|
| Status |
Public on Jul 07, 2022 |
| Title |
Input_ChIP-seq in Beko cells, Hypoxia_Input_2 |
| Sample type |
SRA |
| |
|
| Source name |
Beko pre-T cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Beko
cell type: pre-T cells
treatment: kept for 12 hours at 1% oxygen
chip antibody: none
|
| Treatment protocol |
Mouse pre-T (Beko) cells were treated with DMSO for 24 hours.
|
| Growth protocol |
Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi: 10.3791/55907)
Library-prep kit: Diagenode MicropPlex Library Preparation kit v2 (C05010012).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using TopHat v.2.1.1. or Hisat2 v.2.2.1
Count tables were generated from BAM files using the summarizeOverlaps function.
ChIP-seq aligment was performed using Bowite 2 v.2.3.5.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 and followed by MSPC to combine peak sets.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Count tables of raw read counts per gene in csv format.
Supplementary_files_format_and_content: ChIP-seq: bigWig files.
|
| |
|
| Submission date |
Jan 19, 2022 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Tobias Friedrich |
| E-mail(s) |
tobias.friedrich@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE194003 |
Characterization of the crosstalk between Notch signaling and hypoxia |
|
| Relations |
| BioSample |
SAMN25122605 |
| SRA |
SRX13832296 |
