Nature - USA (2020-06-25)

4

nature research | reporting summary

October 2018

Animals and other organisms

Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research

Laboratory animals Female athymic nu/nu mice (Hsd:Athymic Nude-Foxn1nu, Envigo) were used at 8 weeks of age.

Wild animals not applicable

Field-collected samples not applicable

Ethics oversight The authors confirm that all animal experiments were performed in accordance with relevant guidelines and regulations. All

studies were approved by the Yale University Institutional Animal Care and Use Committee.

Note that full information on the approval of the study protocol must also be provided in the manuscript.

ChIP-seq

Data deposition

Confirm that both raw and final processed data have been deposited in a public database such as GEO.

Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links

May remain private before publication.

We did not generate ChIP-seq data in this study. Rather, we analyzed published and publicly available data. Raw ChIP-seq

data corresponding to dox-induced IDH1 R132H mutant (MUT) and uninduced parental (PAR) astrocyte cell lines after 40

passages in culture, as well as corresponding input data, were accessed from publicly available SRA data (SRP082568) from

experiments previously published in Turcan, S. et al. Mutant-IDH1-dependent chromatin state reprogramming, reversibility,

and persistence. Nat Genet 50, 62-72, doi:10.1038/s41588-017-0001-z (2018).

Files in database submission Not applicable. See comment above.

Genome browser session

(e.g. UCSC)

not applicable

Methodology

Replicates Not applicable. See comment above.

Sequencing depth Not applicable. See comment above.

Antibodies Not applicable. See comment above.

Peak calling parameters Not applicable. See comment above.

Data quality Not applicable. See comment above.

Software See comment above. For ChIP-seq analysis, data from Turcan, S. et al. Mutant-IDH1-dependent chromatin state

reprogramming, reversibility, and persistence. Nat Genet 50, 62-72, doi:10.1038/s41588-017-0001-z (2018) was aligned to

the GRhg38 (hg38) genome build using Bowtie2 (v2.3.4.1). H3K9me3 peaks were called using HOMER (v4.10) using

findPeaks with options -style histone -size 1000 -minDist 2500, filtered by P = 0.01.

Flow Cytometry

Plots

Confirm that:

The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).

The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of identical markers).

All plots are contour plots with outliers or pseudocolor plots.

A numerical value for number of cells or percentage (with statistics) is provided.

Methodology

Sample preparation For the EJ2 and EJ5 assays, reporter cells were washed with PBS, collected by trypsinization, then assayed for GFP expression by

flow cytometry. For cell cycle analysis, cells were fixed with cold ethanol for 1 h at 4C, then stained with Propidium iodide

solution.

Instrument Becton Dickinson FACSCalibur