|
| Status |
Public on Oct 12, 2018 |
| Title |
rat_atac_1 |
| Sample type |
SRA |
| |
|
| Source name |
unsorted nuclei from cerebellum
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
brain region: cerebellum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cerebellum was dissected and nuclei were isolated. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013; 2015) with the following modifications: nuclei were resuspended in ice-cold lysis buffer, omitting incubation step on ice and centrifuged. Transposition reaction was performed for 30 min at 37°C using Tn5 transposase from Nextera. DNA fragments were purified and size selected using AMPure XP beads to yield 100-700bp fragments.
Libraries were generated using the Nextera DNA Library Preparation Kit. ATAC-seq libraries from mouse and human cerebellum were sequenced on the Illumina HiSeq2500 to obtain 50bp paired-end reads, and libraries generated from rat cerebellum were sequenced on Illumina HiSeq 2500 NextSeq 500 to obtain 75bp paired-ended reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter sequences were trimmed and reads were filtered depending on quality using Trim Galore! (trim_galore --stringency 3 --fastqc --paired *_R1_2.fastq.gz *_R2_2.fastq.gz).
Reads that passed the filter were aligned using Bowtie2 (Langmead and Salzberg, 2012) to the Rattus norvegicus reference genome (rn6).
Duplicate reads were removed using SAMtools (Li et al., 2009).
For data visualization, tdf files were generated using igvtools.
Genome_build: rn6
Supplementary_files_format_and_content: tdf format for visualization in IGV
|
| |
|
| Submission date |
Jul 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiao Xu |
| E-mail(s) |
xxu@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Department |
Laboratory of Molecular Biology
|
| Lab |
Nathaniel Heintz
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE101916 |
Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Rat ATAC-Seq] |
| GSE101918 |
Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia |
|
| Relations |
| BioSample |
SAMN07417161 |
| SRA |
SRX3038920 |
