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Sample GSM2183948

Query DataSets for GSM2183948

Status

Public on Aug 10, 2016

Title

1.CCIC-G9a

Sample type

SRA

Source name

T5088-CCICs

Organism

Homo sapiens

Characteristics

ID: T5088
cell type: colon cancer stem cells
sorting marker: CD133

Treatment protocol

T5088 CRC cells sorting by CD133 marker

Growth protocol

DMEM/F12, stem cell medium

Extracted molecule

genomic DNA

Extraction protocol

Millipore EZ-ChIP #17-371 kit
(1)DNA-end repair,3'-dA overhang and ligation of methylated sequencing adaptor.(2)PCR amplification and size selection (usually 100-300bp,including adaptorsequence).(3)Qualified library forsequencing. Which follow illumina instruction

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 4000

Data processing

Starting fromthe Illumina GA Pipeline v1.5, the range of base quality values is from 2 to 41
ChIP-seq reads were aligned to the hg19 genome assembly using
After filtering, the clean data was then mapped to the reference genome by SOAPaligner/SOAP2 (Version: 2.21t).
MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2) : The candidate peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value < le-05
Genome_build: hg19
Supplementary_files_format_and_content: wig

Submission date

Jun 01, 2016

Last update date

May 15, 2019

Contact name

SHIH-TING CHA

Organization name

National Taiwan University

Street address

6F., No.2, Syu-jhou Road,

City

TAIPEI

ZIP/Postal code

886

Country

Taiwan

Platform ID

GPL20301

Series (1)

GSE82131

HiSeq Chip-seq analysis of whole genomic landscape of G9a and H3K9me2-targeted in CCICs

Relations

BioSample

SAMN05195185

SRA

SRX1814973

Supplementary file	Size	Download	File type/resource
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr1.wig.gz	11.1 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr10.wig.gz	6.4 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr11.wig.gz	6.3 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr11_gl000202_random.wig.gz	1.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr12.wig.gz	6.5 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr13.wig.gz	4.5 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr14.wig.gz	4.2 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr15.wig.gz	3.7 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr16.wig.gz	3.6 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17.wig.gz	3.9 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17_ctg5_hap1.wig.gz	2.5 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17_gl000203_random.wig.gz	647 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17_gl000204_random.wig.gz	2.8 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17_gl000205_random.wig.gz	7.3 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr17_gl000206_random.wig.gz	268 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr18.wig.gz	3.5 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr18_gl000207_random.wig.gz	426 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr19.wig.gz	2.7 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr19_gl000208_random.wig.gz	3.9 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr19_gl000209_random.wig.gz	2.3 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr1_gl000191_random.wig.gz	1.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr1_gl000192_random.wig.gz	11.9 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr2.wig.gz	11.8 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr20.wig.gz	2.9 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr21.wig.gz	1.5 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr21_gl000210_random.wig.gz	321 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr22.wig.gz	1.6 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr3.wig.gz	9.7 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr4.wig.gz	9.2 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr4_ctg9_hap1.wig.gz	1.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr4_gl000193_random.wig.gz	5.8 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr4_gl000194_random.wig.gz	3.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr5.wig.gz	8.6 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6.wig.gz	8.1 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_apd_hap1.wig.gz	394 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_cox_hap2.wig.gz	9.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_dbb_hap3.wig.gz	1.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_mann_hap4.wig.gz	2.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_mcf_hap5.wig.gz	2.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_qbl_hap6.wig.gz	3.7 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr6_ssto_hap7.wig.gz	1.3 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr7.wig.gz	7.5 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr7_gl000195_random.wig.gz	8.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr8.wig.gz	7.1 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr8_gl000196_random.wig.gz	314 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr8_gl000197_random.wig.gz	266 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr9.wig.gz	5.4 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr9_gl000198_random.wig.gz	2.0 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr9_gl000199_random.wig.gz	4.6 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chr9_gl000201_random.wig.gz	295 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrM.wig.gz	1.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000211.wig.gz	5.8 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000212.wig.gz	4.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000213.wig.gz	675 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000214.wig.gz	4.8 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000215.wig.gz	410 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000216.wig.gz	7.3 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000217.wig.gz	1.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000218.wig.gz	4.6 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000219.wig.gz	8.7 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000220.wig.gz	7.9 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000221.wig.gz	1.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000222.wig.gz	1.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000223.wig.gz	317 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000224.wig.gz	8.3 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000225.wig.gz	9.6 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000226.wig.gz	444 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000227.wig.gz	725 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000228.wig.gz	952 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000229.wig.gz	1.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000230.wig.gz	1.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000231.wig.gz	1.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000232.wig.gz	2.1 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000233.wig.gz	1010 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000234.wig.gz	2.0 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000235.wig.gz	1.4 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000236.wig.gz	234 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000237.wig.gz	913 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000238.wig.gz	379 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000239.wig.gz	279 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000240.wig.gz	828 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000241.wig.gz	2.2 Kb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000242.wig.gz	444 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000243.wig.gz	433 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000244.wig.gz	264 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000245.wig.gz	282 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000246.wig.gz	541 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000247.wig.gz	325 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000248.wig.gz	329 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrUn_gl000249.wig.gz	244 b	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrX.wig.gz	5.4 Mb	(ftp)(http)	WIG
GSM2183948_1.CCIC-G9a_treat_afterfiting_chrY.wig.gz	54.4 Kb	(ftp)(http)	WIG
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file