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Sample GSM3900113 Query DataSets for GSM3900113
Status Public on Feb 01, 2021
Title shScramble POL II LPS 45min
Sample type SRA
 
Source name Marcophages
Organism Mus musculus
Characteristics cell type: Bone marrow derived macrophages
genotype: wild type
strain: FVB/Hsd
chip antibody: anti-total RNA pol II, Santa Cruz sc-899
Treatment protocol Cells were treated for 45 min with LPS (10 ng/ml) before harvesting.
Growth protocol Primary bone marrow cells were cultured in DMEM containing 10% North American FBS, 1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells to allow for differentiation into macrophages for 7 days before the experiments were performed.
Extracted molecule genomic DNA
Extraction protocol Ca. 100-150 mill. cells were fixed with 1% formaldehyde for 10 min. Nuclear lysates were prepared, sonicated to reach an average fragment length of 300 bp, whereafter protein-DNA complexes were immunoprecipitated with specific antibodies.
DNA libraries of immunoprecipiated DNA were prepared for sequencing on the Illumina NextSeq as previously described (Ostuni, 2013).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against RNA pol II
GSM1634808
Data processing Pol II raw data were downloaded from GEO (GSM1634808) and re-analysed
Reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp and a False Discovery Rate (FDR) cut-off <0.01 were used. Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA from primary bone marrow-derived macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia (http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist.bed.gz) were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: Tracks (*.bigWig files)
 
Submission date Jun 20, 2019
Last update date Feb 02, 2021
Contact name Viviana Piccolo
E-mail(s) viviana.piccolo@ieo.it
Organization name European Institute of Oncology (IEO)
Department Department of Experimental Oncology
Lab Gioacchino Natoli Lab
Street address Via Adamello 16
City Milano
State/province Milano
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL13112
Series (2)
GSE133104 A first exon termination checkpoint that preferentially suppresses extragenic transcription [ChIPseq_BMDM_POLII]
GSE133109 A first exon termination checkpoint that preferentially suppresses extragenic transcription
Relations
Reanalysis of GSM1634808
BioSample SAMN12100490
SRA SRX6099380

Supplementary file Size Download File type/resource
GSM3900113_PolII_BMDM_scramle_LPS_mm10_SRR1916905_mm10_unique.mapped.bw 193.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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