|
| Status |
Public on Apr 01, 2024 |
| Title |
KO-R837-6h-rep2 [RNA Pol II ChIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow Derived Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: AbFlex® RNA Pol II antibody, Cat#91151, lot number 26520003
genotype: N4bp1 KO
cell type: Bone Marrow Derived Macrophages
treatment: R837 6h
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were aligned to the mouse reference (GRCm38) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads. MACS2 was used to call peaks.
Assembly: GRCm38
Supplementary files format and content: Peak calls in bed format relative to the input per sample
|
| |
|
| Submission date |
Nov 29, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Rohit Reja |
| E-mail(s) |
rejar@gene.com
|
| Phone |
+1-650-467-7615
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE218954 |
Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis [ChIP-seq] |
| GSE218958 |
Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis |
|
| Relations |
| BioSample |
SAMN31923089 |
| SRA |
SRX18410276 |
