|
Status |
Public on Feb 03, 2015 |
Title |
44_T1_input |
Sample type |
SRA |
|
|
Source name |
Colon primary tissue
|
Organism |
Homo sapiens |
Characteristics |
sample id: 44 fraction: Input antibody: n/a tissue: Colon tumor (adenocarcinoma)
|
Treatment protocol |
not applicable
|
Growth protocol |
not applicable
|
Extracted molecule |
genomic DNA |
Extraction protocol |
For hmeDIP-seq, Illumina libraries were prepared from sonicated genomic DNA followed by immunoprecipitation with anti-5hmC antibody (Active Motif, 39791) and sequenced. For TET2 ChIP-seq, formaldehyde cross-linked material was immunoprecipitated with anti-TET2 antibody (SantaCruz sc-136926) followed by Illumina adapter ligation and sequencing.
|
|
|
Library strategy |
MeDIP-Seq |
Library source |
genomic |
Library selection |
5-methylcytidine antibody |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
Colon tumor (adenocarcinoma) SUL_CRC2_44T1_hmC_Inp.689.s_5 hmeDIP-seq SUL_CRC2_44T1_hmC_Inp.689.s_5
|
Data processing |
Alignments: Illumina reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA Wap counting: counts of overlapping reads in 300bp windows centered around Inifinium array probes (overlapping windows merged), with overlapping reads in control subtracted Wide promoter counting: counts of overlapping reads in 3500bp windows, 3000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted Narrow promoter counting: counts of overlapping reads in 1500bp windows,1000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted Gene counting: counts of overlapping reads in windows from TSS to TES (overlapping windows merged), with overlapping reads in control subtracted Genome_build: hg18 Supplementary_files_format_and_content: *.counts.bed: bed file with score set to number of reads overlapping a feature (minimum 1) Supplementary_files_format_and_content: *.rpkm.bed: bed file with score set to RPKM based on reads overlapping a feature (minimum reads 1)
|
|
|
Submission date |
Jun 03, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Chandra Chilamakuri |
E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
Organization name |
Cancer Research UK Cambridge Institute
|
Street address |
Robinson Way
|
City |
Cambridge |
ZIP/Postal code |
CB2 0RE |
Country |
United Kingdom |
|
|
Platform ID |
GPL10999 |
Series (2) |
GSE47590 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq] |
GSE47592 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer |
|
Relations |
BioSample |
SAMN02189737 |
SRA |
SRX290520 |