title: VSX2-Adult human ChIP-Seq Input, Rep1

value: Adult

value: White

value: untreated


title: U87MG_ID2_1

status: Public on Jul 13 2022

type: SRA

city: Seoul

first: Sang-Hun

last: Choi

address: Anamro 145

department: Biotechnology

country: South Korea

institute: Korea University

library_source: transcriptomic

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text file which includes: 1) FPKMs, 2) read counts

molecule: total RNA

organism: Homo sapiens

source_name: Glioblastoma cells

growth_protocol: U87MG cells were grown in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50µg/ml).

extract_protocol:
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
Libraries were prepared for QuantSeq3' mRNA by using hg19(UCSC) platform. All procedures were proceeded by ebiogen coporation.
Lexogen (Quant-Seq library prep kit)

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Malignant glioma-derived cells

tag: treatment

value: ID2 lentivirus for 24 hours

tag: genotype

value: ID2 overexpression


title: Irradiated cell 1 Bio Rep 1

city: Ljubljana

first: Bostjan

last: Markelc

email: bmarkelc@gmail.com, bmarkelc@onko-i.si

state: Ljubljana

address: Zaloska cesta 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

data_processing:
tophat v2.1.0
cufflinks-2.2.1
htseq  0.9.1
Genome_build: GRCm38 release 88
Supplementary_files_format_and_content: txt

organism: Mus musculus

source_name: Tumor endothelial cells

growth_protocol: Murine colon adenocarcinoma cells (MC38) were a gift from Dr. Lee Gorden (Vanderbilt University, Nashville, TN, USA). Cells were transduced with lentiviruses to obtain MC38 mCherry cells. Cells were cultured in DMEM (MC38) supplemented with 10% (v/v) fetal bovine serum and 1% penicillin-streptomycin. All cells were maintained in a humidified incubator with 5% CO2 at 37°C. Cells were used at passage number < 10 and were routinely tested negative for Mycoplasma with MycoAlertTM Mycoplasma Detection Kit (Lonza). A 100 µl of cell suspension in 0.9% NaCl (2.5 x 105 cells) was injected subcutaneously on the right flank.

extract_protocol:
Dissected tumors were finely chopped with scalpels and the obtained fragments digested in HBSS (with Calcium and Magnesium; GIBCO) containing a mix of Collagenases 1 and 3 (Worthington; 3 mg ml−1), dispase II (Roche; 7 mg ml−1), DNase I (Invitrogen; 2 U ml−1) and left at 37 °C with gentle agitation for 20 minutes. A total of 25x106 cells were stained in a final volume of 100 μl of antibody mix for 15-20 minutes, in ice, protected from light. Cells were subsequently washed with 2 ml PBS-5% FBS, centrifuged at 500g for 5 minutes and resuspended in 500 μl PBS-5% FBS. 7-AAD was added right before the sample acquisition. Sorting was performed by using a Fusion cell sorter (BD Biosciences). The dissociated cells were centrifuged at 500g for 5 minutes, resuspended in PBS-5% FBS and filtered through 50 μm cell strainers before being counted and used for flow cytometry. 100 cells per population were sorted in 4 μl of lysis mix (0.4% Triton X + RNAse Inhibitor (1:20), dNTPS (10 mM), Oligo dT (10 μM) - according to the original Smart-seq2 protocol49) for bulk RNAseq, and 1 cell per well of a 96 well plate for single cell RNAseq, and immediately processed for RNA-sequencing or stored at -80 °C.
A 5.7 μl of retro-transcription mix (see reference for details) was added to each sample. Retro-transcription was carried out according to the original Smart-seq2 protocol and cDNA was then pre-amplified for 15 cycles. After PCR pre-amplification, cDNA was purified using Ampure XP magnetic beads according to the manufacturer's instructions, in a ratio of 0.8 to 1 with cDNA, resuspended in 17.5 μl of buffer EB (Qiagen) and stored at –20 °C. Quality and concentration of the cDNA generated were assessed using High-Sensitivity Bioanalyzer kit (Agilent). 1 ng of pre-amplified cDNA was tagmented and indexed with Nextera XT DNA Sample Preparation kit (Illumina) according to the manufacturer's instructions. The product was purified with AMPure XP beads (1:1 ratio) and eluted in 17.5 μl of EB buffer (Qiagen). Samples were loaded on a High-Sensitivity DNA chip (Agilent Technologies) to check for library size and quality and concentration measured with Qubit High-Sensitivity DNA kit (Invitrogen). Libraries were pooled to a final concentration ranging between 2 nM and 10 nM and sequenced with Illumina Hiseq 4000 (25 bp single-end read) at the Wellcome Trust Centre for Human Genetics in Oxford.

treatment_protocol: Once tumors reached 80-100 mm3 mice were randomly assigned to experimental groups. Mice were anesthetized under inhalation with isoflurane and led shielded with only the tumors exposed to radiation. Tumors received  15 Gy X-ray radiation treatment (300 kV, dose rate of 2.25 Gy per minute) delivered to tumors using a Gulmay RS320 irradiation system (Gulmay Medical Ltd).

tag: strain

tag: tumor model

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation

tag: time point

value: 48 h after treatment

tag: experiment type

value: single cell

value: FACS sorted tumor endothelial cells


title: U87MG_ID1_2

value: ID1 lentivirus for 24 hours

value: ID1 overexpression


title: Irradiated cell 1 Bio Rep 2


title: Untreated cell 96 Bio Rep 2


title: Untreated cell 95 Bio Rep 3


title: U87MG_GFP_3

value: control lentivirus for 24 hours

value: control


title: Untreated cell 94 Bio Rep 2


title: Untreated cell 95 Bio Rep 2


title: spinal cord - ALS - H3K27Ac [ALS #30]

city: Boston

first: Wanjin

last: Li

state: Massachusetts

address: 240 longwood Ave

department: Cell Biology

country: USA

institute: Harvard Medical School

description:
8401
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

library_source: genomic

data_processing:
Library strategy: CUT&Tag
For ATAC-seq, paired-end 41x41 bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500 to access open vs closed chromatin regions. Data was processed following ATAC-seq guidelines by Harvard FAS informatics. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --very-sensitive -k 10.
For RNA-seq, libraries were sequenced on an Illumina NextSeq500 instrument with paired 38bp reads. Reads were aligned to the mm9 UCSC mouse transcriptome with Salmon and expression values were determined with DESeq2.
For CUT&Tag,paired-end 41x41bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --local --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Genome_build: mm9 for mouse, hg19 for human
Supplementary_files_format_and_content: bigWig files were generated by deeptools version 3.0.2

molecule: genomic DNA

source_name: spinal cord

extract_protocol:
ATAC-seq was performed according to the standard protocol.
For RNA-seq, RNA was extracted from wildtype or Ripk1D325A/D325A;Ripk3-/- MEFs using Quick-RNA MiniPrep kit (Zymo Research) with the in-column DNase treatment. Libraries were prepared and sequenced by the Bauer Core facility at Harvard University.
For CUT&Tag, the nuclei were isolated and the protein enriched DNA regions were obtained using standard CUT&Tag protocol.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ripk1D325A/D325A;Ripk3-/- MEFs treated with vehicle or TNFα with or without Nec-1s

tag: patient

value: ALS #30

tag: cut&tag antibody


title: U87MG_GFP_1


title: Irradiated cell 1 Bio Rep 3


title: Untreated cell 93 Bio Rep 3


title: Untreated cell 94 Bio Rep 3


title: U87MG_GFP_2


title: Untreated cell 93 Bio Rep 2


title: spinal cord - ALS - H3K27Ac [ALS #38]

description:
8402
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

value: ALS #38


title: Untreated cell 92 Bio Rep 2


title: Untreated cell 92 Bio Rep 3


title: spinal cord - ALS - H3K27Ac [ALS #32]

description:
32
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

value: ALS #32


title: spinal cord - ALS - H3K4me1 [ALS #30]

description:
8369
ALS_me1_no_input_relaxed_no26_enriched_FDR0.05.bed


title: spinal cord - ALS - H3K27Ac [ALS #36]

description:
33
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

value: ALS #36


title: U87MG_ID1_3

value: Brain


title: spinal cord - ALS - p-S166-RIPK1 [ALS #38]

description:
8386
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: Untreated cell 91 Bio Rep 3

value: untreated


title: Untreated cell 91 Bio Rep 2


title: Untreated cell 90 Bio Rep 2


title: spinal cord - control - H3K27Ac [control #42]

description:
29
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

value: control #42


title: spinal cord - control - H3K27Ac [control #73]

description:
30
ALS_Ac_no_input_relaxed_no26_enriched_FDR0.05.bed

value: control #73


title: Untreated cell 90 Bio Rep 3

value: colon adenocarcinoma cells (MC38)


title: spinal cord - ALS - p-S166-RIPK1 [ALS #36]

description:
17
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: U87MG_ID1_1

value: Malignant glioma-derived cells


title: Untreated cell 89 Bio Rep 3


title: Untreated cell 89 Bio Rep 2


title: Untreated cell 88 Bio Rep 2


title: Untreated cell 88 Bio Rep 3


title: Untreated cell 87 Bio Rep 3


title: Untreated cell 86 Bio Rep 3


title: spinal cord - control - p-S166-RIPK1 [control #42]

description:
13
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: spinal cord - control - p-S166-RIPK1 [control #31]

description:
12
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed

value: control #31


title: spinal cord - ALS - SMARCC2 [ALS #38]


title: Untreated cell 85 Bio Rep 3

value: single cell


title: Untreated cell 85 Bio Rep 2

value: FACS sorted tumor endothelial cells


title: spinal cord - control - SMARCC2 [control #42]


title: Untreated cell 86 Bio Rep 2


title: Untreated cell 87 Bio Rep 2


title: Untreated cell 84 Bio Rep 2


title: spinal cord - ALS - H3K4me1 [ALS #32]

description:
GEN00198000
ALS_me1_no_input_relaxed_no26_enriched_FDR0.05.bed


title: spinal cord - control - H3K4me1 [control #70]

description:
GEN00197615
ALS_me1_no_input_relaxed_no26_enriched_FDR0.05.bed

value: control #70


title: Untreated cell 84 Bio Rep 3


title: Untreated cell 83 Bio Rep 2


title: Untreated cell 83 Bio Rep 3


title: spinal cord - control - p-S166-RIPK1

description:
GEN00197607
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: spinal cord - ALS - p-S166-RIPK1 [ALS #32]

description:
16
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: Untreated cell 82 Bio Rep 3


title: KD2_repeat2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome hg38 by STAR aligner (version 2.7.5a)
Gene counts were quantified by STAR feature count function
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using Python

growth_protocol: SW480 cells were cultured in DMEM Medium with 10% FBS.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacther's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: model

tag: source tissue

value: colon

tag: source gender

value: Male


title: spinal cord - control - p-S166-RIPK1 [control #73]

description:
14
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: spinal cord - ALS - SMARCC2 [ALS #30]


title: Untreated cell 81 Bio Rep 2


title: Untreated cell 82 Bio Rep 2


title: KD2_repeat1


title: spinal cord - ALS - p-S166-RIPK1 [ALS #30]

description:
15
ALS_phR_no_input_relaxed_30323638314270_enriched_FDR0.05.bed


title: spinal cord - control - SMARCC2 [control #73]


title: Untreated cell 80 Bio Rep 3


title: KD1_repeat1


title: spinal cord - control - H3K4me1 [control #42]

description:
GEN00197997
ALS_me1_no_input_relaxed_no26_enriched_FDR0.05.bed


title: Untreated cell 80 Bio Rep 2


title: NC_repeat2

value: NC


title: Untreated cell 78 Bio Rep 2


title: NC_repeat1


title: Untreated cell 79 Bio Rep 3


title: Untreated cell 78 Bio Rep 1


title: spinal cord - ALS - H3K4me1 [ALS #36]

description:
GEN00198001
ALS_me1_no_input_relaxed_no26_enriched_FDR0.05.bed


title: RNA-seq_NASH_7

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Single-read sequencing was performed using the NextSeq 500 (Illumina). Pair-end sequencing was performed using the NovaSeq 6000 (Illumina).
All data was analysed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Trim Galore! (Galaxy version 0.4.3.1) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the hg38 or mm10 version of the human and mouse genome, respectively, using STAR (Galaxy version 2.7.7a). Strand specificity and read counting was performed with Infer Experiment (Galaxy version 2.6.4.1) and featureCounts (Galaxy version 2.0.1), respectively. Next, we used DESeq2 (Galaxy version 2.11.40.6+galaxy1) for differential expression analysis and the resulting data was annotated with Annotate DESeq2/DEXSeq output tables (Galaxy version 1.1.0).
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Excel (xlsx) files containing DESeq2 outputs.

source_name: Human liver tissue

growth_protocol: FL83B mouse hepatocytes (ATCC®, #CRL-2390™) were grown in F-12K medium (Thermo Fisher Scientific, #21127030) supplemented with 10% fetal bovine serum (growth medium). Cells were maintained at 37°C, 95% O2 and 5% CO2.

extract_protocol:
Cells were collected in TRI Reagent (Sigma #T9424), following which RNA was purified using Direct-zol™ RNA MiniPrep (Zymo Research, #R2050).
Libraries from human liver tissue and wild type FL83B cells were prepared with TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020599). Libraries from knockout FL83B cells and their corresponding non-targeting controls were prepared with TruSeq Stranded mRNA Library Kit (Illumina, #20020595).

treatment_protocol: FL83B cells were incubated in 400 µM palmitate diluted in growth medium for 24 h. One percent BSA diluted in growth medium was used as control. Moreover, gene knockout was achieved by the CRISPR-Cas9 system, using non-targeting agRNA (control) and Tcf4 or Mafk sgRNA.

tag: tissue/cell type

value: Liver

tag: condition

value: NASH


title: Untreated cell 78 Bio Rep 3


title: Untreated cell 77 Bio Rep 3


title: RNA-seq_Healthy_4

value: Healthy


title: RNA-seq_NASH_8


title: RNA-seq_NASH_5


title: KD1_repeat2


title: Untreated cell 77 Bio Rep 1


title: RNA-seq_Healthy_2


title: RNA-seq_Healthy_3


title: RNA-seq_Healthy_1


title: Untreated cell 76 Bio Rep 3


title: Untreated cell 81 Bio Rep 3


title: Untreated cell 77 Bio Rep 2


title: Untreated cell 75 Bio Rep 3


title: Untreated cell 75 Bio Rep 2


title: Untreated cell 76 Bio Rep 1


title: NASH_8

data_processing:
Pair-end sequencing of the libraries was performed using the Illumina NextSeq 500.
All data was analysed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Cutadapt (Galaxy version: 1.16.5) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the hg38 or mm10 version of the human and mouse genome, respectively, using Bowtie2 (Galaxy version 2.3.4.3+galaxy0). Low quality reads (phred < 30) were filtered out with Filter (Galaxy Version 2.4.1) and duplicated reads were removed with MarkDuplicates (Galaxy version 2.18.2.2). Next, we used Genrich (Galaxy version 0.5+galaxy2) for peak calling (q-value < 0.05), while ChIPseeker (Galaxy version, #1.18.0+galaxy1) was used to annotate peaks.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Excel (xlsx) files containing Genrich outputs.

extract_protocol:
Nuclei from human liver (15 mg) were isolated using with the Nuclei EZ Prep kit (Sigma-Aldrich, #NUC101) and a glass dounce homogenizer (25 strokes with lose pastel and 25 strokes with tight pastel in ice-cold Nuclei EZ Lysis Buffer). Nuclei were filter through a 40 μm cell strainer and counted before ATAC-seq. On the other hand, Fl83B mouse hepatocytes were seeded in 60 mm plates 24 h before BSA or PAL treatment. Nuclei from human liver and mouse hepatocytes were then used for ATAC-seq as previously described (PMID: 28846090).
Library preparation was performed as previously described (PMID: 28846090).

treatment_protocol: FL83B cells were incubated in 400 µM palmitate diluted in growth medium for 24 h. One percent BSA diluted in growth medium was used as control.


title: NASH_7


title: Untreated cell 75 Bio Rep 1


title: RNA-seq_NASH_6


title: Healthy_3


title: NASH_5


title: Healthy_2


title: Healthy_1


title: Untreated cell 74 Bio Rep 3


title: Untreated cell 74 Bio Rep 1


title: Untreated cell 74 Bio Rep 2


title: SF10592_spatial_proteomics

city: San Francisco

first: Aaron

last: Diaz

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

library_source: other

data_processing:
The SP data were normalized by ROI surface area. The ST data were normalized against the 75th percentile of signal, i.e. Q3 normalization. MUlti-Subject SIngle Cell deconvolution (MuSiC) was used for deconvolution of the spatial transcriptomics data based on cell-type signatures determined from snRNA-seq data used as input. Heatmaps were generated via pheatmap package (https://cran.r-project.org/web/packages/pheatmap/index.html). To validate putative ligand-receptor interactions via ST, the expression of each ligand-receptor pair obtained from CellChat were used to calculate a Pearson's correlation coefficient across ROIs. These were adjusted for multiple-hypothesis testing via fdrtool. Representative IF images for specific pathways were obtained based on sorting for correlation and then for expression of ligand-receptor pairs in that pathway.
Assembly: hg38
Supplementary files format and content: Read count; image data
Library strategy: Spatial proteomics

molecule: protein

source_name: Brain

extract_protocol: For the spatial transcriptomics assay, FFPE tissue blocks were reviewed for tumor purity and 10, 5 µm sections were cut by the UCSF Neurosurgery Tissue Core. Slides were baked at 37°C overnight and then deparaffinized, rehydrated, antigen-retrieved for 20 min at 100°C, and digested with proteinase-K 0.1 ug/ml for 15 min in a Leica BOND-RX. Samples were post-fixed in neutral-buffered formalin for 10 min and hybridized to the cancer-transcriptome atlas (>1,800 targets) UV-photocleavable barcode-conjugated RNA in situ hybridization probe set overnight. Samples were washed to remove off-target probes and counterstained with morphology markers for 2 hours. The morphology markers consisted of: 1:25 SYTO13 (Invitrogen), 1:100 anti-CD3 Alexa Fluor 647 (UMAB54, Origene)), 1:200 anti-CD68-Alexa Fluor 594 (KP1, Santa Cruz), and 1:400 anti-GFAP-Alexa Fluor 488 (GA5, Invitrogen). Immunofluorescence imaging, region of interest (ROI) selection, spatially-indexed barcode cleavage and collection were performed on a GeoMx Digital Spatial Profiling instrument (NanoString). Approximately 12 ROIs were collected per sample. Photoreleased GeoMx DSP oligonucleotide tags containing RNA IDs and a UMI were collected from each ROI. After PCR with dual-indexing Illumina i5 and i7 primers, the library was purified with AMPure XP beads (Beckman Coulter), quantitated with a Qubit (Themo Fisher Scientific) and quality was checked with a Bioanalyzer (Agilent). Paired-end sequencing was performed on NextSeq 550 and NextSeq 2000 instruments. For the spatial proteomics assay, FFPE tissue blocks were reviewed for tumor purity and 6, 5 µm sections were cut by the UCSF Neurosurgery Tissue Core. Slides were baked at 37°C overnight, deparaffinized, rehydrated, antigen-retrieved in a pressure cooker for 15 min at 100°C at high pressure. Samples were then incubated overnight with the GeoMx Immune Cell Profiling Protein Core antibodies (NanoString) containing UV-photocleavable barcode-conjugated antibodies against 17 targets and 6 control targets. At the same time, the samples were incubated with morphology antibodies consisting of: SYTO83 (100 nM final concentration), 1:200 anti-CD68-Alexa Fluor 594 (clone KP1), 1:200 anti-CD45-Alexa Fluor 647 (clone 2B11+PD7/26), and 1:400 anti-GFAP-Alexa Fluor 488 (clone GA5). Immunofluorescence imaging, region of interest (ROI) selection, spatially-indexed barcode cleavage and collection were performed on a GeoMx Digital Spatial Profiling instrument (NanoString) by GENEWIZ. Approximately 10 ROIs were collected per sample. The resulting photocleavable barcode tags were subsequently detected and counted using an nCounter Prep Station and Digital Analyzer (NanoString).

tag: progression

value: Primary

tag: diagnosis

value: GBM

tag: age

tag: gender

tag: pair#


title: Untreated cell 73 Bio Rep 3

tag: treatment

value: untreated

tag: cell type


title: Healthy_4

tag: tissue


title: Untreated cell 79 Bio Rep 2

tag: strain

tag: tumor model

tag: time point


title: Untreated cell 76 Bio Rep 2

tag: experiment type


title: SF11331_spatial_proteomics

value: Brain


title: Untreated cell 73 Bio Rep 1


title: Untreated cell 72 Bio Rep 3


title: NASH_6


title: SF11857_spatial_proteomics

value: Recurrent


title: SF4297_spatial_proteomics


title: Untreated cell 72 Bio Rep 2

value: colon adenocarcinoma cells (MC38)


title: Untreated cell 73 Bio Rep 2


title: SF11082_spatial_transcriptomics

data_processing:
The SP data were normalized by ROI surface area. The ST data were normalized against the 75th percentile of signal, i.e. Q3 normalization. MUlti-Subject SIngle Cell deconvolution (MuSiC) was used for deconvolution of the spatial transcriptomics data based on cell-type signatures determined from snRNA-seq data used as input. Heatmaps were generated via pheatmap package (https://cran.r-project.org/web/packages/pheatmap/index.html). To validate putative ligand-receptor interactions via ST, the expression of each ligand-receptor pair obtained from CellChat were used to calculate a Pearson's correlation coefficient across ROIs. These were adjusted for multiple-hypothesis testing via fdrtool. Representative IF images for specific pathways were obtained based on sorting for correlation and then for expression of ligand-receptor pairs in that pathway.
Assembly: hg38
Supplementary files format and content: Read count; image data
Library strategy: Spatial transcriptomics

value: Female


title: SF6621_spatial_proteomics


title: SF11720 spatial_proteomics


title: SF12407_spatial_transcriptomics


title: SF11873_spatial_transcriptomics


title: Untreated cell 71 Bio Rep 3


title: Untreated cell 72 Bio Rep 1


title: Untreated cell 71 Bio Rep 1


title: Untreated cell 70 Bio Rep 2


title: Untreated cell 71 Bio Rep 2


title: SF11331_spatial_transcriptomics


title: SF4297_spatial_transcriptomics


title: SF11720_spatial_transcriptomics


title: SF6621_spatial_transcriptomics


title: Untreated cell 69 Bio Rep 3


title: SF11857_spatial_transcriptomics


title: SF12754_spatial_transcriptomics


title: Untreated cell 70 Bio Rep 1


title: SF10592_spatial_transcriptomics


title: Untreated cell 68 Bio Rep 3


title: Untreated cell 70 Bio Rep 3


title: HUDEP2_NT_IgG

city: Memphis

first: Mitchell

middle: J

last: Weiss

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: CUT&RUN

data_processing:
BWA mem mapping to hg19
normalized signal (bw file) was generated using s3norm_pipeline.py -r mean
Assembly: hg19
Supplementary files format and content: bigwiggle and bedgraph

growth_protocol: HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin. Erythroid differentiation of CD34+ cells was performed using a three-phase culture protocol. For phase 1 (days 0-7), cells were maintained at a density of 1-4 × 105 /mL in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin-streptomycin, 3 IU/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, 1 IU erythropoietin, 10 ng/mL SCF, and 1 ng/mL interleukin-3 (IL-3). For phase 2 (days 8-12), IL-3 was omitted from the medium. Cells were maintained at a density of 0.2-0.8 × 106/mL. For phase 3 (days 12-18), IL-3 and SCF were omitted, the holo-transferrin concentration was increased to 1 mg/mL, and the cells were maintained at a density of 1-2 × 106/mL.

extract_protocol: Library construction for DNA sequencing was performed using a NEBNext UltraII DNA Library Prep Kit from NEB (E7645S). Indexed samples were analyzed by paired-end NGS using an Illumina NextSeq Mid-Output (150 cycles) Kit.

treatment_protocol: CD34+ HSPCs cells were eletroporated with NT or VHL sgRNA1 RNP complex. HUDEP2 cells were electroporated with VHL sgRNA1 to isolate VHL Knockout clones.

tag: cell line

tag: antibody

value: IgG


title: Untreated cell 67 Bio Rep 3

value: single cell


title: Untreated cell 68 Bio Rep 2

value: FACS sorted tumor endothelial cells


title: Untreated cell 68 Bio Rep 1


title: Untreated cell 67 Bio Rep 2


title: HUDEP2_VHLKO_P300_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 67 Bio Rep 1


title: CD34_NT_IgG

description: CUT&RUN


title: Untreated cell 66 Bio Rep 3


title: Untreated cell 69 Bio Rep 2


title: HUDEP2_VHLKO_HIF1A_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 66 Bio Rep 2


title: HUDEP2_VHLKO_HIF1b_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_H3K4me3_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 69 Bio Rep 1


title: Untreated cell 65 Bio Rep 3


title: Untreated cell 66 Bio Rep 1


title: HUDEP2_VHLKO_clone1_HIF1b

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 65 Bio Rep 1


title: Untreated cell 64 Bio Rep 2


title: HUDEP2_VHLKO_clone1_H3K4me3

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 64 Bio Rep 3


title: HUDEP2_VHLKO_clone1_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_clone1_H3K4me1

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_H3K4me1_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 63 Bio Rep 3


title: HUDEP2_VHLKO_GATA1_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_clone1_GATA1

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_clone1_H3K27ac

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 63 Bio Rep 2


title: Untreated cell 64 Bio Rep 1


title: HUDEP2_NT_rep1_HIF1b

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 65 Bio Rep 2


title: HUDEP2_NT_rep1_H3K4me1

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_VHLKO_clone1_P300

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 61 Bio Rep 3


title: Untreated cell 62 Bio Rep 3


title: Untreated cell 62 Bio Rep 2


title: HUDEP2_VHLKO_H3K27ac_clone2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_rep1_H3K27ac

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 63 Bio Rep 1


title: Untreated cell 61 Bio Rep 2


title: HUDEP2_NT_rep1_GATA1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 61 Bio Rep 1


title: HUDEP2_NT_P300_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_rep1_H3K4me3

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_rep1_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 60 Bio Rep 2


title: Untreated cell 60 Bio Rep 3


title: HUDEP2_NT_HIF1b_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_H3K4me3_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_HIF1A_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_rep1_P300

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 62 Bio Rep 1


title: Untreated cell 60 Bio Rep 1


title: Untreated cell 59 Bio Rep 2


title: HUDEP2_NT_H3K27ac_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_P300_rep2

description:
CUT&RUN
Illumina NextSeq 550

value: CD34+ HSPCs


title: HUDEP2_NT_GATA1_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 58 Bio Rep 3


title: CD34_VHLKO_P300_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: HUDEP2_NT_H3K4me1_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 57 Bio Rep 3


title: Untreated cell 58 Bio Rep 2


title: Untreated cell 58 Bio Rep 1


title: CD34_VHLKO_IgG

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 57 Bio Rep 2


title: CD34_VHLKO_HIF2A_Rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_HIF2A_Rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 57 Bio Rep 1


title: CD34_VHLKO_HIF1b_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_HIF1b_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 56 Bio Rep 2


title: Untreated cell 56 Bio Rep 1


title: CD34_VHLKO_HIF1A_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 55 Bio Rep 2


title: Untreated cell 55 Bio Rep 3


title: CD34_VHLKO_H3K4me3_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 59 Bio Rep 3


title: Untreated cell 55 Bio Rep 1


title: CD34_VHLKO_HIF1A_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 54 Bio Rep 3


title: Untreated cell 54 Bio Rep 1


title: Untreated cell 59 Bio Rep 1


title: CD34_VHLKO_H3K27ac_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_H3K4me1_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 56 Bio Rep 3


title: CD34_VHLKO_H3K4me1_Rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 53 Bio Rep 3


title: CD34_VHLKO_GATA1_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_H3K27ac_Rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_VHLKO_H3K4me3_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 52 Bio Rep 3


title: Untreated cell 53 Bio Rep 1


title: Untreated cell 53 Bio Rep 2


title: Untreated cell 52 Bio Rep 2


title: CD34_NT_P300_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 52 Bio Rep 1


title: CD34_NT_HIF2A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 51 Bio Rep 1


title: CD34_NT_P300_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_NT_HIF1b_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 51 Bio Rep 2


title: CD34_Vehicle_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 51 Bio Rep 3


title: CD34_NT_HIF1A_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_NT_HIF1A_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_NT_H3K4me3_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 50 Bio Rep 2


title: CD34_VHLKO_GATA1_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 50 Bio Rep 1


title: CD34_NT_H3K4me1_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_NT_H3K4me3_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 49 Bio Rep 3


title: Untreated cell 49 Bio Rep 1


title: CD34_NT_H3K27ac_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 48 Bio Rep 3


title: CD34_NT_H3K4me1_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_NT_H3K27ac_Rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 48 Bio Rep 2


title: CD34_NT_GATA1_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 47 Bio Rep 2


title: Untreated cell 48 Bio Rep 1


title: CD34_NT_HIF1b_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: CD34_FG4592_HIF1A_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 50 Bio Rep 3


title: CD34_NT_GATA1_rep1

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 46 Bio Rep 3


title: CD34_FG4592_HIF1A_rep2

description:
CUT&RUN
Illumina NextSeq 550


title: Baseeditor_Clone2_NT_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 47 Bio Rep 1


title: Untreated cell 49 Bio Rep 2


title: Untreated cell 46 Bio Rep 2


title: Baseeditor_Clone2_MotifB_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Baseeditor_Clone2_MotifA_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 45 Bio Rep 3


title: Untreated cell 45 Bio Rep 2


title: Untreated cell 54 Bio Rep 2


title: Baseeditor_Clone1_MotifB_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Baseeditor_Clone2_MotifAB_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 46 Bio Rep 1


title: Baseeditor_Clone1_NT_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 45 Bio Rep 1


title: Baseeditor_Clone1_MotifAB_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 47 Bio Rep 3


title: Untreated cell 44 Bio Rep 3


title: A549_VHLKO1_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 44 Bio Rep 1


title: Untreated cell 44 Bio Rep 2


title: A549_VHLKO_HIF2A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 43 Bio Rep 3


title: Baseeditor_Clone1_MotifA_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 43 Bio Rep 2


title: Untreated cell 43 Bio Rep 1


title: Untreated cell 42 Bio Rep 3


title: A549_NT_HIF2A

description:
CUT&RUN
Illumina NextSeq 550


title: combined_VHLKO_BCL11A rep2

description: Capture-C

data_processing:
CaptureC data was analyzed using the original captureC pipeline (https://github.com/Hughes-Genome-Group/captureC)
Assembly: hg19
Supplementary files format and content: bw

growth_protocol: Erythroid differentiation of CD34+ cells was performed using a three-phase culture protocol. For phase 1 (days 0-7), cells were maintained at a density of 1-4 × 105 /mL in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin-streptomycin, 3 IU/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, 1 IU erythropoietin, 10 ng/mL SCF, and 1 ng/mL interleukin-3 (IL-3). For phase 2 (days 8-12), IL-3 was omitted from the medium. Cells were maintained at a density of 0.2-0.8 × 106/mL. For phase 3 (days 12-18), IL-3 and SCF were omitted, the holo-transferrin concentration was increased to 1 mg/mL, and the cells were maintained at a density of 1-2 × 106/mL.

extract_protocol: none provided by the submitter

treatment_protocol: CD34+ HSPCs cells eletroporated with NT or VHL sgRNA1 RNP complex. Capture-C was performed using NlaIII enzyme as described before. All experiments were performed in 2 biological replicates. Biotin-labeled DNA probes are listed in supplemental Table 5a in this related manuscript. The libraries were sequenced on an Illumina Nextseq 550 with paired-end sequencing.

tag: cells


title: Untreated cell 42 Bio Rep 2


title: combined_VHLKO_BCL11A rep1

description: Capture-C


title: Untreated cell 42 Bio Rep 1


title: Untreated cell 41 Bio Rep 3


title: combined_NT_BCL11A rep1

description: Capture-C


title: Untreated cell 41 Bio Rep 2


title: Untreated cell 40 Bio Rep 3


title: CaptureC_VHLKO_HS3_rep2

description: Capture-C


title: CaptureC_VHLKO_HBBP1_rep2

description: Capture-C


title: combined_NT_BCL11A rep2

description: Capture-C


title: CaptureC_VHLKO_HBBP1_rep1

description: Capture-C


title: Untreated cell 40 Bio Rep 2


title: Untreated cell 41 Bio Rep 1


title: CaptureC_VHLKO_BGLT3_rep2

description: Capture-C


title: CaptureC_VHLKO_HS3_rep1

description: Capture-C


title: A549_NT_HIF1A

description:
CUT&RUN
Illumina NextSeq 550


title: Untreated cell 40 Bio Rep 1


title: Untreated cell 39 Bio Rep 2


title: CaptureC_VHLKO_BGLT3_rep1

description: Capture-C


title: Untreated cell 39 Bio Rep 3


title: CaptureC_NT_HS3_rep2

description: Capture-C


title: Untreated cell 39 Bio Rep 1


title: CaptureC_NT_HS3_rep1

description: Capture-C


title: CaptureC_NT_HBBP1_rep2

description: Capture-C


title: CaptureC_NT_HBBP1_rep1

description: Capture-C


title: CaptureC_NT_BGLT3_rep2

description: Capture-C


title: CaptureC_NT_BGLT3_rep1

description: Capture-C


title: Untreated cell 38 Bio Rep 1


title: Untreated cell 37 Bio Rep 3


title: Untreated cell 38 Bio Rep 2


title: Untreated cell 37 Bio Rep 2


title: Untreated cell 37 Bio Rep 1


title: NIH3T3_siALDOA_R2

city: Würzburg

first: Elmar

last: Wolf

address: Am Hubland

department: Chair of Biochemistry and Molecular Biology

country: Germany

institute: University of Würzburg

data_processing:
fastq files were generated from base calls using bcl2fastq.
alignment to mm10 using bowtie2 2.2.7
reads were randomly subsampled to equal numbers per sample
count tables were created using GenomicAlignments in R
genes with fewer than 12 reads across all samples were dropped
Assembly: mm10
Supplementary files format and content: CPMs

molecule: polyA RNA

growth_protocol: cells were grown in DMEM + 10% FCS + 1% Pen-Strep

extract_protocol:
RNA was extracted using the RNeasy Mini Kit
Library was prepared with the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina. 13 PCR cycles were used for library amplification.

treatment_protocol: 48 h siRNA treatment (control vs. Aldoa knockdown)

value: fibroblast

value: Aldolase A (Aldoa)-targeting siRNAs, 48 h, replicate 2


title: Untreated cell 38 Bio Rep 3


title: NIH3T3_siCTR_R3

value: non-targeting control siRNAs, 48 h, replicate 3


title: Untreated cell 36 Bio Rep 3


title: Untreated cell 36 Bio Rep 2


title: NIH3T3_siCTR_R1

value: non-targeting control siRNAs, 48 h, replicate 1


title: Untreated cell 35 Bio Rep 2


title: NIH3T3_siALDOA_R1

value: Aldolase A (Aldoa)-targeting siRNAs, 48 h, replicate 1


title: Untreated cell 34 Bio Rep 3


title: Untreated cell 35 Bio Rep 3


title: NIH3T3_siALDOA_R3

value: Aldolase A (Aldoa)-targeting siRNAs, 48 h, replicate 3


title: Untreated cell 33 Bio Rep 3


title: Untreated cell 35 Bio Rep 1


title: Untreated cell 34 Bio Rep 1


title: Primary MC38 tumor vehicle #1

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

country: Canada

institute: University of Ottawa

data_processing:
Processed raw sequences with fastp to perform automatic adapter trimming, and default sequence quality filtering (>60% of bases with Q≥15)
Quantified transcripts from GENCODE vm25 with salmon v1.3.0 using --gcBias flag and genomic decoys in index
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object with four samples (two replicates of two conditions), using the model ~condition (cell type/treatment)
Calculated fold changes using the lfcShrink() function with the apeglm method.
Assembly: GRCm38
Supplementary files format and content: salmon transcript quantification: Quantifrication of GENCODE vm25 transcripts using salmon v1.3.0
Supplementary files format and content: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two conditions, including results for all genes retained after filtering

source_name: Colon adenocarcinoma

extract_protocol:
Snap-frozen tumors were mechanically disrupted and total RNA was extracted using the total RNA purification kit by Norgen Biotech Corp, following the manufacturer's guidelines. Quantification of total RNA samples was performed with a Qubit HS RNA assay (ThermoFisher Scientific) and fragment size was evaluated with a Fragment Analyzer HS NGS assay (AATI). A RNA Quality Number (RQN) of 6.0 or higher was considered satisfactory for library construction. Library construction was performed with a Truseq RNA v2 (Illumina) with unique barcodes compatible with the Illumina NextSeq 500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: injected cell line

value: Colon adenocarcinoma

value: 10 consecutive daily IP injection of saline


title: Primary MC38 tumor vehicle #2


title: Primary MC38 tumor vanoxerine #1

value: 10 consecutive daily IP injection of vanoxerine (25mg/kg)


title: Untreated cell 33 Bio Rep 1

value: untreated


title: Untreated cell 32 Bio Rep 3


title: Untreated cell 33 Bio Rep 2


title: Mm_AMB_N381

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description: mAMB rep./nucleus #381

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Reads from were aligned with STAR (version 2.6.1) against the GENCODE M16 mouse genome annotation for the GRCm38 assembly, supplemented with the Cre and mCherry sequences. Duplicate alignments were removed using Picard Tools (version 2.18.21). Digital expression matrices were generated from the deduplicated alignments using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> software suite (version 2.3.0), specifically the `DigitalExpression` program, counting all unique alignments to both exons and introns.
Assembly: GRCm38
Supplementary files format and content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell counts.

molecule: nuclear RNA

source_name: single neuron nucleus

extract_protocol:
On the next day, nAmb tissue was homogenized and purified by density-gradient centrifugation into a single-nuclei suspension as previously described (Habib et al., 2016; Todd et al., 2020). The single-nuclei suspension was sorted by FACS to isolate one H2b-mCherry+ nucleus per well of three 96-well plates, which were then centrifuged at 2,500rcf, frozen on dry ice, and stored at -80°C until use.
After purifying the RNA by RNA-clean SPRI reagents (1.5x ratio of SPRI to sample), cDNA libraries were generated from polyadenylated mRNA of each sample using Smart-Seq2 (Picelli et al., 2014), modified as previously described (Tao et al., 2021). Illumina sequencing libraries were prepared from single-nuclei cDNA samples as described previously (Tao et al., 2021) and then sequenced by Illumina Next-Seq 500.

treatment_protocol: The ventrolateral medulla of five male Chat-Cre mice was injected with a Cre-dependent reporter virus, AAV-DIO-H2b-mCherry. Four weeks later, at the age of 27 weeks, mice were rapidly decapitated for brain extraction to avoid stress related changes in nuclear mRNA. Following immediate brain extraction, 1 mm thick coronal sections of hindbrain through the nAmb’s full rostral-caudal extent (Bregma -6.5 mm to -8.0 mm) were cut and immersed in ice-cold RNA-later (Qiagen catalog # 76106). After at least 30 minutes in ice-cold RNA-later, the nAmb was visualized under a fluorescence stereomicroscope (Zeiss Discovery V8) and dissected, then stored in RNA-later overnight at 4°C.

value: brain

tag: brain region

value: nucleus ambiguus


title: Mm_AMB_N382

description: mAMB rep./nucleus #382


title: Mm_AMB_N380

description: mAMB rep./nucleus #380


title: Mm_AMB_N383

description: mAMB rep./nucleus #383


title: NIH3T3_siCTR_R2

value: non-targeting control siRNAs, 48 h, replicate 2


title: Mm_AMB_N379

description: mAMB rep./nucleus #379


title: Untreated cell 32 Bio Rep 2

value: colon adenocarcinoma cells (MC38)


title: Untreated cell 36 Bio Rep 1

value: single cell


title: Mm_AMB_N378

description: mAMB rep./nucleus #378


title: Mm_AMB_N377

description: mAMB rep./nucleus #377


title: Untreated cell 31 Bio Rep 3

value: FACS sorted tumor endothelial cells


title: Untreated cell 34 Bio Rep 2


title: Mm_AMB_N384

description: mAMB rep./nucleus #384


title: Mm_AMB_N376

description: mAMB rep./nucleus #376


title: Primary MC38 tumor vanoxerine #2


title: Mm_AMB_N375

description: mAMB rep./nucleus #375


title: Untreated cell 31 Bio Rep 2


title: Mm_AMB_N374

description: mAMB rep./nucleus #374


title: Untreated cell 31 Bio Rep 1


title: Mm_AMB_N373

description: mAMB rep./nucleus #373


title: Untreated cell 30 Bio Rep 1


title: Untreated cell 30 Bio Rep 3


title: Untreated cell 30 Bio Rep 2


title: Mm_AMB_N371

description: mAMB rep./nucleus #371


title: Mm_AMB_N372

description: mAMB rep./nucleus #372


title: Untreated cell 29 Bio Rep 3


title: Untreated cell 29 Bio Rep 2


title: Mm_AMB_N370

description: mAMB rep./nucleus #370


title: Mm_AMB_N368

description: mAMB rep./nucleus #368


title: Mm_AMB_N367

description: mAMB rep./nucleus #367


title: Mm_AMB_N366

description: mAMB rep./nucleus #366


title: Untreated cell 32 Bio Rep 1


title: Untreated cell 28 Bio Rep 3


title: Untreated cell 28 Bio Rep 2


title: Mm_AMB_N365

description: mAMB rep./nucleus #365


title: Untreated cell 28 Bio Rep 1


title: Untreated cell 27 Bio Rep 2


title: Untreated cell 27 Bio Rep 1


title: Mm_AMB_N361

description: mAMB rep./nucleus #361


title: Mm_AMB_N363

description: mAMB rep./nucleus #363


title: Untreated cell 26 Bio Rep 2


title: Mm_AMB_N360

description: mAMB rep./nucleus #360


title: Mm_AMB_N362

description: mAMB rep./nucleus #362


title: Untreated cell 26 Bio Rep 1


title: Mm_AMB_N359

description: mAMB rep./nucleus #359


title: Mm_AMB_N369

description: mAMB rep./nucleus #369


title: Untreated cell 29 Bio Rep 1


title: Untreated cell 25 Bio Rep 3


title: Untreated cell 27 Bio Rep 3


title: Mm_AMB_N357

description: mAMB rep./nucleus #357


title: Untreated cell 25 Bio Rep 1


title: Untreated cell 25 Bio Rep 2


title: Untreated cell 24 Bio Rep 1


title: Mm_AMB_N364

description: mAMB rep./nucleus #364


title: Untreated cell 24 Bio Rep 3


title: Untreated cell 23 Bio Rep 3


title: Untreated cell 24 Bio Rep 2


title: Mm_AMB_N354

description: mAMB rep./nucleus #354


title: Mm_AMB_N356

description: mAMB rep./nucleus #356


title: Mm_AMB_N352

description: mAMB rep./nucleus #352


title: Mm_AMB_N353

description: mAMB rep./nucleus #353


title: Untreated cell 26 Bio Rep 3


title: Untreated cell 23 Bio Rep 1


title: Mm_AMB_N350

description: mAMB rep./nucleus #350


title: Untreated cell 23 Bio Rep 2


title: Untreated cell 22 Bio Rep 3


title: Mm_AMB_N358

description: mAMB rep./nucleus #358


title: Mm_AMB_N348

description: mAMB rep./nucleus #348


title: Untreated cell 22 Bio Rep 2


title: Mm_AMB_N355

description: mAMB rep./nucleus #355


title: Mm_AMB_N347

description: mAMB rep./nucleus #347


title: Mm_AMB_N346

description: mAMB rep./nucleus #346


title: Untreated cell 21 Bio Rep 2


title: Mm_AMB_N351

description: mAMB rep./nucleus #351


title: Untreated cell 21 Bio Rep 3


title: Mm_AMB_N345

description: mAMB rep./nucleus #345


title: Untreated cell 21 Bio Rep 1


title: Untreated cell 20 Bio Rep 3


title: Mm_AMB_N341

description: mAMB rep./nucleus #341


title: Untreated cell 20 Bio Rep 2


title: Untreated cell 19 Bio Rep 2


title: Untreated cell 20 Bio Rep 1


title: Untreated cell 19 Bio Rep 3


title: Mm_AMB_N343

description: mAMB rep./nucleus #343


title: Mm_AMB_N339

description: mAMB rep./nucleus #339


title: Mm_AMB_N342

description: mAMB rep./nucleus #342


title: Mm_AMB_N349

description: mAMB rep./nucleus #349


title: Untreated cell 19 Bio Rep 1


title: Mm_AMB_N340

description: mAMB rep./nucleus #340


title: Untreated cell 22 Bio Rep 1


title: Mm_AMB_N336

description: mAMB rep./nucleus #336


title: Mm_AMB_N337

description: mAMB rep./nucleus #337


title: Untreated cell 18 Bio Rep 2


title: Mm_AMB_N338

description: mAMB rep./nucleus #338


title: Mm_AMB_N335

description: mAMB rep./nucleus #335


title: Untreated cell 18 Bio Rep 1


title: Mm_AMB_N334

description: mAMB rep./nucleus #334


title: Untreated cell 17 Bio Rep 3


title: Untreated cell 17 Bio Rep 2


title: Mm_AMB_N344

description: mAMB rep./nucleus #344


title: Mm_AMB_N333

description: mAMB rep./nucleus #333


title: Untreated cell 16 Bio Rep 3


title: Untreated cell 17 Bio Rep 1


title: Mm_AMB_N332

description: mAMB rep./nucleus #332


title: Untreated cell 18 Bio Rep 3


title: Untreated cell 16 Bio Rep 2


title: Mm_AMB_N331

description: mAMB rep./nucleus #331


title: Untreated cell 16 Bio Rep 1


title: Mm_AMB_N328

description: mAMB rep./nucleus #328


title: Untreated cell 14 Bio Rep 3


title: Mm_AMB_N330

description: mAMB rep./nucleus #330


title: Mm_AMB_N329

description: mAMB rep./nucleus #329


title: Mm_AMB_N324

description: mAMB rep./nucleus #324


title: Mm_AMB_N326

description: mAMB rep./nucleus #326


title: Untreated cell 15 Bio Rep 3


title: Mm_AMB_N325

description: mAMB rep./nucleus #325


title: Untreated cell 15 Bio Rep 1


title: Mm_AMB_N323

description: mAMB rep./nucleus #323


title: Untreated cell 14 Bio Rep 1


title: Mm_AMB_N322

description: mAMB rep./nucleus #322


title: Untreated cell 13 Bio Rep 3


title: Untreated cell 13 Bio Rep 2


title: Untreated cell 13 Bio Rep 1


title: Mm_AMB_N321

description: mAMB rep./nucleus #321


title: Untreated cell 12 Bio Rep 3


title: Mm_AMB_N319

description: mAMB rep./nucleus #319


title: Untreated cell 12 Bio Rep 2


title: Mm_AMB_N317

description: mAMB rep./nucleus #317


title: Untreated cell 15 Bio Rep 2


title: Mm_AMB_N318

description: mAMB rep./nucleus #318


title: Untreated cell 11 Bio Rep 3


title: Mm_AMB_N327

description: mAMB rep./nucleus #327


title: Untreated cell 12 Bio Rep 1


title: Mm_AMB_N315

description: mAMB rep./nucleus #315


title: Mm_AMB_N316

description: mAMB rep./nucleus #316


title: Untreated cell 14 Bio Rep 2


title: Mm_AMB_N312

description: mAMB rep./nucleus #312


title: Untreated cell 11 Bio Rep 1


title: Untreated cell 10 Bio Rep 3


title: Mm_AMB_N320

description: mAMB rep./nucleus #320


title: Mm_AMB_N314

description: mAMB rep./nucleus #314


title: Mm_AMB_N313

description: mAMB rep./nucleus #313


title: Mm_AMB_N311

description: mAMB rep./nucleus #311


title: Untreated cell 9 Bio Rep 2


title: Untreated cell 9 Bio Rep 1


title: Untreated cell 10 Bio Rep 1


title: Untreated cell 10 Bio Rep 2


title: Untreated cell 9 Bio Rep 3


title: Mm_AMB_N310

description: mAMB rep./nucleus #310


title: Mm_AMB_N307

description: mAMB rep./nucleus #307


title: Mm_AMB_N309

description: mAMB rep./nucleus #309


title: Mm_AMB_N308

description: mAMB rep./nucleus #308


title: Untreated cell 8 Bio Rep 3


title: Untreated cell 8 Bio Rep 2


title: Mm_AMB_N306

description: mAMB rep./nucleus #306


title: Untreated cell 8 Bio Rep 1


title: Untreated cell 11 Bio Rep 2


title: Mm_AMB_N305

description: mAMB rep./nucleus #305


title: Untreated cell 7 Bio Rep 2


title: Untreated cell 7 Bio Rep 3


title: Untreated cell 7 Bio Rep 1


title: Mm_AMB_N303

description: mAMB rep./nucleus #303


title: Untreated cell 6 Bio Rep 3


title: Mm_AMB_N301

description: mAMB rep./nucleus #301


title: Mm_AMB_N300

description: mAMB rep./nucleus #300


title: Mm_AMB_N299

description: mAMB rep./nucleus #299


title: Untreated cell 6 Bio Rep 2


title: Mm_AMB_N304

description: mAMB rep./nucleus #304


title: Untreated cell 6 Bio Rep 1


title: Untreated cell 5 Bio Rep 3


title: Mm_AMB_N296

description: mAMB rep./nucleus #296


title: Mm_AMB_N297

description: mAMB rep./nucleus #297


title: Mm_AMB_N295

description: mAMB rep./nucleus #295


title: Untreated cell 5 Bio Rep 1


title: Untreated cell 4 Bio Rep 3


title: Untreated cell 5 Bio Rep 2


title: Untreated cell 4 Bio Rep 2


title: Untreated cell 4 Bio Rep 1


title: Mm_AMB_N291

description: mAMB rep./nucleus #291


title: Mm_AMB_N294

description: mAMB rep./nucleus #294


title: Mm_AMB_N292

description: mAMB rep./nucleus #292


title: Untreated cell 3 Bio Rep 3


title: Untreated cell 3 Bio Rep 2


title: Mm_AMB_N302

description: mAMB rep./nucleus #302


title: Untreated cell 3 Bio Rep 1


title: Untreated cell 2 Bio Rep 3


title: Mm_AMB_N290

description: mAMB rep./nucleus #290


title: Untreated cell 2 Bio Rep 2


title: Mm_AMB_N289

description: mAMB rep./nucleus #289


title: Mm_AMB_N298

description: mAMB rep./nucleus #298


title: Mm_AMB_N288

description: mAMB rep./nucleus #288


title: Mm_AMB_N286

description: mAMB rep./nucleus #286


title: Mm_AMB_N293

description: mAMB rep./nucleus #293


title: Mm_AMB_N287

description: mAMB rep./nucleus #287


title: SAS, siIGFBP3-72h, 1

city: Bunkyo-ku

first: Atsushi

last: Kaida

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Hisat2 (version 2.0.1) was used to align the data to reference genome.
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: Homo_sapiens_Ensembl_GRCh38.101
Supplementary files format and content: Microsoft Excel file includes FPKM values for each sample

source_name: Tongue

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard DNBSEQ protocol.

value: Tongue

value: SAS

value: Squamous cell carcinoma

tag: genotype

value: IGFBP3 knockdown

value: siRNA, 72 h


title: SAS, siIGFBP3-72h, 2


title: Untreated cell 1 Bio Rep 3


title: Mm_AMB_N284

description: mAMB rep./nucleus #284


title: Untreated cell 1 Bio Rep 1


title: SAS, siCont, 2

value: Control

value: siRNA


title: Mm_AMB_N285

description: mAMB rep./nucleus #285


title: SAS, siCont, 1


title: SAS, siIGFBP3-48h, 2

value: siRNA, 48 h


title: HUDEP2_VHLKO_ATAC_clone2

description: ATAC-seq

data_processing:
Raw reads were trimmed to remove the Tn5 adaptor sequence using skewer (version 0.2.2), then mapped to hg19 using BWA-MEM (version 0.7.16a). Duplicated multi-mapped reads were removed with SAMtools (version 0.17). ATAC-seq peaks were called using MACS2 (version 2.1.1) with the following parameters: macs2 callpeak --nomodel --shift --100 --extsize 200.
Assembly: hg19
Supplementary files format and content: bw

growth_protocol: Erythroid differentiation of CD34+ cells was performed using a three-phase culture protocol. For phase 1 (days 0-7), cells were maintained at a density of 1-4 × 105 /mL in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin-streptomycin, 3 IU/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, 1 IU erythropoietin, 10 ng/mL SCF, and 1 ng/mL interleukin-3 (IL-3). For phase 2 (days 8-12), IL-3 was omitted from the medium. Cells were maintained at a density of 0.2-0.8 × 106/mL. For phase 3 (days 12-18), IL-3 and SCF were omitted, the holo-transferrin concentration was increased to 1 mg/mL, and the cells were maintained at a density of 1-2 × 106/mL. HUDEP-2 cells were maintained in expansion medium consisting of SFEM (Stem Cell Technologies, #09650) supplemented with 50 ng/mL recombinant human stem cell factor (SCF) (R&D systems, #255-SC), 1 μg/mL doxycycline (Sigma-Aldrich, #D9891), 0.4 μg/mL dexamethasone (Sigma-Aldrich #D4902), 3 IU/mL erythropoietin (Epogen, Amgen), and 1% penicillin-streptomycin solution (Gibco, #15140122).

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. For each sample, 5-6 × 104 cells were lysed with buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, then the lysate was washed and incubated with Tagment DNA TDE1 Enzyme (Illumina) for 30 min at 37°C. DNA was purified with a Qiagen MinElute PCR Purification Kit.
Library fragments were amplified using NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541) and custom primers (table S4) with unique dual indexes. PCR amplification cycles were in accordance with the manufacturer’s instructions. PCR products were purified using AMPure XP beads (Beckman Coulter, A63881) at a 1:1 ratio according to the manufacturer’s instructions. Purified PCR products sized from 150 bp to 1 kb were purified from E-Gel EX Agarose Gels, 2% (Thermo Fisher, G401002). Libraries were pooled and sequenced in paired-end mode by using an Illumina HiSeq kit.

tag: cell


title: HUDEP2_VHLKO_ATAC_clone1

description: ATAC-seq


title: Mm_AMB_N282

description: mAMB rep./nucleus #282


title: Untreated cell 2 Bio Rep 1


title: Mm_AMB_N283

description: mAMB rep./nucleus #283


title: Mm_AMB_N281

description: mAMB rep./nucleus #281


title: HUDEP2_WT_ATAC_rep2

description: ATAC-seq


title: HUDEP2_WT_ATAC_rep1

description: ATAC-seq


title: SAS, siIGFBP3-48h, 1


title: Untreated cell 1 Bio Rep 2


title: Mm_AMB_N280

description: mAMB rep./nucleus #280


title: CD34_VHLKO_ATAC_rep2

description: ATAC-seq

value: CD34+ HSPCs


title: Mm_AMB_N279

description: mAMB rep./nucleus #279


title: Mm_AMB_N278

description: mAMB rep./nucleus #278


title: CD34_NT_ATAC_rep1

description: ATAC-seq


title: Lung_Disseminated_Tumor_Cells

city: Lausanne

first: Fabio

last: De Martino

address: EPFL SV ISREC UPBRI Station 19

institute: EPFL

data_processing:
Fastq files were aligned to the human genome (hg38) to produce a count matrix using 10X Cell Ranger (v5.0.1).
The resulting count matrix was then filtered to exclude all cells with UMI count in mitochondrial genes > than 20% of all counts. Following these initial filtering steps, statistical analyses were conducted using the Seurat software v4.0. Default Seurat settings were used to ensure conservative clusters. Differential expression analyses were conducted using the FindMarkers function in Seurat.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrices outputted by 10X Cell Ranger (v5.0.1)

source_name: FACS-sorted MCF7 cells based on RFP expression

growth_protocol: We transcriptionally profiled single MCF7 cells isolated from either primary breast tumor or lung tissues

extract_protocol: 10x Genomics Chromium V3.1 kit. Reads configuration: 28 base-pairs (bp) (10X Index + UMI) and 91 bp (Read 2)

value: Lung

tag: tag

value: RFP


title: Y-TZP_rough_Saos-2_Cells_Exposed_rep1

type: RNA

city: NANCY

first: Laëtitia

last: CHEZEAU

address: Campus Artem, 2 allée André Guinier

department: Institut Jean Lamour

country: France

institute: Université de Lorraine

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4851B SurePrint G3 Human Gene Expression 8*60 K v2 microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were quantile normalized using the software Solo (http://www-microarrays.u-strasbg.fr/Solo/index.html).

source_name: Human epithelial bone cell derived from osteosarcoma, Exposed to Y-TZP rough surface disc

label_protocol: For each of the 8 samples (4 control and 4 exposed cells per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kit (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Plus Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Saos-2 epithelial cell line is derived from bone of an eleven-year old child suffering from osteosarcoma and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in McCoy's (modified) 5A medium (Gibco™, Fisher Scientific) supplemented with 1% penicillin/streptomycin; 0.05% amphotericin B, and 15% fetal calf serum (Sigma-Aldrich ®, Saint Quentin Fallavier, France). Cells were cultured in humid atmosphere (37 °C, 5% CO2).

extract_protocol: Cells were lysed with buffer RLT plus containing β-mercaptoethanol (Qiagen®). Total RNA was extracted and purified using a RNeasy Plus Mini Kit, Qiagen® (cat. No 74136). RNA purity was assessed by spectrophotometry using a BioSpecNano® (Shimadzu). RNA quality and integrity was assessed by microfluidic capillary  electrophoresis using an RNA 6000 Nano Kit and 2100 Bioanalyzer (Agilent). All RNA samples were of high purity and integrity, as demonstrated by A260/A280 ratios above 2, and RNA integrity number above 9.2. Total RNA were stored at −80 °C until further use.

treatment_protocol: 180 000 Saos-2 cells for each experiment (n = 4) were cultured without (control) or with yttria zirconia discs with rough (Ra=1 µm) surface states for 96h, in 12-well plates (Sarstedt® order 83.3921300) at 30 000 cells/ml and 2 ml per well in McCoy’s medium.

tag: tissue source

value: bone

tag: gender

value: female

tag: age

value: 11 years child with osteosarcoma

value: Exposed to Y-TZP rough surface disc


title: Y-TZP_rough_Saos-2_Cells_Exposed_rep4

tag: cell type

value: Human epithelial bone cell derived from osteosarcoma

tag: treatment


title: Saos-2_Cells_Control_rep4

source_name: Human epithelial bone cell derived from osteosarcoma, control

value: control


title: Saos-2_Cells_Control_rep3


title: Y-TZP_rough_Saos-2_Cells_Exposed_rep3


title: Mm_AMB_N277

description: mAMB rep./nucleus #277

tag: strain

tag: tissue

value: brain

value: nucleus ambiguus


title: Mm_AMB_N276

description: mAMB rep./nucleus #276


title: Primary_Breast_ Tumor_Cells

value: Mammary gland


title: Saos-2_Cells_Control_rep2


title: Y-TZP_rough_Saos-2_Cells_Exposed_rep2


title: Saos-2_Cells_Control_rep1


title: Mm_AMB_N273

description: mAMB rep./nucleus #273


title: Mm_AMB_N274

description: mAMB rep./nucleus #274


title: Mm_AMB_N272

description: mAMB rep./nucleus #272


title: CD34_NT_ATAC_rep2

description: ATAC-seq


title: Mm_AMB_N275

description: mAMB rep./nucleus #275


title: VKO_rep1

description: RNA-seq

data_processing: gene expression quantification was performed using Kallisto (v0.43.1).

extract_protocol:
RNA from approximately 0.5 to 1 million cells was extracted using the RNeasy Plus Kit (QIAGEN).
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to enrich for polyA+ RNA and create libraries for HiSeq4000 sequencing (Illumina).

treatment_protocol: CD34+ HSPCs cells eletroporated with NT or VHL sgRNA1 RNP complex.

value: VHL sgRNA1 RNP complex


title: NT_rep1

description: RNA-seq

value: NT sgRNA


title: CD34_VHLKO_ATAC_rep1

description: ATAC-seq


title: Mm_AMB_N269

description: mAMB rep./nucleus #269


title: NT_rep2

description: RNA-seq


title: Mm_AMB_N271

description: mAMB rep./nucleus #271


title: Mm_AMB_N270

description: mAMB rep./nucleus #270


title: Mm_AMB_N268

description: mAMB rep./nucleus #268


title: VKO_rep2

description: RNA-seq


title: Mm_AMB_N266

description: mAMB rep./nucleus #266


title: Mm_AMB_N267

description: mAMB rep./nucleus #267


title: Mm_AMB_N265

description: mAMB rep./nucleus #265


title: Mm_AMB_N264

description: mAMB rep./nucleus #264


title: Mm_AMB_N263

description: mAMB rep./nucleus #263


title: Mm_AMB_N262

description: mAMB rep./nucleus #262


title: HeLa_siBRAF_Mut1

city: Tokyo

first: Yoshiaki

last: Kobayashi

address: 2-11-16 Yayoi, Bunkyo-ku

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy3-labeled RNAs were fragmented using the Gene Expression Hybridization Kit (Agilent Technologies) and hybridized to a SurePrint G3 Human GE Microarray (version 3, 8 × 60 K) (Agilent Technologies) at 65ºC for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing:
Signals were quantified by Feature Extraction version 12.1.1.1 (Agilent Techinologies).
Quality filtering was peformed using the following parameters;
ControlType = 0
gIsPosAndSignif = 1
gIsFeatNonUnifOL = 0
gIsWellAboveBG = 1
gIsSaturated = 0
gIsFeatPopnOL = 0
In addition, normalization of signal intensity was performed using quantile method.

label_protocol: cDNA and Cy3-labeled RNA were synthesized using the Quick Amp Labeling kit for One Color (Agilent Technologies).

growth_protocol: A HeLa cell suspension (1.0 × 10^5 cells/mL) was inoculated into a well of 24-well culture plate 1 day before transfection.

extract_protocol: Total RNA was purified using FastGene RNA Premium Kit (NIPPON Genetics) and the quality of the total RNA was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were transfected three times with 50 nM of each siRNA using Lipofectamine 2000 (Thermo Fisher Scientific). At 24 h after last transfection, cells were harvested from three wells per one sample.

value: HeLa

value: cervical cancer cells

tag: source gender


title: HeLa_siBRAF_WT

description: Gene expression


title: Mm_AMB_N261

description: mAMB rep./nucleus #261


title: PCBP1_3rd

city: Urumqi

first: Aishanjiang

last: Yusufujiang

address: Tianchi road 91

department: Neurology

country: China

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38

organism: Rattus norvegicus

source_name: PCBP1 overexpression in PC12 cell

growth_protocol: The PC12 cells were ground into fine powder before RNA extraction.

extract_protocol:
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted with TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.

tag: transfection

value: PCBP1 overexpression


title: PCBP1_2nd

tag: cell line


title: PCBP1_1st


title: HeLa_siBRAF_Mut1_2'-OMe

description: Gene expression


title: HeLa_siBRAF_WT_2'-OMe

description: Gene expression


title: Ctrl_3rd

source_name: PC12 cell (control plasmid)

value: control plasmid


title: HeLa_siBRAF_Mut2_2'-OMe

description: Gene expression


title: Mm_AMB_N259

description: mAMB rep./nucleus #259


title: Mm_AMB_N260

description: mAMB rep./nucleus #260


title: HeLa_siBRAF_Mut2

description: Gene expression


title: Mm_AMB_N258

description: mAMB rep./nucleus #258


title: HeLa_siBRAF_WT&Mut

description: Gene expression


title: Ctrl_2nd


title: Mm_AMB_N257

description: mAMB rep./nucleus #257


title: Ctrl_1st


title: HeLa_mock_control

description: Gene expression

value: mock


title: Mm_AMB_N256

description: mAMB rep./nucleus #256


title: CR_9_H3K4me1

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads were aligned to the mm10 reference genome using ”bwa aln” (v0.6.2-r126).
Unmapped reads (reads with a MAPQ smaller than 1), reads that mapped outside of chr1-19 and chrX, as well as duplicate reads were removed using samtools (v0.1.18).
Merged BAM files of each group were binarized using the “BinarizeBam” command. Then, the chromatin state model was trained using the “LearnModel” command for 8 outcome states.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file of genomic bins coordinate and their relative associated 'chromatin state' flag, obtained as described in metadata information

source_name: Liver 12m CR rep6

growth_protocol: Inbred C57BL/6 female mice of 3, 6 and 12 months of age were fed with standard diet (SD). The fourth C57BL/6 female group were fed  30% caloric restriction (CR) diet.

extract_protocol:
Chromatin was extracted using a PAT-ChIP protocol
Library were prepared in according to HT-ChIP-Seq Library Preparation protocol

treatment_protocol: Mice were sacrificed by cervical dislocation and livers were washed in phosphate buffer (PBS) and incubated overnight at room temperature (RT) in 4% formalin solution. Formalin-fixed samples were then dehydrated by increasing concentration of ethanol (from 70% to 100%) and subsequently included in paraffin.

value: liver

tag: chip antibody

value: Caloric restriction

value: 12 months

tag: Sex


title: CR_79_H3K4me1

source_name: Liver 12m CR rep8

value: female


title: CR_81_H3K4me1

source_name: Liver 12m CR rep9


title: CR_78_H3K4me1

source_name: Liver 12m CR rep7


title: CR_7_H3K4me1

source_name: Liver 12m CR rep4


title: CR_8_H3K4me1

source_name: Liver 12m CR rep5


title: Juvenile, Thymus, 4

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: Sample name: Juvenile Thymus Technical Replicate 6

data_processing:
The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline (version 3.1.0). The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix.
Genome_build: Zebrafish Ensembl GRCz11 reference
Supplementary_files_format_and_content: h5 count matrices from the NovaSeq platforms

organism: Danio rerio

source_name: sorted live thymus cells

growth_protocol: Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital (ARCH) guidelines.

extract_protocol:
Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted (85 um nozzle) on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50,000 and 100,000 cells were sorted per sample, assessed by Trypan blue staining, and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL.
Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits (10x Genomics, Inc.). A targeted recovery of 6,000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide (Rev D). The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core (https://bauercore.fas.harvard.edu/) on an Illumina NovaSeq 6000 using an SP flow cell (Read 1: 28 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 91 cycles).
scRNA-Seq

value: sorted live thymus cells

tag: developmental stage

value: Juvenile

value: 4 weeks post-fertilization

tag: cardiac bleed

value: no

tag: dissection buffer

value: 0.5% BSA in HBSS, no Ca2+ or Mg2+

tag: dissection temperature

value: room temperature


title: CR_6_H3K4me1

source_name: Liver 12m CR rep3


title: Mm_AMB_N255

description: mAMB rep./nucleus #255

value: brain

tag: brain region

value: nucleus ambiguus


title: Mm_AMB_N254

description: mAMB rep./nucleus #254


title: Mm_AMB_N253

description: mAMB rep./nucleus #253


title: CR_5_H3K4me1

source_name: Liver 12m CR rep2


title: SD_76_H3K4me1

source_name: Liver 12m SD rep6

value: Standard diet


title: SD_74_H3K4me1

source_name: Liver 12m SD rep5


title: Juvenile, Thymus, 2

description: Sample name: Juvenile Thymus Technical Replicate 3


title: CR_4_H3K4me1

source_name: Liver 12m CR rep1


title: SD_73_H3K4me1

source_name: Liver 12m SD rep4


title: Adult, Thymus, 2

description: Sample name: Adult Thymus Lck 2

value: Adult

value: 3 months post-fertilization

value: yes


title: Mm_AMB_N252

description: mAMB rep./nucleus #252

source_name: single neuron nucleus


title: Juvenile, Thymus, 1

description: Sample name: Juvenile Thymus Technical Replicate 1


title: SD_72_H3K4me1

source_name: Liver 12m SD rep3


title: SD_71_H3K4me1

source_name: Liver 12m SD rep2


title: SD_21_H3K4me1

source_name: Liver 12m SD rep1


title: Mm_AMB_N251

description: mAMB rep./nucleus #251


title: Adult, Thymus, 1

description: Sample name: Adult Thymus Lck 1


title: Mm_AMB_N250

description: mAMB rep./nucleus #250


title: SD_698_H3K4me1

source_name: Liver 6m SD rep5

value: 6 months


title: KM, Myeloid, 5

description: Sample name: Myeloid 27

source_name: sorted kidney marrow granulocytes

value: sorted kidney marrow granulocytes

value: GESTALT

value: 4.5 months post-fertilization

value: 0.5% BSA in DPBS, no Ca2+ or Mg2+

value: on ice


title: SD_139_H3K4me1

source_name: Liver 6m SD rep3

value: liver

value: female


title: SD_132_H3K4me1

source_name: Liver 6m SD rep2


title: SD_146_H3K4me1

source_name: Liver 6m SD rep4


title: SD_677_H3K4me1

source_name: Liver 3m SD rep7

value: 3 months


title: SD_684_H3K4me1

source_name: Liver 3m SD rep8


title: Mm_AMB_N248

description: mAMB rep./nucleus #248


title: SD_125_H3K4me1

source_name: Liver 6m SD rep1


title: Mm_AMB_N249

description: mAMB rep./nucleus #249


title: SD_655_H3K4me1

source_name: Liver 3m SD rep4


title: SD_648_H3K4me1

source_name: Liver 3m SD rep3


title: SD_662_H3K4me1

source_name: Liver 3m SD rep5


title: KM, Lym, Prog, 4

description: Sample name: Lymphoid 49

source_name: sorted kidney marrow lymphoid and progenitor cells

value: 4 months post-fertilization


title: SD_634_H3K4me1

source_name: Liver 3m SD rep1


title: KM, Lym, Prog, 5

description: Sample name: Lymphoid 27

value: sorted kidney marrow lymphoid and progenitor cells


title: KM, Myeloid, 3

description: Sample name: Myeloid 44


title: Mm_AMB_N243

description: mAMB rep./nucleus #243

source_name: single neuron nucleus

value: brain


title: Mm_AMB_N244

description: mAMB rep./nucleus #244

value: nucleus ambiguus


title: KM, Myeloid, 4

description: Sample name: Myeloid 49


title: CR_9_H3K27ac

source_name: Liver 12m CR rep6

value: Caloric restriction

value: 12 months


title: Mm_AMB_N245

description: mAMB rep./nucleus #245


title: Mm_AMB_N242

description: mAMB rep./nucleus #242


title: Juvenile, Thymus, 3

description: Sample name: Juvenile Thymus Technical Replicate 5

source_name: sorted live thymus cells

value: sorted live thymus cells

value: Juvenile

value: 4 weeks post-fertilization

value: no

value: 0.5% BSA in HBSS, no Ca2+ or Mg2+

value: room temperature


title: Mm_AMB_N247

description: mAMB rep./nucleus #247


title: SD_641_H3K4me1

source_name: Liver 3m SD rep2

value: Standard diet


title: Mm_AMB_N246

description: mAMB rep./nucleus #246


title: KM, Lym, Prog, 2

description: Sample name: Lymphoid 24

value: GESTALT

value: Adult

value: yes

value: 0.5% BSA in DPBS, no Ca2+ or Mg2+

value: on ice


title: KM, Lym, Prog, 3

description: Sample name: Lymphoid 44

value: sorted kidney marrow lymphoid and progenitor cells

value: 4 months post-fertilization


title: Mm_AMB_N241

description: mAMB rep./nucleus #241

value: brain

value: nucleus ambiguus


title: SD_670_H3K4me1

source_name: Liver 3m SD rep6

value: liver

value: 3 months

value: female


title: CR_78_H3K27ac

source_name: Liver 12m CR rep7

value: Caloric restriction

value: 12 months


title: Adult, Thymus, 4

description: Sample name: Thymus 24

value: sorted live thymus cells

value: 0.5% BSA in HBSS, no Ca2+ or Mg2+


title: CR_7_H3K27ac

source_name: Liver 12m CR rep4


title: KM, Myeloid, 2

description: Sample name: Myeloid 24

source_name: sorted kidney marrow granulocytes

value: sorted kidney marrow granulocytes


title: SD_76_H3K27ac

source_name: Liver 12m SD rep7

value: Standard diet


title: CR_4_H3K27ac

source_name: Liver 12m CR rep1


title: CR_8_H3K27ac

source_name: Liver 12m CR rep5


title: CR_6_H3K27ac

source_name: Liver 12m CR rep3


title: Mm_AMB_N240

description: mAMB rep./nucleus #240


title: KM, Lym, Prog, 1

description: Sample name: Lymphoid 22

value: GESTALT

value: Adult


title: Mm_AMB_N238

description: mAMB rep./nucleus #238


title: SD_72_H3K27Ac

source_name: Liver 12m SD rep4


title: CR_5_H3K27ac

source_name: Liver 12m CR rep2


title: SD_71_H3K27ac

source_name: Liver 12m SD rep3


title: SD_74_H3K27ac

source_name: Liver 12m SD rep5


title: Mm_AMB_N239

description: mAMB rep./nucleus #239


title: SD_75_H3K27ac

source_name: Liver 12m SD rep6


title: MΦ Dusp6 KO_3

city: Beijing

first: Chenyang

last: Zhang

address: 5 Yiheyuan Road

institute: College of Future Technology, Peking University

data_processing:
RNA libraries were sequenced by Illumina NovaSeq 6000.
Raw reads were trimmed with Trim Galore! and then aligned to rat reference genome (rnor6) by HISAT2.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: Counts_Matrix.csv: Comma-separated text file includes raw counts.

source_name: Macrophage

extract_protocol:
Single-cell suspensions of infarcted cardiac tissues were obtained by digestion with Liberase DL (Roche, 5401160001). Macrophages were stained with fluorescence-labeled antibodies against cell surface markers: anti-rat CD45 (OX-1)-PE-Cy7 (BD Biosciences, 561588) and anti-rat macrophage (HIS36)-PE (eBioscience, 12-0660-82) and selected by flow cytometry (MoFlo XDP). Selected macrophages were harvested directly into Trizol reagent. Total amounts and integrity of RNA samples were assessed using RNA Nano 6000 Assay Kit of Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared using KAPA RNA HyperPrep Kit (8098140702, Roche).

value: Sprague Dawley

tag: genotype

value: cardiac infiltrated macrophages

value: myocardial infarction for 72h


title: MΦ Dusp6 KO_2


title: CR_81_H3K27ac

source_name: Liver 12m CR rep9


title: Mm_AMB_N237

description: mAMB rep./nucleus #237

source_name: single neuron nucleus


title: SD_153_H3K27ac

source_name: Liver 6m SD rep5

value: 6 months


title: SD_21_H3K27ac

source_name: Liver 12m SD rep1


title: Mm_AMB_N236

description: mAMB rep./nucleus #236

value: brain


title: SD_698_H3K27ac

source_name: Liver 6m SD rep6


title: MΦ Dusp6 KO_1


title: SD_22_H3K27ac

source_name: Liver 12m SD rep2


title: SD_139_H3K27ac

source_name: Liver 6m SD rep3


title: Mm_AMB_N235

description: mAMB rep./nucleus #235

value: nucleus ambiguus


title: SD_146_H3K27ac

source_name: Liver 6m SD rep4

value: liver


title: Adult, Thymus, 3

description: Sample name: Thymus 22

source_name: sorted live thymus cells

value: 4 months post-fertilization

value: yes

value: room temperature


title: SD_132_H3K27ac

source_name: Liver 6m SD rep2

value: female


title: MΦ WT_3

value: WT


title: KM, Myeloid, 1

description: Sample name: Myeloid 22

source_name: sorted kidney marrow granulocytes

value: 0.5% BSA in DPBS, no Ca2+ or Mg2+

value: on ice


title: MΦ WT_1


title: Mm_AMB_N232

description: mAMB rep./nucleus #232


title: SD_125_H3K27ac

source_name: Liver 6m SD rep1

value: Standard diet


title: SD_670_H3K27ac

source_name: Liver 3m SD rep6

value: 3 months


title: MΦ WT_2


title: SD_684_H3K27ac

source_name: Liver 3m SD rep8


title: Mm_AMB_N233

description: mAMB rep./nucleus #233


title: SD_662_H3K27ac

source_name: Liver 3m SD rep5


title: CR_79_H3K27ac

source_name: Liver 12m CR rep8

value: Caloric restriction

value: 12 months


title: SD_648_H3K27ac

source_name: Liver 3m SD rep3


title: SD_677_H3K27ac

source_name: Liver 3m SD rep7


title: Mm_AMB_N231

description: mAMB rep./nucleus #231

source_name: single neuron nucleus


title: SD_655_H3K27ac

source_name: Liver 3m SD rep4


title: SD_641_H3K27ac

source_name: Liver 3m SD rep2


title: SD_634_H3K27ac

source_name: Liver 3m SD rep1


title: CR_79_H3K27me3

source_name: Liver 12m CR rep6


title: CR_78_H3K27me3

source_name: Liver 12m CR rep5


title: Mm_AMB_N228

description: mAMB rep./nucleus #228


title: Mm_AMB_N234

description: mAMB rep./nucleus #234


title: CR_9_H3K27me3

source_name: Liver 12m CR rep4


title: CR_8_H3K27me3

source_name: Liver 12m CR rep3


title: Mm_AMB_N227

description: mAMB rep./nucleus #227


title: lymphatic endothelial cells, medium without MCF-7 cells

city: Schlieren

first: Giovanna

last: Azzarito

address: Wagistrasse 14

department: Reproductive endocrinology

institute: University Hospital Zurich

description:
LEC_CTR_1
LEC_CTR_2
LEC_CTR_3
gene expression data from endothelial cells co-cultured with pericytes and treated with vehicle (DMSO)

hyb_protocol: 15 ug of cRNA were subjected to 2nd-cylce ss-cDNA synthesis. 5.5 ug of the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin. Hybridization to Clariom S Assay, human (Applied Biosystems, 902927) is performed for 16 hr at 45°C with rotation at 60 rpm in the GeneChip Hybridization Oven 645 (00-0331, 110/220V). GeneChips were washed and stained in the CheneChip Fluidics Station 450 (00-079).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G System (00-0213).

data_processing: The data were analyzed with GeneChip Command Console Software (GCC) v5.0. The obtained CEL files were up-loaded to the Transcriptome Analysis Console (TAC, applied biosystems) and analysis was performed by the software (Limma-based, eBayes).

label: biotin

source_name: human lymphatic endothelial cell line, in medium without MCF-7, control

label_protocol: Biotinylation was prepared according to the protocol (GeneChipTM WT PLUS Reagent Kit) from 5.5 ug total RNA.

growth_protocol: HUVECs were cultured in Collagen coated flasks under standard tissue culture conditions (37 °C, 5 % CO2) in complete growing media: EBM-2 (Endothelial Basal Medium-2) supplemented with Glutamax (1x), antibiotic-antimycotic (AA: 100 μg/ml streptomycin, 100 μg/ml penicillin and 0.025 μg/ml amphotericin B), LSGS (2% v/v FCS, 1 µg/ml hydrocortisone, 10 ng/ml human Epidermal Growth Factor, 3ng/ml human basic Fibroblast Growth Factor, 10 µg/ml heparin) and 10% FCS (Fetal Calf Serum).  LECs were propagated in EGM™-2MV BulletKit™ Growth Medium containing EBM-2 (Endothelial Basal Medium-2) supplemented with human Epidermal Growth Factor (hEGF), Vascular Endothelial Growth Factor (VEGF), R3-Insulin-like Growth Factor-1 (R3-IGF-1), Ascorbic Acid, Hydrocortisone, human Fibroblast Growth Factor-Beta (hFGF-β), Fetal Bovine Serum (FBS) and Gentamicin/Amphotericin-B (GA).  MCF-7 cells (epithelial cancer cells) were cultured in DMEM/F12 medium supplemented with Glutamax (1x), antibiotic-antimycotic (AA 100 μg/ml streptomycin, 100 μg/ml penicillin and 0.025 μg/ml amphotericin B) and FBS (10%).

extract_protocol: Total RNA was extracted by using the Quick-RNA MiniPrep Kit (ZymoResearch) according to the manufacture’s protocol. RNA integrity was checked by determinig the ratio of absorbance at 260 nm and 280 nm / 230 nm respectively. The samples were frozen at -80 °C and shipped to the Gene expression Affymetrix facility in dry ice.

treatment_protocol: Endothelial cells are plated in 35mm tissue cultures dishes (HUVECs in collagen-coated) and after allowing them to adhere, the cells were starved for 7h (steroid-free medium). Starving media was replaced with CM supplemented with 0.4% FCS. After 20h of CM treatment, cells were lysed using RNA Lysis buffer. CM was formed by MCF-7 cells: normal growth medium was replaced with treatment medium with and without E2 (2.5% steroid-free medium). After 24h the treatment medium was replaced with serum free medium for 48h.The supernatant containing all factors secreted by the cells, was harvested from the cultures, centrifuged and filtered through 0.2 µm syringe filters. As control was used serum free medium not added to cells but treated in the same condition.

value: human lymphatic endothelial cells

tag: origin

value: Dermal Microvascular_Pooled

tag: transfection with mir193a

value: no

tag: treatment with cm

tag: treatment with cm-mirna193

tag: treatment medium

value: vehicle (DMSO)

tag: growth protocol

value: 2D (cellular monolayer)

tag: culture protocol


title: lymphatic endothelial cells, CM by MCF-7 cells

description:
LEC_CM_1
LEC_CM_2
LEC_CM_3
gene expression data from endothelial cells co-cultured with pericytes and treated with estradiol (E2)

source_name: human lymphatic endothelial cell line, in medium collected from MCF-7 CTR

tag: cell type

value: estradiol (E2)


title: CR_4_H3K27me3

source_name: Liver 12m CR rep1

tag: strain

tag: tissue

value: liver

tag: treatment

tag: age


title: CR_6_H3K27me3

source_name: Liver 12m CR rep2

tag: chip antibody

tag: Sex


title: vascular endothelial cells, CM by MCF-7 cells

description:
HUVEC_CM_1
HUVEC_CM_2
HUVEC_CM_3
gene expression data from endothelial cells cultured alone and treated with estradiol (E2)

source_name: human vascular endothelial cell line, in medium collected from MCF-7 CTR

value: human vascular endothelial cells

value: Umbilical Vein

value: yes


title: Mm_AMB_N226

description: mAMB rep./nucleus #226

value: brain

value: nucleus ambiguus


title: SD_75_H3K27me3

source_name: Liver 12m SD rep7

value: female


title: SD_76_H3K27me3

source_name: Liver 12m SD rep8

value: Standard diet


title: Mm_AMB_N230

description: mAMB rep./nucleus #230


title: SD_74_H3K27me3

source_name: Liver 12m SD rep6


title: Mm_AMB_N229

description: mAMB rep./nucleus #229


title: Mm_AMB_N224

description: mAMB rep./nucleus #224


title: Mm_AMB_N225

description: mAMB rep./nucleus #225


title: SD_71_H3K27me3

source_name: Liver 12m SD rep3


title: SD_73_H3K27me3

source_name: Liver 12m SD rep5


title: SD_22_H3K27me3

source_name: Liver 12m SD rep2


title: K562, LRF_overexpression, hemin/EPO, 3h

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

data_processing:
Basecalling, de-multiplexing and filtering of low quality reads was performed within the Torrent Suite 5.12.3
Reads were trimmed with trimmomatic (Version 0.38) with the following parameters SLIDINGWINDOW:30:15 MINLEN:25
ChIP-seq datasets were mapped to hg38 using Bowtie2 with the --very-sensitive-local preset
BigWig files were created using the deeptools bamCoverage function with the following parameters: --outFileFormat 'bigwig'  --binSize 1  --normalizeUsing RPKM. The initial alignments, that include redundant alignments were used to generate the bigWig files, to account for the high degree of sequence duplication within the HBB locus that can mask LRF/ZBTB7A occupancy.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells from studied experimental conditions were cross-linked with 1% formaldehyde. After quencing and cell lysis, chromatin was sonicated with a LABSONIC M sonicator (Sartorius) to generate 150-300bp DNA fragments.
Library preparation from ChIP-isolated DNA was performed using the Ion Xpress™ Plus Fragment Kit and the Ion Xpress™ Barcode Adapters 1-16 Kit (both from ThermoFischer). The protocol for 200bp read-length libraries and for 50-100ng input DNA was employed with some modifications. Due to the small amount of input DNA (10ng) and to avoid adapter concatamerization 1μl of P1 adapter and IonXpress™ Barcodes was used instead of 2μl. Adapter ligation and dual bead size selection for 200bp read length fragments was performed using AMPure XP beads. The size selected libraries were then amplified for 16 cycles.

tag: cell line

value: erythroleukemia

value: Anti-ZBTB7A (Abcam, #ab70208)

value: LRF overexpression, hemin/EPO, 3h


title: Mm_AMB_N223

description: mAMB rep./nucleus #223

source_name: single neuron nucleus

tag: brain region


title: SD_21_H3K27me3

source_name: Liver 12m SD rep1

value: 12 months


title: SD_72_H3K27me3

source_name: Liver 12m SD rep4


title: Mm_AMB_N222

description: mAMB rep./nucleus #222


title: SD_153_H3K27me3

source_name: Liver 6m SD rep5

value: 6 months


title: K562, untransfected, hemin/EPO, 3h

value: hemin/EPO, 3h


title: vascular endothelial cells, CM by MCF-7 pre-transfected with mimic CTR

description:
HUVEC_CM mimic CTR_1
HUVEC_CM mimic CTR_2
HUVEC_CM mimic CTR_3
gene expression data from endothelial cells cultured alone and treated with estradiol (E2)

source_name: human vascular endothelial cell line, in medium collected from MCF-7 pre-transfected with mimic CTR

value: no


title: SD_698_H3K27me3

source_name: Liver 6m SD rep6


title: SD_146_H3K27me3

source_name: Liver 6m SD rep4


title: Mm_AMB_N220

description: mAMB rep./nucleus #220


title: vascular endothelial cells, medium without MCF-7 cells

description:
HUVEC_CTR_1
HUVEC_CTR_2
HUVEC_CTR_3
gene expression data from endothelial cells cultured alone and treated with vehicle (DMSO)

source_name: human vascular endothelial cell line, in medium without MCF-7, control

value: vehicle (DMSO)

value: 2D (cellular monolayer)


title: K562, untransfected

value: no treatment


title: lymphatic endothelial cells+MCF-7epithelial cells, miRNA193a

description:
LEC+MCF-7_miR193a_1
LEC+MCF-7_miR193a_2
LEC+MCF-7_miR193a_3
gene expression data from endothelial cells co-cultured with pericytes and treated with vehicle (DMSO)

source_name: human lymphatic endothelial cell line+ MCF-7 epithelial cells, miRNA193a

value: human lymphatic endothelial cells

value: Dermal Microvascular_Pooled+epithelial cancer cell

value: 3D (spheroids)


title: SD_132_H3K27me3

source_name: Liver 6m SD rep2

value: liver


title: K562, negative_control

value: rabbit IgGs (Sigma, #I5006)


title: vascular endothelial cells, CM by MCF-7 pre-transfected with miRNA193a

description:
HUVEC_CM miR193a_1
HUVEC_CM miR193a_2
HUVEC_CM miR193a_3
gene expression data from endothelial cells cultured alone and treated with vehicle (DMSO)

source_name: human vascular endothelial cell line, in medium collected from MCF-7 pre-transfected with miR193a

value: human vascular endothelial cells

value: Umbilical Vein

value: yes


title: SD_684_H3K27me3

source_name: Liver 3m SD rep7

value: Standard diet

value: 3 months

value: female


title: SD_139_H3K27me3

source_name: Liver 6m SD rep3

value: 6 months


title: SD_662_H3K27me3

source_name: Liver 3m SD rep4


title: SD_677_H3K27me3

source_name: Liver 3m SD rep6


title: K562, LRF_overexpression

value: erythroleukemia

value: Anti-ZBTB7A (Abcam, #ab70208)

value: LRF overexpression


title: Mm_AMB_N217

description: mAMB rep./nucleus #217

value: brain

value: nucleus ambiguus


title: SD_655_H3K27me3

source_name: Liver 3m SD rep3


title: Mm_AMB_N216

description: mAMB rep./nucleus #216


title: SD_634_H3K27me3

source_name: Liver 3m SD rep1


title: SD_648_H3K27me3

source_name: Liver 3m SD rep2


title: Mm_AMB_N221

description: mAMB rep./nucleus #221

source_name: single neuron nucleus


title: CR_78_H3K4me3

source_name: Liver 12m CR rep4

value: Caloric restriction

value: 12 months


title: CR_79_H3K4me3

source_name: Liver 12m CR rep5


title: SD_125_H3K27me3

source_name: Liver 6m SD rep1


title: CR_9_H3K4me3

source_name: Liver 12m CR rep3


title: Mm_AMB_N214

description: mAMB rep./nucleus #214


title: CR_6_H3K4me3

source_name: Liver 12m CR rep1


title: CR_8_H3K4me3

source_name: Liver 12m CR rep2


title: Mm_AMB_N215

description: mAMB rep./nucleus #215


title: Mm_AMB_N218

description: mAMB rep./nucleus #218


title: SD_76_H3K4me3

source_name: Liver 12m SD rep8


title: Mm_AMB_N219

description: mAMB rep./nucleus #219


title: Mm_AMB_N213

description: mAMB rep./nucleus #213


title: Mm_AMB_N212

description: mAMB rep./nucleus #212


title: SD_73_H3K4me3

source_name: Liver 12m SD rep5


title: SD_74_H3K4me3

source_name: Liver 12m SD rep6


title: SD_71_H3K4me3

source_name: Liver 12m SD rep3


title: SD_72_H3K4me3

source_name: Liver 12m SD rep4


title: SD_22_H3K4me3

source_name: Liver 12m SD rep2


title: lymphatic endothelial cells+MCF-7 epithelial cells, mimic CTR

description:
LEC+MCF-7_mimic CTR_1
LEC+MCF-7_mimic CTR_2
LEC+MCF-7_mimic CTR_3
gene expression data from endothelial cells co-cultured with pericytes and treated with estradiol (E2)

source_name: human lymphatic endothelial cell line+ MCF-7 epithelial cells, mimic CTR

value: human lymphatic endothelial cells

value: Dermal Microvascular_Pooled+epithelial cancer cell

value: no

value: estradiol (E2)

value: 3D (spheroids)


title: SD_75_H3K4me3

source_name: Liver 12m SD rep7

value: liver


title: SD_670_H3K27me3

source_name: Liver 3m SD rep5

value: Standard diet


title: Mm_AMB_N210

description: mAMB rep./nucleus #210


title: Mm_AMB_N211

description: mAMB rep./nucleus #211


title: SD_153_H3K4me3

source_name: Liver 6m SD rep3


title: SD_21_H3K4me3

source_name: Liver 12m SD rep1


title: SD_132_H3K4me3


title: SD_146_H3K4me3

source_name: Liver 6m SD rep2


title: SD_684_H3K4me3

source_name: Liver 3m SD rep7

value: 3 months


title: Mm_AMB_N207

description: mAMB rep./nucleus #207

source_name: single neuron nucleus


title: SD_655_H3K4me3

source_name: Liver 3m SD rep3

value: female


title: Mm_AMB_N206

description: mAMB rep./nucleus #206


title: SD_670_H3K4me3


title: SD_641_H3K4me3

source_name: Liver 3m SD rep2


title: SD_662_H3K4me3

source_name: Liver 3m SD rep4


title: Mm_AMB_N205

description: mAMB rep./nucleus #205


title: Mm_AMB_N204

description: mAMB rep./nucleus #204


title: SD_634_H3K4me3

source_name: Liver 3m SD rep1


title: Mm_AMB_N203

description: mAMB rep./nucleus #203


title: Viewpoint C3, replicate 2

first: Anaïs

last: LE NABEC

address: Station 19

data_processing:
library strategy: 4C-seq
base-calling, alignment, filtering, peak-calling, ouput files are generated with pipe4C pipeline
Assembly: hg19
Supplementary files format and content: rds and wig.gz files

source_name: SAEC

growth_protocol: Airway epithelial cell medium (PromoCell).Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1,5% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested with DpnII, then with NlaIII
200 ng of 4C libraries was used fo inverse PCR with primers and Illumina adapters (P5 and P7) for different viewpoints, with Expand™ Long Template PCR System (Roche) (as described in Krijger et al, 2020). The second inverse PCR were realized with 8-nt index sequence. Inverse PCR for each step were purified by using Nucleomag PCR beads, with a ratio 1.  Sequencing were realized on MiniSeq of Illumina, as single-end reads with 75-bp read length and generated FastQ files.

value: SAEC

value: small airway epithelial cells


title: Viewpoint C3, replicate 1


title: Mm_AMB_N209

description: mAMB rep./nucleus #209


title: Mm_AMB_N202

description: mAMB rep./nucleus #202


title: Viewpoint PGJB2, replicate 1


title: Viewpoint C3, replicate 3