 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 22, 2021 |
| Title |
GRO-DT40-Ri_GFP2 |
| Sample type |
SRA |
| |
|
| Source name |
DT40 cell line
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: B lymphocyte
genotype: IgL(-) AIDR1 Ri GFP2 2-3
cell type: Bursal lymphooma
age: Unknown
|
| Treatment protocol |
The GRO-seq was done as previously described (Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (80-. ). 322, 1845–1848.)
|
| Growth protocol |
DT40 cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Hyclone), 1 % chicken serum (Biowest), 1X GlutaMAX (Gibco), 50 µM β-mercaptoethanol (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 41 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleus were prepared from about 20 millions cells of each line. The GRO-seq was done as previously described (Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (80-. ). 322, 1845–1848.)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: GRO-seq
The reads from libraries were aligned with Bowtie2 (Langmead and Salzberg, 2012) to the customized Gallus_gallus-4.0 genome with the reporter construct appended as an extra chromosome. The alignment was done as previously described (Meng et al., 2014).
Genome_build: GalGal4
Supplementary_files_format_and_content: Aligned-reads bed files were seperated by strand and then converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).
|
| |
|
| Submission date |
Jul 15, 2021 |
| Last update date |
Oct 22, 2021 |
| Contact name |
Yaakov Maman |
| Organization name |
Bar-Ilan University
|
| Department |
Azrieli Faculty of Medicine
|
| Lab |
Genome Instability & Cancer
|
| Street address |
Henrietta Szold 8
|
| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE180176 |
Immunoglobulin enhancers increase RNA polymerase 2 stalling at somatic hypermutation target sequences [GRO-seq] |
| GSE180178 |
Immunoglobulin enhancers increase RNA polymerase 2 stalling at somatic hypermutation target sequences |
|
| Relations |
| BioSample |
SAMN20245097 |
| SRA |
SRX11457857 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5454745_GRO-DT40-Ri_GFP2_minus.bw |
20.0 Mb |
(ftp)(http) |
BW |
| GSM5454745_GRO-DT40-Ri_GFP2_plus.bw |
19.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
