NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4255722 Query DataSets for GSM4255722
Status Public on Jan 08, 2020
Title 100169 ERY input
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics chip ab: none
strain: C57BL6
developmental stage: adult
cell isolation markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119+, CD44+, FSCLow
cell type: erythroblast
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part# IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Mapping to reference genome with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm10 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Macs
Supplementary_files_format_and_content: broadpeak, peaks from Sicer
 
Submission date Jan 07, 2020
Last update date Jan 08, 2020
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL17021
Series (2)
GSE143265 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [histones]
GSE143271 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Relations
BioSample SAMN13750833
SRA SRX7517442

Supplementary file Size Download File type/resource
GSM4255722_100169.mm10.bw 2.3 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap