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Sample GSM2095203 Query DataSets for GSM2095203
Status Public on Aug 25, 2016
Title DEX2_GR chip seq library_STARRseq
Sample type SRA
 
Source name human GR chip seq library cloned into STARR-seq plasmid
Organism Homo sapiens
Characteristics cell line: A549
transfection: transfected with STARR-seq library
agent: dex
Treatment protocol transfected with STARR-seq library at 50% confluence, after 48H treated with 100 nM DEX or etoh control for 3 h, then harvested
Growth protocol A549 cells grown in F12K medium with 10%FCS
Extracted molecule total RNA
Extraction protocol Qiagen total RNAmidi-prep, two rounds of oligodT dynabead (invitrogen) to harvest mRNA
gene specific RT primer used to reverse transcribe only the mRNA encoded by the plasmid pool, then nested PCR to amplify spliced reporter transcripts and index for sequencing
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description STARR-seq- Reporter-RNA-seq
Data processing Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Bam files were converted to Bed files for down stream analysis using BamtoBed function of the bedTools suite.
Genome_build: hg19
Supplementary_files_format_and_content: .bed (columns: Chromosome, Start, Stop, Bed Name (RNAME field in the BAM alignment)/ mate (1 or 2), Counts, Strand). bed files report the abundance of fragments generated in a reporter plasmid-specific RNA-seq experiment performed after transfecting the reporter plasmids contained in [4] into A549 cells and treating the cells with either 100 nM dexamethasone or ethanol. In the context of [1] and [5], the files contain the abundance of RNA transcribed from the reporter vectors (from the plasmid pools described in [4] and [7]). [1] and [5] contain the location and abundance of the RNA species transcribed from the transfected reporter plasmids after treatment with either 100 nM dexamethasone or with ethanol as a control.
 
Submission date Mar 21, 2016
Last update date May 15, 2019
Contact name Christopher Vockley
E-mail(s) christopher.vockley@gmail.com
Organization name Duke University
Street address 101 science drive rm 2193
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL15520
Series (2)
GSE79428 Direct GR binding sites potentiate clusters of TF binding across the human genome [5]
GSE79432 Direct GR binding sites potentiate clusters of TF binding across the human genome
Relations
BioSample SAMN04570626
SRA SRX1650249

Supplementary file Size Download File type/resource
GSM2095203_CV32_CV33-S2.bed.gz 148.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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