|
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.
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|
|
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 |