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Sample GSM4801079 Query DataSets for GSM4801079
Status Public on Jun 18, 2021
Title Uhrf_WT_rep2
Sample type SRA
 
Source name V65 mESC
Organism Mus musculus
Characteristics cell type: mESC
strain: V65
genotype: WT + Uhrf1 FLAG TAG
Treatment protocol N/A
Growth protocol mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.
Extracted molecule genomic DNA
Extraction protocol Cells were washed once with PBS and fixed with 1% formaldehyde (methanol-free) for 10 minutes at room temperature with rotation. The formaldehyde was quenched with 125 mM glycine for five minutes at room temperature. Cells were spun at 500g for 10 minutes at 4°C and washed twice with ice-cold PBS supplemented with Protease Inhibitor cOmpleteTM. Subsequent work was performed on ice and with buffers cooled to 4°C. The pellet was lysed in L3B buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate (DOC), 0.5% N-lauroylsarcosine, 1x protease inhibitors) and sonicated in a 130 µL milliTUBE in a Covaris E220 for 7 min until most of the fragments were 200- 700 base pairs long (settings: duty cycle 5%, peak incident power 140 Watts, cycles per burst 200). Lysates were supplemented with 1% Triton-X-100 and centrifuged at full speed for five minutes at 4°C, the supernatant containing the sonicated chromatin was transferred to a new tube.
In parallel, Protein G magnetic beads (Invitrogen) were blocked and conjugated to an antibody by washing them twice in PBS with 0.5% BSA and resuspended in 200 μl of PBS with 0.5% BSA per IP. Anti-Flag (1 μg, Millipore/Sigma F1804) was added and bound to the beads by rotating >1 hour at room temperature. Blocked antibody conjugated magnetic beads were added to the tube containing the chromatin and incubated over night at 4°C. The beads were then washed twice with each of the following: TFWBI (20 mM Tris-HCl/pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), TF-WBIII (250 mM LiCl, 1% Triton X-100, 0.7% DOC, 10 mM Tris-HCl/pH 8, 1 mM EDTA), and 10 mM Tris-HCl pH8. Beads were resuspended in 24 μl of tagmentation buffer and 1 μl of Tn5 transposase (Illumina 15027866, 15027865) and then incubated at 37ºC for five minutes in a thermocycler. Tagmentation reactions were removed and beads were washed twice with WBI and TET (0.2% Tween-20, 10 mM Tris-HCl/pH 8.0, 1 mM EDTA) (twice). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (NEB) for 1 hour at 55°C and 8 hours at 65°C to reverse crosslink, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads and incubated with another 1 μl of Proteinase K for 1 hour at 55°C, eluates were combined. Finally, DNA was purified with AMPure XP beads (sample-to-beads ratio 1:2). Relative quantitation was performed using SYBR-green as in (Schmidl et al, 2015; PMID:26280331) using 2 μl of DNA. Libraries were amplified according to the Cq values obtained in the previous step (12 cycles were used), purified using AMPure XP beads and eluted in 15 μl of water. 
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIPmentation
Data processing The ChIPseq data as well as the control input sequencing were aligned to the mouse mm9 reference genome using BWA mem using the default parameter. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Genome build: mm9
processed data files format and content: bigWig coverage files
 
Submission date Sep 23, 2020
Last update date Jul 04, 2021
Contact name Helene Kretzmer
E-mail(s) kretzmer@molgen.mpg.de
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Meissner Lab
Street address Ihnestraße 63
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL24247
Series (1)
GSE158460 Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements
Relations
BioSample SAMN16249185
SRA SRX9179192

Supplementary file Size Download File type/resource
GSM4801079_Uhrf_WT_rep2.bw 165.4 Mb (ftp)(http) BW
GSM4801079_V6.5_Uhrf1_rep2.broadPeak.bed.gz 1.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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