|
| Status |
Public on Jan 21, 2022 |
| Title |
CTCF_NICD_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/+ Mx1Cre
cre: Mx1Cre induction 2ug/g b.w. poly(I:C)
facs sorting: Target population from bone marrow: CD45.2+ eGFP+ Lin- Sca1+ cKit+
group_chip: NICD_TCFWT_CTCF
group_cells: NICD_TCFWT
replicate: rep1
chip antibody: 1μg CTCF antibody (Diagenode Cat# C15410210, RRID:AB_2753160)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed on chromatin from 20,000 sortedLSK cells. Sorted cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies Cat# 28906), quenched with 0.125 M glycine and frozen at -80 °C and stored until further processing.
ChIP reaction was performed with Diagenode True MicroChIP Kit (Diagenode Cat# C01010130) with modifications of the manual detailed below. Lysed samples were sonicated using Diagenode Bioruptor Pico (Diagenode Cat# B01060010).
ChIP and input libraries for sequencing were prepared with MicroPlex Library Preparation Kit (Diagenode Cat# C0101134). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter Cat# A63880).
sequencing protocol: The libraries were sequenced by Gene Expression Core Facility of EPFL using the Illumina NextSeq 500 platform and the 75-bp paired-end configuration to obtain at least 30 million reads per sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
77061-RNIC_S2
|
| 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 (0.7.13).
Properly paired good quality reads were filtered with samtools (v1.5) 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 --call-summits (CTCF) or --broad --broad-cutoff 0.1 (Other ChIP).
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) |
| GSE169117 |
Genome-wide histone mark and CTCF profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [ChIP-seq] |
| GSE169121 |
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology. |
|
| Relations |
| BioSample |
SAMN18341046 |
| SRA |
SRX10372524 |
