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Sample GSM4206985 Query DataSets for GSM4206985
Status Public on Oct 19, 2022
Title LSK_Pcgf1_f/f_RING1B_2
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: B6CBAF1/J
cell type: LSK (Lin-, cKIt+, sca1+) cells
passage: 8-10 weeks
genotype: Pcgf1 fl/fl
antibody: anti RING1B (in house)
Growth protocol Culture with TSt4 stroma cells by IMDM supplemented with IL7, SCF,Fl3L
Extracted molecule genomic DNA
Extraction protocol ChIP for FLAG, RING1B, SUZ12, H3K27me3 and H3K27ac were performed as described previously (Isono et al., 2013). Cultured IdHP cells were cross-linked with 1% formaldehyde/PBS for 10 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with indicated antibodies. ChIP for H2AK119ub was performed as described before (Mochizuki-Kashio et al., 2015). Cultured IdHP cells were cross-linked with 0.5% formaldehyde/PBS for 2 min at 37℃. Chromatin was sheared and used for each immunoprecipitation.
ChIP products and fragmented DNAs fragmentd by MNase were subjected to library preparation by NEBNext UltraⅡ DNA library preparation kit for Illumina(E7645; New England Biolabs).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description LSK_Pcgf1_f/f_RING1B_2
Data processing For ChIP-seq without spike-in genome, reads were aligned to mm9 using bowtie2(Langmead et al., 2012). ChIP-seq experiments which contained a spike-in genome were aligned against concatenated genome of mm9 and dm3 using bowtie2 and resulting SAM files were then split such that reads aligning to mouse and drosophilia were placed in separate files. The SAM files were converted to the BAM format using Samtools, version 1.6.0 (Li et al., 2009). The PCR duplicates were removed by Picardtools (http://broadinstitute.Github.io/picard).
he BAM files were converted to bigwig files by deepTools2 (Ramirez et al. 2016) for visualization. For comparison across ChIP-seq samples without spike-in genome, the bigwig files were normalized to reads per million mapped sequence reads (RPKM). For ChIP-seq with spike-in genome, RPKM were further normalized according to normalization factors calculated as 1 over the number of reads (per million) mapping to drosophilia as previously reported(Orland et al., 2016).
Genome_build: mm9 or concateenated genomes of Mm9 and dm3
Supplementary_files_format_and_content: bigwig files described in the data processing step columns
 
Submission date Dec 06, 2019
Last update date Oct 19, 2022
Contact name Junichiro Takano
E-mail(s) junichiro.takano@riken.jp
Organization name RIKEN
Department IMS
Lab Developmental Genetics
Street address Tsurumi-ku-Suehirocho-1-7-22
City Yokohama-shi
State/province Kanagawa-kwn
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL19057
Series (2)
GSE141559 Gene regulation by PCGF1 in hematopoietic progenitor cells [ChIP, MNaseSeq]
GSE141560 Hematopoietic progenitor cells
Relations
BioSample SAMN13496775
SRA SRX7278163

Supplementary file Size Download File type/resource
GSM4206985_DK18007_36_06.bw 44.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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