|
| Status |
Public on Feb 03, 2015 |
| Title |
42_T1_bound |
| Sample type |
SRA |
| |
|
| Source name |
Colon primary tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 42
fraction: hmC_bound fraction
antibody: anti 5-hmC rabbit polyclonal (Active Motif, catalog# 39791, lot# 02511003)
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_42T1_hmC_bnd.689.s_5
hmeDIP-seq
SUL_CRC2_42T1_hmC_bnd.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 |
SAMN02189734 |
| SRA |
SRX290517 |
| Named Annotation |
GSM1152875_SUL_CRC2_42T1_hmC_bnd_genes_counts.bed.gz |
| Named Annotation |
GSM1152875_SUL_CRC2_42T1_hmC_bnd_promoters_narrow_counts.bed.gz |
| Named Annotation |
GSM1152875_SUL_CRC2_42T1_hmC_bnd_promoters_wide_counts.bed.gz |
| Named Annotation |
GSM1152875_SUL_CRC2_42T1_hmC_bnd_WaP_counts.bed.gz |
