title: DIPG48_H3K27me3_1

value: WT


title: MTD-Gal4 driven CG2678 KD Rhi-ChIP biological replicate 1

status: Public on May 15 2022

type: SRA

city: Vienna

first: Lisa

last: Baumgartner

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

library_source: genomic

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.3.0) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: 25˚C, 12h dark/light

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library for Illumina (NEB).

tag: tissue

value: ovary

tag: genotype

tag: antibody

value: anti-Rhi antibody (Rhino#1_3573gly)


title: DIPG36_HRP_1

city: Rehovot

first: Efrat

last: Shema

address: Herzl St 234

department: Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
Library strategy: CUT&RUN
Paiered-end reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20). Reads were mapped to human genome (hg19, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools, and broad peaks were called using MACS2 against the corresponding HRP samples as background control (parameters: -f BAMPE --SPMR --nomodel --extsize 100 --keep-dup auto -q 0.05).  MLL1 were called using narrow peaks. Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Supplementary_files_format_and_content: Peaks files were constructed using MACS2 against the corresponding HRP samples as background control

organism: Homo sapiens

source_name: Patient-derived DIPG cells (SU-DIPG 36)

growth_protocol: DIPG cells were cultured in Tumor Stem Media (TSM) consisting of a 1:1 mixture of DMEM/F12 (Invitrogen) and Neurobasal (-A) (Invitrogen), with addition of B27(-A) (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah Biotechnology), human-EGF (20 ng/ml) (Shenandoah Biotechnology), human PDGF-AA (20 ng/ml) (Shenandoah Biotechnology), human PDGF-BB (20 ng/ml) (Shenandoah Biotechnology) and heparin (10 ng/ml) (Stemcell Technologies). Cells were passaged every week.

extract_protocol:
CUT&RUN assay was done as described in Skene et al (2017) with slight modifications as follows. Cells were harvested and counted with 200000 cells per reaction. Permeabilized cells, bound to Concanavalin A-coated beads were mixed with individual primary antibody (see antibody list) and incubated overnight at 4°C while rotating. Secondary antibody, anti-rabbit HRP was used as a negative control. pAG-MNase enzyme was added to each sample followed by incubation step of 1 hour at 4°C. Targeted digestion was done by 15 minutes incubation on ice block (0°C) under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609).
Libraries were prepared from 1-20ng of DNA as previously described by Blecher-Gonen et al (2013). Paired end sequencing was done on a Next-Seq 500 instrument (Illumina) using a V2 150 cycles mid output kit.

value: Brain

tag: part

value: Brianstem

tag: tumor

value: DIPG

tag: genotype/variation


title: Gossypol, 1 µg/ml SAMPLE 12

type: RNA

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

country: USA

institute: USDA-ARS

description:
Gossypol, 1 µg/ml
Test

hyb_protocol: SYBR Green qPCR reaction mixtures contained 5 ng of total RNA-derived cDNAs, forward primer, reverse primer and 1X iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). The thermal cycle conditions were as follows: 3 min at 95°C, followed by 40 cycles at 95°C for 10 s, 65°C for 30 s and 72°C for 30 s. The qPCR reactions were performed in 96-well clear plates sealed by adhesives with a CFX96 real-time system-C1000 Thermal Cycler (Bio-Rad Laboratories).

data_processing:
Rpl32 mRNA was selected as the internal reference for qPCR analysis for this cell type (HKG).
1% DMSO treatment was used as sample control
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Gos normalized to Rpl32 and DMSO worksheet reports normalized signal (against housekeeping genes and sample control), where deltadeltaCt = delta(Ct_Target )− delta(Ct_DMSO)
Gos fold Change worksheet reports test/control (i.e., test/DMSO control) ratios. The 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: RAW264.7 cells

label_protocol: The cDNAs were synthesized from total RNA using SuperScript II reverse transcriptase (Life Technologies). The cDNA synthesis mixture (20 μl) contained 2.5 μg total RNA, 2.4 μg oligo(dT)12-18 primer, 0.1 μg random primers, 500 μM dNTPs, 10 mM DTT, 40 units RNaseOUT and 200 units SuperScript II reverse transcriptase in 1X first-strand synthesis buffer (Life Technologies). The cDNA synthesis reactions were incubated at 42°C for 50 min. The cDNA samples were stored in -80°C freezer and diluted with water to 1 ng/µl before qPCR analyses.

extract_protocol: Total RNA was extracted from mouse macrophages with Trizol reagent followed by DNase I treatment.

tag: cell type

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

tag: activation agent

value: Gossypol, 1 ug/ml

tag: time

value: 2 h


title: Gossypol, 1 µg/ml SAMPLE 11

description:
Gossypol, 1 µg/ml
Test


title: DIPG38_HRP_1

source_name: Patient-derived DIPG cells (SU-DIPG 38)


title: Gossypol, 1 µg/ml SAMPLE 10

description:
Gossypol, 1 µg/ml
Test


title: Gossypol, 5 µg/ml SAMPLE 13

description:
Gossypol, 5 µg/ml
Test

value: Gossypol, 5 ug/ml


title: DIPG36_K27M_1


title: rhino transheterozygous KO rhi18-7_rhig2m11 input 1


title: DIPG17_H3K27me3_1

source_name: Patient-derived DIPG cells (SU-DIPG 17)


title: rhino transheterozygous KO rhi18-7_rhig2m11 CG2678-ChIP biological replicate 1


title: DIPG17_H3K4me3_1


title: DIPG17_H3K27ac_1


title: rhino transheterozygous KO rhi18-7_rhig2m11 Rhi-ChIP biological replicate 1


title: DIPG17_K27M_1


title: DIPG13_H3K4me3_1

source_name: Patient-derived DIPG cells (SU-DIPG 13)


title: Gossypol, 0.5 µg/ml SAMPLE 9

description:
Gossypol, 0.5 µg/ml
Test

value: Gossypol, 0.5 ug/ml


title: Gossypol, 0.5 µg/ml SAMPLE 8

description:
Gossypol, 0.5 µg/ml
Test


title: DIPG17_HRP_1


title: w1118 input 1


title: DIPG13_K27M_1


title: Gossypol, 0.5 µg/ml SAMPLE 7

description:
Gossypol, 0.5 µg/ml
Test


title: DIPG13_H3K27me3_1


title: MTD-Gal4 driven control KD input 3

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: DIPG13_H3K27ac_1


title: Gossypol, 0.1 µg/ml SAMPLE 5

description:
Gossypol, 0.1 µg/ml
Test

value: Gossypol, 0.1 ug/ml


title: Gossypol, 0.1 µg/ml SAMPLE 6

description:
Gossypol, 0.1 µg/ml
Test


title: DIPG6_HRP_2

source_name: Patient-derived DIPG cells (SU-DIPG 6)


title: DIPG13_HRP_1


title: DIPG6_MLL1_2


title: DIPG13_K27M_2


title: DIPG13_MLL1_2


title: MTD-Gal4 driven control KD input 2


title: RNA_seq_basal_cells_WT_Aged_ex3 [Aging_3]

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

library_source: transcriptomic

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STAR (version 2.6.0c) with the GENCODE vM25 annotation gtf file after trimming adaptor sequences and low quality bases by cutadapt- 1.18.
The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 and the expression level of each gene was calculated as FPKM using DESeq2 v1.30.0 with the GENCODE vM25 annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: A tsv file includes FPKM values for each sample.

extract_protocol:
Subcutaneous fat was removed from the skin with a scalpel, and the whole skin was trypsinized at 37 °C for an hour to separate the epidermis and the dermis. The cell suspensions were filtered through strainers (70-μm, BD Falcon), collected by centrifugation (300 × g, 5 min) and suspended in Dulbecco’s modified Eagle’s medium (Ca-). Cell suspensions were incubated with Pacific Blue anti-human/mouse CD49f (Biolegend) antibody and eFluor660 anti-mouse CD34 (Biolegend) antibody for 30 min on ice, washed twice with PBS and subjected to flow cytometric analysis. Cell isolation was performed on a FACSAria Ⅲ sorter. RNA was extracted from CD49f positive and CD34 negative cells using the RNeasy Micro Kit (Qiagen). Quality RNA samples were selected (RIN>7).
RNA-seq libraries were generated using the TruSeq Stranded mRNA library prep kit (Illumina) and the libraries were sequenced on NextSeq 500 (Illumina).

tag: strain

tag: postnatal day

value: 24 months

tag: group

value: aged

tag: tissue/cell type

value: interfollicular epidermal basal cells from plantar skin


title: DIPG13_HRP_2


title: MTD-Gal4 driven control KD H3K9me2-ChIP biological replicate 2

value: anti-H3K9me2 antibody (mAbcam 1220)


title: DMSO, 1% SAMPLE 3

description:
DMSO, 1%
Control

value: DMSO, 1%


title: RNA_seq_basal_cells_WT_Aged_ex2 [Aging_2]

value: WT


title: w1118 CG2678-ChIP biological replicate 1

value: ovary


title: w1118 Rhi-ChIP biological replicate 1

value: anti-Rhi antibody (Rhino#1_3573gly)


title: MTD-Gal4 driven control KD H3K9me3-ChIP biological replicate 3

value: anti-H3K9me3 antibody (active motif 39161)


title: DMSO, 1% SAMPLE 2

description:
DMSO, 1%
Control


title: RNA_seq_basal_cells_WT_high_fat_diet_ex3 [HFD_3]

value: 5 months

value: high fat diet fed (HFD)


title: DIPG6_K27M_2

value: Brain

value: Brianstem

value: DIPG


title: RNA_seq_basal_cells_WT_high_fat_diet_ex2 [HFD_2]


title: RNA_seq_basal_cells_WT_Aged_ex1 [Aging_1]


title: MTD-Gal4 driven control KD H3K9me3-ChIP biological replicate 2


title: WT Tumor 4 untreated

city: Houston

first: manisha

last: singh

state: TX

address: 1901,East road

institute: MDACC

data_processing:
After completion of the S5 run, the raw sequence files (fastq files) were aligned to the mouse genome (MM10) reference sequence by the Ion Torrent Browser using the default parameters. The genes and transcripts annotations that were used was retrieved from the Ensembl data base. Aligned BAM files were used for further analysis.
After filtering, the aligned reads were normalized and quantified using the DEseq algorithm by the StrandNGS program. Next, statistical analysis was performed using the Moderated T-test to determine significant differentially expressed genes based on the replicates of each condition. After significant DEGs were identified, significant fold change was determined and genes that had a significant fold change of 2.0x or higher were listed. GSEA was then run for each condition.
Assembly: MM10
Supplementary files format and content: Singh_GEO_Processed_data_files.xlsx ("Quant all" sheet represents normalized data).

organism: Mus

source_name: Control tumor

growth_protocol: B16 tumors were established by subcutaneous inoculation, and allowed to grow for 7 days

extract_protocol:
Total RNA of dissected tumors was extracted using Qiagen RNeasy Mini Kit (Cat# 74104). The RNA quality was checked by using a Agilent RNA 6000 nano kit (Cat# 5067-1511).
cDNA libraries were constructed using Ion Total RNA-Seq Kit v2 from ThermoFisher (Cat# 4479789) and manufacturers recommended protocol.

treatment_protocol: Mice were untreated or treated with anti-PD-L1 antibody,3 times every 3 days then 3 days after the 3rd treatment tumors were excised.

value: B16 melanoma

tag: tumor type

value: WT syngeneic

tag: treatment

value: untreated

tag: replicate


title: DMSO, 1% SAMPLE 1

description:
DMSO, 1%
Control

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

value: 2 h


title: Gossypol, 0.1 µg/ml SAMPLE 4

description:
Gossypol, 0.1 µg/ml
Test

value: Gossypol, 0.1 ug/ml


title: RNA_seq_basal_cells_WT_cont_ex3 [Cont_3]

value: control (nomal diet fed)

value: interfollicular epidermal basal cells from plantar skin


title: MTD-Gal4 driven control KD Rhi-ChIP biological replicate 3

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: RNA_seq_basal_cells_WT_cont_ex2 [Cont_2]

value: WT


title: 208782.cyst.INPUT

city: Boston

first: Margherita

last: Boieri

state: MA

address: 55 Fruit Street

institute: Masachusetts General Hospital

data_processing:
Alignment: BWA
Density map: IGV Density tool
ChIP seq coverage analyis: IGV
Peaks identification: MACS2peak caller
Pathway Erichment analysis: GSEA
Genome_build: mm10
Supplementary_files_format_and_content: list of EMT genes upregulated in tumor vs. cyst
Supplementary_files_format_and_content: all enhancers up or downregulated in tumor vs cyst

extract_protocol:
Chromatin extracted from formalin-fixed cells was fragmented with a Branson 250 sonifier, solubilized and immunoprecipitated with H3K27ac antibody (Active Motif, Inc., Carlsbad, CA) overnight at 4°C. Antibody-chromatin complexes were pulled down with protein G-Dynabeads (Life Technologies), washed, and eluted.
Immunoprecipitated DNA was extracted with AMP Pure beads (Beckman Coulter) after crosslink reversal, RNase A, and proteinase K treatment. ChIP DNA was quantified with Qubit.

treatment_protocol: 10-30 mg of tumor was cut on dry ice and minced on ice with a razor blade. Samples were then resuspended in 1ml cold PBS and fixed in 1% formaldehyde for 15 minutes at room temperature. Glycine was added for 5 minutes at room temperature. Samples were washed and resuspended in cold PBS and homogenized with a syringe.

tag: strain background

value: Balb/c

value: injected with CD4+ T cells

value: Breast tumor


title: 188847.cyst.INPUT

tag: tissue


title: 208782.cyst.H3K27ac

tag: chip antibody

value: H3K27ac antibody (Active Motif, Inc., Carlsbad, CA)


title: MTD-Gal4 driven control KD Rhi-ChIP biological replicate 2

value: ovary

tag: genotype

tag: antibody

value: anti-Rhi antibody (Rhino#1_3573gly)


title: WT Tumor 3 untreated


title: RNA_seq_basal_cells_WT_cont_ex1 [Cont_1]

value: 5 months


title: MV4;11_MS40_GROseq_rep2

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

description: nascent RNA

data_processing:
Basecalls performed using Illuminal CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: MV4;11 cells

growth_protocol: MV4;11 cells were grown in RPMI1640 base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
Cells were subjected to nuclear run-on for 5minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: MV4;11 cells were treated with 0.5 µM of MS40, or DMSO, for 4 days.


title: RNA_seq_basal_cells_WT_high_fat_diet_ex1 [HFD_1]

value: high fat diet fed (HFD)


title: WT Tumor 1 untreated

value: B16 melanoma

value: WT syngeneic


title: WT Tumor 2 untreated

value: untreated


title: 209503.tumor.H3K27ac


title: 188847.cyst.H3K27ac


title: WT Tumor 3 anti-PD-L1

source_name: Treated tumor


title: 209503.tumor.INPUT


title: 128651.tumor.INPUT


title: WT Tumor 2 anti-PD-L1


title: MV4;11_DMSO_GROseq_rep2

description: nascent RNA

value: DMSO


title: MV4;11_DMSO_GROseq_rep1

description: nascent RNA


title: total RNA (polyA selected) from MTD-Gal4 CG2678 KD biological  rep3

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

molecule: polyA RNA

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)
polyA selection, RNA-seq

tag: age

value: 7 days old


title: T13_3

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

description: IECs from TgSTAT6vt mice

data_processing: FPKM

source_name: Jejunum

extract_protocol: none provided by the submitter

value: Jejunum

value: primarily isolated Intestinal epithelial cells

value: STAT6vt IEC specific overexpression


title: NO B cells Tumor 4 untreated

value: B cells depleted


title: WT Tumor 4 anti-PD-L1


title: total RNA (polyA selected) from MTD-Gal4 rhino KD biological  rep2

value: w, MTD/+; MTD/+; MTD/pW20>rhi_sh[attP2]/;


title: total RNA (polyA selected) from MTD-Gal4 CG2678 KD biological  rep2


title: MV4;11_MS40_GROseq_rep1

description: nascent RNA


title: total RNA (polyA selected) from MTD-Gal4 rhino KD biological  rep1


title: total RNA (polyA selected) from MTD-Gal4 CG2678 KD biological  rep1


title: C13_3

description: IECs from WT mice

value: WT


title: total RNA (polyA selected) from MTD-Gal4 rhino KD biological  rep3


title: total RNA (polyA selected) from MTD-Gal4 control KD biological  rep3

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: NO B cells Tumor 3 untreated


title: T13_1

description: IECs from TgSTAT6vt mice


title: NO B cells Tumor 2 untreated


title: total RNA (polyA selected) from MTD-Gal4 control KD biological  rep2


title: T13_2

description: IECs from TgSTAT6vt mice


title: CG2678deltaZAD CG2678-ChIP

description:
CG2678deltaZAD_in
internally 3xFLAF-tagged CG2678 harboring a deletion of the ZAD, expressed from endogenous locus instead of WT protein (RMCE)

value: w;; CG2678RMCE[3xFLAG-deltaZAD]/TM3,Sb;


title: NO B cells Tumor 1 untreated


title: 128651.tumor.H3K27ac

value: Balb/c

tag: genotype/variation

value: injected with CD4+ T cells

value: Breast tumor

value: H3K27ac antibody (Active Motif, Inc., Carlsbad, CA)


title: CG2678deltaZnFarray2 CG2678-ChIP

description:
CG2678deltaZnFarray2_in
internally 3xFLAF-tagged CG2678 harboring a deletion of the second ZnF array, expressed from endogenous locus instead of WT protein (RMCE)

value: ovary


title: C13_2

description: IECs from WT mice

tag: cell type


title: C13_1

description: IECs from WT mice


title: total RNA (polyA selected) from MTD-Gal4 control KD biological  rep1


title: WT Tumor 1 anti-PD-L1

value: B16 melanoma

value: WT syngeneic


title: CG2678deltaZnFarray1 CG2678-ChIP

description:
CG2678deltaZnFarray1_in
internally 3xFLAF-tagged CG2678 harboring a deletion of the first ZnF array, expressed from endogenous locus instead of WT protein (RMCE)


title: NO B cells Tumor 4 anti-PD-L1


title: IKO_3

description: IECs from Sirt6 KO mice

value: Sirt6 IEC specific knockout


title: L_plaque

city: Stanford

first: Patricia

last: Nguyen

state: California

address: 300 Pasteur Dr

department: Cardiovascular Medicine

institute: Stanford University

description:
norm_matrix.txt
counts_matrix.txt

data_processing:
FASTQ read were demultiplexed and alligned using 10X Genomics' Cell Ranger.
Matrices were read into Seurat and log normalized.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_matrix.txt,  norm_matrix.txt (Log normalized values, with patient ID and tissue appended to cell barcodes)

source_name: patient L

extract_protocol:
Cells were enzymatically digested from explanted coronary arteries.
10x Chromium instrument 3' whole transcriptome manufacturer protocol.
scRNA-seq

tag: individual

value: patient L

value: coronary artery

value: T cells


title: CG2678deltaZAD input

description: internally 3xFLAF-tagged CG2678 harboring a deletion of the ZAD, expressed from endogenous locus instead of WT protein (RMCE)


title: CG2678deltaZnFarray2 input

description: internally 3xFLAF-tagged CG2678 harboring a deletion of the second ZnF array, expressed from endogenous locus instead of WT protein (RMCE)


title: NO B cells Tumor 2 anti-PD-L1


title: CG2678deltaZnFarray1 input

description: internally 3xFLAF-tagged CG2678 harboring a deletion of the first ZnF array, expressed from endogenous locus instead of WT protein (RMCE)


title: IKO_2

description: IECs from Sirt6 KO mice

value: Jejunum

value: primarily isolated Intestinal epithelial cells


title: K_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient K

value: patient K


title: IKO_1

description: IECs from Sirt6 KO mice


title: K_blood

description:
norm_matrix.txt
counts_matrix.txt

value: peripheral blood


title: Ctr_3

description: IECs from LoxP mice

value: LoxP


title: NO B cells Tumor 1 anti-PD-L1

value: B cells depleted


title: J_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient J

value: patient J


title: 3xFLAG-CG2678 Rhi-ChIP

description:
CG2678FLAG_in
internally 3xFLAF-tagged CG2678 expressed from endogenous locus instead of WT protein (RMCE)

value: w;; CG2678RMCE[S161-3xFLAG]/TM3,Sb;

value: anti-Rhi antibody (Rhino#1_3573gly)


title: SHEDs biol rep 3

city: Chongqing

first: Jie

last: Li

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

country: China

institute: Chongqing Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: dental pulp

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: dental pulp

tag: cell line

value: primary cell

value: mesenchymal stem cells

value: stem cells from human exfoliated deciduous teeth (SHEDs)

value: WT

value: cultured with pTDM


title: 3xFLAG-CG2678 CG2678-ChIP

value: ovary


title: J_blood

description:
norm_matrix.txt
counts_matrix.txt

value: T cells


title: SHEDs biol rep 2


title: Ctr_1

description: IECs from LoxP mice

value: Jejunum


title: RhiGCN4 input

description: Rhino construct with GCN4 dimerization domain in place of CSD


title: SHEDs biol rep 1


title: NO B cells Tumor 3 anti-PD-L1

tag: strain

value: B16 melanoma


title: I_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient I

value: patient I

value: coronary artery


title: Ctr_2

description: IECs from LoxP mice

value: primarily isolated Intestinal epithelial cells

value: LoxP


title: DFCs biol rep 3

source_name: dental follicle

value: dental follicle

value: dental follicle cells (DFCs)


title: RhiGCN4 CG2678-ChIP

description:
RhiGCN4_in
Rhino construct with GCN4 dimerization domain in place of CSD

source_name: ovary


title: tgt_Ni rep3

city: Gainesville

first: Leticia

last: Pollo-Oliveira

state: FL

address: 1355 Museum Dr

department: Microbiology and Cell Science

institute: University of Florida

description:
tgt in Ni 3
vc_sv_t3ni_rz_ec_S19_L002

data_processing:
Sequencing was performed in the HiSeq 2500 System (Illumina) with 76 bp Paired End sequencing and 40 million reads per sample.
Twenty four fastq files were generated and the quality of the raw reads was checked using the FastQC tool.
Trimmomatic was used to remove the adaptors sequences at the beginning of the reads.
The genome was indexed using Bowtie2 and the mapping was performed using TopHat.
Read counts were obtained using htseq-count script.
ARSyN method was applied for batch normalization and the result was checked by Principal Component Analysis (PCA).
rpkm normalization was applied, and the differential expression (DE) was assessed using the Limma package.
Genome_build: The Escherichia coli strain K-12 MG1655 genome fasta and gff files (GCF_000005845.2_ASM584v2_genomic) were downloaded from National Center for Biotechnology Information website (https://www.ncbi.nlm.nih.gov/).
Supplementary_files_format_and_content: Processed_data_GEO_RNAseq_LPO_2021 is in Excel format and coints: A. reads per sample; B. transcripts differential expression (log2FC and p-values); C. list of significant differentially expressed genes.

organism: Escherichia coli

source_name: whole cell extract

growth_protocol: Three biological replicates of WT and Δtgt strains were grown overnight in LB medium and saturated cultures were diluted to OD600 of 0.5 in 20 mL of LB or in 20 mL of LB medium added by 2 mM NiCl2·6H2O (Sigma Aldrich). Cells were incubated at 37°C with continuous shaking and harvested during exponential phase (OD600 0.6-0.8) for RNA isolation.

extract_protocol:
RNA was stabilized with RNAprotect Bacteria Reagent (Qiagen #76506) and isolated using the RNeasy Mini Kit (Qiagen # 74104). The quality and quantity of total RNA was evaluated using the Agilent RNA 6000 Nano Kit on an Agilent Bioanalyzer. rRNA was removed using Ribo-Zero™ Magnetic Kit* (Gram-Negative Bacteria) Epicentre.
The RNA sequencing library was prepared with TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were analyzed on a Bioanalzyer for average base pair distribution, and quantified using Qubit Fluorometric Quantitation (Thermo Fisher Scientific).
TruSeq RNA Library Prep Kit v2 (Illumina): Oligo-dT beads capture polyA tails. Captures the coding transcriptome (without strand information).

treatment_protocol: Samples were grown in LB (no treatment) or LB supplemented with 2 mM NiCl2.

value: tgt mutant

value: 2 mM nickel


title: H_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient H

value: patient H


title: RhiGCN4 FLAG-ChIP

value: anti-FLAG antibody (Sigma F1804-1MG)


title: G_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient G

value: patient G


title: 3xFLAG-CG2678 input

description: internally 3xFLAF-tagged CG2678 expressed from endogenous locus instead of WT protein (RMCE)

value: w;; CG2678RMCE[S161-3xFLAG]/TM3,Sb;


title: DFCs biol rep 2

value: primary cell

value: mesenchymal stem cells

value: WT

value: cultured with pTDM


title: F_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient F

value: patient F

value: T cells


title: Rhiarthinge input

description: Rhino construct with artificial hinge domain

value: ovary


title: DFCs biol rep 1


title: tgt_Ni rep1

description:
tgt in Ni 1
vc_sv_t1ni_rz_ec_S18_L002


title: WT_Ni rep3

description:
WT in Ni 3
vc_sv_m3ni_rz_ec_S17_L002

value: wild type


title: ASCs biol rep 3

source_name: adipose

value: adipose

value: adipose-derived stromal/stem cells (ASCs)


title: F_blood

description:
norm_matrix.txt
counts_matrix.txt

value: peripheral blood


title: WT_Ni rep1

description:
WT in Ni 1
vc_sv_m1ni_rz_ec_S16_L002


title: Rhiarthinge FLAG-ChIP

description:
Rhiarthinge_in
Rhino construct with artificial hinge domain


title: MTD-Gal4 driven UASz2678 Rhi-ChIP

value: w, MTD/+; MTD/+; MTD/pUASz>CG2678[attP2]/;

value: anti-Rhi antibody (Rhino#1_3573gly)


title: WT_Ni rep2

description:
WT in Ni 2
vc_sv_m2ni_rz_ec_S22_L002

value: 2 mM nickel


title: ASCs biol rep 1


title: ASCs biol rep 2


title: C_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient C

value: patient C

value: coronary artery


title: D_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient D

value: patient D


title: tgt_Ni rep2

description:
tgt in Ni 2
vc_sv_t2ni_rz_ec_S23_L002

value: tgt mutant


title: MTD-Gal4 driven UASz2678 CG2678-ChIP


title: B_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient B

value: patient B


title: Rhiarthinge CG2678-ChIP


title: tgt_LB rep3

description:
tgt in LB 3
vc_sv_t3lb_rz_ec_S15_L002


title: tgt_LB rep2

description:
tgt in LB 2
vc_sv_t2lb_rz_ec_S14_L002


title: tgt_LB rep1

description:
tgt in LB 1
vc_sv_t1lb_rz_ec_S13_L002


title: E_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient E

value: patient E


title: OVCAR3, shScramble

city: Guangzhou

first: Xiaolin

last: Luo

state: Guangdong

address: 651 Dongfeng East Road

department: Gynecology Oncology

institute: Sun Yat'sen University Cancer Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Differential expression analysis was carried out using Deseq with a cut-off of P <0.05 and abs (log2FC) >1.0. The R programming language and ggplot2 package was used to generate heatmaps.
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

growth_protocol: The ovarian carcinoma cell lines, HO8910, OVCAR3 and SKOV3, were obtained from Sun Yat-sen University Cancer Center. All cell lines were thawed from early passage stocks and passaged for less than 6 months. The cell lines used in this study were periodically monitored for mycoplasma using Hoechst staining. The cells were maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (Invitrogen, Carlsbad, CA) at 37 °C and 5% CO2.

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed at Beijing CapitalBio Technology Co., Ltd. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Ovarian cancer cells

value: WT

value: No treatment


title: OVCAR3, shTRAF4

value: TRAF4 knockdown


title: iso1 Rhi-ChIP biological replicate 2

value: ovary


title: WT_LB rep3

description:
WT in LB 3
vc_sv_m3lb_rz_ec_S12_L002

value: wild type


title: MTD-Gal4 driven UASz2678 input


title: HO8910, shTRAF4


title: HO8910, shScramble


title: WT_LB rep2

description:
WT in LB 2
vc_sv_m2lb_rz_ec_S21_L002


title: A_plaque

description:
norm_matrix.txt
counts_matrix.txt

source_name: patient A

value: patient A

value: T cells


title: iso1 Rhi-ChIP biological replicate 1


title: small RNAs from w1118 ovaries

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

extract_protocol:
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)
Libraries were prepared by ligation of 3' and 5' barcoded adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.


title: tbx5 enh knockout - diff rep 2

city: Dallas

first: Daniel

last: Armendariz

address: 5323 Harry Hines Boulevard

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description:
scRNA-seq
KO_SC_DF.h5ad
KO_CM_DF.h5ad

data_processing:
Provided datasets are for combined DAA267 and DAA269 scRNA-seq libraries.
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 6.0.0, 10X Genomics). Cellplex barcodes and library assignments can be found in KO_cmo_bc.csv and cellplex_library_assignments.csv supplementary files respectively. Both knockout sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in KO_SC_DF.h5ad supplementary file.
The Louvain cluster defining cardiomyocytes was isolated and re-clustered using Louvain. Clusters corresponding to cardiomyocyte gene signatures were selected and clustering above repeated to identify cardiomyocyte subpopulations. Dataset contained in KO_CM_DF.h5ad supplementary file.
processed data files format and content:H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
processed data files format and content:H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

source_name: H9-derived cardiomyocytes

growth_protocol: H9 ESCs were maintained feeder-free in mTeSR Plus (Stemcell Tech. 100-0276) according to suggested manufacturer’s instructions on Matrigel (Corning 354277) coated plates, passaged every 3-4 days with DPBS/0.5 mM EDTA and plated in 2 uM thiazovivin (Sigma SML1045) supplemented mTeSR Plus overnight.

extract_protocol:
Library prepared following 10x v3.1 Dual Index with Cell Multiplexing protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.

treatment_protocol: At 80-90% confluency, media was replaced with 3 uM CHIR99021 (Tocris 4423) supplemented CDM3 (RPMI 1640, Sigma R8758; 0.5 mg/ml human albumin, ScienCell OsrHSA; 211 ug/ml L-ascorbic acid 2-phosphate, Sigma A8960) for 48 hours followed by 2 uM Wnt-C59 (Cayman 16644) supplemented CDM3 for 48 hours with subsequent media changes every 2 days with CDM3 alone.

tag: differentiation day


title: iso1 CG2678-ChIP biological replicate 1


title: SW620_day17_rep3-CRISPRi

city: Beijing

first: Kequan

last: Lin

address: Qinghua Yuan #1

institute: Tsinghua University

data_processing:
Library strategy: CRISPRi
Quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.2).
DNA-seq data were mapped to the reference genome(hg38) using Bowtie.
The reads of each sgRNA oligo (targeting to one gene or no target) were counted by user-defined scripts.
The differential expression analysis between the day0 group and day17 group was quantified using excel (t test).
Genome_build: hg38
Supplementary_files_format_and_content: rawcount

extract_protocol:
Genomic DNA was extracted following the instructions of QIAamp DNA Blood Midi Kit (QIAGEN, Dusseldorf, Germany; 51183).
100 μg genomic DNA of each biological replicate was used for library construction. sgRNA region was amplified and incorporated with a barcode by two-round PCR.

value: treatment

tag: cultured time

value: 18 days


title: SW620_day17_rep2-CRISPRi


title: SW620_day17_rep4-CRISPRi


title: large screen - lane 1 - seq 2

description:
scRNA-seq
Large_SC_DF.h5ad
Large_CM_DF.h5ad

data_processing:
Provided datasets are for combined DAA243-250 scRNA-seq libraries.
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 3.1.0, 10X Genomics). All large screen sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Doublets were removed using the HTO libraries. HTO barcodes used can be found in Large_CM_bc.csv supplemental file. In short, we assigned HTO tags to cells using the saturation curve method described in Drop-seq (Macosko et al, 2015). Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in Large_SC_DF.h5ad supplementary file.
The Louvain clusters defining cardiomyocytes and mesoderm cells were isolated and re-clustered using Louvain. Clusters corresponding to cardiomyocyte and smooth muscle cells were selected and clustering above repeated to identify cardiomyocyte subpopulations. Dataset contained in Large_CM_DF.h5ad supplementary file.
processed data files format and content:H5AD file containing count matrix and cluster classifications for combined large screen scRNA-seq.
processed data files format and content:H5AD file containing count matrix and cluster classifications for CM subpopulations in combined large screen scRNA-seq.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

extract_protocol:
Library prepared following 10x v3.1 gene expression protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.


title: SW620_day0_rep4-CRISPRi

value: control


title: WT_LB rep1

description:
WT in LB 1
vc_sv_m1lb_rz_ec_S20_L002


title: tbx5 enh knockout - diff rep 1

description:
scRNA-seq
KO_SC_DF.h5ad
KO_CM_DF.h5ad


title: SW620_day0_rep3-CRISPRi


title: w1118 H3K9me3-ChIP biological replicate 1

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.3.0) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library for Illumina (NEB).

value: anti-H3K9me3 antibody (active motif 39161)


title: iso1 input 2


title: eWAT ISO_3

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing reads were mapped to the mouse genome mm9 or hg19 using STAR (v2.4.2a), tag counts were summarized at the gene level using HOMER, allowing only one read per position per length. Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v1.1) specifying the -count gene option. Data analysis was performed in R studio (v2022.2.0)
Codes and scripts used to process and analyze data have been deposited to GitHub: https://github.com/LasseKMarkussen/Lipolysis-regulates-major-transcriptional-programs-in-brown-adipocytes
Assembly: mm9
Supplementary files format and content: Raw_Gene_Count_Matrix.txt contains raw gene counts for the entire dataset

source_name: eWAs

growth_protocol: eWAT was isolated from lean male C57/BL6J mice (Charles River), all non-adipose tissue was removed, and the tissue was minced with a scalpel. The tissue was digested for 15 minutes at 37oC and 130 rpm in degradation buffer (collagenase type 1 (Worthington, #LS004196) in Krebs-Ringer buffer (adjusted to pH=7,4 containing 1% BSA). The cell suspension was then filtered through a double 250 µm filter to a sterile tube. The filter and suspension were washed with Krebs-Ringer buffer containing 1% BSA to stop the digestion of the tissue. A long syringe was inserted, and the tube was left for 2-5 minutes to allow the mature adipocytes to float to the top before removing the infranatant with the syringe. Cells were distributed in a 24-well plate (50,000 cells per well) in a gel mix consisting of 1:1 gelin-S and glycosil-S (ESI-BIO HyStem®-C Hydrogel Kit, #GS1005) and 30 μL Extralink (ESI-BIO HyStem®-C Hydrogel Kit, #GS1005). Gelation occurred after 60 minutes, and 700 μL DMEM (Sigma-Aldrich, #D6249) with high glucose (4500 mg/L) –with 10% FBS and 1% penicillin/streptomycin (Lonza, #09-757F) was added to the wells. The cells were incubated at 37oC, 5% CO2 for 2 days prior to investigations.

extract_protocol:
total RNA was harvested using TRIzol reagent and isolated using the chloroform-isopropanol method. cDNA was transcribed using the QuantiTect Reverse Transcription Kit (Qiagen, #205311).
RNA-seq was performed according to the instructions by the manufacturer (TruSeq2, Illumina) using 500ng of total RNA for preparation of cDNA libraries.

treatment_protocol: eWAs at day 2 were treated +/- Lipase inhibitors and subsequently +/- ISO for 3 hrs.

value: Primary floated eWAs


title: eWAT Lip+ISO_3


title: eWAT DMSO_3


title: large screen - lane 1 - sgRNA

description: sgRNA Amplicon Library for large screen - lane 1

data_processing:
Provided datasets are for combined DAA259-266 sgRNA amplicon libraries.
sgRNA libraries were mapped using FBA count (Duan et al, 2021). We assigned sgRNA to cells using the saturation curve method described in Drop-seq (Macosko et al, 2015). Dataset contained in Large_SG_DF.h5ad supplementary file.
Multiple sgRNA were designed for each target region. Using a hypergeometric based filter described in the accompanying publication, biased sgRNA were removed. sgRNA for each target were combined to form a single group name. A dictionary was generated which provides individual sgRNA name to combined target name. Dictionary contained in Guide_Dictionary_Filtered.pkl supplementary file.
A dictionary was generated which, for each sgRNA key, provides all the cell barcodes with the given guide. Dictionary contained in CM_Large_sgRNA_Dic_Filtered.pkl supplementary file.
processed data files format and content:Pickle file containing dataframe with count matrix for sgRNA mapping.
processed data files format and content:Pickle file containing dictionary defining filtered sgRNA to target regions.
processed data files format and content:Pickle file containing sgRNA and sgRNA cell assignments.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

extract_protocol:
Library prepared by amplifiying sgRNA from cDNA.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.


title: SW620_day0_rep2-CRISPRi


title: iso1 input 1


title: w1118 H3K9me3-ChIP biological replicate 2


title: eWAT Lip_3


title: w1118 H3K9me2-ChIP biological replicate 1

value: anti-H3K9me2 antibody (mAbcam 1220)


title: eWAT Lip+ISO_2


title: SW620_day17_rep1-CRISPRi


title: eWAT Lip_2


title: w1118 HP1-ChIP biological replicate 1

value: anti-HP1 antibody (DSHB C1A9)


title: eWAT ISO_2


title: AT6-2

data_processing:
Paired-end raw reads were trimmed using cutadapt (with the parameters -q 25 -m 30), and mapped to genome hg19 (Gencode) using bowtie2 (with the parameter --local).
Following alignment, mitochondrial genes are removed from the analysis, and duplicated reads were removed using picard-tools.
Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads, and broad peaks were called using MACS2 (with the parameters --bw 120 -B -f BAMPE --SPMR –B --shift -50 --extsize 100 -keep-dup all -q 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: Peaks detected by MACS2

source_name: Patient-derived DIPG culture (SU-DIPG 6)

extract_protocol:
Sample preparation was conducted as previously described by Buenrostro et al, with modifications described by Lara-Astiaso and colleges
Two sequential 9-cycle and 5-cycle PCR were performed in order to enrich small tagmentated DNA fragments. Libraries were prepared using KAPA HiFi HotStart ready mix. After the first PCR, the libraries were selected for small fragments using SPRI cleanup (0.65x). Then a second PCR was performed with the same conditions in order to obtain the final library.

treatment_protocol: no treatment

value: Brain

tag: region

value: Brianstem

tag: tumor

value: DIPG


title: SW620_day0_rep1-CRISPRi

tag: treatment


title: w1118 input 2


title: AT6-1


title: w1118 input 3


title: AT48-2

source_name: Patient-derived DIPG culture (SU-DIPG 48)

value: WT


title: eWAT Lip_1


title: eWAT Lip+ISO_1


title: MTD-Gal4 driven control KD input 1

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: w1118 Rhi-ChIP biological replicate 2

value: anti-Rhi antibody (Rhino#1_3573gly)


title: eWAT ISO_1


title: eWAT DMSO_1


title: MTD-Gal4 driven control KD CG2678-ChIP biological replicate 1

value: ovary


title: AT48-1


title: eWAT DMSO_2


title: MTD-Gal4 driven control KD Rhi-ChIP biological replicate 1


title: AT13-1

source_name: Patient-derived DIPG culture (SU-DIPG 13)


title: w1118 CG2678-ChIP biological replicate 2


title: AT13-2


title: HFD-JGF mice

status: Public on May 14 2022

city: Jiangmen

first: Xiu

last: Zhou

address: Pengjiang

department: School of Biotechnology and Health Sciences

institute: Wuyi University

description:
Test
Six-week-old male C57BL/6J mice were purchased from the Guangdong Medical Laboratory Animal Center. Mice were maintained under standard management conditions (temperature of 25 ± 2°C and a 12-hour light-dark cycle) and performed in accordance with procedures approved by the Animal Care and Ethics Committee at Wuyi University (Jiangmen, Guangdong). After 1 weeks of acclimatization, mice were randomly assigned into three groups and fed with either a chow (8% calories from fat, 21% calories from protein, and 71% calories from carbohydrate), a HFD (45% calories from fat, 20% calories from protein and 35% calories from carbohydrate), or a HFD supplemented with 0.6% (w/w) OLE-JGF (HFD-JGF) ad libitum for 10 weeks.
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using LightCycler® 96 real-time PCR system
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
For the normalization it uses the average of three housekeeping genes:fatty acid synthase (FAS), sterol regulatory element-binding protein (SREBP-1c), acetyl-CoA carboxylase (ACC), LKB1, peroxisome proliferator–activated receptor-γ coactivator-1α (PGC-1α), nuclear factor-erythroid-derived 2-like 2 (Nrf2), mitochondrial transcription factor A (Tfam), mitochondrial DNA (mtDNA), uncoupling protein 2 (UCP2), cluster of dif-ferentiation 68 (CD68), monocyte chemoattractant protein-1 (MCP-1), tumor necrosis factor-α (TNF-α) and β-actin
Matrix normalized worksheet reports normalized signal (against housekeeping genes).

source_name: C57BL/6J mice

label_protocol: RNA concentration was measured by using a NanoDrop One/One . For reverse transcription to cDNA, 2 μg of RNA were incubated with the ReverTra AceTM qPCR RT Master Mix  at 37°C for 15 min followed by 5 min at 50°C and 5 min at 98°C. The qPCR was performed using SYBR Green qPCR SuperMix  for amplifing targeted genes, using three-step annealing on the LightCycler® 96 real-time PCR system according to the manufacturer’s instructions.

growth_protocol: Mice were maintained under standard management conditions (temperature of 25 ± 2°C and a 12-hour light-dark cycle).Cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) and Ham's F-12 (1:1) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin, 1% insulin transferrin selenium solution, and 40 ng/ml dexamethasone .

extract_protocol: Total RNA of liver or cell was extracted by using RNAiso Plus kit  according to manu-facturer´s instructions.

treatment_protocol: After 1 weeks of acclimatization, mice were randomly assigned into three groups and fed with either a chow (8% calo-ries from fat, 21% calories from protein, and 71% calories from carbohydrate), a HFD (45% calories from fat, 20% calories from protein and 35% calories from carbohydrate), or a HFD supplemented with 0.6% (w/w) OLE-JGF (HFD-JGF) ad libi-tum for 8 weeks. Diets were stored at -20°C and changed twice a week during the experiments.Cells were treated with 0.25 mM OA dissolved in 5% BSA for 24 h followed by the admin-istration of 10, 40 or 80 μM OLE or 10 μM metformin for 24 h.

tag: protocol

value: HFD-JGF

tag: Sex

value: male


title: OA-induced liver (AML-12) cells

description:
Test
Alpha mouse liver 12 (AML-12) cells were purchased from American Type Culture Collection (ATCC, USA). Cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) and Ham's F-12 (1:1) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Guangzhou, China), 1% insulin transferrin selenium solution (LV-Biotech, Shenzhen, China), and 40 ng/ml dexamethasone (Sigma, Guangzhou, China). Cells were treated with 0.25 mM OA (Sigma, Guangzhou, China) dissolved in 5% BSA for 24 h followed by the admin-istration of 10, 40 or 80 μM OLE or 10 μM metformin (Sigma, Guangzhou, China) for 25 h.
SAMPLE 5

source_name: Alpha Mouse Liver 12

value: OA-induced


title: LKB1 activator-metformin intervented OA-induced liver (AML-12) cells

description:
Test
Alpha mouse liver 12 (AML-12) cells were purchased from American Type Culture Collection (ATCC, USA). Cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) and Ham's F-12 (1:1) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Guangzhou, China), 1% insulin transferrin selenium solution (LV-Biotech, Shenzhen, China), and 40 ng/ml dexamethasone (Sigma, Guangzhou, China). Cells were treated with 0.25 mM OA (Sigma, Guangzhou, China) dissolved in 5% BSA for 24 h followed by the admin-istration of 10, 40 or 80 μM OLE or 10 μM metformin (Sigma, Guangzhou, China) for 27 h.
SAMPLE 7


title: 260-A039109

city: Frankfurt

first: Florestan

middle: Johannes

last: Koll

address: Theodor-Stern-Kai 7

department: Department of Urology

country: Germany

institute: University Hospital Frankfurt, Goethe University

data_processing:
Post-Sequencing QC  Post-sequencing QC metrics (QC0, QC1, QC2, and QC3) detect four different sample failure modes. QC0 detects degraded RNA or poor quality / quantity samples, by assessing the percentage of overall reads being allocated to the positive process control probe for each sample. QC1 detects samples with insufficient read depth; this is evaluated by setting the cut-off at the minimum number of reads that can be allocated to each sample for the data set to be repeatable. QC2 detects samples with minimal expression variability, of which is determined by the median log2 (CPM) for negative control probes. QC3 detects samples with elevated gDNA background, which is caused by incomplete digestion of gDNA by the DNase enzyme.
Data are returned from the sequencer in the form of demultiplexed FASTQ files, with four files per original well of the assay. The HTG EdgeSeq Parser was used to align the FASTQ files to the probe list to collate the data. Data are provided as data tables of raw, QC raw, log2 CPM (counts per million), and median normalized data.
Supplementary files format and content: Processed data files contain raw data (xlsx) and median normalized and log2-transformed counts.

source_name: MIBC, FFPE

extract_protocol:
A 1mm punch was taken from FFPE blocks of a representative tumor area with at least 50% tumor content. RNA was isolated using the “truXTRAC FFPE total NA Kit – Column” (Covaris, Woburn, MA, USA)
HTP Processing:  Samples were processed in accordance with manufacturers recommendations, HTG EdgeSeq processing (instrument method). Samples were transferred to a standard 96-well micro-titer plate, referred to as the sample plate.      Target capture was done by the HTG EdgeSeq chemistry. Briefly, the nuclease protection probes (NPPs) were added to the lysed samples in the sample plate in excess amount and hybridized to the target mRNA. Then S1 nuclease was added to digest non-hybridized RNA and excess NPPs, thus producing a stoichiometric amount of target mRNA NPP duplexes. After the S1 digestion was completed, the processed sample was transferred to a new 96-well micro-titer plate with a v-bottom, referred to as the stop plate, and S1 digestion was terminated by the addition of termination solution followed by heat denaturation of S1 enzyme.
Library Preparation   Each processed sample from the stop plate was used as a template to set up PCR reactions with specially designed primers, referred to as tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. HTG has developed 12 forward and eight reverse primer tags; therefore, up to 96 samples can be analyzed simultaneously on an Illumina sequencing platform. The library was prepared using a PCR with OneTaq (New England Biolabs) and EdgeSeq PCR tag primers (HTG molecular). Following, the PCR, clean-up procedures was performed with AMPure cleanup beads (Beckman) .The library was then quantified in with Accuclear fluorescent dye (Biotium) and a Molecular Devices SpectraMax plate reader. All samples and controls were quantified in triplicate.    Following quantification, the HTG Library Calculator software was used to ensure there was a sufficient concentration of sample for library pooling and to determine the appropriate dilutions for building the library pool. All samples processed within this study had sufficient PCR product to be pooled for sequencing.  The HTG Library Calculator was also determined the volume and specific type of denaturation reagents to be used for the library. The library was denatured by adding 0.2N NaOH to the library tube. The tube was then vortexed, spun down, and incubated for five minutes at room temperature. Cold HT1 buffer (Illumina) was added to the library tube, followed by the addition of 200 mM Tris pH 7.4 to neutralize the NaOH. The sample was vortexed and spun down.   PhiX control adaptor-ligated library was spiked in at a concentration of 12.5 pM to the pooled library. The library was vortexed and spun down for a final time. The denatured library was loaded (1,300 µL) into the appropriate well of the NextSeq sequencing cartridge. The concentration of the pooled library loaded on the NextSeq flow cell was 1.7 pM.        The sequencing was performed on the Illumina NextSeq 550 sequencer in accordance with manufacturer’s recmendations but also including two HTG custom sequencing primers.  The sequencing data on mRNA expression of target genes were imported into HTG EdgeSeq Parser software for alignment and quantification of the reads. The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data.

tag: tissue

value: MIBC

tag: gender

value: m

tag: pt-stage


title: OLE therapy OA-induced liver (AML-12) cells

description:
Test
Alpha mouse liver 12 (AML-12) cells were purchased from American Type Culture Collection (ATCC, USA). Cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) and Ham's F-12 (1:1) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Guangzhou, China), 1% insulin transferrin selenium solution (LV-Biotech, Shenzhen, China), and 40 ng/ml dexamethasone (Sigma, Guangzhou, China). Cells were treated with 0.25 mM OA (Sigma, Guangzhou, China) dissolved in 5% BSA for 24 h followed by the admin-istration of 10, 40 or 80 μM OLE or 10 μM metformin (Sigma, Guangzhou, China) for 26 h.
SAMPLE 6

value: OLE therapy OA-induced


title: 260-A039093


title: Chow mice

description:
Control
Six-week-old male C57BL/6J mice were purchased from the Guangdong Medical Laboratory Animal Center (Fo-shan, Guangdong, China). Mice were maintained under standard management conditions (temperature of 25 ± 2°C and a 12-hour light-dark cycle) and performed in accordance with procedures approved by the Animal Care and Ethics Committee at Wuyi University (Jiangmen, Guangdong). After 1 weeks of acclimatization, mice were randomly assigned into three groups and fed with either a chow (8% calories from fat, 21% calories from protein, and 71% calories from carbohydrate), a HFD (45% calories from fat, 20% calories from protein and 35% calories from carbohydrate), or a HFD supplemented with 0.6% (w/w) OLE-JGF (HFD-JGF) ad libitum for 8 weeks.
SAMPLE 1

value: Chow


title: 260-A039097


title: 260-A039121

value: f


title: 260-A039105


title: 260-A039082


title: 260-A039102


title: 2-DG capTG rep2

city: Shanghai

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
read counting
Genome_build:  hg19_GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human OSCC cell line

growth_protocol: The cal27 cells were seeded in 6-well plates and treated with different CM for 24 hours.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tongue mucosa

tag: culture media

value: high glucose DMEM with 2-DG


title: 0 capTG rep3

value: glucose-deprived DMEM


title: 0 capTG rep1


title: 260-A039087

tag: age


title: 0 TG rep3


title: 260-A039113


title: 2-DG capTG rep3


title: 260-A039130


title: H TG rep3

value: high glucose DMEM


title: Normal liver (AML-12) cells

description:
Control
Alpha mouse liver 12 (AML-12) cells were purchased from American Type Culture Collection (ATCC, USA). Cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) and Ham's F-12 (1:1) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Guangzhou, China), 1% insulin transferrin selenium solution (LV-Biotech, Shenzhen, China), and 40 ng/ml dexamethasone (Sigma, Guangzhou, China). Cells were treated with 0.25 mM OA (Sigma, Guangzhou, China) dissolved in 5% BSA for 24 h followed by the admin-istration of 10, 40 or 80 μM OLE or 10 μM metformin (Sigma, Guangzhou, China) for 24 h.
SAMPLE 4

value: Normal


title: HFD mice

description:
Test
Six-week-old male C57BL/6J mice were purchased from the Guangdong Medical Laboratory Animal Center (Fo-shan, Guangdong, China). Mice were maintained under standard management conditions (temperature of 25 ± 2°C and a 12-hour light-dark cycle) and performed in accordance with procedures approved by the Animal Care and Ethics Committee at Wuyi University (Jiangmen, Guangdong). After 1 weeks of acclimatization, mice were randomly assigned into three groups and fed with either a chow (8% calories from fat, 21% calories from protein, and 71% calories from carbohydrate), a HFD (45% calories from fat, 20% calories from protein and 35% calories from carbohydrate), or a HFD supplemented with 0.6% (w/w) OLE-JGF (HFD-JGF) ad libitum for 9 weeks.
SAMPLE 2

value: HFD


title: H capTG rep1


title: 2-DG TG rep3


title: 2-DG TG rep1


title: 2-DG TG rep2


title: 0 capTG rep2


title: H TG rep2


title: FL LMPP rep2 (ATAC-seq)

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

description:
2_FL_LMPP
FL_LMPP_mapq10_ppr.IDR0.1.filt.narrowPeak

data_processing:
RNA-seq: RNA-sequence pre-processing  RNA-sequenced reads were trimmed TrimGalore (Babraham Bioinformatics) for removal of adapter –and low quality sequences. Resulting reads were then mapped onto the mouse genome build mm10 with STAR (Dobin et al, 2013)  and post-processed with RSEM (http://deweylab.github.io/RSEM/) (Li et al, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build mm10 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options and tested for differential gene expression using the DESeq2 package ( https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html) (Love et al, 2014 #38) via HOMER getDifferentialExpression.pl.  Differential genes with adjusted p-value <= 0.05 were considered significantly different.
ATAC-seq: Reads were trimmed using TrimGalore and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.5) (Langmead et al, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.21.4) and files were further filtered for mapq score of 10 using Samtools (v. 1.9). Peak calling from the mapq10 filtered bam files (duplicates) was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From each processed duplicate, the Optimal peak set was used for downstream analysis.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: RNA-seq: Raw count matrix derived with HOMER tools analyzeRepeats.pl rna mm10 -condenseGenes -count exons -raw -d {path-to-tagdirs}
Supplementary_files_format_and_content: ATAC-seq: IDR-processed MACS2 peak file. Filtered bam-files were processed with Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively.

source_name: Lymphoid-primed multipotent progenitor

extract_protocol:
ATAC-seq: Briefly, sorted cells (same populations as in RNA-seq) were rinsed with HBSS, lysed and immediately after added tagmentation reaction mix including Nextera Tn5 transposase (Illumina). After 30  min incubation at 37C, samples were cleaned up using ChIP DNA Clean and Concentrator (Zymo Research). The libraries were constructed and barcoded using a Nextera library preparation kit(Illumina). The final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio for ~100-150bp cutoff DNA size) using Ampure XP beads (Beckman-Coulter). Each biological sample was run in duplicates. Libraries were sequenced paired-end on Nextseq 500 using the 150cycles high output V2 kit (Illumina), to an approximate depth of 100 million reads.
ATAC-seq:  ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers Libraries were run paired-end on the Illumina NexSeq500.

value: fetal liver

value: Lymphoid-primed multipotent progenitor


title: 0 TG rep1


title: H capTG rep3


title: H capTG rep2


title: 2-DG capTG rep1


title: 0 TG rep2


title: H TG rep1


title: FL LMPP rep1 (ATAC-seq)

description:
1_FL_LMPP
FL_LMPP_mapq10_ppr.IDR0.1.filt.narrowPeak


title: FL CD41- HSC (scATAC-seq)

data_processing:
R1 and R3 contain biological read, R2 contains the cell barcode.
Preprocessing: The majority of the analysis was carried out with the Single Nucleus Analysis Pipeline for ATAC-seq SnapATAC (Fang et al., 2020). Read pre-processing was carried out as follows: 1) Snaptools dex-fastq was used to integrate the 10X barcode into the read name of read 1 and read 3. 2) The resulting, demultiplexed fastq-files were trimmed in paired-end mode with TrimeGalore which is a wrapper script for Cutadapt (Kechin et al., 2017). 3) Trimmed fastq-files were aligned to mm10 (Assembly version GRCm38.p5) with snaptools align-paired-end using bwa as the aligner. 4) The resulting bam-file was downscaled to approximately the same number of high-quality reads per cell (~135.000) and used as input for snap-file generation using snaptools snap-pre (settings: --min-mapq=30 --min-flen=0 --max-flen=1000 --keep-chrm=FALSE --keep-single=FALSE --keep-secondary=FALSE --overwrite=True --min-cov=100) (reads aligning to chrM were filtered out at this step) followed by a 5000 bp bin cell-by-bin matrix creation with snaptools snap-add-bmat. The resulting snap-files were imported into R (v.3.6.0) as a combined object for all samples, with the createSnap function from the SnapATAC-package (development version).
Single-cell ATAC-seq processing: Barcode and bin filtering  Prior to downstream analysis we filter for high-quality barcodes on two criteria: 1) Fragment coverage; 2) and promoter_ratio which is the ratio of fragments in promoter regions / all passed fragments.   Number of fragments in promoters were derived by calculating the total number of fragments in the mm10 promoter regions provided with the 10X cellranger-atac pipeline (10x Genomics single cell ATAC Cell Ranger software). Barcodes with a fragment coverage > 4.15 a promoter_ratio > 0.27 and < 0.8 were included in the analysis. In total 2,403 FL CD41– HSCs, 2,310 ABM CD41– HSCs, 1,123 ABM CD41int HSCs and 2,986 adult MkPs passed the barcode QC. Additionally the cell-by-bin matrix was converted to a binary matrix and the bins with the top 5% highest coverage (mainly invariant features such as promoters of house-keeping genes) as well as bins overlapping mm10 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were filtered out and omitted from downstream analyses.    Cell-by-bin based dimension reduction and clustering  SnapATAC utilizes diffusion maps for dimensionality reduction. The cell-by-bin matrix was used as input for SnapATACs runDiffusionMaps calculating 50 eigenvectors. These were pair-wised plotted and after visual inspection the first eight were selected for pairwise Euclidean distance calculation between every two cells followed by k-nearest neighbor (k=50) clustering. Cells in samples or clusters were visualized as a two-dimensional UMAP representation using the runViz function from the SnapATAC-package.    Peak calling and identification of differentially accessible regions (DARs)  Peaks were called on a per-sample-basis with MACS2 via the SnapATAC runMACS (Zhang et al., 2008) functions with the settings: --nomodel --shift 100 --ext 200 --qval 5e-2 -B --SPMR. The resulting narrowPeak peak files were imported into R and combined to one non-redundant peak list with the GenomicRanges package (v. 1.36.1). A cell-by-peak matrix was created with createPmat from SnapATAC, followed by matrix binarization.   Differentially accessible regions (DARs) between ABM CD41– and ABM CD41int HSCs or ABM CD41– HSCs and FL HSCs were identified with findDAR from the SnapATAC-package (test.method=”exactTest”, bcv(biological coefficient of variation)=0.1). 1014 regions were identified for ABM CD41int HSCs and 83 for ABM CD41– HSCs in the ABM CD41int vs CD41– HSC comparison and 17859 for the ABM CD41– HSC and 39224 for the FL CD41– HSC in the FL vs ABM CD41– HSC comparison. If less than 2000 regions were identified, the top 2000 most enriched peaks were used for UMAP visualization and motif analysis.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Binarized peak-by-cell matrix.

source_name: Hematopoietic stem cell

extract_protocol:
Cells were FACS sorted based on the following surface parameters. FL CD41- HSC: CD3-Gr1-B220-ter119-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41-, ABM CD41- HSC: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41-,  ABM CD41int HSC: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41+, ABM MkP: :CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1-CD150+CD41+. Nuclei were isolated according to Low cell input nuclei isolation protocol (RevD 10x Genomics single cell ATAC).
scATAC-seq libraries were prepared according to the Chromium Next GEM Single Cell ATAC Reagent Kits User Guide (v1.1 chemistry) (10x Genomics;) by the Center for Translational Genomics (CTG), Lund University. Nuclei were sequenced on Illumina NovaSeq 6000 with ~81,000-235,000 read pairs per cell and reads fastq-files were generated with the cellranger-atac mkfastq command.

value: Hematopoietic stem cell


title: ABM LMPP rep2 (ATAC-seq)

description:
2_ABM_LMPP
BM_LMPP_mapq10_ppr.IDR0.1.filt.narrowPeak

value: adult bone marrow

value: 12 weeks


title: ABM LMPP rep1(ATAC-seq)

description:
1_ABM_LMPP
BM_LMPP_mapq10_ppr.IDR0.1.filt.narrowPeak


title: LOUCY cell line with  ICN construct, ICN overexpression. Replicate 1 [ICN+1]

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analysis was performed in R version 3.6.3. The Affy package, version 1.64.0, was used for Robust Multichip Average (RMA) normalization.

label: biotin

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions

value: LOUCY

tag: genotype/variation

value: ICN construct, ICN overexpression

value: with doxycyline


title: ABM CD41- HSC (scATAC-seq)

tag: cell type


title: FL HSC rep2 (ATAC-seq)

description:
2_FL_HSC
FL_HSC_mapq10_ppr.IDR0.1.filt.narrowPeak


title: M36_sample_5_RIF

city: Cape Town

first: Tracey

last: Calvert-Joshua

state: Western Cape

address: Robert Sobukwe Road, Bellville

department: South African National Bioinformatics Institute (SANBI)

country: South Africa

institute: University of the Western Cape

data_processing:
FastQC checks in Galaxy showed that the data was of high quality (mean PHRED > 30). Reads were trimmed, and adapter sequences were removed using Trimmomatic V.0.38 with a PHRED = 20 and a sliding window of 4 (Bolger et al., 2014).
Reads were alignedusing BWA-MEM 0.17.1
Quality of the bam files were checked using Samtools 1.9
Some of the bam files were converted to wiggle files for further analysis, using the RSeQC package in Galaxy
Assembly: H37Rv (NC00096.3)
Supplementary files format and content: Diffrential expression analysis was carried out using Limma voom (TMM normalization) in Galaxy. Although these files were not needed for this analysis
Supplementary files format and content: tabular files with DE genes called using limma voom (TMM) to compare expression of genes exposed to rifampicin versus those grown under no rifampicin treatment

organism: Mycobacterium tuberculosis

growth_protocol: Cultures were grown in 7H9 media until mid-log phase

extract_protocol:
RNA extraction was carried out using the FastBlue RNA extraction kit (MP Biomedicals). Ribosomal depletion was performed, with the bacterial option as probes for hybridization of rRNA (TruSeq Total RNA). Primer design and RNA-seq were done by the Agricultural Research Council (ARC) sequencing facility using the TruSeq DNA and RNA CD Indexes (I7 and I5 adapters).
TruSeq Stranded mRNA Library

treatment_protocol: exposed to RIF for 24 hours

value: Rifampicin-resistant

tag: genotype

value: 1/4 MIC rifampicin

value: 24 hours


title: ABM MkP (scATAC-seq)

source_name: Hematopoietic progenitor

value: Hematopoietic progenitor


title: M36_sample_4_RIF

tag: cell line


title: LOUCY cell line with  ICN construct, no overexpression. Replicate 2 [ICN-2]

value: ICN construct, no overexpression

value: without doxycyline


title: LOUCY cell line with MEF2C and ICN construct, MEF2C ICN overexpression. Replicate 1 [M_ICN+1]


title: M36_sample_3_RIF


title: LOUCY cell line with  ICN construct, ICN overexpression. Replicate 3 [ICN+3]


title: LOUCY cell line with MEF2C and ICN construct, MEF2C ICN overexpression. Replicate 2 [M_ICN+2]


title: LOUCY cell line with MEF2C and ICN construct, MEF2C ICN overexpression. Replicate 3 [M_ICN+3]


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-DL1 condition. Replicate 3 [M_DL1+3]

value: with doxycyline, grown on OP9-DL1


title: FL HSC rep1 (ATAC-seq)

description:
1_FL_HSC
FL_HSC_mapq10_ppr.IDR0.1.filt.narrowPeak

tag: strain


title: M36_sample_2_RIF


title: LOUCY cell line with  ICN construct, no overexpression. Replicate 3 [ICN-3]


title: M36_sample_1_RIF


title: LOUCY cell line with  ICN construct, ICN overexpression. Replicate 2 [ICN+2]


title: LOUCY cell line with MEF2C and ICN construct, no overexpression. Replicate 2 [M_ICN-2]


title: LOUCY cell line with  ICN construct, no overexpression. Replicate 1 [ICN-1]


title: ABM HSC rep2 (ATAC-seq)

description:
2_ABM_HSC
BM_HSC_mapq10_ppr.IDR0.1.filt.narrowPeak


title: LOUCY cell line with MEF2C and ICN construct, no overexpression. Replicate 3 [M_ICN-3]


title: M35_sample_3_CONT


title: M35_sample_2_CONT


title: LOUCY cell line with MEF2C and ICN construct, no overexpression. Replicate 1 [M_ICN-1]


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-DL1 condition. Replicate 2 [M_DL1+2]


title: ABM HSC rep1(ATAC-seq)

description:
1_ABM_HSC
BM_HSC_mapq10_ppr.IDR0.1.filt.narrowPeak


title: M35_sample_1_CONT


title: FL LMPP rep3 (RNA-seq)

description:
3-FL-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt

extract_protocol:
RNA-seq: Cells were FACS sorted based on the following surface parameters. FL HSC: CD3-Gr1-B220-ter119-7AAD-cKit+Sca1+CD48-CD150+Flt3-, FL LMPP: CD3-Gr1-B220-ter119-7AAD-cKit+Sca1+CD48+CD150-Flt3+, ABM HSC: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48-CD150+Flt3-. ABM LMPP: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48+CD150-Flt3+.Total RNA was isolated with RNAzol according to manufacturers protocol (Sigma) and analyzed on an Agilent 2100 Bioanalyzer with the RNA 6000 nano kit (Agilent).
RNA-seq: RNA was prepared for sequencing with the SMART-Seq v4 Ultra Low Input RNA Library Prep Kit according to manufacturer’s instructions (Takara Bio USA, Inc.). Amplified cDNA was purified using Ampure XP beads (Beckman-Coulter). 125pg cDNA was used for tagmentation with Nextera XT DNA library preparation kit (Illumina) quantified by Agilent 2100 Bioanalyzer (High sensitivity DNA kit).  Libraries were indexed using the Nextera XT v2 indexing kit (Illumina).


title: M33_sample_3_RIF


title: M33_sample_4_RIF


title: FL LMPP rep2 (RNA-seq)

description:
2-FL-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: M33_sample_2_RIF


title: M33_sample_5_RIF


title: FL LMPP rep1 (RNA-seq)

description:
1-FL-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: M33_sample_1_RIF


title: ABM LMPP rep3 (RNA-seq)

description:
3-ABM-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: ABM LMPP rep2 (RNA-seq)

description:
2-ABM-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-DL1 condition. Replicate 1 [M_DL1+1]


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-DL1 condition. Replicate 2 [M_DL1-2]

value: without doxycyline, grown on OP9-DL1


title: M32_sample_3_CONT


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-DL1 condition. Replicate 3 [M_DL1-3]


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-GFP condition. Replicate 3 [M_GFP+3]

value: with doxycyline, grown on OP9-GFP


title: ABM LMPP rep1(RNA-seq)

description:
1-ABM-LMPP
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-DL1 condition. Replicate 1 [M_DL1-1]


title: M32_sample_1_CONT


title: FL HSC rep2 (RNA-seq)

description:
2-FL-HSC
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt

value: fetal liver


title: ABM CD41int HSC (scATAC-seq)


title: M30_sample_3_RIF


title: M32_sample_2_CONT


title: FL HSC rep1 (RNA-seq)

description:
1-FL-HSC
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: M30_sample_2_RIF


title: ABM HSC rep3 (RNA-seq)

description:
3-ABM-HSC
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt


title: HDFa_EBC-1013_72h

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 72h

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

growth_protocol: Adult human dermal fibroblasts (HDFa, ThermoFisher Scientific) were cultured in Medium 106 supplemented with Low Serum Growth Supplement (LSGS) and gentamycin. Cells were maintained in a humidified incubator (37°C, 5% CO2) and passaged using tryspin/versene at 80% confluency.  All cells were confirmed mycoplasma negative prior to use using MycoAlert (Promega).  HDFa were used between p3 and p10 for all assays.

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: HDFa were seeded into T25 flasks (Nunc) at a density of 2.5 × 104 cells per flask (5 ml).  After reaching 80% confluency, the growth medium was aspirated and replaced with 5 ml of fresh medium containing vehicle (ethanol) or 100 ng/ml EBC-1013.  At 0, 0.5, 1, 2, 4, 8, 24, 48 and 72 h, the growth medium was aspirated, cells washed twice with fresh medium before RNA extraction.

tag: cell

tag: time


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-GFP condition. Replicate 2 [M_GFP+2]


title: LOUCY cell line with MEF2C construct, MEF2C overexpression, grown OP9-GFP condition. Replicate 1 [M_GFP+1]


title: HDFa_EBC-1013_48h

scan_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 48h


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-GFP condition. Replicate 2 [M_GFP-2]

value: without doxycyline, grown on OP9-GFP


title: HDFa_EBC-1013_24h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 24h


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-GFP condition. Replicate 1 [M_GFP-1]


title: HDFa_EBC-1013_02h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 2h

value: 2 h


title: ABM HSC rep1(RNA-seq)

description:
1-ABM-HSC
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt

value: adult bone marrow

value: Hematopoietic stem cell


title: LOUCY cell line with MEF2C construct, no overexpression, grown OP9-GFP condition. Replicate 3 [M_GFP-3]

value: LOUCY


title: HDFa_EBC-1013_08h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 8h

value: 8 h


title: LOUCY cell line with MEF2C construct, MEF2C overexpression. Replicate 2 [M+2]

value: MEF2C construct, MEF2C overexpression

value: with doxycyline


title: LOUCY cell line with MEF2C construct, no overexpression. Replicate 3 [M-3]

value: MEF2C construct, no overexpression


title: HDFa_EBC-1013_0h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 0h

value: 0 h


title: HDFa_EBC-1013_04h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 4h

value: 4 h


title: M29_sample_3_CONT

value: Rifampicin-resistant


title: HDFa_EBC-1013_01h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 1h

value: 1 h


title: LOUCY cell line with MEF2C construct, MEF2C overexpression. Replicate 3 [M+3]


title: KPPC;Col1pdxKO mouse PDAC 5

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

data_processing:
STAR
HTSEQ
DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: pancreatic tumor

growth_protocol: Mice with standard housing conditions

extract_protocol:
Direct-zol RNA extraction kit (Zymo)
Illumina TrueSeq stranded mRNAseq Library

treatment_protocol: Mice received no treatment

value: pancreatic tumor

tag: detailed genotype


title: M30_sample_1_RIF

value: 1/4 MIC rifampicin

value: 24 hours


title: ABM HSC rep2 (RNA-seq)

description:
2-ABM-HSC
analyzeRepeats_ABM_and_FL_HSC_LMPP.raw.exon_count_matrix.condenseGenes.txt

value: 12 weeks


title: M29_sample_4_CONT


title: LOUCY cell line with MEF2C construct, MEF2C overexpression. Replicate 1 [M+1]


title: M27_sample_4_RIF


title: M29_sample_1_CONT


title: M29_sample_2_CONT


title: KPPC;Col1pdxKO mouse PDAC 4


title: M27_sample_3_RIF


title: toyocamycin_72hr_2

city: Nutley

first: Ying

last: Wang

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health Center for Discovery and Innovation

data_processing:
Sequenced reads were aligned to the GRCh38.100 reference genome using STAR version 2.7.5a and gene-level counts were generated by setting the `quantMode GeneCounts` flag.
Differential expression analysis was performed using EdgeR. The `filterByExpr` function in EdgeR was then used to determine genes with sufficiently large counts to be included in downstream differential expression testing
The filtered count matrix was then normalized using TMM normalization and differential expression testing was performed using the `glmTreat` function with the minimal required fold-change threshold set to log2(1) for significant differential gene expression (FDR < 0.1).
Assembly: GRCh38.100
Supplementary files format and content: Tab-delimited count matrix of raw counts from STAR ReadsPerGene.out files
Supplementary files format and content: Differential expression table from edgeR topTags output with an additional column describing the contrast tested

source_name: Colorectal

extract_protocol:
RNA from experiments in biological triplicates was isolated using RNeasy Mini Plus Kit (QIAGEN) following the manufacturer’s instructions.
RNA amount and purity was measured using Qubit 3.0, and (3) Agilent2100 was used to check for RNA Integrating Number (RIN). Samples with RIN values of >8.5 were sent to Novogene Library construction. Briefly, the polyA enrichment library preparation was performed to construct 250-300 bp insert cDNA library. Sequencing was performed using paired end reads (150 bp, average 40 million reads per sample) on the HiSeq2500 platform.

value: Colorectal

value: toyocamycin

tag: batch


title: toyocamycin_72hr_3

tag: treatment


title: KPPC;Col1pdxKO mouse PDAC 1


title: KPPC mouse PDAC 4

value: KPPC


title: M27_sample_1_RIF


title: M27_sample_2_RIF


title: toyocamycin_24hr_2


title: toyocamycin_48hr_2


title: LOUCY cell line with MEF2C construct, no overexpression. Replicate 2 [M-2]

value: without doxycyline


title: HDFa_Vehicle_24h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 24h

value: Vehicle


title: KPPC mouse PDAC 3


title: HDFa_Vehicle_72h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 72h


title: toyocamycin_10hr_2


title: HDFa_Vehicle_48h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 48h


title: KPPC;Col1pdxKO mouse PDAC 2


title: HDFa_EBC-1013_0.5h

source_name: Adult human dermal fibroblast (HDFa) cells treated with 100 ng/ml EBC-1013 for 0.5h


title: KPPC mouse PDAC 2


title: LOUCY cell line with MEF2C construct, no overexpression. Replicate 1 [M-1]

value: LOUCY


title: HDFa_Vehicle_02h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 2h

value: 2 h


title: HDFa_Vehicle_01h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 1h


title: HDFa_Vehicle_0.5h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 0.5h


title: HDFa_Vehicle_04h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 4h


title: HDFa_Vehicle_08h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 8h

value: 8 h


title: KPPC mouse PDAC 1


title: toyocamycin_72hr_1


title: M26_sample_3_CONT


title: toyocamycin_10hr_1


title: HDFa_Vehicle_0h

source_name: Adult human dermal fibroblast (HDFa) cells treated with vehicle (ethanol) for 0h


title: toyocamycin_2hr_1


title: M26_sample_1_CONT


title: M24_sample_2_RIF


title: 1-1 08302016

city: Boston

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation kit was miRcury biofluids (Exiqon).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were not multiplexed. Type of Starting Material was total RNA.

value: Plasma

tag: condition

value: Healthy Subject

tag: time of day

value: morning

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: subject id


title: 2-1 08302016

tag: tissue


title: ATAC_231_GATA3_rep2

city: Grand Forks

first: Archana

last: Dhasarathy

state: ND

address: 1301 N. Columbia Road, STOP 9061, STOP 9037

department: Biomedical Sciences

institute: UNIVERSITY OF NORTH DAKOTA

data_processing:
Reads were filtered based on a mean base quality score >20.
Adapter sequences were removed with the Cutadapt function.
Reads were mapped to the mm10 or hg19 genome using Bowtie 0.12.8 with parameters '-I 0 -X 2000 -m 1'.
The offset parameters suggested by Buenrostro et al (Nat. Methods, 2013) were applied to each mapped read.
Alignments to chrM were filtered out with samtools.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Signal tracks were generated from either the full ATAC-seq fragment or only the 9bp footprint at 5' ends of reads, via conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format by UCSC utility bedGraphToBigWig.
Peak calls were made by PeaKDEck with parameters '-sig 0.0001 -bin 300 -back 3000 -npBack 2500000'.
Assembly: mm10, hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: peak calls in BED format

growth_protocol: DMEM (with L-Glutamine, and 15 mM HEPES) + 10% FBS was used for NMuMG cells. DMEM + 10%FBS was used for MDA-MB-231 cells.

extract_protocol:
MinElute (before PCR, Qiagen) and AMPure XP (after PCR, Beckman Coulter) were used for DNA purification.
Cells were lysed with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Nuclei were treated with Tn5 Transposase (Illumina). The total of 8 PCR cycles were performed to recover and amplify the DNA fragments at open chromatin.

treatment_protocol: Increasing number of NMuMG cells were used to optimize the ATAC seq protocol. Cells are cultured using DMEM+10% FBS medium.  To collect the cell pellet, cells were washed with 1X PBS, and trypsinize with 0.25% Trypsin-EDTA (1X).  Cells are counted by the Countess cell counter (Invitrogen)

tag: passages


title: A+Input

city: Changsha

first: Shen

last: Li

address: 110 Xiangya Road

department: School of Basic Medical Science

institute: Central South University

data_processing:
Raw data (Fastq files) was processed by FASTQC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence  by Trimmomatic, then mapped to hg38whole genome using bwa
The bam file generated by the unique mapped reads as an input file, using MACS2 software for callpeak with cutoff qvalue < 0.05
ChIP-seq signal tracks were visualized through Integrative Genomics Viewer
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: EBV positive Akata

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator.
ChIP-seq libraries were prepared using the NEBNext® UltraTMII DNA Library Preparation Kit (#E7645S) complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using AMPure® XP Beads(Beckman Coulter,#A63881) from Beckman Coulter. Libraries were validated using Qubit Kit.

value: EBV positive Akata

tag: cell type

value: Burkitt lymphomas cell line

tag: chip antibody


title: dmso_72hr_2

tag: cell line

value: dmso


title: M26_sample_2_CONT

value: Rifampicin-resistant

tag: genotype


title: A-BRD7

source_name: EBV negative Akata

value: EBV negative Akata

value: BRD7（CST， #14910）


title: toyocamycin_2hr_2

value: Colorectal

value: toyocamycin


title: dmso_72hr_1


title: A+BRD7


title: M23_sample_2_CONT


title: 6-2 08302016

value: afternoon


title: dmso_48hr_2


title: M24_sample_3_RIF

value: 1/4 MIC rifampicin

value: 24 hours


title: 5-3 08302016

value: Plasma

value: evening


title: SS664, scRNAseq

last: Quiat

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
10x Genomics
nuclear RNA

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pinna

extract_protocol:
Nuclei were isolated from flash frozen tissue as previously described (PMID: 34043278)
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Multiple

value: Pinna

tag: phenotype

value: microtia

tag: age

value: pediatric


title: 6-3 08302016

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: dmso_72hr_3

value: dmso

tag: time


title: SS658, scRNAseq

description:
10x Genomics
nuclear RNA

value: normal

value: 6 years


title: ATAC_231_GATA3_rep1


title: M23_sample_1_CONT

value: Rifampicin-resistant


title: M24_sample_1_RIF


title: SS16, scRNAseq

description:
10x Genomics
nuclear RNA

value: 5 years


title: 5-2 08302016

value: afternoon


title: 6-1 08302016

value: morning


title: A-Input

value: EBV negative Akata

value: Burkitt lymphomas cell line


title: M21_sample_3_RIF

value: 1/4 MIC rifampicin

value: 24 hours


title: M23_sample_3_CONT


title: 1-2 08302016

value: Plasma


title: M21_sample_2_RIF


title: dmso_24hr_2

value: Colorectal

tag: batch


title: dmso_10hr_2

tag: treatment


title: 3-2 08302016

tag: condition

value: Healthy Subject


title: M20_sample_3_CONT


title: Meg-01, sodium propionate, 500 micro molar, rep2

city: Erlangen

first: Michael

last: Frech

address: Ulmenweg 18

department: Department of Internal Medicine 3 - Rheumatology and Immunology

institute: University Hospital Erlangen

data_processing:
Raw data of FASTQ format were processed through fastp.
Paired-end clean reads were aligned to the reference genome (GRCh38/hg38) using the Spliced Transcripts Alignment to a Reference (STAR, v2.6.1d) software.
FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene.
The count output was utilized to identify differentially expressed genes using DESeq2 version v1.26.0.
Assembly: hg38
Supplementary files format and content: FeatureCounts transcript-level abundance tab-separated text file

source_name: cell line

extract_protocol:
RNA was extracted using a RNeasy Mini kit (qiagen, USA) according to the manufacturer's instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cell line

value: megakaryoblast

value: sodium propionate, 500 µM, 48 hours


title: 4-2 08302016

tag: time of day

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)