|
| Status |
Public on Jan 21, 2022 |
| Title |
NICD_TCFKO_ATAC-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
BM LSK (Lin- Sca1+ cKit+)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J; Sv/129
transgene: R26 N1IC lox/+ Tcf7 lox/lox Mx1Cre
cre: Mx1Cre induction 2ug/g b.w. poly(I:C)
group: NICD_TCFKO
cell type: BM LSK (Lin- Sca1+ cKit+)
replicate: 1
batch: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50'000 LSK cells were isolated from induced bone marrow and processed as in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Library was amplify using NEBNext High-Fidelity 2X PCR Master Mix and size selection was performed using Agencourt AMPure XP beads.
sequencing protocol: Prepared libraries were sequenced on the Illumina NextSeq 500 with paired-end 2x75nt reads to obtain at least 35 million reads per sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC3_R1_L001
|
| Data processing |
Illumina bcl2fastq 2.19.1 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed.
Reads were aligned to mouse genome build mm10 using BWA-MEM (0.7.15).
Properly paired good quality reads were filtered with samtools (v1.3.1) using samtools view -b -h -f 0x2 -q 2.
Peaks were called using MACS2 (2.1.1.20160309 ) using macs2 callpeak -t -f BAMPE -g mm -B --nomodel --nolambda -q 0.05 --keep-dup all --broad --broad-cutoff 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each ChIP sample - generated by MACS2
|
| |
|
| Submission date |
Mar 17, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Nadine Fournier |
| E-mail(s) |
nadine.fournier@sib.swiss
|
| Organization name |
Agora Cancer Research Center & Swiss Institute of Bioinformatics
|
| Lab |
Translational Data Science Facility
|
| Street address |
Agora Cancer Research Center, Bugon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE169118 |
Chromatin accessibility profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [ATAC-seq_mouse] |
| GSE169121 |
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology. |
|
| Relations |
| BioSample |
SAMN18341014 |
| SRA |
SRX10372534 |
