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Sample GSM826718 Query DataSets for GSM826718
Status Public on Jan 19, 2012
Title RPC1_Rep2
Sample type SRA
Source name Mouse liver cells
Organism Mus musculus
Characteristics strain: C57/BL6
tissue: liver
chip antibody: RPC1
chip antibody manufacturer: Made in our lab
chip antibody catalog number: CS377, raised against the C-terminus of RPC1, peptide PKRPLIFDTNEFHIPLVT, see (Sepehri and Hernandez 1997)),
chiip antibody lot/batch: none
Treatment protocol They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.
Growth protocol C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.
Extracted molecule genomic DNA
Extraction protocol Chromatin from cell lysates was sonicated and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Reads mapping at a unique place on the genome (uniquely matching tags) and matching without any mismatch were mapped by Eland. Reads mapping at multiple places on the reference genome (repeated tags) were aligned using “fetchGWI” ( The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. ere aligned using “fetchGWI” ( The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. Signal from enriched regions were converted into wig format. Genome build: NCBI37/mm9
Submission date Nov 02, 2011
Last update date May 15, 2019
Contact name David Bernasconi
Organization name University of Lausanne
Department CIG
Lab Nouria Hernandez
Street address Quartier Sorge, Bat. Génopode
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platform ID GPL11002
Series (1)
GSE33421 A Multiplicity of Factors Contributes to Selective RNA polymerase III occupancy of a Subset of RNA polymerase III Genes in Mouse Liver
SRA SRX104146
BioSample SAMN00749934

Supplementary file Size Download File type/resource
GSM826718_RPC1.Rep2.wig.txt.gz 551.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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