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SRX10372521: GSM5176626: NICD_TCFKO_rep3_Input; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 35.5M spots, 2.9G bases, 1Gb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide histone mark and CTCF profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [ChIP-seq]
show Abstracthide Abstract
NOTCH1 is a well-established lineage specifier for T cells and amongst the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape during T-ALL initiation is unknown. Here we demonstrate an essential role for the high-mobility-group transcription factor Tcf1 in orchestrating chromatin accessibility and topology allowing for aberrant Notch1 signaling to convey its oncogenic function. Although essential, Tcf1 is not sufficient to initiate leukemia. The formation of a leukemia-prone landscape at the distal Notch1-regulated Myc enhancer, which is fundamental to this disease, is Tcf1-dependent and occurs within the earliest progenitor stage even before cells adopt a T lymphocyte or leukemic fate. Moreover, we discovered an additional evolutionarily conserved Tcf1-regulated enhancer element, in the distal Myc-enhancer, which is important for the transition of pre-leukemic cells to full-blown disease. Overall design: Histone marks and CTCF ChIP comparisons of sorted LSK derived from C57BL/6J; Sv/129 compound mice with Notch1 induced or Tcf1 knocked-down.
Sample: NICD_TCFKO_rep3_Input
SAMN18341049 • SRS8487308 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction 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.
Experiment attributes:
GEO Accession: GSM5176626
Links:
Runs: 1 run, 35.5M spots, 2.9G bases, 1Gb
Run# of Spots# of BasesSizePublished
SRR1399508735,530,5452.9G1Gb2022-01-23

ID:
13690435

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