|
| Status |
Public on Jun 15, 2019 |
| Title |
ATAC-seq_iPSC-induced lower motor neurons_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ATAC-seq_iPSC-induced lower motor neurons
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-induced lower motor neurons
|
| Growth protocol |
Human primary fetal astrocytes were cultured according to the ScienCell protocol (catalog #1801).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, snap frozen in dry ice, and stored at -80C. Cells were washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with Ampure XP beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MS139_YSMS16
processed data file:
motor.atac.seq.narrowPeak
motor.atac-seq.bigwig
|
| Data processing |
All reads were trimmed to 50 bp prior to processing. For libraries having undergone paired-end sequencing, only the first read was used.
All libaries were processed using the ENCODE ATAC-seq pipeline (December 2017).
Optimal IDR and optimal overlap peaks called by MACS2 were used.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format
|
| |
|
| Submission date |
Feb 11, 2019 |
| Last update date |
Jun 15, 2019 |
| Contact name |
Yin Shen |
| E-mail(s) |
Yin.Shen@ucsf.edu
|
| Phone |
4155023403
|
| Organization name |
UCSF
|
| Department |
Department of Neurology
|
| Lab |
Shen Lab
|
| Street address |
513 Parnassus Ave
|
| City |
SAN FRANCISCO |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94143-0410 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE113480 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [ATAC-seq] |
| GSE113483 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes |
|
| Relations |
| BioSample |
SAMN10910623 |
| SRA |
SRX5359794 |
