|
Status |
Public on Feb 03, 2015 |
Title |
24_NC_bound |
Sample type |
SRA |
|
|
Source name |
Colon primary tissue
|
Organism |
Homo sapiens |
Characteristics |
sample id: 24 fraction: hmC_bound fraction antibody: anti 5-hmC rabbit polyclonal (Active Motif, catalog# 39791, lot# 02511003) tissue: Normal Colon Close to tumor
|
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 |
Normal Colon Close to tumor SLX-3717.607.s_6 hmeDIP-seq SLX-3717.607.s_6
|
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 |
SAMN02189724 |
SRA |
SRX290507 |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_genes_counts.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_genes_rpkm.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_narrow_counts.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_narrow_rpkm.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_wide_counts.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_wide_rpkm.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_WaP_counts.bed.gz |
Named Annotation |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_WaP_rpkm.bed.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_WaP_counts.bed.gz |
118.8 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_WaP_rpkm.bed.gz |
376.9 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_genes_counts.bed.gz |
249.7 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_genes_rpkm.bed.gz |
379.9 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_narrow_counts.bed.gz |
239.5 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_narrow_rpkm.bed.gz |
271.8 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_wide_counts.bed.gz |
241.2 Kb |
(ftp)(http) |
BED |
GSM1152865_SUL_CRC2_24NC_hmC_bnd_promoters_wide_rpkm.bed.gz |
280.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |