|
| Status |
Public on Mar 13, 2024 |
| Title |
Hippocampus, IS13_S3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Brain
tissue region: Hippocampus
group: IS1
maternal treatment: IS
offspring age: P65
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hippocampi were bisected, flash-frozen in liquid nitrogen, and stored at -80°C. For ATAC-seq, nuclei were isolated from tissue using iodixanol gradient and DNA was transposed with Tn5 transposase followed by MinElute Reaction Cleanup kit purification. DNA was quantified using the PicoGreen dsDNA Assay Kit.
ATAC-seq library preparation was performed in accordance with the ATAC-seq protocol as described by Buenrostro et al. (2015). Libraries were assessed for quality using electrophoresis on an Agilent Bioanalyzer (Agilent) and size-selected for 200~800 bp fragments.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
annotated_IS_peaks_atacseq.txt
|
| Data processing |
Raw sequencing reads were aligned to the rat reference genome (rn6) using HISAT2 (Kim et al., 2019).
MACS was utilized to assess sites of chromatin accessibility in ATAC-seq samples
diffReps (Shen et al., 2013) was run on the processed samples to find differential sites for the comparisons to the IS control group (ID, IDch, or ISch vs IS).
The atacseq.txt and chipseq.txt files are the annotation peak lists obtained from MACS software. The fold change for each peak is computed as the ratio of the read count in the peak to the maximum of the local and global lambda values.
Local Lambda: MACS2 computes a local lambda value for each peak, which is a measure of the local background noise around the peak.
Global Lambda: MACS2 also computes a global lambda value, which is a measure of the background noise across the entire genome.
Assembly: rn6
Supplementary files format and content: tab-delimited text peaks file
|
| |
|
| Submission date |
Sep 27, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Aarthi Ramakrishnan |
| E-mail(s) |
aarthi.ramakrishnan@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Street address |
1425 Madison Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE244206 |
ATAC and histone H3K9me3 landscapes reveal long-term epigenomic effects of fetal-neonatal iron deficiency in rat hippocampus [ATAC-seq] |
| GSE244208 |
ATAC and histone H3K9me3 landscapes reveal long-term epigenomic effects of fetal-neonatal iron deficiency in rat hippocampus |
|
| Relations |
| BioSample |
SAMN37568736 |
| SRA |
SRX21909487 |
