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| Status |
Public on Jan 12, 2016 |
| Title |
18qE_2_USC_RNA_53 |
| Sample type |
SRA |
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| Source name |
Human colorectal cancer cell-line HCT116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
clone: 18qE Deletion Clone 2
time point: RNA extracted on day D
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| Growth protocol |
HCT116 cells and HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin until 80% confluent.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was prepared using Trizol (Life Technologies, Carlsbad, CA)
For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For 4C-seq, cells were cross linked using 1% formalehyde for 10 minutes and nuclei were isolated, followed by chromatin is digested with a first restriction enzyme (DpnII) and ligated. After reverse cross-linking, DNA is treated with secondary restriction enzyme (Csp6I) followed by second ligation.
RNA-seq:Single-end libraries were prepared using the Illumina TruSeqV2 Sample Prep Kit (Catalog #15596-026), starting with 1 ug total RNA. Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an NextSeq500.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an Illumina HiSeq2000 or NextSeq500
4C-seq: Libraries were made through inverse PCR using primers that anneal to the bait fragment-end, customized barcode and adaptor seqeunces. Libraries were sequenced using an Illumina HiSeq2500
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina Casava (version: BCL2FASTQ Conversion Software 1.8.4) was used for basecalling.
RNA-seq reads were aligned to hg19 genome assembly using Tophat2 after trimming some raw reads using the quality score in Partek Flow version 3. HTSeq 0.6.1 was used to count aligend sequencing reads (bam file) using htseq-count script ( options: -format=bam -m=intersectio-strict -stranded=no). Also gencodev19 gff file was used for running htseq-count script.
ChIP-seq reads were aligned to hg19 genome assembly using bwa (0.6.2)and bam file was converted to bed file using bedtools. Bed files were converted to sgr files for visualization using a script from Sole-Search program.
4C-seq: Processed files of sequenced 4C-seq reads is from 4Cseqpipe program (http://compgenomics.weizmann.ac.il/tanay/?page_id=367)
hg19
processed data files format and content: RNA-seq: Tab-delimited text files that include counts for each gene
processed data files format and content: ChIP-seq: SGR files which are tab-delimited graph format showing base coordinates and scores.
processed data files format and content: 4C-seq: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins. Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns: column 1 – the starting coordinate of the 1kb bin column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin column 3 – the 80th percentile of values in the window column 4 – the 20th percentile of values in the window column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 50kb
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| Submission date |
Sep 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peggy Farnham |
| Organization name |
University of Southern California
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| Department |
GMCB
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| Lab |
NRT6514
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| Street address |
1450 Biggy St.
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| City |
LA |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE72631 |
Effects on the transcriptome upon deletion of distal elements are not correlated with the size of H3K27Ac peaks in human cells |
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| Relations |
| BioSample |
SAMN04032620 |
| SRA |
SRX1184005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1867010_18qE_2_USC_RNA_53.txt.gz |
223.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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