title: GS-9_abemaciclib_REP_B

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

description: Library name: 24049a044

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, central nervous system

growth_protocol: LN18 and LN229 glioma cell lines were cultured in DMEM (Gibco, Carlsbad, CA, US) supplemented with 10% fetal calf serum (Thermo Fisher Scientific, Waltham, MA, US) and 50 µg/mL Gentamicin (Thermo Fisher Scientific, Waltham, MA, US). GS-9 cells were grown in Neurobasal®-A medium (Gibco, Carlsbad, CA, US) supplemented with 2% B27 without vitamin A (Invitrogen, Waltham, MA, US), 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA, US), and 0.02 µg/mL fibroblast growth factor (FGF) and epidermal growth factor (EGF) (PeproTech, Cranbury, NJ, US).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were treated with 2µM (LN229), 0.75µM (LN18), or 3µM (GS-9) of abemaciclib for 48 hours, or corresponding concentration of DMSO solvent.

value: tumor, central nervous system

value: glioma

value: parental

value: abemaciclib


title: in vitro Daxx WT microglia LPS-24h-3 [15395]

status: Public on Jun 22 2026

type: SRA

city: Bonn

first: Paolo

last: Salomoni

address: Venusberg-Campus 1, Building 99

country: Germany

institute: DZNE

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15395_merged

library_source: transcriptomic

data_processing:
Raw FASTQ files were trimmed by Trimgalore and aligned to genome mm10 by STAR. SAM files were filter by mapq>=10 and transformed to BAM by samtools. Gene count table was created by featureCounts.
Assembly: mm10
Supplementary files format and content: read counts from featureCounts

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for contruction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

tag: tissue

value: brain

tag: cell type

value: microglia

tag: genotype

value: Cx3cr1CreERT,Daxx wt/wt

tag: treatment

value: Tamoxifen, LPS


title: in vitro Daxx KO microglia LPS-24h-1 [15396]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15396_merged

value: Cx3cr1CreERT,Daxx flox/flox


title: in vitro Daxx WT microglia LPS-24h-2 [15394]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15394_merged


title: GS-9_abemaciclib_REP_A

description: Library name: 24049a043

organism: Homo sapiens

tag: cell line


title: Bone marrow MNCs, Human, Patient 2, untreated

city: Salamanca

first: Rósula

last: Garcia Navas

state: Salamanca

address: Campus Miguel de Unamuno, P. Universidad de Coimbra s/n. Lab.1

country: Spain

institute: Centro de Investigación del Cáncer

description:
Library name: S12077Nr5
BM-MNCs from newly diagnosed CML patient. Untreated control.

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20)
Adapter trimming was performed using Skewer (v0.2.2). No quality trimming was applied.
Trimmed reads were aligned to mm10 (mouse) or hg19-cegat (human) using STAR aligner (v2.7.3). In human samples, pseudoautosomal regions on chromosome Y were masked
Differential expression analysis was performed using DESeq2 (v1.24.0) in R (v4.0.4), applying a negative binomial model to raw gene counts
Assembly: Mouse: GRCm38 (mm10) Human: GRCh37 (hg19); pseudoautosomal regions on chrY were masked
Supplementary files format and content: Tab-delimited text files including raw read counts (raw_counts.tsv), normalized counts (normalized_counts.tsv), and differential expression analysis results (*_DEA.tsv, *_significant_DEA.tsv). Rows represent Ensembl gene IDs; columns correspond to sample names (library name).

source_name: Bone marrow

growth_protocol: Mouse samples: Bone marrow was isolated directly after treatment in vivo without prior culture. Human samples: BM-MNCs were cultured for 48h ex vivo in IMDM supplemented with recombinant human Flt3L, SCF, IL-3, IL-6, and TPO prior to RNA extraction.

extract_protocol:
Total RNA was extracted from bone marrow cells using the QIAGEN RNeasy Plus Mini Kit, following the manufacturer’s instructions. RNA integrity was confirmed using Qubit 4
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche), following the manufacturer’s protocol. Paired-end sequencing was performed on an Illumina NovaSeq 6000 platform

treatment_protocol: Mouse: Mice were treated orally with imatinib (IMA, 60 mg/kg, once daily) and/or BI-3406 (50 mg/kg, twice daily) for 5 weeks. BI-3406 was administered every 6 hours, following a 5 days on / 2 days off schedule. Control,non-transgenic mice and SOS1 KO received vehicle under the same regimen. Human: BM-MNCs from newly diagnosed CML patients were treated ex vivo for 48 hours in IMDM medium supplemented with recombinant human Flt3L, SCF, IL-3, IL-6, and TPO. Treatments included 500 nM imatinib, 1 µM BI-3406, or their combination. Untreated controls were cultured in parallel in the same medium without inhibitors.

value: Bone marrow

value: BM


title: SKO_24hDMSO_3

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

description: Library name: Sample 30

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: Prostate

growth_protocol: SKO, DKO, DKOcr105, and TKO cells were cultured in DMEM/high glucose (Gibco 11995-065) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% FBS (Corning MT35010CV). DKOcr298 was cultured in phenol-red free DMEM/high glucose (Gibco 31053-028) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% charcoal-stripped FBS (Millipore Sigma F6765).

extract_protocol:
Total RNA was extracted using a Qiagen AllPrep RNA/DNA mini kit (Qiagen 80204) according to the manufacturer's protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: TKO and DKOcr298 cells were treated with BET inhibitors (500nM ZEN or 1µM JQ1) for 24hrs with corresponding vehicle (DMSO) controls; TKO and DKOcr298 were treated with BET inhibitor (500nM ZEN), DNA methyltransferase inhibitor (100nMdAZA), or the combination (500nM ZEN + 100nM dAZA) daily for 72 hrs with corresponding vehicle (DMSO) controls.

value: Prostate

value: SKO

value: Prostate Cancer Cell Line

value: DMSO 24hr


title: TKO_24hDMSO_1

description: Library name: Sample 31

value: TKO


title: in vitro Daxx KO microglia LPS-6h-2 [15391]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15391_merged


title: in vitro Daxx WT microglia LPS-24h-1 [15393]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15393_merged


title: SKO_24hDMSO_2

description: Library name: Sample 29


title: in vitro Daxx KO microglia LPS-6h-3 [15392]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15392_merged


title: in vitro Daxx KO microglia LPS-6h-1 [15390]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15390_merged


title: GS-9_DMSO_REP_C

description: Library name: 24049a039

value: DMSO


title: GS-9_DMSO_REP_B

description: Library name: 24049a038

value: tumor, central nervous system


title: Met3_AKP_replicate2

city: New York

first: Norihiro

last: Goto

state: NY

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

description: Library name: ATAC_1237_Met

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were merged using Samtools.
Peaks were called on the merged BAM using MACS2.
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: ngoto_ATACseq_met_peak_tiled_reads.txt.gz is a tab delimited text of counts for filtered peaks

molecule: genomic DNA

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated by TrypLE Express for 10 min at 37ºC, passed through a 40 μm filter, and a total of 50,000 cells were centrifuged and washed twice with PBS. Cells are resuspended in 50 μl of buffer with TDE1 enzyme and incubated at 37°C for 30 min with gentle agitation. DNA was isolated using the Qiagen MinElute PCR Purification Kit.
ATAC-seq libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. 2 x 75 paired-end sequencing was performed on an Illumina NextSeq 500.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: TKO_72hZEN_1

description: Library name: Sample 49

value: 500nM ZEN 72hr


title: Primary3_AKP_replicate1

description: Library name: ATAC_1242_Primary


title: in vitro Daxx WT microglia LPS-6h-3 [15389]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15389_merged

value: brain


title: SKO_24hDMSO_1

description: Library name: Sample 28


title: in vitro Daxx WT microglia LPS-6h-2 [15388]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15388_merged

value: microglia


title: Met2_AKP_replicate3

description: Library name: ATAC_1188_Met


title: TKO_72hDMSO_1

description: Library name: Sample 46

value: DMSO 72hr


title: GS-9_DMSO_REP_A

description: Library name: 24049a037

value: glioma

value: parental


title: in vitro Daxx WT microglia LPS-6h-1 [15387]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15387_merged

value: Cx3cr1CreERT,Daxx wt/wt

value: Tamoxifen, LPS


title: DKOcr298_72hZEN_3

description: Library name: Sample 27

value: Prostate


title: in vitro Daxx KO microglia control-3 [15386]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15386_merged

value: Cx3cr1CreERT,Daxx flox/flox

value: Tamoxifen, PBS


title: LN18_abemaciclib_REP_C

description: Library name: 24049a030

value: abemaciclib


title: in vitro Daxx KO microglia control-2 [15385]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15385_merged


title: DKOcr298_72hZEN_2

description: Library name: Sample 26

value: Prostate Cancer Cell Line


title: Met1_AKP_replicate3

description: Library name: ATAC_1027_Met


title: in vitro Daxx KO microglia control-1 [15384]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15384_merged


title: LN18_abemaciclib_REP_B

description: Library name: 24049a029


title: in vitro Daxx WT microglia control-3 [15383]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15383_merged


title: DKOcr298_72hZEN_1

description: Library name: Sample 25


title: TKO_72hCombo_3

description: Library name: Sample 42

value: TKO

value: 500nM ZEN + 100nM dAZA 72hr


title: TKO_72hdAZA_1

description: Library name: Sample 43

value: 100nM dAZA 72hr


title: in vitro Daxx WT microglia control-2 [15382]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15382_merged


title: in vitro Daxx WT microglia control-1 [15381]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15381_merged


title: DKOcr298_72hDMSO_3

description: Library name: Sample 24


title: LN18_abemaciclib_REP_A

description: Library name: 24049a028

value: tumor, central nervous system


title: in vitro microglia LPS-72h-3 [LPS_72h_3_S18]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_72h_3_S18

value: wild type

value: LPS


title: in vitro microglia LPS-72h-2 [LPS_72h_2_S17]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_72h_2_S17

value: brain

value: microglia


title: LN18_DMSO_REP_C

description: Library name: 24049a027

value: glioma

value: DMSO


title: DKOcr298_72hDMSO_2

description: Library name: Sample 23

value: DMSO 72hr


title: LN18_DMSO_REP_B

description: Library name: 24049a026

value: parental


title: in vitro microglia LPS-72h-1 [LPS_72h_1_S16]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_72h_1_S16


title: in vitro microglia LPS-48h-3 [LPS_48h_3_S15]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_48h_3_S15


title: DKOcr298_72hDMSO_1

description: Library name: Sample 22

value: Prostate


title: in vitro microglia LPS-48h-2 [LPS_48h_2_S14]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_48h_2_S14


title: in vitro Daxx KO NPCs+Cre-1 [S514Nr2]

description:
20200214_countTable_daxxKo.txt
S514Nr2

source_name: E13.5 embryo cortex

value: E13.5 embryo cortex

value: neuron progenetor cells

value: Daxx flox/flox

value: Transfection with Cre construct


title: in vitro Daxx KO NPCs+Cre-2 [S514Nr7]

description:
20200214_countTable_daxxKo.txt
S514Nr7


title: LN18_DMSO_REP_A

description: Library name: 24049a025


title: in vitro microglia LPS-48h-1 [LPS_48h_1_S13]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_48h_1_S13


title: DKOcr298_72hdAZA_3

description: Library name: Sample 21

value: Prostate Cancer Cell Line


title: in vitro microglia LPS-24h-3 [LPS_24h_3_S12]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_24h_3_S12


title: LN229_sgAMBRA1_abemaciclib_REP_C

description: Library name: 24049a024

value: abemaciclib


title: in vitro microglia LPS-24h-2 [LPS_24h_2_S11]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_24h_2_S11


title: TKO_24hJQ1_2

description: Library name: Sample 35

value: TKO

value: 1µM JQ1 24hr


title: in vitro Daxx KO microglia LPS-48h-3 [15404]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15404_merged

value: Cx3cr1CreERT,Daxx flox/flox

value: Tamoxifen, LPS


title: Bone marrow MNCs, Human, Patient 1, BI3406

description:
Library name: S12077Nr3
BM-MNCs from newly diagnosed CML patient treated ex vivo with 1 µM BI-3406 for 48h.

value: Bone marrow


title: TKO_24hJQ1_3

description: Library name: Sample 36


title: DKOcr298_72hdAZA_2

description: Library name: Sample 20

value: 100nM dAZA 72hr


title: in vitro microglia LPS-24h-1 [LPS_24h_1_S10]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_24h_1_S10

value: brain

value: microglia

value: wild type

value: LPS


title: in vitro microglia LPS-6h-3 [LPS_6h_3_S9]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_6h_3_S9


title: LN229_sgAMBRA1_abemaciclib_REP_B

description: Library name: 24049a023

value: tumor, central nervous system

value: glioma


title: in vitro microglia LPS-6h-2 [LPS_6h_2_S8]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_6h_2_S8


title: in vitro Daxx WT microglia LPS-48h-3 [15401]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15401_merged

value: Cx3cr1CreERT,Daxx wt/wt


title: in vitro microglia LPS-6h-1 [LPS_6h_1_S7]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_6h_1_S7


title: in vitro microglia LPS-2h-3 [LPS_2h_3_S6]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_2h_3_S6


title: LN229_sgAMBRA1_DMSO_REP_C

description: Library name: 24049a021

value: DMSO


title: in vitro microglia LPS-2h-1 [LPS_2h_1_S4]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_2h_1_S4

value: PBS


title: DKOcr298_72hCombo_2

description: Library name: Sample 17

value: Prostate

value: Prostate Cancer Cell Line

value: 500nM ZEN + 100nM dAZA 72hr


title: in vitro Daxx KO microglia LPS-24h-3 [15398]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15398_merged


title: LN229_sgAMBRA1_DMSO_REP_B

description: Library name: 24049a020


title: in vitro microglia control-2 [Control_2_S2]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
Control_2_S2


title: DKOcr298_72hCombo_1

description: Library name: Sample 16


title: in vitro microglia control-1 [Control_1_S1]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
Control_1_S1

value: no treatment


title: Freshly isolated mouse hepatocyte DRIP-seq

city: Szeged

first: Lajos

last: Mates

address: Temesvari krt. 62.

department: Institute of Genetics

country: Hungary

institute: Biological Research Centre

description: RNA/DNA hybrids isolation and identification

data_processing:
Library strategy: DRIP-seq
The read mapping was performed using the Burrows-Wheeler algorithm (bwa) program. Reads were mapped to the Mus musculus reference genome mm10/GRCm38.
Model-based Analysis of ChIP-seq (MACS2) was used for peak calling.
Finally, the ENCODE black list overlapping peaks were removed using BEDTools program
Genome_build: Mus musculus reference genome mm10/GRCm38.
Supplementary_files_format_and_content: The processed data files have BED format, containing the result of MACS2 peak calling after ENCODE black list removal.

source_name: mouse liver

extract_protocol:
DNA extraction, digestion and the precipitation of DNA-RNA hybrids with the S9.6 antibody were  performed as described (Sanz, L.A. and Chedin, F. Nature Protocols 14;1734-1755.(2019).
Standard Illumina protocol.

treatment_protocol: Hepatocyte isolation

tag: strain

value: freshly isolated (4 ° C cooling)

value: liver

value: hepatocyte


title: DKOCr298_24hZEN_3

description: Library name: Sample 15

value: 500nM ZEN 24hr


title: LN229_abemaciclib_REP_C

description: Library name: 24049a009

value: parental

value: abemaciclib


title: GS-9_abemaciclib_REP_C

description: Library name: 24049a045


title: LN229_sgAMBRA1_DMSO_REP_A

description: Library name: 24049a019


title: in vitro Daxx KO microglia LPS-24h-2 [15397]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15397_merged

value: brain

value: microglia

value: Cx3cr1CreERT,Daxx flox/flox

value: Tamoxifen, LPS


title: DKOCr298_24hZEN_2

description: Library name: Sample 14


title: CUT&RUN FOSL2 in SKUT1B

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description: Library name: CR-LMS-SKUT1B-N, Cut_Run

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by Bowtie2
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: hg38
Supplementary files format and content: peaks files: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig files: .bw
Library strategy: CUT&RUN

growth_protocol: human cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Epicypher cut and run protocol v2.1
Epicypher CUTANA™ CUT&RUN Library Prep Kit

tag: disease state

value: Leiomyosarcoma

value: leiomyosarcoma cell


title: CUT&RUN BACH2 in SKUT1B

description: Library name: CR-LMS-SKUT1B-M, Cut_Run


title: LN229_abemaciclib_REP_B

description: Library name: 24049a008

value: tumor, central nervous system

value: glioma


title: CUT&RUN NFIX in SKUT1B

description: Library name: CR-LMS-SKUT1B-L, Cut_Run


title: DKOCr298_24hZEN_1

description: Library name: Sample 13

value: Prostate

value: Prostate Cancer Cell Line


title: CUT&RUN NFIC in SKUT1B

description: Library name: CR-LMS-SKUT1B-K, Cut_Run


title: CUT&RUN NFIB in SKUT1B

description: Library name: CR-LMS-SKUT1B-J, Cut_Run


title: DKOCr298_24hJQ1_3

description: Library name: Sample 12

value: 1µM JQ1 24hr


title: CUT&RUN NFIA in SKUT1B

description: Library name: CR-LMS-SKUT1B-I, Cut_Run


title: LN229_DMSO_REP_C

description: Library name: 24049a003

value: DMSO


title: DKOCr298_24hJQ1_2

description: Library name: Sample 11


title: DKOCr298_24hJQ1_1

description: Library name: Sample 10


title: LN229_DMSO_REP_A

description: Library name: 24049a001


title: DKOCr298_24hDMSO_3

description: Library name: Sample 9

value: DMSO 24hr


title: CUT&RUN NFIC in SKLMS01

description: Library name: CR-LMS-SKLMS01-K, Cut_Run


title: CUT&RUN NFIB in SKLMS01

description: Library name: CR-LMS-SKLMS01-J, Cut_Run


title: DKOCr298_24hDMSO_2

description: Library name: Sample 8


title: 13EP_pos_0_250305_invitro12hr

status: Public on Jun 23 2026

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

description: Library name: Sample 21

data_processing:
Transcript abundance was determined from FASTQ files using Salmon (v1.8.0) and the Ensembl reference transcript sequences. Transcript per million (TPM) values and gene level counts were calculated using the tximport R Bioconductor package (v1.22.0). Differential gene expression analysis was performed with the DESeq2 R Bioconductor package (v 1.44.0) .
Assembly: hg38
Supplementary files format and content: raw counts from DESeq2

extract_protocol:
RNA was harvested using the trizol-chloroform technique followed by the Qiagen Rneasy micro kit.
100ng of total RNA was used to generate RNA-Seq libraries using Illumina stranded mRNA kit (Catalog#: 20040534), following the manufactures protocol.   Libraries prepared with unique dual indexes were pooled at equal molar ratios.

treatment_protocol: Human abdominal subcutaneous adipose tissue was collected 7-10 days before, or 3-hours following, a graded exercise test on a treadmill. In vitro adipocytes were collected 12-hours following incubation with plasma collected either in the resting (no exercise) state, or with plasma collected immediately following sprint-interval exercise or moderate-intensity exercise.

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte

value: MIE Plasma


title: YM115-3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA36627

data_processing:
Sequencing was performed on the NovaSeq 6000 platform in 101-base single-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.3.5.1 and SAMtools ver.1.2.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells using the RNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
The cDNA libraries were constructed according to the manufacturer's instructions using the TruSeq Stranded mRNA Library Prep (Illumina, Inc., San Diego, CA).


title: CUT&RUN NFIA in SKLMS01

description: Library name: CR-LMS-SKLMS01-I, Cut_Run


title: YM115-2

description: Library name: GA36626


title: CUT&RUN H3K4me3 in SKUT1B

description: Library name: CR-LMS-SKUT1B-G, Cut_Run


title: CUT&RUN H3K4me3 in SKLMS01

description: Library name: CR-LMS-SKLMS01-G, Cut_Run


title: 10EC_pos_0_250305_invitro12hr

description: Library name: Sample 19

value: SIE Plasma


title: DKOCr298_24hDMSO_1

description: Library name: Sample 7


title: YM115-1

description: Library name: GA36625


title: CUT&RUN FOSL2 in Leio012

description: Library name: CR-LMS-Leio012-N, Cut_Run


title: CUT&RUN NFIX in Leio012

description: Library name: CR-LMS-Leio012-L, Cut_Run


title: CUT&RUN NFIC in Leio012

description: Library name: CR-LMS-Leio012-K, Cut_Run


title: DMSO-2

description: Library name: GA36623


title: CUT&RUN NFIB in Leio012

description: Library name: CR-LMS-Leio012-J, Cut_Run


title: DKOCr105_24hDMSO_1

description: Library name: Sample 4


title: CUT&RUN NFIA in Leio012

description: Library name: CR-LMS-Leio012-I, Cut_Run


title: CUT&RUN H3K4me3 in Leio012

description: Library name: CR-LMS-Leio012-G, Cut_Run


title: DKO_24hDMSO_3

description: Library name: Sample 3

value: DKO


title: CUT&RUN IgG control in Leio012

description: Library name: CR-LMS-Leio012-C, IgG


title: LS8817, day3, Palbo, rep2, techrep3, ATAC

first: Viviana

middle: I.

last: Risca

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description: Library name: day3_Palbo_Biorep2.3

data_processing:
Adapters were trimmed using cutadapt
Reads were aligned with bowtie2 2.3.4.3 to the hg38 genome. Following this, duplicate reads and reads mapping to the mitochondrial genome were removed.
Bam files were converted to bedpe files, which were then converted to tagAlign files for MACS2 to call peaks on, areas of the genome enriched for aligned sequencing reads, indicating hyperaccessibility. MACS2 parameters were -g 2.7e9 -p 0.2 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits.
Reproducible peaks across technical replicates per condition were kept using Irreproducible Discovery Rate (Li et al. 2011)
A master nonredundant peak set was generated using a custom iterative peak filtering script which selects the peak with the lowest q-value generated by MACS2 from a set of overlapping peaks
Peaks were fixed to 500bp in length, with 250bp extending from the summit identified by MACS2
Fragment counts under peaks were counted using chromVAR’s getCounts function(Schep et al. 2017)
Assembly: hg38
Supplementary files format and content: Files ending in "scaleFactornorm.bw" are coverage bigwig tracks normalized by sequencing depth. Files ending in "scaleFactornorm_cutsCoverage.bw" are normalized coverage of Tn5 insertion sites (fragment ends). If the file contained the string "merged" it means that bams across biological and technical replicates for that condition were merged prior to generating the bigwig file.
Supplementary files format and content: .narrowPeak files are peaks called for each technical replicate by MACS2.
Supplementary files format and content: summits.bed files are the summits of peaks identified by MACS2

source_name: soft tissue sarcoma

growth_protocol: Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.

extract_protocol:
Cells were treated in culture medium with DNase (Worthington cat# LS002007) at a final concentration of 200 U/mL at 37 °C for 30 mins, then washed twice with PBS at 500g, RT. Approximately ~50,000-60,000 cells were used for each transposition reaction. Following permeabilization, 2.5 µL of Illumina TDE1 enzyme was used for transposition at 37°C for 30 minutes.
Libraries were PCR amplified for 8-13 cycles with Illumina i5 or i7 barcoded primers and were cleaned up pre- and post-amplification following the manufacturer’s instructions using Zymo DNA Clean and Concentrator-5 Kit. Fragment length distribution and DNA amount was quantified via Tapestation and Qubit to assess for quality prior to sequencing.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with either 1 µM palbociclib or 100 nM doxorubicin, with media changes every 2–3 days until harvest.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day3 palbociclib (1uM)


title: HUtSMC ChIP-seq Input

description: Library name: SM HUtSMC Input, ChIP

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by BMA
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs2 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: hg38
Supplementary files format and content: .bigwig

source_name: HUtSMC

growth_protocol: Mouse melanoma cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Following the protocol on: Terranova, Christopher, et al. "An integrated platform for genome-wide mapping of chromatin states using high-throughput ChIP-sequencing in tumor tissues." Journal of visualized experiments: JoVE 134 (2018).
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: Normal

value: HUtSMC

value: Human uterine smooth muscle cells

tag: chip antibody

value: ChIP-seq Input


title: DKOCr105_24hDMSO_2

description: Library name: Sample 5

value: Prostate

value: Prostate Cancer Cell Line


title: DKO_24hDMSO_2

description: Library name: Sample 2


title: HUtSMC ChIP-seq for FOSL2

description: Library name: SM HUtSMC FOSL2, ChIP

value: ChIP-seq for FOSL2


title: HUtSMC ChIP-seq for BACH2

description: Library name: SM HUtSMC BACH2, ChIP

value: ChIP-seq for BACH2


title: HUtSMC ChIP-seq for NFIX

description: Library name: SM HUtSMC NFIX, ChIP

value: ChIP-seq for NFIX


title: DKO_24hDMSO_1

description: Library name: Sample 1

value: DMSO 24hr


title: LS8817, day3, Palbo, rep2, techrep1, ATAC

description: Library name: day3_Palbo_Biorep2.1


title: HUtSMC ChIP-seq for NFIC

description: Library name: SM HUtSMC NFIC, ChIP

value: ChIP-seq for NFIC


title: HUtSMC ChIP-seq for NFIB

description: Library name: SM HUtSMC NFIB, ChIP

value: ChIP-seq for NFIB


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO+IMA, rep4

description:
Library name: S12076Nr56
p210BCR/ABL SOS1 knockout transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.

value: Bone marrow

value: p210BCR/ABL, SOS1KO


title: HUtSMC ChIP-seq for NFIA

description: Library name: SM HUtSMC NFIA, ChIP

value: ChIP-seq for NFIA


title: LS8817, day3, Palbo, rep1, techrep2, ATAC

description: Library name: day3_Palbo_Biorep1.2

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO+IMA, rep3

description:
Library name: S12076Nr55
p210BCR/ABL SOS1 knockout transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.


title: SKLMS01 ChIP-seq Input

description: Library name: LMS SKLMS01 Input, ChIP

value: Leiomyposarcoma

value: Human leiomyosarcoma cell line


title: LS8817, day3, Palbo, rep1, techrep1, ATAC

description: Library name: day3_Palbo_Biorep1.1

value: day3 palbociclib (1uM)


title: SKLMS01 ChIP-seq for FOSL2

description: Library name: LMS SKLMS01 FOSL2, ChIP


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO+IMA, rep2

description:
Library name: S12076Nr54
p210BCR/ABL SOS1 knockout transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.


title: SKLMS01 ChIP-seq for BACH2

description: Library name: LMS SKLMS01 BACH2, ChIP


title: LS8817, day3, Doxo, rep2, techrep3, ATAC

description: Library name: day3_Doxo_Biorep2.3

value: day3 doxorubicin (100nM)


title: SKLMS01 ChIP-seq for NFIB

description: Library name: LMS SKLMS01 NFIB, ChIP


title: LS8817, day3, Doxo, rep2, techrep2, ATAC

description: Library name: day3_Doxo_Biorep2.2


title: SKLMS01 ChIP-seq for NFIA

description: Library name: LMS SKLMS01 NFIA, ChIP


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO, rep4

description:
Library name: S12076Nr52
p210BCR/ABL SOS1 knockout transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: LS8817, day3, Doxo, rep2, techrep1, ATAC

description: Library name: day3_Doxo_Biorep2.1


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO, rep3

description:
Library name: S12076Nr51
p210BCR/ABL SOS1knockout transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: Leio012 ChIP-seq for FOSL2

description: Library name: LMS Leio012 FOSL2, ChIP


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO, rep2

description:
Library name: S12076Nr50
p210BCR/ABL SOS1 knockout transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: SKLMS01 ChIP-seq for NFIX

description: Library name: LMS SKLMS01 NFIX, ChIP


title: LS8817, day3, Doxo, rep1, techrep1, ATAC

description: Library name: day3_Doxo_Biorep1.1


title: Leio012 ChIP-seq Input

description: Library name: LMS Leio012 Input, ChIP

value: ChIP-seq Input


title: DKOcr298_72hdAZA_1

description: Library name: Sample 19

value: Prostate

value: Prostate Cancer Cell Line

value: 100nM dAZA 72hr


title: LN229_sgAMBRA1_abemaciclib_REP_A

description: Library name: 24049a022

value: tumor, central nervous system

value: glioma

value: abemaciclib


title: in vitro microglia LPS-2h-2 [LPS_2h_2_S5]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
LPS_2h_2_S5

value: brain

value: microglia

value: wild type

value: LPS


title: Leio012 ChIP-seq for NFIC

description: Library name: LMS Leio012 NFIC, ChIP

value: ChIP-seq for NFIC


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO, rep1

description:
Library name: S12076Nr49
p210BCR/ABL SOS1 knockout transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).

value: Bone marrow

value: p210BCR/ABL, SOS1KO


title: DKOcr298_72hCombo_3

description: Library name: Sample 18

value: 500nM ZEN + 100nM dAZA 72hr


title: in vitro microglia control-3 [Control_3_S3]

description:
20210202_count_byFeatureCount_s2_lpsVitroMgTimeCourseRnaseq.txt
Control_3_S3

value: PBS


title: Leio012 ChIP-seq for NFIB

description: Library name: LMS Leio012 NFIB, ChIP

value: Leiomyposarcoma

value: Human leiomyosarcoma cell line

value: ChIP-seq for NFIB


title: LS8817, day3, Doxo, rep1, techrep2, ATAC

description: Library name: day3_Doxo_Biorep1.2

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day3 doxorubicin (100nM)


title: Leio012 ChIP-seq for BACH2

description: Library name: LMS Leio012 BACH2, ChIP

value: ChIP-seq for BACH2


title: LS8817, day28, Palbo, rep2, techrep3, ATAC

description: Library name: day28_Palbo_Biorep2.3

value: day28 palbociclib (1uM)


title: Leio012 ChIP-seq for NFIA

description: Library name: LMS Leio012 NFIA, ChIP

value: ChIP-seq for NFIA


title: LN229_abemaciclib_REP_A

description: Library name: 24049a007

value: tumor, central nervous system

value: glioma

value: parental

value: abemaciclib


title: OVCAR3_Cis_DAC_R12

city: Bloomington

first: Heather

last: O'Hagan

state: Indiana

institute: Indiana University

description:
Library name: Sample 12
Column name in OV3_RNA_seq_raw_count.txt: Cis_DAC_3

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
Reads were aligned to the hg38 genome followed by calculation of raw read counts using STAR (version 2.7.3a)
Assembly: hg38
Supplementary files format and content: Tab-deliminated file includes raw counts for each sample from STAR

growth_protocol: OVCAR3 cells were cultured in DMEM media with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNAs were collected using RNeasy Mini Kit (QIAgen, 74106)
RNA libraries for RNA-seq were preparing using Illumina TruSeq Stranded mRNA HT Library (Illumina, 20020594) as per the manufacturer’s instructions

treatment_protocol: OVCAR3 cells were mock-treated or treated with cisplatin (15uM, 16h) and/or DAC (100nM, 72h)

value: Primary ovarian cancer cells

value: Cisplatin + DAC

tag: time

value: 72 hour


title: Bone marrow, Mouse, BCR-ABL+, IMA+BI3406, rep4

description:
Library name: S12076Nr48
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily + 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.

value: Bone marrow


title: OVCAR3_Cis_DAC_R11

description:
Library name: Sample 11
Column name in OV3_RNA_seq_raw_count.txt: Cis_DAC_2


title: CUT&RUN IgG control in SKUT1B

description: Library name: CR-LMS-SKUT1B-C, IgG

value: Leiomyosarcoma

value: leiomyosarcoma cell


title: LS8817, day28, Palbo, rep2, techrep2, ATAC

description: Library name: day28_Palbo_Biorep2.2

value: soft tissue sarcoma


title: OVCAR3_Cis_DAC_R10

description:
Library name: Sample 10
Column name in OV3_RNA_seq_raw_count.txt: Cis_DAC_1


title: Bone marrow, Mouse, BCR-ABL+, IMA+BI3406, rep3

description:
Library name: S12076Nr47
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily + 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: LS8817, day28, Palbo, rep2, techrep1, ATAC

description: Library name: day28_Palbo_Biorep2.1

value: liposarcoma


title: CUT&RUN BACH2 in SKLMS01

description: Library name: CR-LMS-SKLMS01-M, Cut_Run


title: OVCAR3_DAC_R9

description:
Library name: Sample 9
Column name in OV3_RNA_seq_raw_count.txt: DAC_3

value: DAC


title: Bone marrow, Mouse, BCR-ABL+, IMA+BI3406, rep2

description:
Library name: S12076Nr46
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily + 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: OVCAR3_DAC_R8

description:
Library name: Sample 8
Column name in OV3_RNA_seq_raw_count.txt: DAC_2


title: OVCAR3_DAC_R7

description:
Library name: Sample 7
Column name in OV3_RNA_seq_raw_count.txt: DAC_1


title: Bone marrow, Mouse, BCR-ABL+, IMA+BI3406, rep1

description:
Library name: S12076Nr45
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily + 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: OVCAR3_Cis_R3

description:
Library name: Sample 6
Column name in OV3_RNA_seq_raw_count.txt: Cis_3

value: Cisplatin


title: LS8817, day28, Palbo, rep1, techrep2, ATAC

description: Library name: day28_Palbo_Biorep1.2

value: TetON FLAG-MDM2


title: OVCAR3_Cis_R2

description:
Library name: Sample 5
Column name in OV3_RNA_seq_raw_count.txt: Cis_2


title: OVCAR3_Cis_R1

description:
Library name: Sample 4
Column name in OV3_RNA_seq_raw_count.txt: Cis_1


title: LS8817, day28, Palbo, rep1, techrep1, ATAC

description: Library name: day28_Palbo_Biorep1.1

value: day28 palbociclib (1uM)


title: OVCAR3_Untreated_R1

description:
Library name: Sample 1
Column name in OV3_RNA_seq_raw_count.txt: UT_1

value: Untreated


title: Bone marrow, Mouse, BCR-ABL+, BI3406, rep2

description:
Library name: S12076Nr42
p210BCR/ABL transgenic mouse treated orally with 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: Zolmi, Replicate 3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

description:
Zolmi_B3
condition_Zolmi_DMSO.csv

data_processing:
QC: FastQC ( v0.11.9 )
Filters: cutadapt ( 1.18 )
Mapping & QC: Tophat2 ( 2.0.13), samtools ( 0.1.19 )
Counting: HTSeq-count ( 0.8.0 )
RNA-seq data were analyzed using FaRLine with the FasterDB database (Benoit-Pilven et al., 2018; Mallinjoud et al., 2014). The differential gene expression (DEG) between conditions was calculated with DESeq2.
Assembly: EnsEMBL Human GRCh37.75 / FasterDB
Supplementary files format and content: Raw counts of each sample
Supplementary files format and content: Differential gene expression analysis

source_name: hES SA001

extract_protocol:
After treatment, total RNA were extracted using the RNeasy Qiagen extraction kit.
Sequencing libraries were prepared according to the llumina TruSeq Stranded mRNA Sample Prep Kit (according to manufacturer’s protocol) (Illumina, San Diego, CA).

treatment_protocol: Mesodermal precursor cells derived from the human wild type embryonic stem cell line SA001 were treated for 24 hours with 50 different marketed drugs at the concentration of 10 µM. Each drug was tested in triplicates.

value: hES SA001

tag: replicate

value: WT

value: Zolmitriptan


title: LS8817, day21, Palbo, rep2, techrep2, ATAC

description: Library name: day21_Palbo_Biorep2.2

value: day21 palbociclib (1uM)


title: Zolmi, Replicate 2

description:
Zolmi_B2
condition_Zolmi_DMSO.csv


title: Zolmi, Replicate 1

description:
Zolmi_B1
condition_Zolmi_DMSO.csv


title: LS8817, day21, Palbo, rep2, techrep1, ATAC

description: Library name: day21_Palbo_Biorep2.1


title: UrapHydro, Replicate 3

description:
UrapHydro_B3
condition_UrapHydro_DMSO.csv

value: Urapidil hydrochloride


title: Bone marrow, Mouse, BCR-ABL+, IMA, rep4

description:
Library name: S12076Nr40
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.

value: IMA


title: Bone marrow, Mouse, BCR-ABL+, BI3406, rep3

description:
Library name: S12076Nr43
p210BCR/ABL transgenic mouse treated orally with 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: UrapHydro, Replicate 2

description:
UrapHydro_B2
condition_UrapHydro_DMSO.csv


title: Bone marrow, Mouse, BCR-ABL+, IMA, rep3

description:
Library name: S12076Nr39
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.


title: TrosChlor, Replicate 3

description:
TrosChlor_B3
condition_TrosChlor_DMSO.csv

value: Trospium chloride


title: TrosChlor, Replicate 2

description:
TrosChlor_B2
condition_TrosChlor_DMSO.csv


title: LS8817, day21, Palbo, rep1, techrep2, ATAC

description: Library name: day21_Palbo_Biorep1.2


title: TrosChlor, Replicate 1

description:
TrosChlor_B1
condition_TrosChlor_DMSO.csv


title: LS8817, day21, Palbo, rep1, techrep1, ATAC

description: Library name: day21_Palbo_Biorep1.1


title: Triflu, Replicate 3

description:
Triflu_B3
condition_Triflu_DMSO.csv

value: Trifluridine


title: OVCAR3_Untreated_R2

description:
Library name: Sample 2
Column name in OV3_RNA_seq_raw_count.txt: UT_2

value: Primary ovarian cancer cells

value: 72 hour


title: Bone marrow, Mouse, BCR-ABL+, IMA, rep1

description:
Library name: S12076Nr37
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.

value: Bone marrow


title: Triflu, Replicate 1

description:
Triflu_B1
condition_Triflu_DMSO.csv


title: Tobra, Replicate 3

description:
Tobra_B3
condition_Tobra_DMSO.csv

value: Tobramycin


title: Triflu, Replicate 2

description:
Triflu_B2
condition_Triflu_DMSO.csv


title: LS8817, day21, Doxo, rep2, techrep1, ATAC

description: Library name: day21_Doxo_Biorep2.1

value: soft tissue sarcoma

value: liposarcoma

value: day21 doxorubicin (100nM)


title: Bone marrow, Mouse, BCR-ABL+, vehicle, rep3

description:
Library name: S12076Nr35
p210BCR/ABL transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).

value: VH


title: Tobra, Replicate 1

description:
Tobra_B1
condition_Tobra_DMSO.csv


title: LS8817, day21, Doxo, rep2, techrep2, ATAC

description: Library name: day21_Doxo_Biorep2.2

value: TetON FLAG-MDM2


title: LS8817, day21, Doxo, rep1, techrep3, ATAC

description: Library name: day21_Doxo_Biorep1.3


title: Bone marrow, Mouse, BCR-ABL+, vehicle, rep4

description:
Library name: S12076Nr36
p210BCR/ABL transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: TetracHCL, Replicate 3

description:
TetracHCL_B3
condition_TetracHCL_DMSO.csv

value: hES SA001

value: Tetracycline HCl


title: Bone marrow, Mouse, BCR-ABL+, vehicle, rep2

description:
Library name: S12076Nr34
p210BCR/ABL transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: TetracHCL, Replicate 2

description:
TetracHCL_B2
condition_TetracHCL_DMSO.csv

value: WT


title: LS8817, day21, Doxo, rep1, techrep2, ATAC

description: Library name: day21_Doxo_Biorep1.2


title: TetracHCL, Replicate 1

description:
TetracHCL_B1
condition_TetracHCL_DMSO.csv


title: Bone marrow, Mouse, BCR-ABL+, vehicle, rep1

description:
Library name: S12076Nr33
p210BCR/ABL transgenic mouse treated with vehicle orally for 5 weeks (5 days on / 2 off).


title: Tobra, Replicate 2

description:
Tobra_B2
condition_Tobra_DMSO.csv


title: Terbi, Replicate 4

description:
Terbi_B4
condition_Terbi_DMSO.csv

value: Terbinafine


title: Terbi, Replicate 2

description:
Terbi_B2
condition_Terbi_DMSO.csv


title: Bone marrow, Mouse, BCR-ABL–, untreated, rep4

description:
Library name: S12076Nr32
Control littermate from CML mouse colony, does not express BCR-ABL1 transgene. Treated with vehicle orally for 5 weeks (5 days on / 2 days off).

value: non-transgenic, WT

value: CT


title: LS8817, day28, Palbo, rep1, techrep3, ATAC

description: Library name: day28_Palbo_Biorep1.3

value: day28 palbociclib (1uM)


title: Terbi, Replicate 1

description:
Terbi_B1
condition_Terbi_DMSO.csv


title: Bone marrow, Mouse, BCR-ABL+, BI3406, rep4

description:
Library name: S12076Nr44
p210BCR/ABL transgenic mouse treated orally with 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: LS8817, day14, Palbo, rep2, techrep3, ATAC

description: Library name: day14_Palbo_Biorep2.3

value: day14 palbociclib (1uM)


title: LS8817, day21, Doxo, rep1, techrep1, ATAC

description: Library name: day21_Doxo_Biorep1.1


title: Tadal, Replicate 3

description:
Tadal_B3
condition_Tadal_DMSO.csv

value: Tadalafil


title: LS8817, day21, Palbo, rep2, techrep3, ATAC

description: Library name: day21_Palbo_Biorep2.3

value: day21 palbociclib (1uM)


title: Bone marrow, Mouse, BCR-ABL–, untreated, rep3

description:
Library name: S12076Nr31
Control littermate from CML mouse colony, does not express BCR-ABL1 transgene. Treated with vehicle orally for 5 weeks (5 days on / 2 days off).

value: Bone marrow


title: OVCAR3_Untreated_R3

description:
Library name: Sample 3
Column name in OV3_RNA_seq_raw_count.txt: UT_3

value: Primary ovarian cancer cells

value: Untreated

value: 72 hour


title: Tadal, Replicate 2

description:
Tadal_B2
condition_Tadal_DMSO.csv


title: LS8817, day14, Palbo, rep2, techrep2, ATAC

description: Library name: day14_Palbo_Biorep2.2

value: soft tissue sarcoma

value: liposarcoma


title: Bone marrow, Mouse, BCR-ABL+, BI3406, rep1

description:
Library name: S12076Nr41
p210BCR/ABL transgenic mouse treated orally with 50 mg/kg BI-3406 twice daily, 5 days on / 2 off, for 5 weeks.


title: Tadal, Replicate 1

description:
Tadal_B1
condition_Tadal_DMSO.csv


title: Bone marrow, Mouse, BCR-ABL–, untreated, rep2

description:
Library name: S12076Nr30
Control littermate from CML mouse colony, does not express BCR-ABL1 transgene. Treated with vehicle orally for 5 weeks (5 days on / 2 days off).


title: Sulba, Replicate 2

description:
Sulba_B2
condition_Sulba_DMSO.csv

value: Sulbactam


title: LS8817, day14, Palbo, rep2, techrep1, ATAC

description: Library name: day14_Palbo_Biorep2.1

value: TetON FLAG-MDM2


title: Sulba, Replicate 1

description:
Sulba_B1
condition_Sulba_DMSO.csv

value: hES SA001


title: Bone marrow, Mouse, BCR-ABL–, untreated, rep1

description:
Library name: S12076Nr29
Control littermate from CML mouse colony, does not express BCR-ABL1 transgene. Treated with vehicle orally for 5 weeks (5 days on / 2 days off).


title: Spiro, Replicate 3

description:
Spiro_B3
condition_Spiro_DMSO.csv

value: WT

value: Spironolactone


title: LS8817, day14, Doxo, rep2, techrep2, ATAC

description: Library name: day14_Doxo_Biorep2.2

value: day14 doxorubicin (100nM)


title: Spiro, Replicate 2

description:
Spiro_B2
condition_Spiro_DMSO.csv


title: 7c, kidney, biological replicate 6

city: Boston

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description: Library name: WM20

data_processing:
Reads were mapped to mouse genome with STAR (version 2.7.11b) and counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: csv file containing raw counts for each sample

molecule: polyA RNA

source_name: Kidney

extract_protocol:
RNA was purified using the Direct-zol RNA mini-prep kit (Zymo Research)
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: 12-month-old male UM-HET3 mice were treated with 7c (repsox, valproate, tranylcypromine, DZNep, CHIR99021, forskolin, TTNPB) or vehicle (50% DMSO / 50% PEG300) for 28 days using subcutaneously-implanted osmotic minipumps (Alzet model # 1004). The doses were as follows: repsox, tranylcypromine, DZNep, CHIR99021, forskolin, TTNPB: 0.1 mg/kg/day, valproate: 1 mg/kg/day

value: Kidney

tag: Sex

value: Male


title: Spiro, Replicate 1

description:
Spiro_B1
condition_Spiro_DMSO.csv


title: 7c, kidney, biological replicate 5

description: Library name: WM19


title: LS8817, day14, Doxo, rep2, techrep1, ATAC

description: Library name: day14_Doxo_Biorep2.1


title: LS8817, day21, Palbo, rep1, techrep3, ATAC

description: Library name: day21_Palbo_Biorep1.3


title: Salbu, Replicate 3

description:
Salbu_B3
condition_Salbu_DMSO.csv

value: Salbutamol


title: UrapHydro, Replicate 1

description:
UrapHydro_B1
condition_UrapHydro_DMSO.csv

value: Urapidil hydrochloride


title: Salbu, Replicate 2

description:
Salbu_B2
condition_Salbu_DMSO.csv


title: LS8817, Cycling, rep4, techrep3, ATAC

description: Library name: Cycling_Biorep4.3


title: Salbu, Replicate 1

description:
Salbu_B1
condition_Salbu_DMSO.csv


title: CUT&RUN FOSL2 in SKLMS01

description: Library name: CR-LMS-SKLMS01-N, Cut_Run

value: Leiomyosarcoma

value: leiomyosarcoma cell


title: Roxit, Replicate 3

description:
Roxit_B3
condition_Roxit_DMSO.csv

value: Roxithromycin


title: 7c, kidney, biological replicate 4

description: Library name: WM18


title: LS8817, Cycling, rep4, techrep2, ATAC

description: Library name: Cycling_Biorep4.2


title: Bone marrow, Mouse, BCR-ABL+, IMA, rep2

description:
Library name: S12076Nr38
p210BCR/ABL transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.

value: Bone marrow

value: IMA


title: Roxit, Replicate 1

description:
Roxit_B1
condition_Roxit_DMSO.csv


title: Roxit, Replicate 2

description:
Roxit_B2
condition_Roxit_DMSO.csv


title: RosuCalci, Replicate 3

description:
RosuCalci_B3
condition_RosuCalci_DMSO.csv

value: Rosuvastatin Calcium


title: control (vehicle), kidney, biological replicate 4

description: Library name: WM17


title: LS8817, Cycling, rep4, techrep1, ATAC

description: Library name: Cycling_Biorep4.1

value: soft tissue sarcoma

value: liposarcoma


title: control (vehicle), kidney, biological replicate 3

description: Library name: WM16


title: RosuCalci, Replicate 2

description:
RosuCalci_B2
condition_RosuCalci_DMSO.csv


title: LS8817, Cycling, rep3, techrep3, ATAC

description: Library name: Cycling_Biorep3.3

value: TetON FLAG-MDM2


title: RosuCalci, Replicate 1

description:
RosuCalci_B1
condition_RosuCalci_DMSO.csv

value: hES SA001


title: control (vehicle), kidney, biological replicate 2

description: Library name: WM15


title: Rivar, Replicate 3

description:
Rivar_B3
condition_Rivar_DMSO.csv

value: WT

value: Rivaroxaban


title: LS8817, Cycling, rep3, techrep2, ATAC

description: Library name: Cycling_Biorep3.2


title: control (vehicle), kidney, biological replicate 1

description: Library name: WM14


title: Rivar, Replicate 1

description:
Rivar_B1
condition_Rivar_DMSO.csv


title: Rivar, Replicate 2

description:
Rivar_B2
condition_Rivar_DMSO.csv


title: Rised, Replicate 3

description:
Rised_B3
condition_Rised_DMSO.csv

value: Risedronate


title: Med1512_KDM2B

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
*library strategy: CUT&RUN
Paired-end reads of 50 bp were mapped to the human genome hg38 (Gencode GRCh38.p12) using BWA after adapter trimming with Trim_galore. Duplicated reads were marked with biobambam2 and only non-duplicated reads were retained using samtools. All samples had more than 5 million fragments. Bigwig files were generated from the center 80 bp of fragments smaller than 2000 bp and normalized to 10M fragments. Peaks were called using MACS2 with stringent and lower cutoffs, and only reproducible peaks were retained using bedtools.
Assembly: hg38
Supplementary files format and content: bw

extract_protocol:
Approximately 500,000 live cells were mixed with 50,000 Drosophila S2 cells per reaction. For CUT&RUN, we followed EpiCypher CUTANA protocol. In brief, we first isolated nuclei by incubating cells on ice for 5 min in Buffer A with protease inhibitor and 0.1% Triton X-100.  After centrifugation at 1750 x g for 2 min at 4 °C, nuclei were resuspended in Wash buffer. Bio-Mag®Plus Concanavalin-A (Con A) coated beads (BP531, Bangs Laboratories) activated in Binding buffer were then added to the nuclei and rotated for 10 min at room temperature. 1 μg primary antibody with 0.25 μg Spike-in antibody (61686, Active Motif) diluted in Antibody buffer was added to the bead-nuclei mixture and incubated for 2 hours at room temperature. Beads were washed twice with Digitonin buffer and incubated with pAG-MNase for 10 min at room temperature. Beads were then washed twice with Digitonin buffer, incubated with 2 mM CaCl2 for 2 hours at 4 °C, and quenched by adding Stop buffer. DNA was released from the beads by incubating them for 10 min at 37 °C and purified by CUTANA DNA purification kit (SKU:14-0050, EpiCypher). Antibodies used for CUT&RUN: Negative control IgG (AB-105-C, R&D systems), H3K27me3 (07-449, MilliporeSigma), H3K4me3 (C15410003, Diagenode), H3K4me1 (39298, Active Motif), EZH2 (39076, Active Motif) and KDM2B (09-864, MilliporeSigma). Buffers for CUT&RUN: Buffer A: 10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol; CUT&RUN Wash buffer: 20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, protease inhibitor cocktail (11873580001, Sigma-Aldrich); CUT&RUN Binding buffer: 20 mM HEPES-KOH (pH 7.9), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; CUT&RUN Digitonin buffer: CUT&RUN Wash buffer with 0.01% digitonin; CUT&RUN AApproximately 500,000 live cells were mixed with 50,000 Drosophila S2 cells per reaction. For CUT&RUN, we followed EpiCypher CUTANA protocol. In brief, we first isolated nuclei by incubating cells on ice for 5 min in Buffer A with protease inhibitor and 0.1% Triton X-100.  After centrifugation at 1750 x g for 2 min at 4 °C, nuclei were resuspended in Wash buffer. Bio-Mag®Plus Concanavalin-A (Con A) coated beads (BP531, Bangs Laboratories) activated in Binding buffer were then added to the nuclei and rotated for 10 min at room temperature. 1 μg primary antibody with 0.25 μg Spike-in antibody (61686, Active Motif) diluted in Antibody buffer was added to the bead-nuclei mixture and incubated for 2 hours at room temperature. Beads were washed twice with Digitonin buffer and incubated with pAG-MNase for 10 min at room temperature. Beads were then washed twice with Digitonin buffer, incubated with 2 mM CaCl2 for 2 hours at 4 °C, and quenched by adding Stop buffer. DNA was released from the beads by incubating them for 10 min at 37 °C and purified by CUTANA DNA purification kit (SKU:14-0050, EpiCypher). Antibodies used for CUT&RUN: Negative control IgG (AB-105-C, R&D systems), H3K27me3 (07-449, MilliporeSigma), H3K4me3 (C15410003, Diagenode), H3K4me1 (39298, Active Motif), EZH2 (39076, Active Motif) and KDM2B (09-864, MilliporeSigma). Buffers for CUT&RUN: Buffer A: 10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol; CUT&RUN Wash buffer: 20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, protease inhibitor cocktail (11873580001, Sigma-Aldrich); CUT&RUN Binding buffer: 20 mM HEPES-KOH (pH 7.9), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; CUT&RUN Digitonin buffer: CUT&RUN Wash buffer with 0.01% digitonin; CUT&RUN Antibody buffer: CUT&RUN Digitonin buffer with 2 mM EDTA; CUT&RUN 2X Stop buffer: 340 mM NaCl, 20 mM EDTA, 4 mM EGTA; CUT&RUN Stop buffer: Into 1 mL of 2X Stop buffer stock, add 5 μL of 10 mg/mL RNase A and 3.3 μL of 15 mg/mL GlycoBlue™ Coprecipitant (AM9516, ThermoFisher).ntibody buffer: CUT&RUN Digitonin buffer with 2 mM EDTA; CUT&RUN 2X Stop buffer: 340 mM NaCl, 20 mM EDTA, 4 mM EGTA; CUT&RUN Stop buffer: Into 1 mL of 2X Stop buffer stock, add 5 μL of 10 mg/mL RNase A and 3.3 μL of 15 mg/mL GlycoBlue™ Coprecipitant (AM9516, ThermoFisher).
Libraries were constructed using xGen ssDNA & Low-Input DNA Prep by following the manufacturer’s instructions (IDT 10009817). Purified libraries were evaluated with TapeStation (Agilent) using the High Sensitivity D1000 reagents (5067-5585, Agilent) and sequenced on NovaSeq6000 sequencer to generate 50 bp paired-end reads.


title: CUT&RUN BACH2 in Leio012

description: Library name: CR-LMS-Leio012-M, Cut_Run


title: 7c, kidney, biological replicate 3

description: Library name: WM13

value: Kidney


title: Rised, Replicate 2

description:
Rised_B2
condition_Rised_DMSO.csv


title: Med1512_EZH2


title: DMSO-1

description: Library name: GA36622

value: DMSO


title: 7c, kidney, biological replicate 2

description: Library name: WM12

value: Male


title: Rised, Replicate 1

description:
Rised_B1
condition_Rised_DMSO.csv


title: Ribav, Replicate 3

description:
Ribav_B3
condition_Ribav_DMSO.csv

value: Ribavirin


title: Med1512_IgG


title: 7c, kidney, biological replicate 1

description: Library name: WM11


title: Ribav, Replicate 1

description:
Ribav_B1
condition_Ribav_DMSO.csv


title: Ribav, Replicate 2

description:
Ribav_B2
condition_Ribav_DMSO.csv


title: Rcmb37_H3K4me3


title: Ranit, Replicate 3

description:
Ranit_B3
condition_Ranit_DMSO.csv

value: Ranitidine


title: Ranit, Replicate 2

description:
Ranit_B2
condition_Ranit_DMSO.csv


title: 7c, liver, biological replicate 6

description: Library name: WM10r

source_name: Liver

value: Liver


title: Rcmb37_H3K4me1


title: Ranit, Replicate 1

description:
Ranit_B1
condition_Ranit_DMSO.csv


title: 7c, liver, biological replicate 5

description: Library name: WM9r


title: QuinaHCL, Replicate 3

description:
QuinaHCL_B3
condition_QuinaHCL_DMSO.csv

value: Quinapril HCl


title: Rcmb37_H3K27me3


title: QuinaHCL, Replicate 2

description:
QuinaHCL_B2
condition_QuinaHCL_DMSO.csv


title: 7c, liver, biological replicate 4

description: Library name: WM8r


title: QuinaHCL, Replicate 1

description:
QuinaHCL_B1
condition_QuinaHCL_DMSO.csv


title: Rcmb37_KDM2B


title: control (vehicle), liver, biological replicate 4

description: Library name: WM7r


title: PropHydro, Replicate 3

description:
PropHydro_B3
condition_PropHydro_DMSO.csv

value: Propranolol hydrochloride


title: Rcmb37_EZH2


title: PropHydro, Replicate 1

description:
PropHydro_B1
condition_PropHydro_DMSO.csv


title: PropHydro, Replicate 2

description:
PropHydro_B2
condition_PropHydro_DMSO.csv


title: control (vehicle), liver, biological replicate 3

description: Library name: WM6r


title: Rcmb37_IgG


title: PrazHydro, Replicate 3

description:
PrazHydro_B3
condition_PrazHydro_DMSO.csv

value: Prazosin hydrochloride


title: control (vehicle), liver, biological replicate 2

description: Library name: WM5r


title: control (vehicle), liver, biological replicate 1

description: Library name: WM4r


title: Pirac, Replicate 3

description:
Pirac_B3
condition_Pirac_DMSO.csv

value: Piracetam


title: Med1512_H3K4me3


title: Pirac, Replicate 2

description:
Pirac_B2
condition_Pirac_DMSO.csv


title: 7c, liver, biological replicate 3

description: Library name: WM3r


title: Pirac, Replicate 1

description:
Pirac_B1
condition_Pirac_DMSO.csv


title: Piogl, Replicate 3

description:
Piogl_B3
condition_Piogl_DMSO.csv

value: Pioglitazone


title: Med1512_H3K27me3


title: Med1512_H3K4me1


title: 7c, liver, biological replicate 2

description: Library name: WM2r


title: Piogl, Replicate 1

description:
Piogl_B1
condition_Piogl_DMSO.csv


title: Piogl, Replicate 2

description:
Piogl_B2
condition_Piogl_DMSO.csv


title: KDM2BKO_EZH2_s5

value: medulloblastoma cell line


title: PentIseth, Replicate 2

description:
PentIseth_B2
condition_PentIseth_DMSO.csv

value: Pentamidine isethionate salt


title: PrazHydro, Replicate 1

description:
PrazHydro_B1
condition_PrazHydro_DMSO.csv

value: hES SA001


title: 7c, liver, biological replicate 1

description: Library name: WM1r


title: KDM2BKO_EZH2_s4


title: PentIseth, Replicate 1

description:
PentIseth_B1
condition_PentIseth_DMSO.csv

value: WT


title: Colon cells, amoeba infected, 8 days

city: Shanghai

first: Shaokun

last: Pan

state: Shanghai

address: 131, Dong'an Rd

country: China

institute: Fudan University

description:
Library name: P3
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed using Cell Ranger software (v8.0.0, 10x Genomics). The pipeline included demultiplexing, barcode processing, gene counting, and data aggregation. Reads were aligned to the mouse reference genome (GRCm39-2024-A). Filtered feature-barcode matrices were generated for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: Tap-separated values files and matrix files

source_name: Colon

extract_protocol:
The colon tissues from mice were dissected and cut into small pieces. Tissues were digested in HBSS buffer (with Mg²⁺/Ca²⁺) containing collagenase IV (2 mg/mL) and DNase I (40 U/mL) at 37°C for 30 minutes. The resulting cell suspension was filtered through a 40 µm strainer, washed, and re-suspended in PBS containing 2% FBS. For infected samples (P2, P3), colonic tissues were harvested on day 6 or day 8 post Entamoeba histolytica infection.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 kit (10x Genomics) according to the manufacturer’s instructions. Briefly, single cells were encapsulated into Gel Beads-in-Emulsion (GEMs) using a microfluidics-based partitioning system. Cell lysis and reverse transcription of poly-A tailed mRNA were performed within each droplet to generate barcoded full-length cDNA. The barcoded cDNA was amplified by PCR, and Illumina sequencing adapters (P5 and P7) were added during library construction. Libraries were quantified and quality-checked before sequencing.

value: Colon

value: tisse


title: Nicor, Replicate 2

description:
Nicor_B2
condition_Nicor_DMSO.csv

value: Nicorandil


title: Nicor, Replicate 3

description:
Nicor_B3
condition_Nicor_DMSO.csv


title: EZH2_control_s3


title: PentIseth, Replicate 3

description:
PentIseth_B3
condition_PentIseth_DMSO.csv


title: Colon cells, amoeba infected, 6 days

description:
Library name: P2
10x Genomics


title: Bone marrow, Mouse, BCR-ABL+, SOS1KO+IMA, rep1

description:
Library name: S12076Nr53
p210BCR/ABL SOS1 knockout transgenic mouse treated orally with 60 mg/kg imatinib once daily for 5 weeks.

value: Bone marrow

value: p210BCR/ABL, SOS1KO


title: Nicor, Replicate 1

description:
Nicor_B1
condition_Nicor_DMSO.csv


title: Nepaf, Replicate 3

description:
Nepaf_B3
condition_Nepaf_DMSO.csv

value: Nepafenac


title: Colon cells, uninfected

description:
Library name: P1
10x Genomics


title: Nepaf, Replicate 2

description:
Nepaf_B2
condition_Nepaf_DMSO.csv


title: KDM2BKO_KDM2B_s5


title: Nepaf, Replicate 1

description:
Nepaf_B1
condition_Nepaf_DMSO.csv


title: Molsi, Replicate 3

description:
Molsi_B3
condition_Molsi_DMSO.csv

value: Molsidomine


title: spleen Multiome, TVA, ATAC

city: Chicago

first: Hao

last: Fan

state: IL

address: 900 E 57TH ST

institute: University of Chicago

description: Library name: Spleen TVA ATAC

library_source: genomic single cell

data_processing:
First, datasets were preprocessed with Seurat to remove low-quality and outlier nuclei. The criteria applied were total RNA-seq feature (total RNA-seq feature > 100 for sample TVA2, and total RNA-seq feature > 0 for sample CON2), mitochondrial percentage < 25%, nucleosome signal < 3, and TSS (transcription start site) enrichment score >1. To further refine the dataset, we utilized the Median Absolute Deviation (MAD) method (Germain et al., 2020) to identify and remove outlier and low-quality cells. The MAD is calculated as MAD = median(|Xi - median(X)|), where Xi represents the quality control (QC) metric for each cell, specifically the log10 total RNA count or log10 total ATAC count. This approach provides a robust measure of variability within the dataset, minimizing the influence of extreme outliers.
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz; filtered_feature_bc_matrix.h5

source_name: spleen

extract_protocol:
We isolated nuclei from 4 cryopreserved spleen cell samples and constructed single nuclei gene expression libraries and single nuclei ATAC libraries on the 10x Genomics Chromium System using the 10x Chromium Multiome kit. Each library was sequenced with ~200 million pair end reads (PE150) on Illumina NovaSeq.
All data was generated using the 10x Chromium Single Cell Multiome platform. For each sample, the analysis input is the Cell Ranger ARC output, then we applied Seurat v5.1.0 (Hao et al., 2024) and Signac v 1.13.0 (Stuart et al., 2021) to create a multi-omic Seurat object with paired gene expression and DNA accessibility profiles for each sample.

value: spleen

value: Splenic cell


title: Molsi, Replicate 2

description:
Molsi_B2
condition_Molsi_DMSO.csv


title: KDM2BKO_KDM2B_s4


title: KDM2B_control_s3


title: spleen Multiome, TVA, GEX

description: Library name: Spleen TVA RNA


title: Molsi, Replicate 1

description:
Molsi_B1
condition_Molsi_DMSO.csv


title: spleen Multiome, CON, ATAC

description: Library name: Spleen CON ATAC


title: ManumA, Replicate 4

description:
ManumA_B4
condition_ManumA_DMSO.csv

value: Manumycine A


title: ManumA, Replicate 3

description:
ManumA_B3
condition_ManumA_DMSO.csv


title: KDM2B_control_s2


title: ManumA, Replicate 1

description:
ManumA_B1
condition_ManumA_DMSO.csv


title: Manid, Replicate 3

description:
Manid_B3
condition_Manid_DMSO.csv

value: Manidipine


title: spleen Multiome, CON, GEX

description: Library name: Spleen CON RNA


title: KDM2BKO_H3K4me1_s5


title: Manid, Replicate 2

description:
Manid_B2
condition_Manid_DMSO.csv


title: Multiome, TVA, ATAC

description: Library name: Lung TVA ATAC

source_name: Lung

value: Lung

value: lung infiltrating cells


title: Manid, Replicate 1

description:
Manid_B1
condition_Manid_DMSO.csv


title: KDM2BKO_H3K4me1_s4

value: medulloblastoma cell line


title: Lisin, Replicate 2

description:
Lisin_B2
condition_Lisin_DMSO.csv

value: Lisinopril


title: Multiome, TVA, GEX

description: Library name: Lung TVA RNA


title: Lisin, Replicate 4

description:
Lisin_B4
condition_Lisin_DMSO.csv

value: hES SA001


title: Lisin, Replicate 1

description:
Lisin_B1
condition_Lisin_DMSO.csv

value: WT


title: Multiome, CON, ATAC

description: Library name: Lung CON ATAC


title: Levof, Replicate 3

description:
Levof_B3
condition_Levof_DMSO.csv

value: Levofloxacin


title: Levof, Replicate 2

description:
Levof_B2
condition_Levof_DMSO.csv


title: H3K4me1_control_s2


title: Multiome, CON, GEX

description: Library name: Lung CON RNA


title: Leflu, Replicate 3

description:
Leflu_B3
condition_Leflu_DMSO.csv

value: Leflunomide


title: KDM2BKO_H3K4me3_s5


title: Levof, Replicate 1

description:
Levof_B1
condition_Levof_DMSO.csv


title: in vivo IFANR KO microglia pIC 12h-2

data_processing:
Raw FASTQ files were trimmed by Trimgalore (ver. 0.6.10).
Read alignment to genome (mm10) and read count of transposable elements were done by SQuIRE (ver. 0.9.9.92).
Assembly: mm10
Supplementary files format and content: TE read counts

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 5 ng of total RNA was used for construction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

value: brain

value: microglia

value: IFANR KO

value: poly I:C

tag: timepoint


title: H3K4me1_control_s3


title: Leflu, Replicate 2

description:
Leflu_B2
condition_Leflu_DMSO.csv


title: Leflu, Replicate 1

description:
Leflu_B1
condition_Leflu_DMSO.csv


title: in vivo IFANR KO microglia pIC 12h-1


title: KDM2BKO_H3K4me3_s4


title: H3K4me3_control_s3


title: Ketoc, Replicate 3

description:
Ketoc_B3
condition_Ketoc_DMSO.csv

value: Ketoconazole


title: in vivo IFANR WT microglia pIC 12h-2

value: IFANR WT


title: Ketoc, Replicate 2

description:
Ketoc_B2
condition_Ketoc_DMSO.csv


title: EZH2_control_s2


title: Ketoc, Replicate 1

description:
Ketoc_B1
condition_Ketoc_DMSO.csv


title: Indop, Replicate 3

description:
Indop_B3
condition_Indop_DMSO.csv

value: Indoprofen


title: H3K4me3_control_s2


title: in vivo IFANR WT microglia pIC 12h-1


title: Indop, Replicate 1

description:
Indop_B1
condition_Indop_DMSO.csv


title: KDM2BKO_H3K27me3_s5


title: in vivo microglia pIC 5h-3

value: wild type


title: Indop, Replicate 2

description:
Indop_B2
condition_Indop_DMSO.csv


title: IndaMalea, Replicate 3

description:
IndaMalea_B3
condition_IndaMalea_DMSO.csv

value: Indacaterol Maleate


title: KDM2BKO_H3K27me3_s4


title: IndaMalea, Replicate 2

description:
IndaMalea_B2
condition_IndaMalea_DMSO.csv


title: IndaMalea, Replicate 1

description:
IndaMalea_B1
condition_IndaMalea_DMSO.csv


title: H3K27me3_control_s3


title: Glybu, Replicate 3

description:
Glybu_B3
condition_Glybu_DMSO.csv

value: Glyburide


title: in vivo microglia pIC 5h-2


title: in vivo microglia pIC 5h-1


title: Glybu, Replicate 2

description:
Glybu_B2
condition_Glybu_DMSO.csv


title: H3K27me3_control_s2


title: Glybu, Replicate 1

description:
Glybu_B1
condition_Glybu_DMSO.csv


title: Glicl, Replicate 3

description:
Glicl_B3
condition_Glicl_DMSO.csv

value: Gliclazide


title: Glicl, Replicate 2

description:
Glicl_B2
condition_Glicl_DMSO.csv


title: in vivo microglia PBS 5h-3

value: PBS


title: KDM2BKO_IgG_s5

value: medulloblastoma cell line


title: in vivo microglia PBS 5h-2


title: Glicl, Replicate 1

description:
Glicl_B1
condition_Glicl_DMSO.csv

value: hES SA001


title: KDM2BKO_IgG_s4


title: Ganci, Replicate 3

description:
Ganci_B3
condition_Ganci_DMSO.csv

value: WT

value: Ganciclovir


title: in vivo microglia PBS 5h-1


title: Ganci, Replicate 2

description:
Ganci_B2
condition_Ganci_DMSO.csv


title: IgG_control_s3


title: Ganci, Replicate 1

description:
Ganci_B1
condition_Ganci_DMSO.csv


title: in vitro microglia pIC 20-4


title: Furos, Replicate 3

description:
Furos_B3
condition_Furos_DMSO.csv

value: Furosemide


title: IgG_control_s2


title: in vitro microglia pIC 20-3

value: brain


title: Furos, Replicate 2

description:
Furos_B2
condition_Furos_DMSO.csv


title: Med113__KDM2B


title: Furos, Replicate 1

description:
Furos_B1
condition_Furos_DMSO.csv


title: FluoHydro, Replicate 3

description:
FluoHydro_B3
condition_FluoHydro_DMSO.csv

value: Fluoxetine Hydrochloride


title: in vitro microglia pIC 20-2

value: microglia


title: FluoHydro, Replicate 2

description:
FluoHydro_B2
condition_FluoHydro_DMSO.csv


title: Med1712__KDM2B


title: FluoHydro, Replicate 1

description:
FluoHydro_B1
condition_FluoHydro_DMSO.csv


title: in vitro microglia pIC 20-1

value: poly I:C


title: FludAceta, Replicate 2

description:
FludAceta_B2
condition_FludAceta_DMSO.csv

value: Fludrocortisone acetate


title: Rcmb28__KDM2B


title: FludAceta, Replicate 1

description:
FludAceta_B1
condition_FludAceta_DMSO.csv


title: in vitro microglia pIC 8h-4


title: Fluco, Replicate 3

description:
Fluco_B3
condition_Fluco_DMSO.csv

value: Fluconazole


title: Rcmb20__KDM2B


title: Fluco, Replicate 1

description:
Fluco_B1
condition_Fluco_DMSO.csv


title: in vitro microglia pIC 8h-3


title: Fluco, Replicate 2

description:
Fluco_B2
condition_Fluco_DMSO.csv


title: Med2312__KDM2B


title: Fenof, Replicate 3

description:
Fenof_B3
condition_Fenof_DMSO.csv

value: Fenofibrate


title: in vitro microglia pIC 8h-2

value: wild type


title: Fenof, Replicate 2

description:
Fenof_B2
condition_Fenof_DMSO.csv


title: DMB006_KDM2B


title: Fenof, Replicate 1

description:
Fenof_B1
condition_Fenof_DMSO.csv


title: in vitro microglia pIC 8h-1


title: EsomMagne, Replicate 3

description:
EsomMagne_B3
condition_EsomMagne_DMSO.csv

value: Esomeprazole Magnesium


title: Med113__EZH2


title: EsomMagne, Replicate 2

description:
EsomMagne_B2
condition_EsomMagne_DMSO.csv


title: in vitro microglia PBS-4


title: DoxeHydro, Replicate 3

description:
DoxeHydro_B3
condition_DoxeHydro_DMSO.csv

value: Doxepin Hydrochloride


title: in vitro microglia PBS-3


title: EsomMagne, Replicate 1

description:
EsomMagne_B1
condition_EsomMagne_DMSO.csv


title: DoxeHydro, Replicate 1

description:
DoxeHydro_B1
condition_DoxeHydro_DMSO.csv


title: Rcmb28__EZH2


title: PrazHydro, Replicate 2

description:
PrazHydro_B2
condition_PrazHydro_DMSO.csv

value: Prazosin hydrochloride


title: DMSO, Replicate 4

value: DMSO


title: Med1712__EZH2


title: in vitro microglia PBS-2

value: PBS


title: Rcmb20__EZH2


title: DMSO, Replicate 3

value: hES SA001


title: DMSO, Replicate 2

value: WT


title: in vitro microglia PBS-1


title: DMSO, Replicate 1


title: DivaSodium, Replicate 3

description:
DivaSodium_B3
condition_DivaSodium_DMSO.csv

value: Divalproex Sodium


title: Med2312__EZH2


title: DivaSodium, Replicate 2

description:
DivaSodium_B2
condition_DivaSodium_DMSO.csv


title: DMB006_EZH2


title: in vivo Daxx KO microglia TAM 3dpi-4

data_processing:
The fastq files were directly submitted to atacseq pipeline (ver. 1.2.2) from nf-core with arguments “--genome GRCm38“, “--keep_multi_map” and “--min_reps_consensus 2”
Assembly: GRCm38
Supplementary files format and content: bigwig

extract_protocol:
Primary microglia were isolated using MACS® Column-based cell separation with CD11b (Microglia) MicroBeads (Miltenyi Biotec). Additionally, for the in vitro set-ups, cultured primary mouse bone-marrow-derived macrophages (induction of deletion with 4OHT and stimulated with LPS at 3h, 6h and 24h time points) were used as well for ATAC-seq.
Between 50.000 to 100.000 freshly isolated cells were processed immediately for the library construction. The cells were spun down at 500 x g for 5 min and washed with cold PBS. Thereafter, cells were resuspended into a mix of nuclease-free water, 1% digitonin and 10% Tween-20, mixed by vortexing and spun down briefly. The tagmentation reaction was conducted by adding Nextera’s Tn5 Transposase (TDE1) in reaction buffer. The transposition reaction mix was incubated for 30 minutes at 37°C, followed by DNA purification using a MinElute PCR purification kit (Qiagen). ATAC-Seq libraries were generated from tagmented DNA by PCR amplification using Nextera index primers (Illumina) according to manufacturer’s protocol. Then, ATAC-seq libraries were purified using a PCR purification MinElute kit (Qiagen) and quantified using KAPA library quantification kits (Kapa biosystems) and a D1000 assay on a Tapestation 4200 (Agilent).

value: Cx3cr1CreERT,Daxx flox/flox

value: Tamoxifen


title: in vivo Daxx WT, KO microglia TAM 3dpi, 1wpi, 8wpi, scRNAseq_mixed sample

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: 10X genomics

data_processing:
Raw bcl files were demultiplexed using Bcl2fastq2 V2.20 from Illumina and the resulting paired-end scRNA-seq reads were filtered after quality control and matching cell barcodes with the barcode whitelist provided by BD.
Adaptors were trimmed using Cutadapt 1.16 and reads with a PHRED score of >=20 were retained (https://doi.org/10.14806/ej.17.1.200.). Filtered reads were aligned using STAR 2.6.1b121 to a customized genome which contained both the reference genome (mm10, Gencode: GRCm38.p6),  and multiplexing tag sequences for aligning  the transcriptome read and the sample barcode (Hashtag oligo -HTO).
Raw read counts were imported into R (v.4.1.1) as SeuratObject  using Seurat (v4).  The scRNA-seq data matrix was normalized using the NormalizeData function, followed by identification of the top 2000 most variable features (genes) using the vst method in the FindVariableFeatures function.  All genes were scaled and centered using the ScaleData function.
The top 15 principal components (PC) were used to build a shared nearest neighbor (SNN) cell graph, which was then clustered using the Louvain algorithm (resolution = 0.8) implemented in the FindClusters function. The PCs were then mapped onto two dimensions using the Uniform Manifold Approximation and Projection (UMAP) algorithm. Marker genes from Gerrits et al. 2021 were used to manually assign cell type annotations to each cluster124. Clusters not being assigned a microglia or macrophage assignment, including a mixed cluster, were removed for further analysis.
DecontX function of Bioconductor package celda (1.10.0) was used to estimate and remove contamination with ambient RNA.
Assembly: mm10
Supplementary files format and content: rds data file Seurat Object with cell based meta data and normalized counts

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with ad libitum access to regular chow food (ssniff Spezialdiäten GmbH). All experimental procedures were approved by Landesamt für Natur, Umwelt und Verbraucherschutz Nordrhein-Westfalen (LANUV).

extract_protocol:
Microglia from mice brains were isolated using the Adult Brain Dissociation Kit from Miltenyi Biotech (Bergisch Gladbach, Germany) according to the manufacturer’s guidelines. In brief, after euthanasia, mice brains were mechanically and enzymatically digested at 4 oC. Fully digested tissue suspensions were filtered with a 70 µm cell strainer followed by subsequent removal of myelin, cell debris and erythrocytes. The cell suspension was then incubated with CD11b MicroBeads (Miltenyi Biotech) for 15 minutes at 4 °C followed by a separation in MS columns (Miltenyi Biotech) using a magnetic field on a MACS MultiStand and QuadroMACS (Miltenyi Biotech).
Isolated microglia were labeled with unique oligo sample barcodes conjugated to anti- mouse CD45 antibodies (BD Mouse Immune Single-Cell Multiplexing Kit, #633793), pooled in equivalent amounts and loaded on a BD Rhapsody cartridge (BD Bioscience, #400000847) using a BD Rhapsody Express Single-Cell Analysis System. Cell counting was performed using Countess 3 FL automated cell counter (Invitrogen). Pooled samples were diluted using BD Sample Buffer to a final volume of 650µL. Approximately 60,000 cells in total were loaded on a BD Rhapsody cartridge. Cell and bead loading, cell lysis, recovery of mRNA-bound beads, reverse transcription, and exonuclease treatment were performed according to the manufacturer’s instructions (BD Biosciences). Whole-transcriptome library preparation, based on the random-priming strategy, and index PCR steps were performed using the BD Rhapsody mRNA Whole Transcriptome Analysis and Sample Tag Library Preparation Protocol, as per the manufacturer’s recommendations (BD Biosciences), optimized based on “Optimized workflow for single-cell transcriptomics on infectious diseases incl. COVID-19”, STAR Protoc., 2020. Quantification of the final libraries was performed using a Qubit Fluorometer with the Qubit dsDNA HS Kit (ThermoFisher), whereas the size distribution was assessed using the Agilent High-Sensitivity D5000 assay on a TapeStation 4200 system (Agilent Technologies). Paired-end sequencing (2∗75 cycles) was performed on a NovaSeq 6000 System (Illumina) using NovaSeq S1 Reagent Kit (200 Cycles) chemistry.

treatment_protocol: To induce Cre activation, Cx3cr1-CreERT2 positive mice at 6-7-week-old age was administrated with 80 mg/kg/day tamoxifen (T5648, Sigma-Aldrich) via oral gavage for five consecutive days.

value: brain

tag: age

value: 8-16 weeks old

value: Cx3cr1CreERT,Daxx wt/wt and flox/flox


title: DivaSodium, Replicate 1

description:
DivaSodium_B1
condition_DivaSodium_DMSO.csv


title: Dexme, Replicate 3

description:
Dexme_B3
condition_Dexme_DMSO.csv

value: Dexmedetomidine


title: Med113__H3K4me1


title: Dexme, Replicate 2

description:
Dexme_B2
condition_Dexme_DMSO.csv


title: in vivo Daxx KO microglia TAM 3dpi-3

value: microglia


title: Dexme, Replicate 1

description:
Dexme_B1
condition_Dexme_DMSO.csv


title: CyprHydro, Replicate 3

description:
CyprHydro_B3
condition_CyprHydro_DMSO.csv

value: Cyproheptadine hydrochloride


title: Med1712__H3K4me1


title: in vivo Daxx KO microglia TAM 3dpi-2


title: CyprHydro, Replicate 2

description:
CyprHydro_B2
condition_CyprHydro_DMSO.csv


title: CyprHydro, Replicate 1

description:
CyprHydro_B1
condition_CyprHydro_DMSO.csv


title: Rcmb28__H3K4me1


title: in vivo Daxx KO microglia TAM 3dpi-1


title: ChloDipho, Replicate 3

description:
ChloDipho_B3
condition_ChloDipho_DMSO.csv

value: Chloroquine diphosphate


title: ChloDipho, Replicate 2

description:
ChloDipho_B2
condition_ChloDipho_DMSO.csv


title: Rcmb20__H3K4me1


title: Med2312__H3K4me1


title: in vivo Daxx WT microglia TAM 3dpi-3

value: Cx3cr1CreERT,Daxx wt/wt


title: ChloDipho, Replicate 1

description:
ChloDipho_B1
condition_ChloDipho_DMSO.csv


title: Argat, Replicate 3

description:
Argat_B3
condition_Argat_DMSO.csv

value: Argatroban


title: in vivo Daxx WT microglia TAM 3dpi-2


title: Argat, Replicate 2

description:
Argat_B2
condition_Argat_DMSO.csv


title: Argat, Replicate 1

description:
Argat_B1
condition_Argat_DMSO.csv


title: DMB006_H3K4me1


title: in vivo Daxx WT microglia TAM 3dpi-1


title: Amoxa, Replicate 3

description:
Amoxa_B3
condition_Amoxa_DMSO.csv

value: Amoxapine


title: Med113__H3K4me3


title: Amoxa, Replicate 2

description:
Amoxa_B2
condition_Amoxa_DMSO.csv


title: in vivo Daxx KO microglia TAM 1ypi-2 [24605]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24605

data_processing:
Raw FASTQ files were trimmed by Trimgalore and aligned to genome mm10 by STAR. SAM files were filter by mapq>=10 and transformed to BAM by samtools. Gene count table was created by featureCounts.
Assembly: mm10
Supplementary files format and content: read counts from featureCounts

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for contruction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.


title: Amoxa, Replicate 1

description:
Amoxa_B1
condition_Amoxa_DMSO.csv


title: Med1712__H3K4me3


title: in vivo Daxx KO microglia TAM 1ypi-1 [24604]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24604


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R71A_YW56.2_rep2 biol rep 2

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: YW56_14_D

library_source: other

data_processing:
Raw reads were processed with Cutadapt (v5.0) to filter out adapter sequences, trim low-quality bases, and remove reads shorter than 15 bp. Cutadapt was run using a tiling approach across the 3′ adapter as previously described, with parameters -e 0.2, -O 10, -q 30, and -m 45 (error rate, minimum overlap, quality cutoff, and minimum length, respectively). Filtered reads were aligned with bwa-mem2 (v2.2.1) under default parameters to a composite reference comprising the E. coli MG1655 genome (NCBI: NC_000913.3), the relevant plasmid sequence, and either the λ-vir (NCBI: NC_001416.1) or T5 (NCBI: NC_005859.1) phage genome. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6), normalized to sequencing depth based on the total number of reads passing trimming and length filtering. Reads that failed to align with bwa-mem2 were extracted using SAMtools fasta, and the fraction of unmapped reads was calculated using SAMtools flagstat. Genome build: E. coli MG1655 (NC_000913.3); λ-vir (NC_001416.1); T5 (NC_005859.1).
Assembly: ASM584v2
Supplementary files format and content: .fasta — Unmapped reads extracted from BAM alignments using SAMtools fasta. Each file contains all reads from a given sample that failed to align to the composite reference, used as input for downstream MEME motif enrichment analysis and motif counts per sample.

molecule: other

organism: Escherichia coli

extract_protocol:
cDIP elution was performed by removing the supernatant and resuspending beads with 80 µL of IP wash buffer containing 5 µg RNase A (Thermo Fisher Scientific). Inputs were resuspended with 70 µL of the same wash buffer. Both inputs and immunoprecipitation samples were incubated at 37 °C for 30 min. SDS was then added to a final concentration of 1%, along with 25 µg of proteinase K (Thermo Fisher Scientific). Supernatants containing eluted DNA were transferred to new tubes and DNA was isolated with the Monarch Spin PCR and DNA Cleanup kit (NEB), following the Oligonucleotide Cleanup protocol.
Eluted DNA samples were heated at 95 °C for 2 min and immediately placed on ice to denature DNA. Adapter ligation and conversion of ssDNA to dsDNA were performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (IDT). Indexing PCR was performed using NEBNext Ultra II Q5 Master Mix (NEB). Libraries were sequenced on the Element AVITI system in single- or paired-end mode with 150 cycles per end.

tag: sample group


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R71K_YW56.2_rep2 biol rep 2

description: Library name: YW56_16_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R71K_YW56.2_rep1 biol rep 1

description: Library name: YW56_15_D


title: in vivo Daxx WT microglia TAM 1ypi-2 [24603]

first: Paolo

last: Salomoni

institute: DZNE

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24603


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R71A_YW56.2_rep1 biol rep 1

description: Library name: YW56_13_D


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW56.2_rep2 biol rep 2

description: Library name: YW56_12_D


title: Rcmb20__H3K4me3


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW56.2_rep1 biol rep 1

description: Library name: YW56_11_D


title: in vivo Daxx WT microglia TAM 1ypi-1 [24601]

description:
20231029_count_byFeatureCount_s2_daxxKoMgInvivo0d1d1y.txt
24601


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW56.2_rep2 biol rep 2

description: Library name: YW56_10_D


title: in vivo Daxx KO microglia TAM 8wpi-2 [MCB01_68]

description:
20200728_count_byFeatureCount_strand2_daxxKoMgTam.txt
MCB01_68


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW56.2_rep1 biol rep 1

description: Library name: YW56_09_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R241K_YW56.1_rep2 biol rep 2

description: Library name: YW56_08_D


title: DMB006_H3K4me3


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_R241K_YW56.1_rep1 biol rep 1

description: Library name: YW56_07_D


title: Med113__H3K27me3


title: in vivo Daxx KO microglia TAM 8wpi-1 [MCB01_67]

description:
20200728_count_byFeatureCount_strand2_daxxKoMgTam.txt
MCB01_67


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22D_YW56.1_rep2 biol rep 2

description: Library name: YW56_06_D


title: Med1712__H3K27me3


title: pACYC184_Eco_DRT3_3b-intFLAG-1_DRT3b_E22D_YW56.1_rep1 biol rep 1

description: Library name: YW56_05_D


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW56.1_rep2 biol rep 2

description: Library name: YW56_04_D


title: in vivo Daxx WT microglia TAM 8wpi-1 [MCB01_65]

description:
20200728_count_byFeatureCount_strand2_daxxKoMgTam.txt
MCB01_65


title: Rcmb28__H3K27me3


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_YW56.1_rep1 biol rep 1

description: Library name: YW56_03_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW56.1_rep2 biol rep 2

description: Library name: YW56_02_D


title: in vivo Daxx KO microglia TAM 3wpi-3 [4809]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4809


title: pACYC184_Eco_DRT3_3b-intFLAG-1_YW56.1_rep1 biol rep 1

description: Library name: YW56_01_D


title: in vivo Daxx KO microglia TAM 3wpi-2 [4807]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4807


title: Rcmb20__H3K27me3


title: DRT3_MUT_gam_90min_rep3 biol rep 3

description: Library name: YW34_24

extract_protocol:
Cell lysis and DNA extraction was immediately performed following the standard protocol for the QIAprep Spin Miniprep Kit (QIAGEN) and elution in 30 µL nuclease-free water.
Eluted DNA samples were heated at 95 °C for 2 min and immediately placed on ice to denature DNA. Adapter ligation and conversion of ssDNA to dsDNA were performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (IDT). Indexing PCR was performed using NEBNext Ultra II Q5 Master Mix (NEB). Libraries were sequenced on the Element AVITI system in single- or paired-end mode with 75 or 150 cycles per end.


title: DRT3_MUT_gam_90min_rep2 biol rep 2

description: Library name: YW34_23


title: Med2312__H3K27me3


title: DRT3_MUT_gam_90min_rep1 biol rep 1

description: Library name: YW34_22


title: in vivo Daxx KO microglia TAM 3wpi-1 [4805]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4805


title: DRT3_WT_gam_90min_rep3 biol rep 3

description: Library name: YW34_21


title: DMB006_H3K27me3


title: DRT3_WT_gam_90min_rep2 biol rep 2

description: Library name: YW34_20


title: in vivo Daxx WT microglia TAM 3wpi-3 [4826]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4826


title: DRT3_WT_gam_90min_rep1 biol rep 1

description: Library name: YW34_19


title: Med113__IgG


title: in vivo Daxx WT microglia TAM 3wpi-2 [4726]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4726


title: DRT3_MUT_gam_60min_rep2 biol rep 2

description: Library name: YW34_17


title: DRT3_MUT_gam_60min_rep3 biol rep 3

description: Library name: YW34_18


title: Med1712__IgG


title: DRT3_MUT_gam_60min_rep1 biol rep 1

description: Library name: YW34_16


title: in vivo Daxx WT microglia TAM 3wpi-1 [4725]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4725


title: DRT3_WT_gam_60min_rep3 biol rep 3

description: Library name: YW34_15


title: Rcmb28__IgG


title: in vivo Daxx KO microglia TAM 1wpi-4 [4880]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4880


title: DRT3_WT_gam_60min_rep1 biol rep 1

description: Library name: YW34_13


title: in vivo Daxx KO microglia TAM 1wpi-3 [4878]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4878


title: DRT3_MUT_gam_30min_rep3 biol rep 3

description: Library name: YW34_12


title: DRT3_MUT_gam_30min_rep2 biol rep 2

description: Library name: YW34_11


title: Rcmb20__IgG


title: Med2312__IgG


title: DRT3_MUT_gam_30min_rep1 biol rep 1

description: Library name: YW34_10


title: in vivo Daxx KO microglia TAM 1wpi-2 [4877]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4877


title: DRT3_WT_gam_30min_rep3 biol rep 3

description: Library name: YW34_09


title: DMB006_IgG


title: Rcmb28__H3K4me3


title: DRT3_WT_gam_60min_rep2 biol rep 2

description: Library name: YW34_14


title: in vivo Daxx KO microglia TAM 1wpi-1 [4875]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4875


title: DRT3_WT_gam_30min_rep1 biol rep 1

description: Library name: YW34_07


title: DRT3_WT_gam_30min_rep2 biol rep 2

description: Library name: YW34_08


title: DMB006_gRNA28_rep3_batch2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, cleaned reads were mapped to hg38 (Gencode GRCh38.p12) using STAR
Assembly: hg38
Supplementary files format and content: Tab-separated files

extract_protocol:
For RNA-seq in Group 4 MB PDX, freshly isolated DMB006 cells from mouse brains were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 90% of cells were infected. Cells were cultured for 7 days and then collected for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing. For RNA-seq in D283, cells were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 80% of cells were infected. Cells were cultured for 7 days. An aliquot of cells was collected on day 4 or day 7 for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing.
RNA extraction was performed using RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. RNA libraries for RNA-seq were prepared following manufacturer's protocols


title: DRT3_MUT_gam_0min_rep2 biol rep 2

description: Library name: YW34_05


title: DRT3_MUT_gam_0min_rep3 biol rep 3

description: Library name: YW34_06


title: in vivo Daxx WT microglia TAM 1wpi-3 [4904]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4904


title: DMB006_gRNA28_rep2_batch2


title: DRT3_MUT_gam_0min_rep1 biol rep 1

description: Library name: YW34_04


title: Med2312__H3K4me3


title: in vivo Daxx WT microglia TAM 1wpi-2 [4903]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4903


title: DRT3_WT_gam_0min_rep3 biol rep 3

description: Library name: YW34_03


title: DMB006_gRNA28_rep1_batch2


title: DRT3_WT_gam_0min_rep2 biol rep 2

description: Library name: YW34_02


title: in vivo Daxx WT microglia TAM 1wpi-1 [4901]

description:
20210129_count_byFeatureCount_s2_daxxHiraCx3cr1Rnaseq.txt
4901


title: TKO_24hDMSO_3

description: Library name: Sample 33

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

extract_protocol:
Total RNA was extracted using a Qiagen AllPrep RNA/DNA mini kit (Qiagen 80204) according to the manufacturer's protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

value: Prostate

value: TKO

value: Prostate Cancer Cell Line

value: DMSO 24hr


title: in vivo Daxx WT microglia TAM 8wpi-2 [MCB01_66]

description:
20200728_count_byFeatureCount_strand2_daxxKoMgTam.txt
MCB01_66


title: DRT3_WT_gam_0min_rep1 biol rep 1

description: Library name: YW34_01


title: in vivo Daxx KO microglia TAM 3dpi-6 [19788_S12]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19788_S12


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-C117G_rep2_input biol rep 2

description: Library name: YW43_20i_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-C117G_rep1_input biol rep 1

description: Library name: YW43_19i_D


title: DMB006_gRNA10_rep2_batch2


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-G113C_rep2_input biol rep 2

description: Library name: YW43_18i_D


title: DMB006_gRNA10_rep3_batch2


title: in vivo Daxx KO microglia TAM 3dpi-5 [19784_S8]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19784_S8


title: in vitro Daxx WT microglia LPS-48h-1 [15399]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15399_merged

value: Tamoxifen, LPS


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-G113C_rep1_input biol rep 1

description: Library name: YW43_17i_D


title: DMB006_gRNA10_rep1_batch2


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_rep2_input biol rep 2

description: Library name: YW43_16i_D


title: pACYC184_intFLAG-DRT3_3a3b_RT**YVAA_rep1_input biol rep 1

description: Library name: YW43_15i_D


title: in vivo Daxx KO microglia TAM 3dpi-4 [19783_S7]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19783_S7

value: Cx3cr1CreERT,Daxx flox/flox


title: in vivo Daxx KO microglia TAM 3dpi-3 [19782_S6]

description:
20230103_count_byFeatureCount_s2_mgDaxxKo3dpiReseq.txt
19782_S6

value: Tamoxifen


title: pACYC184_Eco_DRT3_3b-intFLAG-1_rep2_input biol rep 2

description: Library name: YW43_14i_D


title: pACYC184_Eco_DRT3_3b-intFLAG-1_rep1_input biol rep 1

description: Library name: YW43_13i_D


title: DMB006_control_rep2_batch2


title: DMB006_control_rep3_batch2


title: pACYC184_Eco_DRT3_3b-intFLAG-1_ncRNAmut-C117G_rep2 biol rep 2

description: Library name: YW43_20_D