|
| Status |
Public on Oct 01, 2024 |
| Title |
KEC, Asy NAQC, HNF1b, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
KEC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KEC
cell type: Kidney epithelial cells
genotype: WT
cell cycle_stage: Asynchronous
chip antibody: HNF1b (ABclonal custom made rabbit polyclonal)
|
| Treatment protocol |
Mitotic cells were obtained with a thymidine block (2mM 24h) followed by an incubation in 5uM STLC (S-trityl-L-cysteine) for 8-14 h
The HNF1β-knockout KEC cell line was created by CRISPR/Cas9 targeting of HNF1b's exon 1.
|
| Growth protocol |
KECs (kidney epithelial cells) were grown in DMEM, 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAs from ChIP or Input were de-crosslinked and extracted with the IPure kit v2 (Diagenode).
Libraries were prepared from 1ng of immunoprecipitated DNA or Inputs with the MicroPlex v2 kit (Diagenode), according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BamCoverage pool of Asy_Naqc_HNF1_1, Asy_Naqc_HNF1_2
Asy_Naqc_HNF1_pool_bamCoverage_CPM.bigwig
Peaks pool of Asy_Naqc_HNF1_1, Asy_Naqc_HNF1_2
gem_Asy_Naqc_HNF1_pool_all_bams.GPS_events.narrowPeak
|
| Data processing |
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with 2 replicates (each replicate was sequenced in two sessions: set1 + set2 )
bams files from set1 and set2 were pooled with samtools merge
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize = 1
Supplementary files format and content: Peaks were called using using GEM version 3.4 http://cgs.csail.mit.edu/gem/, narrowPeak format
|
| |
|
| Submission date |
Oct 11, 2023 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Marco PONTOGLIO |
| E-mail(s) |
[email protected]
|
| Phone |
0610151577
|
| Organization name |
Inserm
|
| Department |
Growth and Signalling
|
| Lab |
Epigeneitc and development
|
| Street address |
Inserm U1016, 24 rue du Faubourg Saint-Jacques
|
| City |
Paris |
| State/province |
Choisir votre état |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE245070 |
Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [ChIPseq_KEC] |
| GSE245087 |
Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B |
|
| Relations |
| BioSample |
SAMN37767854 |
| SRA |
SRX22058391 |
