|
Status |
Public on Apr 01, 2024 |
Title |
WT-R837-6h-rep1 [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: WT 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
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|
|
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 |
SAMN31923092 |
SRA |
SRX18410273 |