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Sample GSM7785441

Query DataSets for GSM7785441

Status

Public on Apr 16, 2024

Title

EXOSC2 AID ESCs, HiC, 20 hr, rep2

Sample type

SRA

Source name

AID-FBEXOSC2 ESCs

Organism

Mus musculus

Characteristics

cell line: AID-FBEXOSC2 ESCs
cell type: mouse embryonic stem cell
treatment: IAA
time: 20 hour

Treatment protocol

EXOSC2 degradation was induced by treatment of IAA (0.5 mM, Sigma, Cat#: I5148) for indicated hours to adherent ESCs.

Growth protocol

AID-FBEXOSC2 ESCs were maintained in a complete ESC culture medium that consisted of DMEM (Corning) supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX (100× stock, Gibco), Penicillin-Streptomycin Solution (100× stock, Corning), MEM nonessential amino acids (100× stock, Gibco), nucleoside mix (100× stock, Millipore), 0.1 mM 2-mercaptoethanol (Gibco), and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, Millipore). The mESCs were seeded onto 0.1% gelatin-coated dishes. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.

Extracted molecule

genomic DNA

Extraction protocol

Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was subjected to MboI digestion, biotin end repairing and ligation, then reverse-crosslinking and DNA purification. The purified DNA was then sonicated and subjected to biotin pull down by C1 Streptavidin beads. Library construction procedures including end repairing, dATP tailing and adaptor ligation were proceeded on beads. Finally, the DNA was eluted and subjected to PCR and size selection for sequencing.
HiC libraries were constructed following TruSeq DNA preparation procedures including end repairing, dATP tailing, adaptor ligation and PCR amplification.

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

Data processing

Paired end raw reads of Hi-C libraries were aligned, processed and iteratively corrected using HiC-Pro (version 2.7.1b). To eliminate the possible effects on data analyses of variable sequencing depths, we combined valid_interaction_rmdup from replicates and randomly sampled equal numbers of valid_interaction_rmdup read pairs (n = 70 million) from each time point of IAA treatment for downstream analyses.
Assembly: mm9
Supplementary files format and content: hic, binary format for storing contact matrices and annotations of chromatin structural features

Submission date

Sep 18, 2023

Last update date

Apr 16, 2024

Contact name

Xue Han

E-mail(s)

xuehan89@126.com

Organization name

Tsinghua University

Department

School of Medicine