|
| Status |
Public on Jun 30, 2023 |
| Title |
MEFs, Δ-C60, Pol II ChIP-seq, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryos
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryos
cell line: Mouse Embryonic Fibroblasts (MEFs)
cell type: Fibroblasts
chip antibody: Pol II (8wg16, Santa Cruz #56767)
genotype: Nelfb -/-; {delta}-C60
treatment: pLenti-{delta}-C60-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP
|
| Growth protocol |
10% FBS in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with IAA at 0.5mM for 6 hours, if indicated, and then fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented with micrococcal nuclease and immunoprecipitated with Pol II or flag antibodies.
ChIP-seq libraries were prepared using the KAPA Hyperprep Library Preparation Kit complemented with Roche SeqCap Adapter Kit A. Post amplification libraries were size selected at 0.7-0.9X using Kapa cleanup beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Raw ChIP-seq data in FASTQ format was aligned to mm10 reference genome using bowtie2
The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
The coverage (the number of reads per bin) track was generated by deepTools. The size of each bin was set at 1bp and the coverage was normalized by Reads Per Kilobase per Million mapped reads (RPKM).
Scores for each gene were calculated by computeMatrix command. The gene bodies were scaled to 3kb and the region between 1kb upstream to TSS and 1.5kb downstream of TES were included in the analysis.
Assembly: mm10
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Jun 06, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Haihui Pan |
| E-mail(s) |
panh@email.gwu.edu
|
| Organization name |
George Washington University
|
| Department |
Biochemistry and Molecular Medicine
|
| Street address |
2121 I St NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20052 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE205504 |
Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN28869542 |
| SRA |
SRX15596405 |
