|
| Status |
Public on Mar 17, 2022 |
| Title |
U5NSC_Del_Jun_3 |
| Sample type |
SRA |
| |
|
| Source name |
AutiCUTandRUN
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: U5 neural stem cells
genotype: Fbw7-/-
antibody: cJun Santa Cruz Cat #sc-1694
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
autocutandrun_protocols.io.pdf
cutandrun_manualdirectligation_protocol.io.pdf
autocutandrun_protocols.io.pdf
cutandrun_manualdirectligation_protocol.io.pdf
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Replicate 3
U5NSC_Jun_Del_merged.bw
|
| Data processing |
Library strategy: CUT&RUN
We used Bowtie2 with options "--end-to-end --very sensitive --no-overlap --no-dovetail --nounal --no-mixed --no-discordant -q -I -10 -X 700" to map the 25bp paired-end Illumina reads to hg19 genome.
CPM normalized bigwig files were generated using bedtools genomecov. Merged bigwig files that represents all three replicates were generating by merging bam files and then converting to bw.
Merged peak set for each target was used for further analysis. FeatureCounts in Subread 1.5.6 was used to count reads mapped to merged peaks in each samples.
Bioconductor package edgeR 3.26.8 was used to detect differential peaks between conditions. The filitered count matrix was normalized by TMM method.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: Bigwig files generated using bedtools genomecov.
Supplementary_files_format_and_content: Bigwig files representing 3 replicates (bam files from 3 replicates merged and converted to bw)
|
| |
|
| Submission date |
Sep 13, 2021 |
| Last update date |
Mar 19, 2022 |
| Contact name |
Heshani Nayanga Thirimanne |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Human Biology
|
| Lab |
Clurman
|
| Street address |
1100 Fairview AV N, D2-213
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE184037 |
Genome-wide mapping of histone modifications and transcription factor occupancy in Fbw7 mutant cells [CUTandRUN] |
| GSE184041 |
Genome-Scale Analysis of Transcriptional Regulation by the Fbw7 Ubiquitin Ligase |
|
| Relations |
| BioSample |
SAMN21416842 |
| SRA |
SRX12163736 |
