|
| Status |
Public on Aug 19, 2021 |
| Title |
Input_wo_IL-6_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Input_wo_IL-6_rep1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: murine breast cancer 4T1 cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, cells were cultured in 20 cm dishes and stimulated using IL-6. Chromatin (5 μg) was prepared using 4 rounds of sonication (30 sec on and 30 sec off) in precooled conditions. DNA disrupted into fragments of 200-1000 bp was immunoprecipitated using Protein-G Dynabeads (Novex) bound with an anti-HA antibody to detect Arid5a (4 μg each). Normal IgG (4 μg) was used as a control, and libraries were constructed from immunoprecipitated DNA.
The ChIP-Seq library of precipitated DNAs was prepared using KAPA Library Preparation Kits for Illumina (Kapa Biosystems).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HA-tagged Arid5a-overexpressing 4T1 cells following stimulation without IL-6 (100 ng/ml)
|
| Data processing |
Prepared libraries were sequenced using a NovaSeq 6000 platform (Illumina), and 101 bp paired-end reads were obtained.
After adapter trimming by Cutadapt ver2.7, the trimmed reads were mapped to the mouse reference genome sequences (mm10) using Bowtie2 ver. 2.3.5.1. Peak calling was performed with MACS2 ver. 2.2.7.1
Genome_build: Sequence reads were aligned to the mouse genome (mm10).
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions
|
| |
|
| Submission date |
Jun 15, 2021 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Daisuke Okuzaki |
| E-mail(s) |
dokuzaki@biken.osaka-u.ac.jp
|
| Phone |
+81-6-6879-4935
|
| Organization name |
Osaka univ.
|
| Department |
Immunology Frontier Research Center
|
| Lab |
Human Immunology （Single Cell Genomics)
|
| Street address |
Yamadaoka 3-1
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE178249 |
The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway (ChIP-Seq) |
| GSE178252 |
The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway |
|
| Relations |
| BioSample |
SAMN19713820 |
| SRA |
SRX11149860 |
