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Series GSE67540 Query DataSets for GSE67540
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)
GSM1649153 Nalm6 cell line [Gro-Seq]
GSM1649154 Nalm6 cell line co-cultured with stromal cells [Gro-Seq]
GSM1649155 REH cell line_1 [Gro-Seq]
Reanalysis of GSM980645
Reanalysis of GSM980644
Reanalysis of GSM1480326
Reanalysis of GSM1006728
Reanalysis of GSM1006729
BioProject PRJNA280216
SRA SRP056832

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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