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Sample GSM1463456 Query DataSets for GSM1463456
Status Public on Aug 02, 2014
Title PG0198_A01
Sample type SRA
 
Source name SW1353 cells
Organism Homo sapiens
Characteristics cell line: SW1353
cell type: Human chodrogenic cells
transfected with: FLAG-tagged HES1
passage: 7-10
chip-antibody: Anti-FLAG M2 Affinity Antibody
chip-antibody: SIGMA
chip-antibody cat. #: F1804
chip-antibody lot #: 088K6011
Growth protocol SW1353 cells transfected with FLAG-tagged HES1 by in DMEM with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
All protocols for TruSeq ChIP Sample Preparation Guide Rev. A (Illmina)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 1.4.2 with the following setting: ChIP gsize(2700000000) mfold (7,30).
Genome_build: hg19
Supplementary_files_format_and_content: PG0198_A01_annotation.xlsx: annotation data of enrich area with neighborhood gene information. Three bed files were generated for UCSC genome browser. Each file represented the site of enrich area (*region.bed), depth of sequencing (*depth.bed), mapping information of unique hit sequence (*read_uniq.bed).
 
Submission date Aug 01, 2014
Last update date May 15, 2019
Contact name Shurei Sugita
E-mail(s) ssugita-tky@umin.ac.jp
Organization name The University of Tokyo
Department Sensory & Motor System Medicine
Street address 7-3-1, Hongo, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8655
Country Japan
 
Platform ID GPL11154
Series (1)
GSE60006 Genome-wide maps of HES1 binding-site in human chondrogenic cell.
Relations
BioSample SAMN02950170
SRA SRX667896

Supplementary file Size Download File type/resource
GSM1463456_PG0198_02_a_depth.bedGraph.gz 67.1 Mb (ftp)(http) BEDGRAPH
GSM1463456_PG0198_02_a_read_uniq.bed.gz 1.2 Gb (ftp)(http) BED
GSM1463456_PG0198_A01_annotation.xlsx 445.1 Kb (ftp)(http) XLSX
GSM1463456_PG0198_A01_region.bed.gz 72.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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