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Sample GSM7135382 Query DataSets for GSM7135382
Status Public on Jun 30, 2023
Title MBD3 ChIP-seq adult mouse cortex animal no. 9
Sample type SRA
Source name cortex
Organism Mus musculus
Characteristics animal: animal no. 9
tissue: cortex
strain: C57BL/6J
Sex: female
age: 14 weeks
chip antibody: MBD3 (Abcam ab157464)
genotype: wild-type
Growth protocol Surgically excised cerebral cortices of wild-type adult (14 weeks) C57BL/6J female mice were purchased from the Jackson Laboratory and shipped frozen.
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation of mouse cortices was performed with the ChIP-IT High Sensitivity® Kit (Active Motif, cat. no 53040) according to the manufacturer’s protocol. Frozen mouse cortices were cut into ~1 mm cubes in 10 mL Complete Tissue Fixation Solution in a 100-mm petri dish and incubated, with rotation, at room temperature for 15. The reaction was quenched with 515 µL Stop Solution followed by incubation at room temperature for 5 minutes. The cross-linked tissues were then homogenized by passing the suspension 20 times through a 20-guage needle attached to a sterile plastic syringe. The tissues were pelleted by centrifugation at 1,250 x g for 3 min at 4 °C and pellets were washed twice with 10 mL ice-cold PBS Wash Buffer. Washed pellets were resuspended in 5 mL Chromatin Prep Buffer supplemented with 5 µL protease inhibitor cocktail (PIC) and 5 µL 100 µM PMSF, incubated on ice for 10 minutes, and homogenized again to lyse cell membranes. Nuclei were pelleted by centrifugation as before, resuspended in 1 mL ChIP buffer, incubated for 10 min on ice, and sonicated in a Bioruptor (Diagenode) sonicator in 200 µL aliquots, each receiving 6 10-min rounds of sonication at high power (30 sec on / 30 sec off). Sonicated samples were clarified by centrifugation for 2 minutes at 4 °C at 16,000 x g and stored at -80 °C. Input DNA was prepared as follows: 25 µL was removed and purified according to the manufacturer’s protocol (briefly, RNAse A treatment, Proteinase K treatment, addition of NaCl and reverse cross-linking at 65 °C for 16 hours, and purification by phenol:chloroform and ethanol extraction) and quantified using a NanoDrop spectrophotometer. 30 µg sheared chromatin was immunoprecipitated overnight at 4 °C by dilution in 200 µL ChIP Buffer supplemented with 5 µL PIC and incubation with 4 µg antibody with 5 µL Blocker. 30 µL washed Protein G agarose beads were added to the reaction and incubated for 3 h. The reactions were then diluted by the addition of 600 µL ChIP buffer and added to ChIP filtration columns, washed 5 times with Wash Buffer AM1, and eluted in 100 µL Elution Buffer AM4. ChIP DNA was purified in the same manner as input DNA and in 36 µL elution volume for ChIP-sequencing.
Libraries were generated from 25 µL of fragmented DNA (range 100-300 bp) using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies (IDT). Size selection was carried out using SparQ beads (QIAGEN) prior to PCR amplification (12 cycles). Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average fragment size was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized, pooled, and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 175 pM (HEK293 cells) or 200pM (mouse cortices) on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Data processing Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FASTQ files were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Trimmed FASTQ files were aligned to hg38 reference genome using bowtie239 v2.4.5 with default parameters.
SAM files were converted to BAM format and unmapped reads were removed with samtools v1.16.1
BAM files were sorted and duplicates were marked with Picard tools v2.18.29 and indexed with samtools.
Significant peaks were identified with the callpeak function from macs2 v2.2.7.1 using the respective input sequencing data for each sample as control and precompiled values for the mappable human genome size.
Assembly: mm39
Supplementary files format and content: narrowPeak (except for input samples)
Submission date Apr 01, 2023
Last update date Jun 30, 2023
Contact name Moshe Szyf
Phone 5143987107
Organization name McGill University
Department Pharmacology & Therapeutics
Street address 3655 Promenade Sir William Osler, Room 1309
City Montreal
State/province QC Quebec
ZIP/Postal code H3G1Y6
Country Canada
Platform ID GPL24247
Series (2)
GSE228706 Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD [mouse ChIP-seq]
GSE228707 Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD
BioSample SAMN34035815
SRA SRX19843234

Supplementary file Size Download File type/resource
GSM7135382_cortex_MBD3_9_peaks.narrowPeak.gz 943.8 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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