title: ESC Nr1h2-FLAG FLAG-ChIP (sample)

description: Library name: Nr_F_Sample

extract_protocol:
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). EPSC medium is made up of DMEM/F-12 basal media supplemented with 20% knockout serum replacement (Thermo Fisher Scientific, 10828-033), 1X L-glutamine, 1X NEAA, 0.1 mM 2-mercaptoethanol, 103 units/ mL recombinant mouse LIF, 3 µM CHIR99021, 1 µM PD0325901, 4 µM JNK Inhibitor VIII (Tocris, 3222), 10 µM SB203580 (Tocris, 1402), 0.3 µM A-419259 (Santa Cruz, SC-361094) and 5 µM XAV939 (Tocris, 3748).  NrESC medium is composed of ESC medium supplemented with 10 µM T0901317. All the ESC lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . Cells were trypsinized, harvested and the cell number was estimated. Cross-linking was performed for 10 × 106 cells using 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M Glycine. Crosslinked cells were resuspended in 1 ml of FA lysis buffer (10 mM Tris–Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche)), nutated at 4 °C for 15 min and spun down at 1300 × g for 5 min at 4 °C. Supernatant was removed and the pellet was re-suspended in 1% SDS lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail). After 15 min of incubation, the pellet was spun down and washed two times with 0.1% lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-1s00, 0.1% NaDOC and protease inhibitor cocktail). Cell pellet was sonicated by Biorupter (Diagenode) for 14 cycles (30 s on and 60 s off for each cycle). Cell debris was removed from the sheared chromatin by centrifugation at 21,000 × g at 4 °C for 30 min. Protein G Dynabeads (Life Technologies) was incubated with antibodies (Nr1h2 ChIP antibody (NB100-1464, Novus Biologicals), FLAG ChIP antibody (F1804, Sigma-Aldrich), H3K9me2 ChIP antibody (Abcam, ab1220), H3K9me3 ChIP antibody (Abcam, ab8898) and H3K27Ac ChIP antibody (ab4729, Abcam)) for 3 h at room temperature and washed three times by PBS with 0.1% TritonX-100. 5% of the sheared chromatin was separated as input while the remaining was subject to overnight incubation with antibody-bound Dynabeads. In total 7 washes were performed to remove unspecific bindings, including three washes with 0.1% SDS lysis buffer, one with 0.1% SDS lysis buffer/0.35 M NaCl, one with 10 mM Tris–Cl (pH 8.0), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and two with TE buffer (pH 8.0). Dynabeads were resuspended in elution buffer (50 mM Tris–HCl (pH 7.5), 10 mM EDTA, 1% SDS) and incubated at 68 °C for 1 h with 1400 rpm shaking. Eluted samples were de-crosslinked at 42 °C for 2 h and 67 °C for 6 h with Pronase (Sigma).
DNA purification was further performed with QIAGEN PCR Purification kit (for inputs) and the QIAGEN MinELute PCR Purification kit (for ChIP samples). Quantitative PCR with CXF384 Real-time System (Bio-Rad) and Kapa SYBR Fast qPCR kit (Kapa Biosystems). For ChIP-seq library preparation, ACCEL-NGS®2S Plus DNA library kit (IDT) and 2S™ Adapter Set A (IDT) was used as per manufacturer’s instruction starting with 5–10 ng DNA for both input and ChIP sample.

value: Nr1h2-FLAG overexpression


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep13 - H3K4me3

status: Public on Apr 10 2025

type: SRA

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

country: United Kingdom

institute: University of Glasgow

description:
Library name: H3K4ME3_K1_HC_3
H3K4me3_RA_Normalised_Counts.csv

library_source: genomic

data_processing:
The fastQ files were quality control checked using FastQC (Andrews, GitHub, v0.11.7) and then aligned to the reference genome and transcriptome GRCh38 (release 102) using Bowtie2 (v2.4.4). Peaks were called using MACS2 (v2.2.8) specifying the appropriate ChIP input for each sample.
The data was batch corrected using the SVA package ComBat-seq based on sample origin and for the fraction of reads within peak regions (FRiPs).
Assembly: GRCh38 (release 102)
Supplementary files format and content: csv file includes normalised counts for each sample in each dataset (H3K4me3 and H3K27me3). Any samples that did not pass QC were removed from the normalised counts files.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from fresh human blood samples by density gradient centrifugation using Ficoll® Paque Plus (Sigma-Aldrich). To isolate CD14+ monocytes, the EasySep human CD14 positive selection kit II (StemCell Technologies) was used following manufacturer’s instructions.

extract_protocol:
Cells were fixed in 1% methanol free formaldehyde, and then lysed. Chromatin samples were sonicated into 200-600 bp long fragments. Chromatin was split into the 10% input control, and the rest was used for either H3K4me3 or H3K27me3 chromatin immunoprecipitation. Input and ChIP'd DNA samples were extracted using the Qiagen MinElute PCR purification kit, as per manufacturer’s instructions.
DNA libraries were prepared for sequencing using the NEBNext Ultra II Directional DNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions. Quality control was performed on the DNA libraries using a high sensitivity DNA Chip (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).
ChIP-Seq (Each sample was sequenced to a depth of ~30 million reads, with fragments undergoing single end sequencing of 75 base pair read lengths.)

tag: tissue

value: Peripheral Blood

tag: cell type

value: Monocyte

tag: subject status

value: Healthy Control


title: genomic DNA from peripheral blood S5

type: genomic

city: Changsha

first: Shijia

last: Rao

state: Hunan

address: Renmin Road

department: dermatology

country: China

institute: Second Xiangya hospital

description:
adult onset still's disease perpheral blood sample
SAMPLE 55

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data was extracted with the champ R package, the results were not normalized.
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy5 and Cy3

source_name: genomic DNA from peripheral blood S5

label_protocol: Standard Illumina Protocol

growth_protocol: no

extract_protocol: We extracted peripheral blood genomic DNA with GeneJET Whole Blood Genomic DNA Purification Mini Kit (Thermo Fisher Scientific). An EZ DNA Methylation Kit (Zymo Research) was used for DNA samples bisulfite conversion.

treatment_protocol: no

tag: gender

value: female

tag: age

tag: sample type

value: blood

tag: disease state

value: adult onset still's disease


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep15 - H3K4me3

description:
Library name: H3K4ME3_K1_HC_5
H3K4me3_RA_Normalised_Counts.csv


title: Wild type Succinate Rep 3

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

country: USA

institute: Cornell University

description: Library name: yku70D_Succinate_Rep3

library_source: transcriptomic

data_processing:
Base calling was performed with the Illumina DRAGON Bio-IT Platform v4.1 and demultiplexed fastq files were generated using Illumina bcl-convert v4.0.3 software.
Sequenced reads were trimmed for adapter sequence and aligned to the predicted transcripts from the R. toruloides IFO0880 genome (v4). TPMs were quantified with Salmon v. 1.10.0 with the --validateMappings setting.
Assembly: Rhodosporidium toruloides IFO0880 (NBRC0880) v.4 (https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary files format and content: Tab-delimited text file with TPM values for each sample

molecule: total RNA

organism: Rhodotorula toruloides

source_name: Yeast cells

growth_protocol: R. toruloides cells were inoculated into yeast extract peptone dextrose (YPD) medium overnight at 28C with constant shaking at 250rpm in constant light so that cells were in exponential growth phase

extract_protocol:
Cells were harvested by centrifugation and flash frozen using liquid nitrogen. RNA was isolated using the Zymo Quick-RNA Fungal/Bacterial Kit according to manufacturer's protocols. 7.5ug of RNA was DNase treated with Invitrogen DNA-free kit according to manufacturer's protocol. RNA integrity was checked via agarose gel and Bioanalyzer.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols.

treatment_protocol: Cells were washed 3 times in yeast nitrogen base with NH4SO4 w/out amino acids + 12 mM K2HPO4 + 38 mM KH2PO4 + 100nM Fe(II)SO4 pH 6.2 (YNB) medium without a carbon source and then transferred to 100ml YNB lacking a carbon source, YNB 1% succinate, or YNB 1% cellobiose as indicated at 0.1 OD/mL and incubated at 28C in constant light with constant shaking at 250rpm for 8h prior to harvesting for RNAseq.

value: Yeast cells

tag: cell line

tag: genotype

tag: treatment

value: YNB 1% succinate

tag: time


title: genomic DNA from peripheral blood S4

description:
adult onset still's disease perpheral blood sample
SAMPLE 54

source_name: genomic DNA from peripheral blood S4


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep15 - Input

description: Library name: Input_K1_HC_5


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep1 - Input

description: Library name: Input_K1_RA_1

value: Rheumatoid Arthritis


title: genomic DNA from peripheral blood S3

description:
adult onset still's disease perpheral blood sample
SAMPLE 53

source_name: genomic DNA from peripheral blood S3

value: male


title: ESC Nr1h2-FLAG FLAG-ChIP (input)

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: Library name: Nr_F_Input

data_processing:
FastQC was used to check the sequence quality. Reads were mapped to the mm9 genome using STAR software with the parameters ‘–alignIntronMax 1 –alignEndsType EndToEnd’. MACS2 were used to call H3K27ac peaks (q-value < 0.05) and Nr1h2 peaks (p-value < 0.01). H3K27ac peaks from samples were merged with bedtools, and read counts for each sample on merged peaks were then calculated using featureCounts. The differential peaks were identified by EdgeR. Significant differential H3K27ac peaks were determined using cutoff p-value < 0.05 and |log2FC| > 1.5. Bigwig files were produced by Deeptools and visualized in WashU Epigenome Browser. Motif enrichment analysis was performed using Homer with function findMotifsGenome.pl. The p-value of known motifs was used for the visualization.  The enrichment analysis of genomic features on differentially upregulated/downregulated Nr1h2 peaks was performed using Fisher’s exact test. The log2-odds ratio and significance p-value was shown in the bar plot. The public ChIP-seq data of Kdm1a (GSE27841) used in Fig. 6 and S6 was downloaded from GEO database. For the analysis of Nr1h2-FLAG and EGFP-FLAG cells, significant differential H3K27ac peaks were determined using cutoff p-value < 0.05 and |log2FC| > 1. Genome-wide H3K9me3 peaks were first determined by MACS2 and featureCounts followed by edgeR workflow similarly using cutoff p-value < 0.05 and |log2FC| > 1. The overlapping peaks with Nr1h2 bound sites were then selected using bedtools intersect function.
Assembly: mm9
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: E14 ESC

value: E14 ESC

value: Embryonic stem cell

value: Wild-type


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep14 - H3K27me3

description:
Library name: H3K27ME3_K1_HC_4
H3K27me3_RA_Normalised_Counts.csv


title: ESC GFP-FLAG H3K9me3-ChIP (antibody)

description: Library name: GFP_Me3_Ch

extract_protocol:
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). NrESC medium is composed of ESC medium supplemented with 10 µM T0901317. All the ESC lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . Cells were trypsinized, harvested and the cell number was estimated. Cross-linking was performed for 10 × 106 cells using 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M Glycine. Crosslinked cells were resuspended in 1 ml of FA lysis buffer (10 mM Tris–Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche)), nutated at 4 °C for 15 min and spun down at 1300 × g for 5 min at 4 °C. Supernatant was removed and the pellet was re-suspended in 1% SDS lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail). After 15 min of incubation, the pellet was spun down and washed two times with 0.1% lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-1s00, 0.1% NaDOC and protease inhibitor cocktail). Cell pellet was sonicated by Biorupter (Diagenode) for 14 cycles (30 s on and 60 s off for each cycle). Cell debris was removed from the sheared chromatin by centrifugation at 21,000 × g at 4 °C for 30 min. Protein G Dynabeads (Life Technologies) was incubated with antibodies (Nr1h2 ChIP antibody (NB100-1464, Novus Biologicals), FLAG ChIP antibody (F1804, Sigma-Aldrich), H3K9me2 ChIP antibody (Abcam, ab1220), H3K9me3 ChIP antibody (Abcam, ab8898) and H3K27Ac ChIP antibody (ab4729, Abcam)) for 3 h at room temperature and washed three times by PBS with 0.1% TritonX-100. 5% of the sheared chromatin was separated as input while the remaining was subject to overnight incubation with antibody-bound Dynabeads. In total 7 washes were performed to remove unspecific bindings, including three washes with 0.1% SDS lysis buffer, one with 0.1% SDS lysis buffer/0.35 M NaCl, one with 10 mM Tris–Cl (pH 8.0), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and two with TE buffer (pH 8.0). Dynabeads were resuspended in elution buffer (50 mM Tris–HCl (pH 7.5), 10 mM EDTA, 1% SDS) and incubated at 68 °C for 1 h with 1400 rpm shaking. Eluted samples were de-crosslinked at 42 °C for 2 h and 67 °C for 6 h with Pronase (Sigma).
DNA purification was further performed with QIAGEN PCR Purification kit (for inputs) and the QIAGEN MinELute PCR Purification kit (for ChIP samples). Quantitative PCR with CXF384 Real-time System (Bio-Rad) and Kapa SYBR Fast qPCR kit (Kapa Biosystems). For ChIP-seq library preparation, ACCEL-NGS®2S Plus DNA library kit (IDT) and 2S™ Adapter Set A (IDT) was used as per manufacturer’s instruction starting with 5–10 ng DNA for both input and ChIP sample.

value: GFP-FLAG overexpression


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep14 - H3K4me3

description:
Library name: H3K4ME3_K1_HC_4
H3K4me3_RA_Normalised_Counts.csv


title: ESC Nr1h2-FLAG +T09 FLAG-ChIP (sample)

description: Library name: NrES_Nr_sample

value: Nr1h2-FLAG overexpression + T09


title: genomic DNA from peripheral blood N47

description:
normal  perpheral blood sample
SAMPLE 47

source_name: genomic DNA from peripheral blood N47

value: normal


title: ESC Nr1h2-FLAG + T09 H3K27ac-ChIP (antibody)

description: Library name: Nr_T_Ac_Ch


title: Wild type Cellobiose Rep 2

description: Library name: yku70D_Cellobiose_Rep2

value: YNB 1% cellobiose


title: genomic DNA from peripheral blood S1

description:
adult onset still's disease perpheral blood sample
SAMPLE 51

source_name: genomic DNA from peripheral blood S1


title: ESC GFP-FLAG H3K27ac-ChIP (input)

description: Library name: GFP_Ac_In


title: ESC GFP-FLAG H3K9me3-ChIP (input)

description: Library name: GFP_Me3_In


title: cbr1D Succinate Rep 2

description: Library name: cbr1D_Succinate_Rep2

value: yku70::HygR cbr1::NatR


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep14 - Input

description: Library name: Input_K1_HC_4

value: Peripheral Blood

value: Monocyte


title: ESC GFP-FLAG H3K27ac-ChIP (antibody)

description: Library name: GFP_Ac_Ch


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep13 - H3K27me3

description:
Library name: H3K27ME3_K1_HC_3
H3K27me3_RA_Normalised_Counts.csv

value: Healthy Control


title: ESC GFP-FLAG +T09 FLAG-ChIP (sample)

description: Library name: GFP_F_T_Sample

value: GFP-FLAG overexpression + T09


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep12 - Input

description: Library name: Input_K1_HC_2


title: cbr1D Succinate Rep 1

description: Library name: cbr1D_Succinate_Rep1


title: genomic DNA from peripheral blood N49

description:
normal  perpheral blood sample
SAMPLE 49

source_name: genomic DNA from peripheral blood N49

value: female

value: blood


title: cbr1D No Carbon Rep 1

description: Library name: cbr1D_NoCarbon_Rep1

value: Yeast cells

value: YNB no carbon source


title: ESC GFP-FLAG FLAG-ChIP (sample)

description: Library name: GFP_F_Sample


title: genomic DNA from peripheral blood N48

description:
normal  perpheral blood sample
SAMPLE 48

source_name: genomic DNA from peripheral blood N48


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep13 - Input

description: Library name: Input_K1_HC_3


title: Wild type Succinate Rep 2

description: Library name: yku70D_Succinate_Rep2

value: YNB 1% succinate


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep12 - H3K27me3

description:
Library name: H3K27ME3_K1_HC_2
H3K27me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood N42

description:
normal  perpheral blood sample
SAMPLE 42

source_name: genomic DNA from peripheral blood N42


title: Wild type Succinate Rep 1

description: Library name: yku70D_Succinate_Rep1


title: ESC Nr1h2-FLAG +T09 FLAG-ChIP (input)

description: Library name: NrES_Nr_input

value: E14 ESC


title: genomic DNA from peripheral blood N46

description:
normal  perpheral blood sample
SAMPLE 46

source_name: genomic DNA from peripheral blood N46

value: male


title: EPSC +T09 Nr1h2 ChIP (input)

description: Library name: EP_T_Nr_input

value: Embryonic stem cell

value: Wild-type


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep12 - H3K4me3

description:
Library name: H3K4ME3_K1_HC_2
H3K4me3_RA_Normalised_Counts.csv


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep11 - H3K27me3

description:
Library name: H3K27ME3_K1_HC_1
H3K27me3_RA_Normalised_Counts.csv


title: cbr1D No Carbon Rep 3

description: Library name: cbr1D_NoCarbon_Rep3


title: cbr1D No Carbon Rep 2

description: Library name: cbr1D_NoCarbon_Rep2


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep10 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_10
H3K4me3_RA_Normalised_Counts.csv


title: ESC GFP-FLAG +T09 FLAG-ChIP (input)

description: Library name: GFP_F_T_Input


title: genomic DNA from peripheral blood N40

description:
normal  perpheral blood sample
SAMPLE 40

source_name: genomic DNA from peripheral blood N40


title: genomic DNA from peripheral blood N45

description:
normal  perpheral blood sample
SAMPLE 45

source_name: genomic DNA from peripheral blood N45


title: genomic DNA from peripheral blood N44

description:
normal  perpheral blood sample
SAMPLE 44

source_name: genomic DNA from peripheral blood N44


title: genomic DNA from peripheral blood N39

description:
normal  perpheral blood sample
SAMPLE 39

source_name: genomic DNA from peripheral blood N39


title: genomic DNA from peripheral blood N43

description:
normal  perpheral blood sample
SAMPLE 43

source_name: genomic DNA from peripheral blood N43


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep10 - Input

description: Library name: Input_K2_HC_10

source_name: Peripheral Blood


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep11 - H3K4me3

description:
Library name: H3K4ME3_K1_HC_1
H3K4me3_RA_Normalised_Counts.csv


title: EPSC Nr1h2 ChIP (input)

description: Library name: EPSC_Nr_input

value: Control


title: Wild type No Carbon Rep 3

description: Library name: yku70D_NoCarbon_Rep3


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep9 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_9
H3K27me3_RA_Normalised_Counts.csv


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep11 - Input

description: Library name: Input_K1_HC_1


title: ESC GFP-FLAG FLAG-ChIP (input)

description: Library name: GFP_F_Input

value: GFP-FLAG overexpression


title: genomic DNA from peripheral blood N41

description:
normal  perpheral blood sample
SAMPLE 41

source_name: genomic DNA from peripheral blood N41

value: normal


title: Wild type No Carbon Rep 2

description: Library name: yku70D_NoCarbon_Rep2

source_name: Yeast cells


title: EPSC +T09 Nr1h2 ChIP (sample)

description: Library name: EP_T_Nr_sample


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep10 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_10
H3K27me3_RA_Normalised_Counts.csv


title: Wild type No Carbon Rep 1

description: Library name: yku70D_NoCarbon_Rep1


title: genomic DNA from peripheral blood N37

description:
normal  perpheral blood sample
SAMPLE 37

source_name: genomic DNA from peripheral blood N37


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep8 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_8
H3K27me3_RA_Normalised_Counts.csv


title: pgr1_untreated_rep2

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: PGR2_U

data_processing:
Quality controls for FASTQ files using FastQC
Trim of low quality read bases from FASTQ files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2.48  genone reference using Salmon
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe ASM294v2.48
Supplementary files format and content: tab-separated .txt table of DESeq2 normalized counts for all the samples

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: S.pombe pgr1 cells

growth_protocol: WT and pgr1 mutant strains were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
Hot phenol extraction
TrueSeq Stranded mRNA sample Prep kit v2 following manufacterer's instructions

treatment_protocol: 1 mM H2O2 during 30 minutes

value: S.pombe pgr1 cells

value: untreated


title: High Light, +10 h (day), rep 3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_N_HL_Lt_p10h___BR3

data_processing:
Reads mapped to genome assembly with STAR (v2.4.0j) using --runThreadN 4 --alignIntronMax 5000
FPKMs calculated with cuffdiff (v2.0.2) using --num-threads 4 --max-bundle-frags 1000000000 --library-type fr-firststrand
Assembly: Chlamydomonas reinhardtii reference genome assembly and annotations, v6.1, from phytozome.net
Supplementary files format and content: tab-delimited text file of transcript abundances for all genes normalized as Fragments Per KB of transcript per Million mapped reads (FPKMs) for each replicate
Supplementary files format and content: tab-delimited text file of transcript abundances for all genes normalized as Fragments Per KB of transcript per Million mapped reads (FPKMs) averaged across three replicates (mean)

organism: Chlamydomonas reinhardtii

source_name: liquid cultures in a photobioreactor

growth_protocol: Cultures were inoculated from precultures grown in Tris-Acetate-Phosphate medium at a starting optical density at 680 nm (OD680) of 0.05 into Seuoka's High Salt Medium in PSI Photobioreactors illuminated with 200 PFD (medium light). Cultures were maintained on a 12 h light at 28°C / 12 h dark at 18° diel cycle. Cultures were allowed to grow in turbidostat mode for at least 2 weeks prior to each experiment. As the low light condition limited growth, cells were first grown for 1 week at medium light, and then the light was changed to low light for at least 1 week before performing the experiments. At the start of each experiment, OD680 was set to 0.4 at the beginning of the dark phase, and the flow of media was stopped in order to monitor changes in culture density.

extract_protocol:
Cell pellets were placed in lysis buffer (50 mM Tris-Cl, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL proteinase K), flash frozen in LN2, and stored at –80°C prior to purification. Total RNA was purified in batches using standard protocols that accompany commerial kits including: TRIzol (Invitrogen), MaXtract HD columns (QIAgen) and miRNeasy Mini  kits (QIAgen). An additional EtOH precipitation was required to remove contaminants from the kit (as judged by the NanoDrop A260/A230 ratio).
standard Illlumina HiSeq compatible libraries

treatment_protocol: All samples were maintained on a 12 h light at 28°C / 12 h dark at 18° diel cycle. Light intensity in the day phase for Medium Light (ML) samples was maintained at 200 PFD. Light intensity in the day phase for Low Light (ML) samples was reduced to 50 PFD. Light intensity in the day phase for High Light (HL) samples was increased to 1000 PFD. Samples were collected from each series at five points over a diel cycle: -2 h (prior to dawn), +2 h (morning), +6 h (afternoon), +10 h (evening), -10 h (after dusk).

value: liquid cultures in a photobioreactor

value: WT

value: 12h light / 12h dark in high light (1000 PFD)

tag: time point

value: +10 h (evening)

tag: light

value: 1000 / 0 PFD (high light)


title: High Light, -10 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_O_HL_Dk_m10h___BR2

value: -10 h (post-dusk)


title: genomic DNA from peripheral blood N38

description:
normal  perpheral blood sample
SAMPLE 38

source_name: genomic DNA from peripheral blood N38

value: female

value: blood


title: pgr1_untreated_rep1

description: Library name: PGR1_U


title: High Light, -10 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_O_HL_Dk_m10h___BR1


title: pgr1_treated_rep2

description: Library name: PGR2_H

value: 30 min 1 mM H2O2


title: WT_treated_rep2

description: Library name: WT2_H

source_name: S.pombe wt cells

value: S.pombe wt cells


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep9 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_9
H3K4me3_RA_Normalised_Counts.csv

value: Peripheral Blood

value: Monocyte

value: Healthy Control


title: High Light, -10 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_O_HL_Dk_m10h___BR3


title: pgr1_treated_rep1

description: Library name: PGR1_H


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep8 - Input

description: Library name: Input_K2_HC_8


title: genomic DNA from peripheral blood N36

description:
normal  perpheral blood sample
SAMPLE 36

source_name: genomic DNA from peripheral blood N36

value: male


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep9 - Input

description: Library name: Input_K2_HC_9


title: genomic DNA from peripheral blood N32

description:
normal  perpheral blood sample
SAMPLE 32

source_name: genomic DNA from peripheral blood N32

value: normal


title: High Light, +6 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_M_HL_Lt_p06h___BR2

value: +6 h (afternoon)


title: genomic DNA from peripheral blood N35

description:
normal  perpheral blood sample
SAMPLE 35

source_name: genomic DNA from peripheral blood N35


title: High Light, +10 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_N_HL_Lt_p10h___BR2


title: High Light, +10 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_N_HL_Lt_p10h___BR1


title: genomic DNA from peripheral blood N34

description:
normal  perpheral blood sample
SAMPLE 34

source_name: genomic DNA from peripheral blood N34


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep8 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_8
H3K4me3_RA_Normalised_Counts.csv


title: EPSC Nr1h2 ChIP (antibody)

description: Library name: EPSC_Nr_sample

source_name: E14 ESC

value: E14 ESC

value: Embryonic stem cell

value: Wild-type

value: Control


title: WT_untreated_rep1

description: Library name: WT1_U

value: untreated


title: High Light, +6 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_M_HL_Lt_p06h___BR3

value: liquid cultures in a photobioreactor

value: WT

value: 12h light / 12h dark in high light (1000 PFD)

value: 1000 / 0 PFD (high light)


title: genomic DNA from peripheral blood N30

description:
normal  perpheral blood sample
SAMPLE 30

source_name: genomic DNA from peripheral blood N30

value: female

value: blood


title: genomic DNA from peripheral blood N29

description:
normal  perpheral blood sample
SAMPLE 29

source_name: genomic DNA from peripheral blood N29


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep6 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_6
H3K27me3_RA_Normalised_Counts.csv

value: Peripheral Blood


title: genomic DNA from peripheral blood N33

description:
normal  perpheral blood sample
SAMPLE 33

source_name: genomic DNA from peripheral blood N33


title: High Light, +6 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_M_HL_Lt_p06h___BR1


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep7 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_7
H3K27me3_RA_Normalised_Counts.csv

value: Monocyte


title: WT_treated_rep1

description: Library name: WT1_H

value: S.pombe wt cells

value: 30 min 1 mM H2O2


title: High Light, -2 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_K_HL_Dk_m02h___BR3

value: -2 h (pre-dawn)


title: WT_untreated_rep2

description: Library name: WT2_U


title: wing disc_yw_L3_6hr_B

city: Marseille

first: Cédric

last: Maurange

address: Parc Scientifique de Luminy

department: Developmental Biology Institute of Marseille (IBDM)

country: France

institute: CNRS

description: Library name: 6 hr_B

data_processing:
RNA-seq reads were aligned to the fly genome (dm6) using STAR 2.7.10a_alpha_220207 software (Dobin et al., 2013) and the Ensembl Drosophila genome assembly BDGP6.32. Then, aligned reads were quantified in each sample using the featureCounts software (Liao et al., 2014) to give a count text file.
Assembly: dm6
Supplementary files format and content: RNAseq_WT_time_course_normalized_genes_counts_filtered.csv

organism: Drosophila melanogaster

source_name: wing imaginal disc

extract_protocol:
RNA was extracted with the Qiagen RNeasy Micro kit (Qiagen, #74004).
Total RNA-Seq libraries were generated from 200 ng or less of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: wing imaginal disc

value: yw


title: wing disc_yw_L3_6hr_A

description: Library name: 6 hr_A


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep7 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_7
H3K4me3_RA_Normalised_Counts.csv

source_name: Peripheral Blood

value: Healthy Control


title: genomic DNA from peripheral blood N31

description:
normal  perpheral blood sample
SAMPLE 31

source_name: genomic DNA from peripheral blood N31

value: normal


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep7 - Input

description: Library name: Input_K2_HC_7


title: High Light, +2 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_L_HL_Lt_p02h___BR3

value: +2 h (morning)


title: High Light, +2 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_L_HL_Lt_p02h___BR2


title: genomic DNA from peripheral blood N26

description:
normal  perpheral blood sample
SAMPLE 26

source_name: genomic DNA from peripheral blood N26

value: male


title: genomic DNA from peripheral blood N28

description:
normal  perpheral blood sample
SAMPLE 28

source_name: genomic DNA from peripheral blood N28


title: wing disc_yw_L3_25hr_A

description: Library name: 25 hr_A


title: wing disc_yw_L3_25hr_B

description: Library name: 25 hr_B


title: wing disc_yw_L3_15hr_B

description: Library name: 15 hr_B


title: genomic DNA from peripheral blood N27

description:
normal  perpheral blood sample
SAMPLE 27

source_name: genomic DNA from peripheral blood N27


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep6 - Input

description: Library name: Input_K2_HC_6


title: High Light, +2 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_L_HL_Lt_p02h___BR1

source_name: liquid cultures in a photobioreactor

value: liquid cultures in a photobioreactor


title: wing disc_yw_L3_15hr_A

description: Library name: 15 hr_A


title: High Light, -2 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_K_HL_Dk_m02h___BR2

value: WT


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep5 - Input

description: Library name: Input_K2_HC_5


title: Low Light, -10 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_J_LL_Dk_m10h___BR2

value: 12h light / 12h dark in low light (50 PFD)

value: -10 h (post-dusk)

value: 50 / 0 PFD (low light)


title: genomic DNA from peripheral blood N23

description:
normal  perpheral blood sample
SAMPLE 23

source_name: genomic DNA from peripheral blood N23

value: female

value: blood


title: Low Light, -10 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_J_LL_Dk_m10h___BR1


title: wing disc_yw_L3_48hr_A

description: Library name: 48 hr_A


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep5 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_5
H3K27me3_RA_Normalised_Counts.csv

value: Peripheral Blood

value: Monocyte


title: High Light, -2 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_K_HL_Dk_m02h___BR1

value: 12h light / 12h dark in high light (1000 PFD)

value: 1000 / 0 PFD (high light)


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep5 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_5
H3K4me3_RA_Normalised_Counts.csv


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep6 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_6
H3K4me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood N24

description:
normal  perpheral blood sample
SAMPLE 24

source_name: genomic DNA from peripheral blood N24


title: Low Light, -10 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_J_LL_Dk_m10h___BR3


title: wing disc_yw_L3_48hr_B

description: Library name: 48 hr_B

value: wing imaginal disc


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep4 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_4
H3K4me3_RA_Normalised_Counts.csv


title: Low Light, +10 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_I_LL_Lt_p10h___BR3

value: +10 h (evening)


title: genomic DNA from peripheral blood N21

description:
normal  perpheral blood sample
SAMPLE 21

source_name: genomic DNA from peripheral blood N21


title: Low Light, +10 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_I_LL_Lt_p10h___BR2


title: genomic DNA from peripheral blood N25

description:
normal  perpheral blood sample
SAMPLE 25

source_name: genomic DNA from peripheral blood N25


title: Tumor, replicate 2, scRNAseq

city: Daejeon

first: Jeong Ho

last: Lee

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
10x Genomics
TU2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
assembly: mm10
Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Fresh mouse brains were collected in ice-cold PIPES solution. Precancerous stage whole-mount SVZ and adjacent CC were dissected under a stereomicroscope68. Cancer samples were visually inspected, and fluorescence signals were examined using a UV gun (Nightsea). Mouse brain tissue was dissociated into a single cell suspension described previously. Briefly, after activating papain (Worthington) for 10 minutes, the tissue sample was incubated in a solution containing papain (0.003 g per 100 mg tissue) and 10 mg/ml DNase I (Worthington) for 15 minutes at 37 °C. The suspension was centrifuges, and the resulting pellet was resuspended in ovomucoid (Worthington), followed by further dissociation by mechanical digestion. The cell suspension was layered onto a 22 % Percoll (Sigma) solution and centrifuged for 10 minutes at 590 x g at 4 °C. The cell pellet was resuspended in ice-cold Hanks balanced salt solution (HBSS) containing 1 % bovine serum albumen (BSA) and 0.1 % glucose, and DAPI was added. DAPI- tdTomato+ cells were then enriched by FACS, and live cells were concentrated by centrifugation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics except for Tumor R1 sample with v2 protocol). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor

value: brain cells

tag: strain

value: C57BL/6 x FVB

value: 18 weeks old


title: Low Light, +10 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_I_LL_Lt_p10h___BR1

value: liquid cultures in a photobioreactor


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep3 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_3
H3K4me3_RA_Normalised_Counts.csv

value: Healthy Control


title: genomic DNA from peripheral blood N20

description:
normal  perpheral blood sample
SAMPLE 20

source_name: genomic DNA from peripheral blood N20

value: normal


title: genomic DNA from peripheral blood N19

description:
normal  perpheral blood sample
SAMPLE 19

source_name: genomic DNA from peripheral blood N19


title: Low Light, +6 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_H_LL_Lt_p06h___BR3

value: WT

value: 12h light / 12h dark in low light (50 PFD)

value: +6 h (afternoon)


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep3 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_3
H3K27me3_RA_Normalised_Counts.csv


title: Late, replicate 3, scRNAseq

description:
10x Genomics
18W-SVZ-3

source_name: SVZ, CC

value: SVZ, CC


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep4 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_4
H3K27me3_RA_Normalised_Counts.csv

value: Peripheral Blood


title: genomic DNA from peripheral blood N18

description:
normal  perpheral blood sample
SAMPLE 18

source_name: genomic DNA from peripheral blood N18

value: male

value: blood


title: Low Light, +6 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_H_LL_Lt_p06h___BR2

value: 50 / 0 PFD (low light)


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep3 - Input

description: Library name: Input_K2_HC_3

value: Monocyte


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep2 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_2
H3K27me3_RA_Normalised_Counts.csv


title: Late, replicate 2, scRNAseq

description:
10x Genomics
18W-MUT-SVZ


title: genomic DNA from peripheral blood N22

description:
normal  perpheral blood sample
SAMPLE 22

source_name: genomic DNA from peripheral blood N22

value: female


title: genomic DNA from peripheral blood N17

description:
normal  perpheral blood sample
SAMPLE 17

source_name: genomic DNA from peripheral blood N17


title: Late, replicate 1, scRNAseq

description:
10x Genomics
18W-SVZ-1


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep2 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_2
H3K4me3_RA_Normalised_Counts.csv

source_name: Peripheral Blood


title: Low Light, +6 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_H_LL_Lt_p06h___BR1


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep4 - Input

description: Library name: Input_K2_HC_4


title: Low Light, +2 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_G_LL_Lt_p02h___BR3

value: +2 h (morning)


title: genomic DNA from peripheral blood N15

description:
normal  perpheral blood sample
SAMPLE 15

source_name: genomic DNA from peripheral blood N15


title: Tumor, replicate 3, scRNAseq

description:
10x Genomics
TU3

value: Tumor

value: brain cells


title: Low Light, +2 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_G_LL_Lt_p02h___BR2


title: genomic DNA from peripheral blood N14

description:
normal  perpheral blood sample
SAMPLE 14

source_name: genomic DNA from peripheral blood N14


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep2  - Input

description: Library name: Input_K2_HC_2


title: Low Light, +2 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_G_LL_Lt_p02h___BR1


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep1 - H3K27me3

description:
Library name: H3K27ME3_K2_HC_1
H3K27me3_RA_Normalised_Counts.csv


title: Tumor, replicate 1, scRNAseq

description:
10x Genomics
GBM-MS-1

value: C57BL/6 x FVB

value: 24  weeks old


title: Intermediate, replicate 3, scRNAseq

description:
10x Genomics
10W-SVZ2

value: 10 weeks old


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep1 - H3K4me3

description:
Library name: H3K4ME3_K2_HC_1
H3K4me3_RA_Normalised_Counts.csv

value: Healthy Control


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep1 - Input

description: Library name: Input_K2_HC_1


title: genomic DNA from peripheral blood N12

description:
normal  perpheral blood sample
SAMPLE 12

source_name: genomic DNA from peripheral blood N12

value: normal


title: Low Light, -2 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_F_LL_Dk_m02h___BR3

value: liquid cultures in a photobioreactor

value: WT

value: 12h light / 12h dark in low light (50 PFD)

value: -2 h (pre-dawn)


title: Low Light, -2 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_F_LL_Dk_m02h___BR2


title: Intermediate, replicate 1, scRNAseq

description:
10x Genomics
10W-SVZ-1

value: SVZ, CC


title: Intermediate, replicate 2, scRNAseq

description:
10x Genomics
10w_mSVZ


title: Low Light, -2 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_F_LL_Dk_m02h___BR1


title: genomic DNA from peripheral blood N16

description:
normal  perpheral blood sample
SAMPLE 16

source_name: genomic DNA from peripheral blood N16

value: male

value: blood


title: Intermediate, replicate 5, scRNAseq

description:
10x Genomics
10W-SVZ4


title: Medium Light, -10 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_E_ML_Dk_m10h___BR3

source_name: liquid cultures in a photobioreactor

value: 12h light / 12h dark in medium light (200 PFD)

value: -10 h (post-dusk)

value: 200 / 0 PFD (medium light)


title: genomic DNA from peripheral blood N10

description:
normal  perpheral blood sample
SAMPLE 10

source_name: genomic DNA from peripheral blood N10

value: female


title: Intermediate, replicate 4, scRNAseq

description:
10x Genomics
10W-SVZ3

value: brain cells


title: SSc3 res

city: London

first: Kristina

middle: Elizabeth Neergaard

last: Clark

state: England

address: Royal Free Hospital, Pond Street

institute: UCL

description: Library name: Sample 12

data_processing:
The tool used for mapping in this analysis is STAR
Assembly: http://ftp.ensembl.org/pub/release-103/gtf/homo_sapiens/Homo_sapiens.GRCh38.103.gtf.gz ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz
Supplementary files format and content: tab delimited text file includes raw counts

source_name: skin

extract_protocol:
RNA was isolated using the RNAeasy mini kit (Qiagen) according to protocol including on-column DNase digestion
Was performed by cambridge genomics

value: skin

value: resident fibroblast

value: systemic sclerosis


title: genomic DNA from peripheral blood N9

description:
normal  perpheral blood sample
SAMPLE 9

source_name: genomic DNA from peripheral blood N9


title: Early, replicate 2, scRNAseq

description:
10x Genomics
4W-SVZ2

value: C57BL/6 x FVB

value: 4 weeks old


title: SSc3 early

description: Library name: Sample 11

value: migratory fibroblast


title: Medium Light, -10 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_E_ML_Dk_m10h___BR2

value: liquid cultures in a photobioreactor

value: WT


title: SSc2 res

description: Library name: Sample 10


title: Early, replicate 1, scRNAseq

description:
10x Genomics
4W-MUT-SVZ


title: genomic DNA from peripheral blood N8

description:
normal  perpheral blood sample
SAMPLE 8

source_name: genomic DNA from peripheral blood N8

value: normal


title: genomic DNA from peripheral blood N13

description:
normal  perpheral blood sample
SAMPLE 13

source_name: genomic DNA from peripheral blood N13


title: SSc1 res

description: Library name: Sample8


title: Control, replicate 3, scRNAseq

description:
10x Genomics
10w_cSVZ

value: SVZ, CC

value: 10 weeks old


title: SSc2 early

description: Library name: Sample 9


title: genomic DNA from peripheral blood N6

description:
normal  perpheral blood sample
SAMPLE 6

source_name: genomic DNA from peripheral blood N6

value: blood


title: genomic DNA from peripheral blood N11

description:
normal  perpheral blood sample
SAMPLE 11

source_name: genomic DNA from peripheral blood N11


title: Medium Light, +10 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_D_ML_Lt_p10h___BR2

value: 12h light / 12h dark in medium light (200 PFD)

value: +10 h (evening)


title: genomic DNA from peripheral blood N7

description:
normal  perpheral blood sample
SAMPLE 7

source_name: genomic DNA from peripheral blood N7

value: male


title: Control, replicate 1, scRNAseq

description:
10x Genomics
SVZ-MS-1

source_name: SVZ, CC


title: Medium Light, +10 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_D_ML_Lt_p10h___BR3

value: 200 / 0 PFD (medium light)


title: Control, replicate 2, scRNAseq

description:
10x Genomics
4W-CONT-SVZ

value: brain cells


title: Early, replicate 3, scRNAseq

description:
10x Genomics
4W-SVZ3


title: genomic DNA from peripheral blood N5

description:
normal  perpheral blood sample
SAMPLE 5

source_name: genomic DNA from peripheral blood N5

value: female


title: genomic DNA from peripheral blood N4

description:
normal  perpheral blood sample
SAMPLE 4

source_name: genomic DNA from peripheral blood N4


title: HC3 early

description: Library name: Sample 5

value: skin

value: healthy control


title: Medium Light, +6 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_C_ML_Lt_p06h___BR3

value: +6 h (afternoon)


title: genomic DNA from peripheral blood N3

description:
normal  perpheral blood sample
SAMPLE 3

source_name: genomic DNA from peripheral blood N3


title: Medium Light, +6 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_C_ML_Lt_p06h___BR2


title: HC2 res

description: Library name: Sample 4

value: resident fibroblast


title: Medium Light, -10 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_E_ML_Dk_m10h___BR1

value: -10 h (post-dusk)


title: HC2 early

description: Library name: Sample 3

value: migratory fibroblast


title: genomic DNA from peripheral blood N1

description:
normal  perpheral blood sample
SAMPLE 1

source_name: genomic DNA from peripheral blood N1


title: HC1 res

description: Library name: Sample 2


title: genomic DNA from peripheral blood N2

description:
normal  perpheral blood sample
SAMPLE 2

source_name: genomic DNA from peripheral blood N2


title: Medium Light, +6 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_C_ML_Lt_p06h___BR1

value: liquid cultures in a photobioreactor

value: WT


title: HC1 early

description: Library name: Sample 1


title: SSc1 early

description: Library name: Sample 7

value: systemic sclerosis


title: Medium Light, +2 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_B_ML_Lt_p02h___BR1

value: +2 h (morning)


title: HC3 res

description: Library name: Sample 6


title: Medium Light, +2 h (day), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_B_ML_Lt_p02h___BR3


title: W.3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
Library name: W.3
BJAB cell line, bBcl-2 Wild Type, replicate 3

data_processing:
Reads were aligned to the human genome hg19 using STAR aligner and gene counts were estimated by RSEM uwing Ensemble transcriptome
Assembly: hg19
Supplementary files format and content: raw gene counts in text format

source_name: WT

extract_protocol:
Total RNA was extracted from three independent samples of each BJAB cell line using the Direct-zol™ RNA MiniPrep Kit following the manufacturer’s instruction
RNA was treated with DNase I, and 500 ng of total RNA was used to prepare 3’ mRNA-seq libraries with the QuantSeq 3'mRNA-Seq FWD Library Prep Kit (LEXOGEN 015.24) for IIIumina, according to the manufacturer’s protocol

value: BJAB cell line

value: bBcl-2 Wild Type


title: CUR50_3

city: Kunming City

first: Kai

last: Wang

state: Yunnan Province

address: No. 2, Puxin Road, Kunming National Economic and Technological Development Zone

department: College of Agriculture and Life Sciences

institute: Kunming University

description: Library name: Sample9

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean data from the samples were used to do de-novo assembly with Trinity. To increase the assembly quality, all the assembled sequences were filtered by CD-HIT and TransRate and assessed with BUSCO.
The clean reads of each sample were mapped back onto the assembled transcriptome using bowtie2 software
RSEM  was used to count the results of the bowtie2 mapping and obtain the number of read counts that mapped to the transcriptome of each sample. The read counts were then processed with the DESeq2  for normalization and diﬀerential expression analysis.
Assembly: Trinity.filter.fasta
Supplementary files format and content: csv files include TPM values for each Sample
Supplementary files format and content: fa file containing assembly sequence

organism: Akebia trifoliata

source_name: leaves

growth_protocol: The cuttings of Akebia trifoliata used in the experiment were sourced from the Akebia trifoliata germplasm resource nursery of the Dongfang Farm Management Bureau in Mile City, Yunnan Province. Three treatments (including control) were set up. For each treatment, 4 healthy individual plants with consistent growth vigor and a plant height of approximately 110 cm were selected as 3 replicates.

extract_protocol:
Take 1 g of Akebia trifoliata leaves from each of the different treatments respectively, and extract RNA using the MJZol total RNA extraction kit (Shanghai Majorbio Bio - Pharm Technology Co., Ltd.). Use 1.3 μg of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A simulated acid rain stress with a pH of 2.0 was set up, and 0 μmol/L (CUR0), 50 μmol/L (CUR50) of CUR were added. The experimental treatment method was as follows: First, different concentrations of CUR solutions were irrigated to the roots of Akebia trifoliata. Each nutrient pot was watered with 500 mL of the solution. The control plants (Control) were watered with an equal amount of distilled water. Then, the irrigation was repeated every 2 days. On the afternoon of the day when the CUR solution was applied, at 18:00, the test materials were sprayed with simulated acid rain with a pH of 2.0 until all the leaves had liquid dripping off. The Control group was sprayed with an equal amount of distilled water. The treatment was stopped after 28 days.

value: leaves

value: 50 μmol/L (CUR50) of CUR

value: treated with curcumin under acid rain stress for 28 days


title: Medium Light, +2 h (day), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_B_ML_Lt_p02h___BR2

source_name: liquid cultures in a photobioreactor

value: 12h light / 12h dark in medium light (200 PFD)

value: 200 / 0 PFD (medium light)


title: CUR50_2

description: Library name: Sample8


title: Medium Light, -2 h (night), rep 3

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_A_ML_Dk_m02h___BR3

value: -2 h (pre-dawn)


title: Medium Light, -2 h (night), rep 2

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_A_ML_Dk_m02h___BR2


title: W.2

description:
Library name: W.2
BJAB cell line, bBcl-2 Wild Type, replicate 2


title: CUR50_1

description: Library name: Sample7


title: CUR0_3

description: Library name: Sample6

value: 0 μmol/L (CUR0) of CUR

value: simulated acid rain stress with a pH of 2.0


title: W.1

description:
Library name: W.1
BJAB cell line, bBcl-2 Wild Type, replicate 1


title: E.3

description:
Library name: E.3
BJAB cell line, bBcl-2 E14A mutant, replicate 3

value: bBcl-2 E14A mutant


title: Medium Light, +10 h (day), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_D_ML_Lt_p10h___BR1

value: +10 h (evening)


title: Medium Light, -2 h (night), rep 1

description:
Cr073.light_intensity.FPKMs.replicates.v6.1.tsv
Cr073.light_intensity.FPKMs.mean.v6.1.tsv
Cr073_A_ML_Dk_m02h___BR1


title: CUR0_1

description: Library name: Sample4


title: E.1

description:
Library name: E.1
BJAB cell line, bBcl-2 E14A mutant, replicate 1


title: V.3

description:
Library name: V.3
BJAB cell line, empty vector control, replicate 3

source_name: EV

value: empty vector


title: CUR0_2

description: Library name: Sample5


title: NIH-3T3 and K562 ATAC (without blocking oligo)

city: Heidelberg

first: Mikael

last: Marttinen

address: Meyerhofstraße 1

country: Germany

institute: EMBL

description: ATAC-seq data for SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines where a blocking oligo was not spiked into microfluidic droplets. Data related to Extended data figure 2, panels A and J.

library_source: genomic single cell

data_processing:
*library strategy: Single-cell Ultra-high-throughput Multiomic sequencing (SUM-seq)
ATAC-seq library base calls were converted to fastq format and demultiplexed by the sample index (i7,see sampleIndexSheet.csv) using bcl-convert (v4.0.3) allowing one mismatch. Demultiplexed reads were aligned to a combined hg38/mm10 reference and fragment file generation was performed with chromap (v0.2.3). Cell barcode filtering was performed per sample index based on number of unique fragments, TSS enrichment score, and fraction of reads in promoter regions. Peak calling was performed for each sample index separately with R package ArchR (v1.0.2). In brief, ArchR utilises MACS2 peak caller to identify peaks for each group of cells, whereafter an iterative overlap peak merging procedure is done to derive a consensus peakset between all samples. Fragments in peaks are counted and a peak by cell matrix is generated. All analysis source code will be available on a separate Git repository upon publication.
Assembly: Hg38/mm10
Supplementary files format and content: 3T3_K562_ATAC_peak_count_matrix_human.mtx, sparse peak matrix
Supplementary files format and content: 3T3_K562_ATAC_barcodes_human.tsv, tab-separated file with cell barcodes for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_features_human.tsv, tab-separated file with peak names (format; chr:start-end) for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_peak_count_matrix_mouse.mtx, sparse peak matrix
Supplementary files format and content: 3T3_K562_ATAC_barcodes_mouse.tsv, tab-separated file with cell barcodes for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_features_mouse.tsv, tab-separated file with peak names (format; chr:start-end) for the peak matrix
Supplementary files format and content: sampleIndexSheet_ATAC.csv, csv file with sample ID matched to demultiplexing index sequence and a description of the sample

organism:
Homo sapiens
Mus musculus

source_name: NIH-3T3 and K562

growth_protocol: Human myelogenous leukemia cells (K562) were cultured in RPMI 1640 medium (Gibco, catalog no. 11875093) supplemented with 10% FBS (Gibco, catalog no. 10270-106), 100 U/ml penicillin/streptomycin (PenStrep, Gibco, catalog no. 15140122) and 1x non-essential amino acids (Gibco, catalog no. 11140050) at 37°C with 5% CO2. Mouse fibroblast cells (NIH-3T3) were cultured in DMEM medium (high glucose, Gibco, catalog no. 11965092) supplemented with 10% FBS, 100 U/ml penicillin/streptomycin and 1x non-essential amino acids at 37 °C with 5% CO2.

extract_protocol:
mouse NIH-3T3 cells were washed once with PBS and dissociated with Accutase (Stem Cell Technologies, catalog no. 07920). Two million NIH-3T3 and K562 cells were collected and fixed in a 3% glyoxal solution (40% glyoxal (Merck, catalog no. 128465) 0.75% acetic acid; 112.5 mM NaOH to adjust the solution to pH5.0) for 7 min at room temperature. For cryopreservation, cells were washed after fixation with RSB-1%BSA-RI (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM DTT, 1% BSA, in-house made RNasin (referred to RNasin hereafter)) and slowly frozen (Freezing buffer: 50 mM Tris-HCl pH 7.5, 5 mM MgAc, 0.1 mM EDTA and 25% glycerol) (cryopreserved cells indicated in sampleindexSheet.csv). On the day of pre-indexing, fresh cells were processed as described above, while cryopreserved cells were thawed slowly on ice and washed with RSB-1%BSA-RI. Nuclei were extracted with 1x lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20, RNasin, 1 mM DTT, 1% BSA, 0.025% IGEPAL CA-630 and 0.01% Digitonin) incubating samples for 5 min on ice. Next, nuclei were washed with wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20, RNasin, 1 mM DTT, 1% BSA) and filtered through a 40 µm cell strainer (Falcon, catalog no. 352340).
Transposome assembly: For accessible DNA transposition transposome assembly, 100 µM of oligonucleotides with the Nextera Read1 sequence and 100 µM of oligonucleotides with a Read2-sample_index-spacer structure were annealed with 100 µM mosaic end-complement oligonucleotides with a 3’ dideoxynucleotide end (ddc) at a 1:1:2 ratio by heating for 95 °C for 3 minutes followed by cooling down to 25 °C at a ramp rate of -1 °C/min (oligonucleotide sequences provided in supplementary table 1). Annealed oligos were mixed with an equal volume of 100% glycerol and stored at -20 °C until use. Finally, the annealed oligos were diluted 1:1 with H2O and mixed at equal volume with in-house produced Tn5 (at 1 mg/ml in 50 mM Tris, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1% NP-40, and 50% glycerol, production details in methods), and incubated for 30-60 min at room temperature. For cDNA/RNA tagmentation transposome preparation, 100 µM of oligonucleotides with a Nextera Read1 sequence overhang were annealed with 100 µM of the Tn5-mosaic end oligonucleotides at a 1:1 (v/v) ratio as described above. Annealed oligos were mixed with an equal volume of 100% glycerol and stored at -20 °C until use. For transposome assembly, annealed oligos were mixed with the in-house produced Tn5 at a 1:1 ratio for 30 min at RT. Assembled Tn5 was stored at -20 °C until use.  Accessible DNA transposition:Isolated and fixed nuclei were resuspended in a transposition mix containing 38.8 mM Tris-acetate, 77.6 mM potassium acetate, 11.8 mM magnesium acetate, and 18.8 % dimethylformamide supplemented with 0.005x protease inhibitor cocktail (Roche, catalog no. 11697498001), 0.4 U/µl SUPERaseIn (Thermo Fisher, catalog no. AM2694), 1.2 U/µl RiboLock (Thermo Fisher, catalog no. EO0382) and the barcoded Tn5 transposomes (1:10 (v/v); 938 µM) and incubated at 30 °C for 30 min with shaking at 400 rpm. The reaction was terminated by adding an equal volume of 2x stop buffer (10 mM Tris-HCl pH 7.5, 20 mM EDTA pH 8.0, 2% BSA).   Reverse transcription: Transposed nuclei were washed 3 times with RSB-1%BSA-RI and resuspended in reverse transcription mix containing 1x RT buffer (50 mM Tris-HCl pH 8.0, 75 mM NaCl, 3 mM MgCl2, 10 mM DTT), 0.5 mM dNTPs, 1 U/µl Protector RNase inhibitor (Roche, catalog no. 3335402001), 0.2 U/µl SUPERaseIn (Thermo Fisher, catalog no. AM2694), 10 U/µl Maxima H Minus RT (Thermo Fisher catalog no. EP0752) and 5 µM of the respective barcoded oligo-dT primer (oligonucleotide sequences provided in supplementary table 1). For a subset of samples 12% PEG 8000 (w/v; Jena Bioscience, CSS-256) was included in the reverse transcription reaction (indicated in sampleIndexSheet.csv). The samples were incubated at 50 °C for 10 min, followed by 3 thermal cycles (8 °C for 12 sec, 15 °C for 45 sec, 20 °C for 45 sec, 30 °C for 30 sec, 42 °C for 2 min and 50 °C for 3 min), and finally incubated at 50 °C for 5 min.   cDNA/RNA tagmentation: Following the RT reaction, all samples were pooled in RSB-RI and washed twice with RSB-1%BSA-RI. The collected nuclei pool was counted, and the following reaction volume was adjusted according to the total number of nuclei (100 µl reaction for each 100,000 nuclei). Nuclei were resuspended in the transposition mix containing 1x transposition buffer (38.8 mM Tris-acetate, 77.6 mM potassium acetate, 11.8 mM magnesium acetate, and 18.8% dimethylformamide and 0.005x protease inhibitor cocktail and a 1:100 ratio (v/v) of assembled Tn5 (93.8 µM) The tagmentation was performed on a shaking thermoblock at 37 °C for 30 min at 400 rpm. The reaction was terminated by adding an equal volume of 2x stop buffer.   Gap filling: Next, the sample pool was washed twice with RSB-1%BSA. Sample pool was resuspended a mix containing 1x RT buffer (50 mM Tris-HCl pH 8.0, 75 mM NaCl, 3 mM MgCl2, 10 mM DTT), 0.5 mM dNTPs, 8 U/µl Maxima H Minus RT (Thermo Fisher catalog no. EP0752) and 2 U/µl Thermolabile Exonuclease I (New England Biolabs, catalog no. M0568S) and incubated for 15 min at 37 °C on a shaking thermoblock at 400 rpm. Afterwards the sample was washed twice with RSB-1%BSA filtered through a 40 µm cell strainer and count.   Cell barcoding: The sample was cleaned prior loading of the 10x Genomics chip using a glycerol-based buffer (50 mM Tris-HCl pH 7.5, 5 mM Mg-acetate, 0.1 mM EDTA, 25% glycerol). For this, nuclei were resuspended in a glycerol-based buffer, layered on top of an additional 500 µl glycerol-based buffer and centrifuged at 800 x g for 15 minutes. The supernatant was discarded, and the pellet was washed twice with RSB-1%BSA and filtered through a 40 µM Flowmi cell strainer (Sigma-Aldrich, catalog no. BAH136800040). The nuclei were counted and loaded into the Chromium Controller (10x Genomics) according to 10x Genomics single-cell-ATAC standard protocol with minor adaptations. In brief, nuclei in 1x Nuclei buffer (10x Genomics) were mixed with barcoding reagents (Barcoding Reagent B, Reducing Reagent B and Barcoding Enzyme). The ”with blocking oligo” libraries were supplemented with ~500 nM of a 3’inverted-dT blocking oligonucleotide (oligonucleotide sequence provided in supplementary table 1). For Chip loading, the standard 10x workflow was followed. In brief, 70 µl of the sample, 50 µl of Barcoding Gel Beads, 40 µl Partitioning Oil were loaded into the respective channels. After the Chromium run, the droplet emulsion was transferred to 10x verified PCR tubes (Eppendorf, catalog no. EP0030124359) and the cell barcoding reaction was run in the thermocycler as follows: 5 min at 72 °C, 30 seconds at 98 °C, 4 or 12 cycles (98 °C 10 seconds, 59 °C 30 seconds and 72 °C 1 min) (cycle amount indicated in sampleindexSheet.csv). In the ”with blocking oligo” library, only 20% of the droplet emulsion was further processed to limit the sequencing requirements. Sample cleanup was performed following the standard 10x Genomics protocol with minor modifications: 125 µl Recovery Reagent was added to sample and inverted 10-15 times. After brief centrifugation, 125 µl of the pink oil phase was discarded and the aqueous phase was mixed with a dynabead cleanup mastermix (182 µl Cleanup Buffer, 13 µl Dynabeads MyOne SILANE and 5 µl Reducing Agent B (10x Genomics)) and incubated for 10 min at RT. Samples were placed on a magnetic separator and washed 2 times with 80% ethanol before eluting them in 42 µl of elution buffer. Finally, samples were subjected to a 1.4x SPRI cleanup (Beckman Coulter, catalog no. B23318).   Pre- and final library amplification: Following GEM generation, cell barcoding and cleanup, samples containing a mixture of single-cell ATAC and RNA libraries were resuspended in the pre-amplification mastermix containing 1x NEBNext HF 2x PCR Master Mix (NEB, catalog no. M0541L) and a combination of three primers: partial-P5-PTO primer (common for both modalities), TruseqR2 (specific for the RNA modality) and an ATAC-spacer primer (specific for ATAC modality) each at a final concentration of 500 nM (oligonucleotide sequences provided in supplementary table 1). Samples were incubated in the thermal cycle as follows: 98 °C 1 mi, 5 cycles of 98 °C for 20 sec, 63 °C for 20 sec and 72 °C for 20 sec), 72 °C for 1 min and then subjected to a 1.2x SPRI cleanup eluting in 42 µl EB buffer (Qiagen). Each sample was split into two fractions and each of them was further amplified with modality-specific primers: a partial-P5-PTO/P7-index-spacer primer pair for the ATAC libraries and a partial-P5-PTO/P7-index-TruseqR2 primer pair for the gene expression libraries (oligonucleotide sequences provided in supplementary table 1). The PCR programme for both library types was as follows: 98 °C for 1 min, 5 cycles of 98 °C for 20 sec, 63 °C for 20 sec and 72 °C for 20 sec followed by a final extension step at 72 °C for 1 min. To estimate the number of endpoint PCR cycles required for each library, 1/20th of the total library volume was used to perform a qPCR reaction using library-specific primers, and the number of cycles required to reach 50% of saturation was calculated. Finalized ATAC libraries were subjected to a 1.2x SPRI cleanup and RNA libraries to 0.72x SPRI cleanup. The concentration of the libraries was measured using Qubit 1x dsDNA-HS (Thermo Scientific, catalog no. Q33230) and the library fragment distribution was assessed using Bioanalyzer High Sensitivity DNA kit (Agilent, catalog no. 5067-4626).

value: NIH-3T3 and K562

value: No treatments performed


title: Control_3

description: Library name: Sample3

value: control

value: distilled water


title: E.2

description:
Library name: E.2
BJAB cell line, bBcl-2 E14A mutant, replicate 2

value: BJAB cell line


title: NIH-3T3 and K562 ATAC (with blocking oligo)

description: ATAC-seq data for SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines where a blocking oligo was spiked into microfluidic droplets. Data related to Figure 1 and Extended data figure 2 (panels B-I).

data_processing:
*library strategy: Single-cell Ultra-high-throughput Multiomic sequencing (SUM-seq)
ATAC-seq library base calls were converted to fastq format and demultiplexed by the sample index (i7,see sampleIndexSheet.csv) using bcl-convert (v4.0.3) allowing one mismatch. Demultiplexed reads were aligned to a combined hg38/mm10 reference and fragment file generation was performed with chromap (v0.2.3). Cell barcode filtering was performed per sample index based on number of unique fragments, TSS enrichment score, and fraction of reads in promoter regions. Peak calling was performed for each sample index separately with R package ArchR (v1.0.2). In brief, ArchR utilises MACS2 peak caller to identify peaks for each group of cells, whereafter an iterative overlap peak merging procedure is done to derive a consensus peakset between all samples. Fragments in peaks are counted and a peak by cell matrix is generated. All analysis source code will be available on a separate Git repository upon publication.
Assembly: Hg38/mm10
Supplementary files format and content: 3T3_K562_ATAC_block_peak_count_matrix_human.mtx, sparse peak matrix
Supplementary files format and content: 3T3_K562_ATAC_block_barcodes_human.tsv, tab-separated file with cell barcodes for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_block_features_human.tsv, tab-separated file with peak names (format; chr:start-end) for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_block_peak_count_matrix_mouse.mtx, sparse peak matrix
Supplementary files format and content: 3T3_K562_ATAC_block_barcodes_mouse.tsv, tab-separated file with cell barcodes for the peak matrix
Supplementary files format and content: 3T3_K562_ATAC_block_features_mouse.tsv, tab-separated file with peak names (format; chr:start-end) for the peak matrix
Supplementary files format and content: sampleIndexSheet_ATAC_block.csv, csv file with sample ID matched to demultiplexing index sequence and a description of the sample

extract_protocol:
mouse NIH-3T3 cells were washed once with PBS and dissociated with Accutase (Stem Cell Technologies, catalog no. 07920). Two million NIH-3T3 and K562 cells were collected and fixed in a 3% glyoxal solution (40% glyoxal (Merck, catalog no. 128465) 0.75% acetic acid; 112.5 mM NaOH to adjust the solution to pH5.0) for 7 min at room temperature. For cryopreservation, cells were washed after fixation with RSB-1%BSA-RI (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM DTT, 1% BSA, in-house made RNasin (referred to RNasin hereafter)) and slowly frozen (Freezing buffer: 50 mM Tris-HCl pH 7.5, 5 mM MgAc, 0.1 mM EDTA and 25% glycerol) (cryopreserved cells indicated in sampleindexSheet.csv). On the day of pre-indexing, fresh cells were processed as described above, while cryopreserved cells were thawed slowly on ice and washed with RSB-1%BSA-RI. Nuclei were extracted with 1x lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20, RNasin, 1 mM DTT, 1% BSA, 0.025% IGEPAL CA-630 and 0.01% Digitonin) incubating samples for 5 min on ice. Next, nuclei were washed with wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20, RNasin, 1 mM DTT, 1% BSA) and filtered through a 40 µm cell strainer (Falcon, catalog no. 352340).
Transposome assembly: For accessible DNA transposition transposome assembly, 100 µM of oligonucleotides with the Nextera Read1 sequence and 100 µM of oligonucleotides with a Read2-sample_index-spacer structure were annealed with 100 µM mosaic end-complement oligonucleotides with a 3’ dideoxynucleotide end (ddc) at a 1:1:2 ratio by heating for 95 °C for 3 minutes followed by cooling down to 25 °C at a ramp rate of -1 °C/min (oligonucleotide sequences provided in supplementary table 1). Annealed oligos were mixed with an equal volume of 100% glycerol and stored at -20 °C until use. Finally, the annealed oligos were diluted 1:1 with H2O and mixed at equal volume with in-house produced Tn5 (at 1 mg/ml in 50 mM Tris, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1% NP-40, and 50% glycerol, production details in methods), and incubated for 30-60 min at room temperature. For cDNA/RNA tagmentation transposome preparation, 100 µM of oligonucleotides with a Nextera Read1 sequence overhang were annealed with 100 µM of the Tn5-mosaic end oligonucleotides at a 1:1 (v/v) ratio as described above. Annealed oligos were mixed with an equal volume of 100% glycerol and stored at -20 °C until use. For transposome assembly, annealed oligos were mixed with the in-house produced Tn5 at a 1:1 ratio for 30 min at RT. Assembled Tn5 was stored at -20 °C until use.
Accessible DNA transposition:Isolated and fixed nuclei were resuspended in a transposition mix containing 38.8 mM Tris-acetate, 77.6 mM potassium acetate, 11.8 mM magnesium acetate, and 18.8 % dimethylformamide supplemented with 0.005x protease inhibitor cocktail (Roche, catalog no. 11697498001), 0.4 U/µl SUPERaseIn (Thermo Fisher, catalog no. AM2694), 1.2 U/µl RiboLock (Thermo Fisher, catalog no. EO0382) and the barcoded Tn5 transposomes (1:10 (v/v); 938 µM) and incubated at 30 °C for 30 min with shaking at 400 rpm. The reaction was terminated by adding an equal volume of 2x stop buffer (10 mM Tris-HCl pH 7.5, 20 mM EDTA pH 8.0, 2% BSA).
Reverse transcription: Transposed nuclei were washed 3 times with RSB-1%BSA-RI and resuspended in reverse transcription mix containing 1x RT buffer (50 mM Tris-HCl pH 8.0, 75 mM NaCl, 3 mM MgCl2, 10 mM DTT), 0.5 mM dNTPs, 1 U/µl Protector RNase inhibitor (Roche, catalog no. 3335402001), 0.2 U/µl SUPERaseIn (Thermo Fisher, catalog no. AM2694), 10 U/µl Maxima H Minus RT (Thermo Fisher catalog no. EP0752) and 5 µM of the respective barcoded oligo-dT primer (oligonucleotide sequences provided in supplementary table 1). For a subset of samples 12% PEG 8000 (w/v; Jena Bioscience, CSS-256) was included in the reverse transcription reaction (indicated in sampleIndexSheet.csv). The samples were incubated at 50 °C for 10 min, followed by 3 thermal cycles (8 °C for 12 sec, 15 °C for 45 sec, 20 °C for 45 sec, 30 °C for 30 sec, 42 °C for 2 min and 50 °C for 3 min), and finally incubated at 50 °C for 5 min.
cDNA/RNA tagmentation: Following the RT reaction, all samples were pooled in RSB-RI and washed twice with RSB-1%BSA-RI. The collected nuclei pool was counted, and the following reaction volume was adjusted according to the total number of nuclei (100 µl reaction for each 100,000 nuclei). Nuclei were resuspended in the transposition mix containing 1x transposition buffer (38.8 mM Tris-acetate, 77.6 mM potassium acetate, 11.8 mM magnesium acetate, and 18.8% dimethylformamide and 0.005x protease inhibitor cocktail and a 1:100 ratio (v/v) of assembled Tn5 (93.8 µM) The tagmentation was performed on a shaking thermoblock at 37 °C for 30 min at 400 rpm. The reaction was terminated by adding an equal volume of 2x stop buffer.
Gap filling: Next, the sample pool was washed twice with RSB-1%BSA. Sample pool was resuspended a mix containing 1x RT buffer (50 mM Tris-HCl pH 8.0, 75 mM NaCl, 3 mM MgCl2, 10 mM DTT), 0.5 mM dNTPs, 8 U/µl Maxima H Minus RT (Thermo Fisher catalog no. EP0752) and 2 U/µl Thermolabile Exonuclease I (New England Biolabs, catalog no. M0568S) and incubated for 15 min at 37 °C on a shaking thermoblock at 400 rpm. Afterwards the sample was washed twice with RSB-1%BSA filtered through a 40 µm cell strainer and count.
Cell barcoding: The sample was cleaned prior loading of the 10x Genomics chip using a glycerol-based buffer (50 mM Tris-HCl pH 7.5, 5 mM Mg-acetate, 0.1 mM EDTA, 25% glycerol). For this, nuclei were resuspended in a glycerol-based buffer, layered on top of an additional 500 µl glycerol-based buffer and centrifuged at 800 x g for 15 minutes. The supernatant was discarded, and the pellet was washed twice with RSB-1%BSA and filtered through a 40 µM Flowmi cell strainer (Sigma-Aldrich, catalog no. BAH136800040). The nuclei were counted and loaded into the Chromium Controller (10x Genomics) according to 10x Genomics single-cell-ATAC standard protocol with minor adaptations. In brief, nuclei in 1x Nuclei buffer (10x Genomics) were mixed with barcoding reagents (Barcoding Reagent B, Reducing Reagent B and Barcoding Enzyme). The ”with blocking oligo” libraries were supplemented with ~500 nM of a 3’inverted-dT blocking oligonucleotide (oligonucleotide sequence provided in supplementary table 1). For Chip loading, the standard 10x workflow was followed. In brief, 70 µl of the sample, 50 µl of Barcoding Gel Beads, 40 µl Partitioning Oil were loaded into the respective channels. After the Chromium run, the droplet emulsion was transferred to 10x verified PCR tubes (Eppendorf, catalog no. EP0030124359) and the cell barcoding reaction was run in the thermocycler as follows: 5 min at 72 °C, 30 seconds at 98 °C, 4 or 12 cycles (98 °C 10 seconds, 59 °C 30 seconds and 72 °C 1 min) (cycle amount indicated in sampleindexSheet.csv). In the ”with blocking oligo” library, only 20% of the droplet emulsion was further processed to limit the sequencing requirements. Sample cleanup was performed following the standard 10x Genomics protocol with minor modifications: 125 µl Recovery Reagent was added to sample and inverted 10-15 times. After brief centrifugation, 125 µl of the pink oil phase was discarded and the aqueous phase was mixed with a dynabead cleanup mastermix (182 µl Cleanup Buffer, 13 µl Dynabeads MyOne SILANE and 5 µl Reducing Agent B (10x Genomics)) and incubated for 10 min at RT. Samples were placed on a magnetic separator and washed 2 times with 80% ethanol before eluting them in 42 µl of elution buffer. Finally, samples were subjected to a 1.4x SPRI cleanup (Beckman Coulter, catalog no. B23318).
Pre- and final library amplification: Following GEM generation, cell barcoding and cleanup, samples containing a mixture of single-cell ATAC and RNA libraries were resuspended in the pre-amplification mastermix containing 1x NEBNext HF 2x PCR Master Mix (NEB, catalog no. M0541L) and a combination of three primers: partial-P5-PTO primer (common for both modalities), TruseqR2 (specific for the RNA modality) and an ATAC-spacer primer (specific for ATAC modality) each at a final concentration of 500 nM (oligonucleotide sequences provided in supplementary table 1). Samples were incubated in the thermal cycle as follows: 98 °C 1 mi, 5 cycles of 98 °C for 20 sec, 63 °C for 20 sec and 72 °C for 20 sec), 72 °C for 1 min and then subjected to a 1.2x SPRI cleanup eluting in 42 µl EB buffer (Qiagen). Each sample was split into two fractions and each of them was further amplified with modality-specific primers: a partial-P5-PTO/P7-index-spacer primer pair for the ATAC libraries and a partial-P5-PTO/P7-index-TruseqR2 primer pair for the gene expression libraries (oligonucleotide sequences provided in supplementary table 1). The PCR programme for both library types was as follows: 98 °C for 1 min, 5 cycles of 98 °C for 20 sec, 63 °C for 20 sec and 72 °C for 20 sec followed by a final extension step at 72 °C for 1 min. To estimate the number of endpoint PCR cycles required for each library, 1/20th of the total library volume was used to perform a qPCR reaction using library-specific primers, and the number of cycles required to reach 50% of saturation was calculated. Finalized ATAC libraries were subjected to a 1.2x SPRI cleanup and RNA libraries to 0.72x SPRI cleanup. The concentration of the libraries was measured using Qubit 1x dsDNA-HS (Thermo Scientific, catalog no. Q33230) and the library fragment distribution was assessed using Bioanalyzer High Sensitivity DNA kit (Agilent, catalog no. 5067-4626).


title: V.1

description:
Library name: V.1
BJAB cell line, empty vector control, replicate 1


title: Control_1

description: Library name: Sample1


title: Control_2

description: Library name: Sample2


title: NIH-3T3 and K562 RNA (with blocking oligo)

description: RNA-seq data for SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines where a blocking oligo was spiked into microfluidic droplets. Data related to Figure 1 and Extended data figure 2 (panels B-I).

data_processing:
*library strategy: Single-cell Ultra-high-throughput Multiomic sequencing (SUM-seq)
RNA-seq library base calls were converted to fastq format using bcl-convert (v4.0.3). The cell barcode (i5) was concatenated to the sample index and UMI (Read2), whereafter reads were demultiplexed by sample index (see sampleIndexSheet.csv) using Je (v2.0.RC), allowing for two mismatches. Read alignment to a combined Hg38/mm10 reference and gene expression matrix generation for each demultiplexed sample was conducted with STARsolo (v.2.7.9a). For each sample, cell calling was performed with EmptyDrops (v.1.16). Feature by cell matrices were merged between samples, and finally features found in a minimum of 10-25 cells were retained. All analysis source code will be available on a separate Git repository upon publication.
Assembly: Hg38/mm10
Supplementary files format and content: 3T3_K562_RNA_block_count_matrix.mtx, sparse gene expression count matrix
Supplementary files format and content: 3T3_K562_RNA_block_barcodes.tsv, tab-separated file with cell barcodes for the gene expression matrix (columns)
Supplementary files format and content: 3T3_K562_RNA_block_features.tsv, tab-separated file with feature names for the gene expression matrix (rows)
Supplementary files format and content: sampleIndexSheet_RNA_block.csv, csv file with sample ID matched to demultiplexing index sequence and a description of the sample


title: GNS166_0_n9

status: Public on Apr 09 2025

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

institute: Biodonostia

description: Library name: Sample 7

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering.
Data filtering steps: (1) Remove the reads containing the adaptor(adaptor pollution);  (2) Remove reads whose N content is greater than 5%;  (3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. Version v1.5.2. Parameters -l 15 -q 0.2 -n 0.05
Bowtie2 was used to map the clean reads to the reference gene sequence. Version：v2.2.5. Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM was used to calculate the gene expression level of each sample. Version：v1.2.8. Parameters：-p 8 --forward-prob 0 --paired-end
Assembly: GRCh38.p13
Supplementary files format and content: Normalized and raw counts of all 8 samples
Supplementary files format and content: excel document (xlsx) and txt

growth_protocol: Patient-derived glioma stem cell lines (GNS166) were kindly provided by Dr. Steve Pollard and cultured in adhesion in DMEM/F12 media (Gibco) supplemented with 100 U/mL penicillin and streptomycin, 2 mM of L-Glutamine, 1 % N2 (Gibco), 2 % B27 (Gibco), 1.34 % D-(+)-Glucose solution 45 % (Sigma-Aldrich), 20 ng/mL basic Fibroblast Growth Factor (bFGF, Gibco) and 20 ng/mL epidermal growth factor (EGF, Sigma-Aldrich).

extract_protocol:
Total RNA was isolated using trizol (Life Technologies, Carlsbad, CA, USA).
1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification. Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis 7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: GNS166 cells were cultured with 5 µM of DDI199 for 48 h, and pellets were then taken for RNAseq

tag: group

value: Control

value: GNS166 Control

tag: replicate


title: NIH-3T3 and K562 RNA (without blocking oligo)

description: RNA-seq data for SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines where a blocking oligo was not spiked into microfluidic droplets. Data related to Extended data figure 2, panels A and J.

data_processing:
*library strategy: Single-cell Ultra-high-throughput Multiomic sequencing (SUM-seq)
RNA-seq library base calls were converted to fastq format using bcl-convert (v4.0.3). The cell barcode (i5) was concatenated to the sample index and UMI (Read2), whereafter reads were demultiplexed by sample index (see sampleIndexSheet.csv) using Je (v2.0.RC), allowing for two mismatches. Read alignment to a combined Hg38/mm10 reference and gene expression matrix generation for each demultiplexed sample was conducted with STARsolo (v.2.7.9a). For each sample, cell calling was performed with EmptyDrops (v.1.16). Feature by cell matrices were merged between samples, and finally features found in a minimum of 10-25 cells were retained. All analysis source code will be available on a separate Git repository upon publication.
Assembly: Hg38/mm10
Supplementary files format and content: 3T3_K562_RNA_count_matrix.mtx, sparse gene expression count matrix
Supplementary files format and content: 3T3_K562_RNA_barcodes.tsv, tab-separated file with cell barcodes for the gene expression matrix (columns)
Supplementary files format and content: 3T3_K562_RNA_features.tsv, tab-separated file with feature names for the gene expression matrix (rows)
Supplementary files format and content: sampleIndexSheet_RNA.csv, csv file with sample ID matched to demultiplexing index sequence and a description of the sample


title: GNS166_5_n6

description: Library name: Sample 2

value: Treated

value: GNS166 treated with DDI199 (5μM)


title: Healthy_control_H16 (mRNA)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on MGISeq-2000 or NovaSeq 6000 platform in a 100+100-base paired-end mode.
On NovaSeq 6000 platform, Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Mapped read counts for each gene-sample combination were quantified with featureCounts ( -M -O --fraction option) of subread-2.0.0 package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: blood

extract_protocol:
Toal RNA was harvested using PAXgene Blood RNA System (BD Biosciences, San Jose, CA).
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

value: blood

value: Healthy


title: Healthy_control_H24 (mRNA)


title: Healthy_control_H14 (mRNA)


title: Healthy_control_H15 (mRNA)


title: GNS166_5_n7

description: Library name: Sample 4


title: GNS166_5_n9

description: Library name: Sample 8


title: GNS166_0_n8

description: Library name: Sample 5


title: GNS166_0_n7

description: Library name: Sample 3


title: GNS166_5_n8

description: Library name: Sample 6


title: GNS166_0_n6

description: Library name: Sample 1


title: Healthy_control_H21 (mRNA)


title: Healthy_control_H9 (mRNA)


title: Healthy_control_H25 (mRNA)


title: V.2

description:
Library name: V.2
BJAB cell line, empty vector control, replicate 2


title: Healthy_control_H7 (mRNA)


title: Healthy_control_H1 (mRNA)


title: Healthy_control_H2 (mRNA)


title: Healthy_control_H8 (mRNA)


title: SEPSIS_patient_P16 (mRNA)


title: SEPSIS_patient_P24 (mRNA)


title: SEPSIS_patient_P11 (mRNA)


title: Healthy_control_H11 (mRNA)


title: SEPSIS_patient_P13 (mRNA)


title: SEPSIS_patient_P14 (mRNA)


title: SEPSIS_patient_P15 (mRNA)


title: SEPSIS_patient_P9 (mRNA)


title: SEPSIS_patient_P10 (mRNA)


title: SEPSIS_patient_P17 (mRNA)


title: Healthy_control_H19 (mRNA)


title: SEPSIS_patient_P28 (mRNA)


title: SEPSIS_patient_P7 (mRNA)


title: SEPSIS_patient_P4 (mRNA)


title: SEPSIS_patient_P2 (mRNA)


title: L10-Input-rep2

city: Bethesda

first: Hye Kyung

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 6

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

source_name: Mammary gland

growth_protocol: Mouse mammary gland tissues were harvested at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665 and at day 10 of lactation (L10) after second pregnancy of Y665H mutant.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: Stage

value: day 10 of lactation (L10)

value: WT

tag: chip-seq antibody

value: IgG


title: L10-Input-rep1

description: Library name: Sample 5

tag: tissue


title: p13-Input-rep2

description: Library name: Sample 2

value: day 13 of pregnant (p13)


title: L1-Input-rep1

description: Library name: Sample 3

value: day 1 of lactation (L1)


title: WT-p13_rep1

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

growth_protocol: RNA-seq was done for the mammary tissues at day 13 and 18 of pregnant (p13, p18) at 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 3000 or Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

value: day 13 of pregnancy (p13)


title: p13-Input-rep1

description: Library name: Sample 1


title: WT-p13_rep3