|
| 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 (http://github.com/dvera/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] |
|
| Relations |
| BioSample |
SAMN10819793 |
| SRA |
SRX5291854 |
