|
| Status |
Public on Jun 19, 2024 |
| Title |
EdU_HU_seq_shNT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
treatment: shNT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Methanol fixed cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-IT chemistry (Macheret M. and Halazonetis T., Nature protocol 2019). DNA was then purified by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation according to the published protocol (Macheret M and Halazonetis T., Nature protocol 2019).
HT-Chip-seq library preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
EduSeq_shNT_HU_merge.bw
|
| Data processing |
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to hg19 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Spike-ins were aligned using mm10 genome assembly
Replicates of the same condition were merged after alignment and spike-in normalization to a single BAM file for the analyses
Peak calling was carried out with epic2 with the following options: -gn hg19 --gaps-allowed 10 --bin-size 400
Assembly: hg19
Supplementary files format and content: *.bed.gz: genomic regions (peaks) called from the merge of the triplicates
Supplementary files format and content: *.bw: bigWig files of the merged replicates
|
| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Stefano Campaner |
| E-mail(s) |
stefano.campaner@iit.it
|
| Organization name |
fondazione Istituto italiano di tecnologia
|
| Department |
Center for Genomic Science
|
| Lab |
Cancer Biology
|
| Street address |
Via adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE236550 |
CDK12 prevents MYC-induced transcription-replication conflicts [EdU-seq] |
| GSE236553 |
CDK12 prevents MYC-induced transcription-replication conflicts |
|
| Relations |
| BioSample |
SAMN36313335 |
| SRA |
SRX20904028 |
