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Sample GSM1411217 Query DataSets for GSM1411217
Status Public on Aug 12, 2014
Title MCF7 NEAT1 CO1 CHART-seq Ethanol treatment, rep1
Sample type SRA
 
Source name MCF-7, ethanol vehicle, NEAT1 CHART
Organism Homo sapiens
Characteristics cell line: MCF-7
cell type: mammary adenocarcinoma cell line
treatment: ethanol vehicle
capture oligo: NEAT1 CO1
antibody: N/A
Extracted molecule genomic DNA
Extraction protocol For CHART-seq, nuclei were isolated from 10^8 MCF-7 cells (ATCC HTB-22) that were crosslinked with 1% formaldehyde for 10 minutes. Nuclei were further crosslinked with 3% formaldehyde for 30 minutes. Chromatin was sheared to a fragment size between 2 kb and 10 kb. Sheared chromatin was incubated overnight with biotinylated DNA oligonucleotides with complementarity to either the NEAT1 or MALAT1 RNAs, and subsequently captured with streptavidin beads. After incubation and washing, captured materials were eluted using RNaseH and subjected to crosslink reversal. DNA was purified by ethanol precipitation and subjected to library construction.
Genomic DNA isolated by CHART enrichment, as well as input DNA, was fragmented using sonication. Sonicated DNA was then subjected to end-repair, A-tailing, ligation to universal adapters, amplification with indexed primers, and size selection using SPRI beads.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description NEAT1 CHART enriched DNA.
Data processing Library strategy: CHART-Seq
Base-calling was performed using Illumina Real Time Analysis software.
Reads were aligned using Bowtie v 0.12.5 with the following options: -m 1 -v 2 -k 1 -X 2000 --best --strata.
After alignment, reads were processed and filtered according to the SPP guidelines, where the genomic positions with a number of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded.
The coverage for each sample represents frequencies of the paired-end reads spanning over a given genomic position, which were corrected for library size and subsequently input normalized.
For analysis of CHART-seq and PSF paired-end ChIP-seq data from untreated MCF-7 cells, coverage was normalized by input as n_norm = [(n+1)/(ni+1)] * [Ni/N], where n, ni, N, and Ni are positional coverage in experiment and input, and total genome coverage in experiment and input, respectively. The resulting normalized coverage files are included in this dataset in bigwig format.
Input-subtracted, normalized read densities of flavopiridol, E2, and respective vehicle CHART-seq were generated using SPP with a bandwidth of 1kb and a step size of 500 bp and are included in this dataset in bigwig format.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: All processed data files are in bigwig format and represent input-normalized CHART-seq or ChIP-seq coverage.
 
Submission date Jun 12, 2014
Last update date May 15, 2019
Contact name Ruslan Sadreyev
Organization name Massachusetts General Hospital
Department Molecular Biology
Lab Bioinfomatics
Street address 185 Cambridge Street
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
 
Platform ID GPL11154
Series (1)
GSE58444 The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites
Relations
BioSample SAMN02853033
SRA SRX593752

Supplementary file Size Download File type/resource
GSM1411217_MCF7_NEAT1_CO1_CHART-seq_Ethanol_treatment_rep1_norm.bw 58.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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