|
| Status |
Public on Jul 05, 2016 |
| Title |
RNA polymerase in pre-B-ALL cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
[Gro-seq] Precursor B acute leukemia cells measured using global nuclear run-on sequencing
[ChIP-Seq] The genome-wide occupancy of ser2 and ser5 phosphorylated RNA pol2 and H3K4me3 was measured in precursor B acute leukemia cells measured using chip-seq.
|
| |
|
| Overall design |
[Gro-seq] Nascent RNA expression profiles were generated at cells in various basal culture conditions.
[ChIP-Seq] Performed from REH and Nalm6 cells cultured under basal culture conditions. Mnase digestion was used for DNA fragmentation. Antibodies against Ser2 and Ser5 phosphorylated RNA polymerase and H3K4me3 compared to input.
******************************
This study includes reanalysis of Samples in Series GSE39878 (GSM980645, GSM980644), GSE60454 (GSM1480326), and GSE41009 (GSM1006728, GSM100672). The processed data files for the reanalyses are linked to GSE67540 as supplementary files (see the GSE67540_README.txt file for additional information).
|
| |
|
| Contributor(s) |
Heinäniemi M, Teppo S, Kaikkonen MU, Bouvy-Liivrand M, Lohi O |
| Citation(s) |
27431763, 33218352 |
| |
| Submission date |
Apr 02, 2015 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Merja Heinäniemi |
| Organization name |
university of eastern finland
|
| Street address |
Yliopistonranta 1
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (21)
|
|
| Relations |
| Reanalysis of |
GSM980645 |
| Reanalysis of |
GSM980644 |
| Reanalysis of |
GSM1480326 |
| Reanalysis of |
GSM1006728 |
| Reanalysis of |
GSM1006729 |
| BioProject |
PRJNA280216 |
| SRA |
SRP056832 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67540_Lymphobl_plus_1e7_fs1e50_res50.bedGraph.gz |
63.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_Lymphoblminus_1e7_fs1e50_res50.bedGraph.gz |
59.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_Nalms_minus_1e7_fs1e50_res50.bedGraph.gz |
48.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_Nalms_plus_1e7_fs1e50_res50.bedGraph.gz |
52.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE67540_README.txt |
825 b |
(ftp)(http) |
TXT |
| GSE67540_REHs_minus_1e7_fs1e50_res50.bedGraph.gz |
57.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_REHs_plus_1e7_fs1e50_res50.bedGraph.gz |
61.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_hESC_minus_1e7_fs1e50_res50.bedGraph.gz |
68.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE67540_hESC_plus_1e7_fs1e50_res50.bedGraph.gz |
72.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
Less...
More...