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| Status |
Public on Apr 20, 2022 |
| Title |
Nfix_mHypoA_25K |
| Sample type |
SRA |
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| Source name |
mHypoA cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Cell line
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| Growth protocol |
Cells were maintained in standard DMEM medium supplemented with 10% FBS and Pen-Strep then harvested using trypsin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added to improve binding to concanavalin A magnetic beads.
Takara SMARTer ThruPlex DNA-seq Kit
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
25,000 cells
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| Data processing |
Library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700.
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q < 0.05). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent genomic binding events.
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| Submission date |
Feb 03, 2020 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Melody Wu |
| E-mail(s) |
mwu@cshl.edu
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE144716 |
Gene regulation by gonadal hormone receptors defines brain sex differences-[CUT&RUN] |
| GSE144718 |
Gene regulation by gonadal hormone receptors defines brain sex differences |
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| Relations |
| BioSample |
SAMN13977692 |
| SRA |
SRX7668944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4294295_mHypoA_Nfix.bw |
42.8 Mb |
(ftp)(http) |
BW |
| GSM4294295_mHypoA_Nfix.narrowPeak.gz |
572.6 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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