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| Status |
Public on Apr 15, 2019 |
| Title |
ompcre_rad21ko_HiC_rep1 |
| Sample type |
SRA |
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| Source name |
mOSNs with Rad21 KO
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| Organism |
Mus musculus |
| Characteristics |
cell type: mOSNs
genotype: ompcre;rad21fl/fl;TdTom
chip antibody: N/A
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| Growth protocol |
HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
HiC-Seq, Paired End
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| Data processing |
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All mouse samples were aligned to mm10, human samples aligned to hg19. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads
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| Submission date |
Dec 14, 2018 |
| Last update date |
May 09, 2019 |
| Contact name |
Daniele Canzio |
| Organization name |
University of California San Francisco
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| Department |
Neurology
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| Street address |
555 Mission Bay Boulevard South
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE115862 |
Antisense lncRNA transcription mediates DNA demethylation to drive stochastic Protocadherin α promoter choice |
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| Relations |
| BioSample |
SAMN10594168 |
| SRA |
SRX5131376 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3514554_ompcre_rad21ko_HiC_rep1.hic |
4.9 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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