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| Status |
Public on Oct 03, 2020 |
| Title |
ChBR.GLU.input |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Pan troglodytes |
| Characteristics |
cell type: glutamatergic neurons
brain area: dorsolateral prefrontal cortex
Sex: Male
age (years): 28
genotype: wild type
antibody: input control chromatin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The dorsolateral prefrontal cortex (DLPFC) tissue specimens were sampled from frozen brains of macaque and chimpanzee subjects, in a region corresponding to human BA9.
Nuclei of glutamatergic or MGE-derived GABAergic neurons were isolated by flow cytometry, using antibodies against neuronal nuclei (anti-NeuN) and MGE-derived GABAergic neurons (anti-SOX6).
Histone modification ChIP-seq was performed using anti-H3K27ac antibodies, and a native MNase-digestion-based protocol.
ChIP-seq libraries were constructed using NEBNext Ultra DNA Library Prep kit.
Sequencing was performed on an Illumina HiSeq 2500 instrument, using a paired-end 50 (PE50) protocol to an average of ∼40 million read pairs per sample.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
MNase-digested genomic DNA
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| Data processing |
Paired-end reads were aligned using Bowtie (version 1.1.2) with the following settings: chunkmbs 512 -S -q -l 40 -n 1 -phred33-quals -p 7 -m 1
H3K27ac-enriched regions (peaks) were called using MACS2 (2.1.1.20160309) using an input control (MNase-digested chromatin) for each sample with the following settings: callpeak -B -f BAMPE –broad –broad-cutoff 0.00001
Peaks coordinates were converted between species using the liftOver tool.
Differentially acetylated H3K27ac peaks were detected with DESeq2 by comparing the sets of biological replicates between cell types or species, using the following criteria: FDR < 0.05, Log2(FC) > 1.
Genome_build: hg38, panTro5, rheMac8
Supplementary_files_format_and_content: H3K27ac ChIP-seq signal traces in BigWig format, constructed using a normalization to 1,000,000 reads in each sample.
Supplementary_files_format_and_content: Peak coordinate files; differentially acetylated analysis tables, in TXT format
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| Submission date |
Oct 02, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Stella Dracheva |
| E-mail(s) |
[email protected]
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Dept. of Psychiatry
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| Street address |
James J. Peters VA Medical Center,130 W Kingsbridge Rd
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| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10468 |
| Country |
USA |
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| Platform ID |
GPL19148 |
| Series (2) |
| GSE158931 |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution [ChIP-Seq] |
| GSE158934 |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution |
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| Relations |
| BioSample |
SAMN16351564 |
| SRA |
SRX9235537 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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