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Sample GSM1599166 Query DataSets for GSM1599166
Status Public on Jul 21, 2015
Title FL_LSK_K4me3_1K_Rep1
Sample type SRA
 
Source name Mouse Embryonic day 14.5 Fetal Liver
Organism Mus musculus
Characteristics strain: B6129SF1 crossed with C57BL/6
cell type: Fetal Liver, Lineage-Sca1+c-Kit+ (LSK)
chip antibody: H3K4me3 (Millipore, catalog# 07-473, lot# 2289139)
Treatment protocol None
Extracted molecule genomic DNA
Extraction protocol [Isolation protocol] FLs were dissected from E14.5 embryos. Single cell suspensions were prepared by dissociating mechanically and expelling the cells through 40 μm Nylon filter, followed by red blood cell lysis (ACK Lysing Buffer, Lonza). To remove non-specific binding, anti-mouse CD16/CD32 (Fc Block, Biolegend) were added into single cell suspensions and incubated 10 min at 4°C. Next, Cells were stained with a cocktail of antibodies against several surface markers, including lineage markers (Ly-6G/Ly-6C, CD45R/B220, CD3ε, TER-119, CD4, CD8a, and CD19), CD117 (c-Kit), and Ly-6A/E (Sca-1). Cells were first subjected to yield sort for Lineage-Sca-1+c-Kit+ (LSK) and collected into 500µL 1×IMDM+20% FBS in a 12×75-mm polystyrene tube. Collected cells were then performed purity sort using the same gate strategy and sorted into 0.8 mL 1×IMDM+50% FBS in a 1.5 mL DNA LoBind tube.
Cells were cross-linked for 5 min with 1% formaldehyde at room temperature prior to quencing with 125mM glycin. Cross-linked cells were sonicated using Covaris S2 sonicator for 14 min with 5% duty, Intensity 3 and Bursts 200. The sonicated lysate was centrifuged at a speed of 14000×g for 10 min under 4°C. The cleared chromatin (10000 cells per 100 µl) in the supernatant was transferred to a new low-bind Eppendorf tube for subsequent microfluidic ChIP.
The ChIPed and input DNA was constructed into libraries by using the ThruPLEX FD Kit (Rubicon Genomics, Ann Arbor, MI, USA). During the amplification step, 11cycles was needed to get enough library from input DNA without over-amplification. 12~13 cycles is needed for ChIPed DNA extracted from 10000 cells. 14~15 cycles is normally required for ChIPed DNA from 1000 or less cells.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Raw sequencing reads were mapped to the human genome (hg19) or mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting. Only uniquly mapped reads were used for analysis
ChIP-seq peaks were identified by two peak caller, MACS (p-value < 10-5) and SPP (z-score > 4) with default parameter setting.
To generate the wig files, the human or mouse genome was divided into 100 bp bins, and the number of uniquely mapped reads were counted in each bin. We normalized the tag counts in each bin according to the total number of uniquely mapped reads. Input reads were processed in the same way and their normalized signals were subtracted from the ChIP-seq tracks.
Normalized wig files were converted to binary bigwig files
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files
 
Submission date Feb 02, 2015
Last update date May 15, 2019
Contact name Kai Tan
Organization name The University of Iowa
Department Internal Medicine
Street address 3292 CBRB, 285 Newton Road
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL17021
Series (1)
GSE65516 A microfluidic device for epigenomic profiling using 100 cells
Relations
BioSample SAMN03324205
SRA SRX863165

Supplementary file Size Download File type/resource
GSM1599166_FL_LSK_K4me3_1K_Rep1.bw 46.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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