|
| Status |
Public on Sep 21, 2016 |
| Title |
Nkx2-1_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Basal ganglia
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
chip antibody: NKX2-1 polyclonal (Santa Cruz Biotechnology #sc-13040 RRID:AB_10015210)
genotype: Wildtype
age: embryonic day 13.5
tissue: Basal ganglia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was micro-dissected and prepared for TF or native ChIP, cross-linked, and sheared. Protein/antibody complexes were isolated with antibodies and collected using Dynabeads.
ChIP-seq libraries were generated using the Ovation Ultralow DR Multiplex System (NuGEN #0330).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Dissociated tissue
|
| Data processing |
Base-calls were performed with CASAVA (v1.8.2) and bcl2fastq (v1.8.4).
ChIP-seq reads were filtered and aligned to whole mouse genome mm9 using BWA (v0.6.2).
Peak-calling was performed with MACS2 (v2.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing coverage and txt files containing MACS2 peak-calls.
|
| |
|
| Submission date |
Aug 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex Nord |
| E-mail(s) |
asnord@ucdavis.edu
|
| Phone |
530-754-5022
|
| Organization name |
University of California Davis
|
| Department |
Neurobiology, Physiology, and Behavior
|
| Street address |
1544 Newton Court
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95618 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE85704 |
Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons (ChIP-Seq) |
| GSE85705 |
Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons |
|
| Relations |
| BioSample |
SAMN05579979 |
| SRA |
SRX2026507 |
