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Sample GSM3579678 Query DataSets for GSM3579678
Status Public on Jan 25, 2019
Title 4k.b.c.G12 [Bru-seq]
Sample type SRA
Source name 4k.b.c.G12
Organism Mus musculus
Characteristics cell type: mESC
hybrid cells: cas/129
Treatment protocol Cells was pulse labeled with 2 mM bromouridine (Bru) for 30 minutes.
Growth protocol Mouse ESCs were maintained on 1% gelatin coated dishes. 46C was grown in GMEM supplemented with 10% FBS and LIF; hybrid cells (Cas/129 and V6.5) in DMEM supplemented with 2i plus LIF.
Extracted molecule total RNA
Extraction protocol Trizol
Nascent RNA was pulled down using anti-BrdU antibodies conjugated magnetic beads. Strand specific cDNA libraries were constructed using 300ng Bru-labeled RNA and sequenced on Illumina HiSeq 2500 with 100bp single end.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
Description Nascent RNA
processed data file: RPKM-9-7-18.txt
Data processing Library strategy: Bru-seq
Reads are mapped to mm10 using bowtie2.
Allele-specific analysis was performed using harp (
RPM-normalized read densities were calculated with bedtools2 (Quinlan and Hall, 2010) genomecov, using a scaling factor of 1000000/(number of parsed reads in library).
Genome_build: mm10
Supplementary_files_format_and_content: *bed: bed files
Supplementary_files_format_and_content: RPKM-9-7-18.txt: Tab-delimited text file
Submission date Jan 25, 2019
Last update date Jan 26, 2019
Contact name David M Gilbert
Organization name Florida State University
Department Biology
Lab Gilbert
Street address 319 Stadium Drive
City Tallahassee
State/province FL
ZIP/Postal code 32306-4295
Country USA
Platform ID GPL17021
Series (2)
GSE114139 Identification of cis elements for temporal and spatial control of DNA replication
GSE114618 Identification of cis elements for temporal and spatial control of DNA replication [Bru-seq]
BioSample SAMN10819793
SRA SRX5291854

Supplementary file Size Download File type/resource
GSM3579678_4k.b.c.G12_clip_svim_q10_psort_supportingReference_castVsSvim_homSnp_reheader.bam.min.2k.bed.gz 6.0 Mb (ftp)(http) BED 6.0 Mb (ftp)(http) BED
GSM3579678_4k.b.c.G12_clip_svim_q10_psort_supportingVariant_castVsSvim_homSnp_reheader.bam.min.2k.bed.gz 6.0 Mb (ftp)(http) BED 6.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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