|
| Status |
Public on Jun 15, 2019 |
| Title |
CUT&RUN-H3K27ac_iPSC-induced lower motor neurons_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-induced lower motor neurons
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-induced lower motor neurons
cut&run antibody: H3K27ac (Active Motif, cat# 39133, lot# 22618011)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&RUN libraries were prepared according to the published protocol (Skene and Henikoff 2017).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MN.H3K27ac.merged.0.05_peaks.narrowPeak
MN.H3K27ac.merged.hg19.bw
|
| Data processing |
library strategy: CUT&RUN
All reads were trimmed to 50 bp with fastp.
Alignment was performed using bowtie2 with the following options: -local -very-sensitive-local -nomixed -no-discordant -phred33 -I 10 -X 700. Picard Tools was used to remove duplicate reads.
Narrow peaks called using MACS2 with a q-value threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format
|
| |
|
| Submission date |
Feb 07, 2019 |
| Last update date |
Apr 08, 2021 |
| 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) |
| GSE113483 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes |
| GSE126211 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN10883278 |
| SRA |
SRX5346384 |
