|
| Status |
Public on Jan 07, 2021 |
| Title |
04.NPC-1.25uM.Six2.r2.sorted |
| Sample type |
SRA |
| |
|
| Source name |
NPC cultured in NPEM (1.25 uM CHIR) for 24 hrs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: nephron progenitor cells
developmental stage: 16.5 days
strain: Swiss Webster
chip antibody: Six2 (ProteinTech, 11562-1-AP)
|
| Growth protocol |
NPEM (Brown et al., 2015)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cortex of moue embryonic kidneys were dissociated and nephron progenitor cells (NPCs) were purified with MACS (Brown et al., 2015). NPCs were fixed in AutoMACS running buffer with 1% formaldeyde for 30 min in room temperature. Chromatin was extracted with SimpleChIP® Sonication Cell and Nuclear Lysis Buffers (Cell Signaling Technology #81804) following manufacturer’s instruction. Sonicated chromatin was immuno-precipitated with the indicated antibodies. The precipitated DNA was subsequently collected with Qiagen minElute reaction cleanup kit (Qiagen, #28204).
Libraries were constructed using ThruPLEX-FD Prep Kit (Clontech, # R400523), and subsequently sequenced by Illumina NextSeq 500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
201803Tcf09
peak coordinates:
peak02.NPC-1.25uM.Six2.txt
|
| Data processing |
Base call by bcl2fastq v. 2.17
Fastq files were aligned using Bowtie 2.
Aligned reads were sorted with samtools (Li et al., 2009).
Duplicate reads were removed with Picard (http://broadinstitute.github.io/picard/index.html).
ChIP-Seq peaks were called using MACS2 (Feng et al., 2012).
wig profiles were generated using QuEST
Genome_build: mm10
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files are available in tar archive on series record.
|
| |
|
| Submission date |
May 13, 2019 |
| Last update date |
Jan 07, 2021 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
amcmahon@med.usc.edu
|
| Phone |
323-442-7847
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell Biol & Regen Med
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St, BCC 312
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE131117 |
Genome-wide map of Tcf/Lef transcription factors, β-catenin, Six2 and chromatin marks in mouse nephron progenitor cells |
| GSE131119 |
Genome-wide map of open chromatin, trancription factor occupancy, chromatin marks and gene expression profiles in mouse nephron progenitor cells |
|
| Relations |
| BioSample |
SAMN11635597 |
| SRA |
SRX5825953 |
