|
| Status |
Public on Sep 26, 2023 |
| Title |
NIH, HS, DMSO, MAL, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
NIH 3T3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH 3T3
cell type: fibroblast
chip antibody: MAL
drug-treatment: DMSO
treatment: heat shock
|
| Treatment protocol |
Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins either in 37°C waterbath (S2R+ cells) or 42°C waterbath (NIH 3T3 cells).
|
| Growth protocol |
Mammalian cell line NIH 3T3 was cultured in DMEM supplemented with 10 % Fetal Bovine Serum (FBS) and maintained in humidified 95% air by 5% CO2 incubator at + 37°C. Schneider cell line (S2R+) cultured in Schneider’s Drosophila Medium (Thermo Fisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (Thermo Fisher Scientific) and 1 x antibiotic-antimycotic solution (penicillin, streptomycin, Amphotericin B; Thermo Fisher Scientific) at +25°C incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
samples were were fixed in 1% PFA for 10 min at RT, homogenized using a pestle in 300 ml of RIPA buffer, and sonicated with Bioruptor (Diagenode). Immunoprecipitations were carried out with 5 µg antibody overnight at 4°C in a rotating wheel.
ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-Seq data sets were aligned using Bowtie2
Assembly: dm6 (BDGP6.87), mm10 (GRCm38)
Supplementary files format and content: bigwig files were generated using DeepTools with RPKM normalization method
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Maria Sokolova |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
Institute of Biotechnology
|
| Lab |
Nuclear Actin Lab
|
| Street address |
Viikinkaari 5
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE243873 |
CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses (ChIP-seq) |
| GSE244232 |
CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses |
|
| Relations |
| BioSample |
SAMN37517909 |
| SRA |
SRX21864857 |
