|
| Status |
Public on May 01, 2017 |
| Title |
Input_ChIPseq_undiff |
| Sample type |
SRA |
| |
|
| Source name |
undifferentiated CAD cells, input
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell line: CAD
differentiation state: undifferentiated
chip antibody: none
|
| Treatment protocol |
To induce neuronal differentiation, sub-confluent CAD cell cultures (50-60%) were transferred to serum-free media (DMEM:HAMS F12 (1:1) supplemented with 2mM Glutamine) and maintained in 15 cm2 culturing dishes for 5 days.
|
| Growth protocol |
CAD cells (Cath.-a-differentiated; generously donated from the Holzbaur Lab at the University of Pennsylvania) were grown in DMEM:HAMS F12 (1:1), supplemented with 2mM Glutamine, 1% penicillin/streptomycin, and 10% Fetal Bovine Serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Shah, P.P. et al. 2013), except that chromatin was sheared to an average size of <500 bp using the Covaris S220 Ultrasonicator. Equal aliquots of sonicated chromatin from undifferentiated and differentiated CAD neurons were used per immunoprecipitation reaction, and 10% of the amount was saved as input. Immunoprecipitation was performed using protein A Dynabeads (Life Technologies).
Sequencing libraries were prepared using NEBNext Ultra library preparation procedure, and then assessed for quality and quantity by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data file: none
|
| Data processing |
NextSeq sequencing data was demultiplexed using bcl2fastq2-v02.14.01.07; the ACSS2 CS DIFF was produced by a separate demultiplexing using bcl2fastq2-v2.15.0.4.
All reads were aligned to the mm10 reference genome using bowtie2.2.1. One alignment was allowed per read and 1 mismatch was allowed in the seed region (-N1 -k1).
Reads were tabulated in fixed windows or to genes provided in the iGenome mm10 UCSC annotations using featureCounts from the subread1.4.6 software package.
ACSS2 ChIP-seq data was normalized to input controls, while all histone acetylation ChIP-seq data was H3-subtracted.
The sub tracks showing a delta in differentiation were created by subtracting Input- or H3-adjusted undifferentiated from differentiated tracks.
Genome_build: GRCm38 (mm10 UCSC)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Jan 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shelley L. Berger |
| E-mail(s) |
bergers@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Berger
|
| Street address |
3400 CIVIC CENTER BLVD
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE76850 |
Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory [ChIP-seq] |
| GSE76854 |
Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory |
|
| Relations |
| BioSample |
SAMN04412706 |
| SRA |
SRX1530240 |
