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| Status |
Public on Mar 13, 2015 |
| Title |
LncHSC-2 IP even probe set tech rep 2 bio rep 1 |
| Sample type |
SRA |
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| Source name |
HPC5 cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow derived hematopoietic progenitor cell line
strain: C57BL/6-cast (B6-cast)
3'-biotin labeled oligo probe set: LncHSC-2 IP even (2,4,6,8,10,12)
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| Treatment protocol |
10 million cells were cross-linked with 1% gluteraldehyde at room temperature for 10 minutes and quenched with 0.125 M glycine for 5 minutes.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked cells were lysed and sonicated to 200-500 bp fragments via bioruptor.
Chromatin fragments were incubated with the indicated biotinylated oligonucleotide probes and enriched material was selected by streptavidin magnet beads. Libraries were constructed using ThruPLEX-FD preparation kit (Rubicon, Ann Arbor, MI)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
technical replicate 2 of biological replicate 1
final.consensus.narrowpeak.bed
hpc5_CHIRP_IP04_treat_pileup.bw
library strategy: ChiRP-seq
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| Data processing |
Reads were mapped with Bowtie2. Uniquely mapped reads were used for peak calling by Macs2. Post-processing steps are described.
ChIRP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.0.6 with 1 mismatch in seed allowed, command=bowtie2 -p12 -k 2 -N 1. Peak calling was performed on uniquely aligned reads (lacking bowtie2 flag XS:i) with Macs2 version 2.0.10.20131216, command=macs2 callpeak -f BAMPE -g mm -m 2 50 --verbose 3 --bdg --SPMR -t treatment.bam -c control.bam , where treatment is RNA bound chromatin DNA and control is input DNA. Post-processing of peak data consisted of three steps. (1) Find concordant regions: Identify all possible regions of overlap among significant peaks called in the four LncHSC-2 and control LacZ experiments. (2) Remove non-specific regions: Exclude regions covered by LacZ peaks and regions not covered by concordant peaks in the two split-probe experiments. Require remaining regions to be covered by peaks in at least one of the two complete probe set experiments. (3) Select consensus peaks: Merge any overlapping regions, select the first intersecting peak from one of the two complete probe set experiments. Exclude the consensus peak if it has any overlap with LacZ peaks.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.
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| Submission date |
Mar 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
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| Phone |
(713) 677-7439
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| Organization name |
Texas A&M University
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| Street address |
2121 W Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE63277 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function |
| GSE66819 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIRP-seq) |
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| Relations |
| BioSample |
SAMN03402217 |
| SRA |
SRX955671 |
| 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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