title: U937-PR9 Zinc Cut&Run RARA antibody replicate 2

data_processing:
Library strategy: Cut&Run
Reads were trimmed of adapters and low-quality reads using Trimmomatic (Bolger et al., 2014) and aligned to the hg19 genome using Bowtie2. PCR duplicates were removed using Samtools and blacklisted reads were removed.
Peaks were called using the SEACR peak calling algorithm. Paired control experiments were used as background and the ‘norm union’ settings were used as thresholding.
Genome_build: hg19
Supplementary_files_format_and_content: Final_Cut&Run_Annotated_PR.csv contains the final 15,412 consensus PML-RARA binding site peaks called using SEACR across both PML-RARA antibody experiments

extract_protocol:
After 5 hours of incubation, Induced and non-induced U937-PR9 cells were washed in fresh RPMI / (10% FBS) medium. Cells were then treated with a hypertonic solution and mild detergent (IGEPAL) followed by clarification through a sucrose gradient to isolate nuclei.
Cut&Run was then performed on isolated nuclei as described (Skene and Henikoff, 2017). In brief, nuclei were resuspended in Cut&Run wash buffer and incubated with 4ug antibody for 12 hours at 4oC. Nuclei were then washed in Cut&Run wash buffer and incubated with PA-MNase for 2 hours at 4oC. Nuclei were washed again in Cut&Run wash buffer, then incubated with CaCl2 for 20 minutes at 0oC to activate the PA-MNase. Stop buffer containing 20mM EDTA was added to cells to stop the CaCl2 induced PA-MNase activity. Nuclei were then incubated at 37 °C with RNase, allowing PA-MNase cut DNA fragments to diffuse into the supernatant. DNA was precipitated using phenol: chloroform/ethanol
Libraries were then prepared using the NEBNext DNA Library prep master mix set and multiplex oligos for Illumina (New England Biolabs). Library quality was assessed using Tapestation E220 high sensitivity (Agilent), and qPCR quantitation was performed using NEB library quant kit. Libraries were sequenced using an Illumina HiSeq 2500 instrument for single-end sequencing.

tag: chip antibody

value: anti-RARA


title: U937-PR9 Zinc Cut&Run RARA antibody replicate 1

status: Public on Dec 14 2022

type: SRA

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: U937-PR9 cells were cultured in RPMI 1640 (Thermo Fisher, A10491), supplemented with 10% fetal bovine serum (Thermo Fisher, 10082147) and incubated at 37°C, 5% CO2.

treatment_protocol: For the zinc induction of U937-PR9 cells, ZnSO4 (Sigma, Z0251) was dissolved in sterile water as a stock solution at 100 mM. ZnSO4 was added directly to the culture medium at a final concentration of 100 μM and incubated at 37°C for 5 hours, as described previously (Martens et al., 2010). For the non-induced U937-PR9 cells, sterile water was added instead of ZnSO4 and incubated under the same conditions.

tag: cell type

value: myeloid cell line

tag: cell line

tag: treatment


title: HeLa cells with SRRM3 transgene, not dox induced

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: polyA-selected RNA

library_source: transcriptomic

data_processing:
Raw reads were mapped with vast-tools align v2.5.1.
Assembly: hg38 (GRCh38), mm10 (GRCm38), rn6 (Rnor_6.0)
Supplementary files format and content: *.cRPKM.txt: Files with raw read counts and cRPKMs for each human, mouse or rat gene in Ensembl.

molecule: total RNA

source_name: HeLa cells

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Illumina strand-specific
Strand-specific polyA-selected

value: HeLa

tag: transgene

value: SRRM3 transgene, not dox induced


title: nonu-1RNASeqRep2

city: Santa Cruz

first: Joshua

last: Arribere

state: CA

address: 1156 High St

department: Department of Molecular, Cell, and Developmental Biology

country: USA

institute: University of California at Santa Cruz

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); nonu-1(srf3015) C. elegans

data_processing:
Reads were mapped to a custom C. elegans genome including annotated splice junctions using STAR v2.5.4b allowing for zero mismatches
All downstream analyses were restricted to uniquely mapping reads
Assembly: Ensembl, WBCel235
Supplementary files format and content: processed jam file containing uniquely-mapping reads with additional information pertaining to gene assignment

organism: Caenorhabditis elegans

growth_protocol: Animals were synchronized by hypochlorite treatment, propagated on NGM plates with OP50 at 16C, and harvested at the L4/young adult stage. Animals were washed off with N50, passed through a 5% sucrose cushion in N50 to remove E. coli, and snap frozen in liquid nitrogen.

extract_protocol:
Animals were lysed by grinding in a mortar and pestle cooled in liquid nitrogen in the presence of frozen PLB (20mM Tris pH8.0, 140mM KCl, 1.5mM MgCl2, 1% Triton). RNA was extracted by trizol.
RNA extracted, rRNA depleted by C. elegans-specific hybridization oligos, libraries  prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina sequencing

tag: strain

tag: genotype

tag: developmental stage

value: young adult

tag: Sex

value: hermaphrodite

tag: tissue

value: whole body

tag: growth conditions

value: NGM + OP50


title: APL patient 1 RNA-seq

data_processing:
Reads were trimmed of adapters and low-quality reads using Trimmomatic (Bolger et al., 2014) and aligned to the hg19 genome using STAR 2 pass aligner
Gene counts were generated using Feature Counts from the Rsubread R package (Liao 2019 NAR) and normalized using the voom normalization approach for differential analysis
Differential analysis comparing uninduced and induced U937-PR9 cells was performed using limma
Genome_build: hg19
Supplementary_files_format_and_content: Log2_Counts_Per_Million_All_RNA-seq.csv: contains the noralised log2 counts per million reads for each dataset, data is normalised by library size
Supplementary_files_format_and_content: Control_vs_Induced_RNA-seq_Limma_DEG.txt contains the 2,314 differentially expressed genes after PML-RARA induction in the U937-PR9 cells

molecule: polyA RNA

source_name: PBMC

extract_protocol:
RNA was extracted from U937-PR9 cells using Trizol reagent (Life Technologies).
Libraries were prepared using the Illumina SureSelect Strand-Specific RNA Library Prep kit following the manufacturer’s instructions
sequenced using an Illumina HiSeq 2500 instrument for paired-end sequencing.

value: Blast cells


title: Week4 Tumor CD103+CD69+ replicate 2

city: Melbourne

first: Franco

last: Caramia

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Adaptor trimming was performed and reads were aligned to the mm10 reference genome using HISAT2.
Aligned reads were quantified using HTSeq
Counts were normalized using RUVIII in R
Assembly: mm10
Supplementary files format and content: comma-delimited text files include normalized counts values for each Sample

organism: Mus musculus

source_name: BREAST, Week4 Tumor CD103+CD69+

extract_protocol:
FACS purified CD8+ T cell subsets were processed for RNA using the RNeasy mini kit (Qiagen) as per the manufacturer's instructions. RNA TapeStation (Agilent, USA) analysis was performed as per the manufacturer's instructions to assess the quantity and quality of RNA material isolated from TNBC tumors
10ng total RNA was used for library preparation according to manufacturer’s instructions (QuantSeq 3' mRNA-Seq FWD, Lexogen)

value: tumor infiltrating T cells

tag: time

value: mammary tumor

tag: facs purified cd8+ t cell subset


title: SPECTRUM-OV-009_S1_CD45N_LEFT_OVARY

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

description:
matrix.h5
GEO_cells.tsv

data_processing:
Mapping and QC with cellranger 3.1.0
Cell type assignment with cellassign 0.99.2
Batch correction with harmony 0.1
Clustering with Seurat v3
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.h5:raw UMI count matrix with cell_ids in columns and genes in rows
Supplementary_files_format_and_content: GEO_cells.tsv:annotation table with cell_ids in rows and meta data in columns

source_name: Adnexa

growth_protocol: Primary samples.

extract_protocol:
Dissociation: Tumor tissue was immediately processed for tissue dissociation. Fresh tissue was cut into 1 mm pieces and dissociated at 37°C using the Human Tumor Dissociation Kit (Miltenyi Biotec) on a gentleMACS Octo Dissociator. After dissociation, single cell suspensions were filtered and washed with ACK (Ammonium-Chloride-Potassium) Lysing Buffer. Cells were stained with Trypan Blue and cell counts and viability were assessed using the Countess II Automated Cell Counter (ThermoFisher) (for detailed protocol see 40). Sorting: Freshly dissociated cells were stained with a mixture of GhostRed780 live/dead marker (TonBo Biosciences) and Human TruStain FcX™ Fc Receptor Blocking Solution (BioLegend). The stained samples were then incubated and stained with Alexa Fluor® 700 anti-human CD45 Antibody (BioLegend). Post staining, they were washed and resuspended in RPMI + 2% FCS and submitted for cell sorting. The cells were sorted into CD45 positive and negative fractions by fluorescence assisted cell sorting (FACS) on a BD FACSAria™ III flow cytometer (BD Biosciences). Positive and negative controls were prepared and used to set up compensations on the flow cytometer. Cells were sorted into tubes containing RPMI + 2% FCS for sequencing.
Flow sorted tumor cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip B (10x Genomics PN 2000060). GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,400-5,000 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics PN 1000075) according to the manufacturer’s protocol. cDNA amplification included 12 cycles and 0.4-419ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR.

tag: sort


title: Week2 Tumor CD103-CD69+ replicate 2

source_name: BREAST, Week2 Tumor CD103-CD69+


title: Week4 Tumor CD103+CD69+ replicate 3


title: SPECTRUM-OV-009_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: U937-PR9 Zinc Cut&Run PML-RARA antibody replicate 2

value: anti-PML-RARA


title: Week2 Tumor CD103+CD69+ replicate 2

source_name: BREAST, Week2 Tumor CD103+CD69+


title: Week1 Tumor CD103-CD69+ replicate 2

source_name: BREAST, Week1 Tumor CD103-CD69+


title: znf-598RNASeqRep2

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); znf-598(srf2119) C. elegans


title: hbs-1RNASeqRep2

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); hbs-1(srf0730) C. elegans


title: wildtypeRNASeqRep2

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004) C. elegans

source_name: unc-54(srf1004) C. elegans


title: SPECTRUM-OV-009_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: SPECTRUM-OV-008_S1_CD45P_LEFT_PARARENAL_LYMPH_NODE_WITH_COLONIC_MESENTARY

description:
matrix.h5
GEO_cells.tsv

source_name: Other


title: Week1 Tumor CD103+CD69+ replicate 2

source_name: BREAST, Week1 Tumor CD103+CD69+


title: SPECTRUM-OV-008_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: U937-PR9 Zinc Cut&Run PML-RARA antibody replicate 1


title: SPECTRUM-OV-008_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Ovarian Clear Cell Carcinoma 53

type: genomic

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

description: FFPE-derived genomic DNA was hybridyzed to OncoScan

hyb_protocol: According to manufacturer's instructions

scan_protocol: The arrays were processed and loaded into the GeneChip® Scanner 3000 7G (Thermo Fisher Scientific/Affymetrix).

data_processing:
The CEL files were generated by Affymetrix Gene Chip Command Console® software (v. 4.0). CEL files containing the raw data were processed via the Affymetrix OncoScan Console (Thermo). CN gains/amplifications were considered when the log R ratio (LRR) was > 0.1, and CN loss/deletions were considered when the LRR was < -0.1. The ASCAT algorithm was used to infer tumor ploidy, allele-specific copy numbers and segmentation. The ASCAT package for R used the following parameters: ascat.predictGermlineGenotypes(platform = "AffyOncoScan") and ascat.runAscat(gamma = 0.9).
Weighted Log2 ratios, Allellic Differences and B-allele frequencies are provided in the matrix tables. Three OSCHP files required manual re-centering.

label: biotin

source_name: primary Ovarian Clear Cell Carcinoma

label_protocol: 80 ng of genomic DNA was subjected to SNP array OncoScan® FFPE (Thermo) according to manufacturer's instructions

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from OCCC FFPE tissue sections using a QIAmp DNA FFPE Tissue kit (Qiagen)

tag: manual re-centering

value: no


title: Ovarian Clear Cell Carcinoma 58


title: Week1 Tumor CD103-CD69+ replicate 1


title: U937-PR9 Control Cut&Run RARA antibody replicate 1


title: SPECTRUM-OV-008_S1_CD45N_LEFT_PARARENAL_LYMPH_NODE_WITH_COLONIC_MESENTARY

description:
matrix.h5
GEO_cells.tsv


title: Week2 Tumor CD103-CD69+ replicate 1


title: Ovarian Clear Cell Carcinoma 53 recurrence

source_name: recurrence Ovarian Clear Cell Carcinoma


title: U937-PR9 Control Cut&Run PML-RARA antibody replicate 2


title: Week1 Tumor CD103+CD69+ replicate 1


title: Ovarian Clear Cell Carcinoma 36

value: yes


title: SPECTRUM-OV-008_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-008_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: APL patient 2  Capture Hi-C

data_processing:
Library strategy: Capture Hi-C
Paired-end fastq files were processed through the HiCUP pipeline (Wingett et al., 2015).
Significant interactions were called on both individual and merged replicate HiCUP bam files using CHiCAGO (Cairns et al., 2016).
Differential CHi-C interactions were called using the statistical framework of GOTHiC (Schoenfelder et al., 2018).
Genome_build: hg19
Supplementary_files_format_and_content: Chicago_Score_5.csv files  contains the CHiCAGO called significant interactions in each dataset. For the Control and Zinc induced datasets, CHiCAGO was called on the 3 merged replicates
Supplementary_files_format_and_content: Consensus_Gained_Interactions_Zinc_vs_Control.csv contains the GOTHiC called differential interactions that were GAINED after Zinc induction (Zinc vs Control)
Supplementary_files_format_and_content: Consensus_Lost_Interactions_Zinc_vs_Control.csv contains th GOTHiC called differential interactions that were LOST after Zinc induction (Zinc vs Control)

extract_protocol:
Hi-C library generation was carried out as described previously (Mifsud et al., 2015). For each condition and each replicate, 20 million cells were fixed in 2% formaldehyde for 5 minutes, cells were incubated on ice for 30 minutes in 25 mL of ice-cold lysis buffer. After overnight digestion with HindIII at 37°C, DNA ends were labelled with biotin-14–dATP (Life Technologies) using a Klenow end-filling reaction. Biotinylated DNA ends were then ligated together in an overnight ligation step using T4 DNA ligase (Invitrogen). After phenol: chloroform/ethanol purification DNA was quantified using Qubit, with a maximum of 40 μg taken forward. DNA was sheared to a peak concentration of around 400 bp, using the manufacturer’s instructions (Covaris). Sheared DNA was then end-repaired, poly adenine tailed, and double size selected using AMPure XP beads to isolate DNA ranging from 250 to 550 bp in size. Ligation fragments marked by biotin were immobilized using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to paired-end adaptors (Illumina). Hi-C libraries were then amplified using PE PCR 1.0 and PE PCR 2.0 primers (Illumina) with 8 PCR amplification cycles.
Capture Hi-C of promoters was carried out with SureSelect target enrichment, using the custom-designed biotinylated RNA bait library and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using PE PCR 1.0 and PE PCR 2.0 primers with 4 PCR amplification cycles. CHi-C libraries were sequenced on the Illumina HiSeq 2000 platform for paired-end sequencing.


title: U937-PR9 Control Cut&Run PML-RARA antibody replicate 1


title: SPECTRUM-OV-007_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Ovarian Clear Cell Carcinoma 32


title: Cntrl Spleen T CM replicate 3

source_name: SPLEEN, Cntrl Spleen T CM

value: Cntrl

value: Spleen

value: CM


title: Cntrl Spleen T Naive replicate 3

source_name: SPLEEN, Cntrl Spleen T Naive

value: Naive


title: APL patient 1  Capture Hi-C


title: Ovarian Clear Cell Carcinoma 28


title: U937-PR9 Induced rep2 Capture Hi-C

value: myeloid cell line


title: SPECTRUM-OV-007_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Ovarian Clear Cell Carcinoma 29


title: Week4 Tumor CD103-CD69+ replicate 2

source_name: BREAST, Week4 Tumor CD103-CD69+


title: U937-PR9 Control Cut&Run RARA antibody replicate 2

value: anti-RARA


title: SPECTRUM-OV-007_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: U937-PR9 Induced rep1 Capture Hi-C


title: Ovarian Clear Cell Carcinoma 24


title: Cntrl Spleen T EM replicate 3

source_name: SPLEEN, Cntrl Spleen T EM

value: EM


title: SPECTRUM-OV-007_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Week4 Tumor CD103+CD69+ replicate 1

source_name: BREAST, Week4 Tumor CD103+CD69+


title: U937-PR9 Control rep2 Capture Hi-C


title: Ovarian Clear Cell Carcinoma 30


title: SPECTRUM-OV-007_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: U937-PR9 Control rep1 Capture Hi-C


title: Ovarian Clear Cell Carcinoma 23


title: Week2 Tumor CD103+CD69+ replicate 1


title: Ovarian Clear Cell Carcinoma 22


title: PBS_control_peritoneal_macs

first: Itai

last: Yanai

address: 435 East. 30th St.

institute: NYU Langone Health

data_processing:
Basecalls was done using cellranger mkfastq V3.0.0
alignment, filtering, counting and umi counting was doe using cellranger count V3.0.0
Genome_build: mouse mm10-3.0.0
Supplementary_files_format_and_content: expression matrix of umi ocunts

source_name: mouse peritoneal macrophages

extract_protocol:
mouse peritoneal cells were isolated by lavage, red blood cells were lysed, and macrophages were isolated by FACS
10x single cell RAN seq V3

treatment_protocol: mice were injected intraperitoneally with Staph for 1h or PBS control

value: peritoneal macrophages

value: control


title: SPECTRUM-OV-007_S1_CD45P_ANTERIOR_ABDOMINAL_WALL

description:
matrix.h5
GEO_cells.tsv


title: Ovarian Clear Cell Carcinoma 21


title: U937-PR9 Induced rep1 omni ATAC-seq

data_processing:
Reads were trimmed of adapters and low-quality reads using Trimmomatic (Bolger et al., 2014) and aligned to the hg19 genome using Bowtie2. PCR duplicates were removed using Samtools and blacklisted reads were removed.
Peaks were called using Macs2 peak caller, with a q-value threshold of 0.01.
For the differential ATAC analysis, DiffBind (Deseq2) was used. A merged set of all peaks from both replicates were used as bins to call peaks. Any bin with an FDR adjusted p-value <= 0.1 was considered as a significant differential ATAC-seq peak.
Genome_build: hg19
Supplementary_files_format_and_content: Final_Combined_ATAC-seq.csv: contains the 90,332 consensus ATAC-seq peak locations and the normalised read build up for each replicateexperiment. It also contains the deseq2 differential calls for each peak.

extract_protocol:
ATAC-seq libraries for Zinc induced and non-induced libraries were generated following the protocol outlined previously (Corces et al., 2017). Briefly 5x105 cells were re-suspended in ATAC-Resuspension buffer (0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin).
 Isolated nuclei were then incubated in a transposition mixture containing 100nM final transposase at 37oC for 30 minutes. DNA was extracted and purified using the Zymo DNA Clean and Concentrator-5 Kit.
 Libraries were pre-amplified with 5 cycles using NEBNext Master Mix, additional cycles were determined by SYBR Green qPCR. DNA was purified (Zymo) after amplification and quantitated using the NEBNext quant kit by qPCR. Paired-end libraries were sequenced on the Illumina HiSeq 2000 platform.


title: Staph_infected_peritoneal_macs

value: Staph infection


title: U937-PR9 Control rep2 omni ATAC-seq


title: SPECTRUM-OV-007_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: Ovarian Clear Cell Carcinoma 18


title: U937-PR9 Induced rep2 omni ATAC-seq


title: SPECTRUM-OV-007_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: Pupal whole brain cells - Mblk-1_inputDNA_rep2

city: Bunkyo-ku

first: Yasuhiro

last: Matsumura

state: Tokyo

department: Department of Biological Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were aligned to the reference genome (Amel_HAv3.1) using Bowtie2 with default parameters.
BAM files were created using samtools.
For peak calling, we used MACS2 and the input DNA sample as a control. Redundant tags at the same location and the same strand by allowing at most 1 tag were filtered out and broad region calling was off. The effective genome size was 270000000. Peak calling q-value thresholds of 0.01, 0.005, or 0.001 were used.
Genome_build: Amel_HAv3.1
Supplementary_files_format_and_content: peak txt  file

organism: Apis mellifera

source_name: Pupal whole brain

growth_protocol: Mushroom bodies or whole brains were dissected under binocular microscopy from cooled and anesthetized honey bees.

extract_protocol: The sample was  centrifuged and the supernatant was collected. Mblk-1 protein-DNA complexes were isolated with antibody.

treatment_protocol: Brains were homogenized with plastic pestles and fixed with formaldehyde. Cells were crushed using zirconium beads (TOMY) and Micro Smash MS-100 (TOMY). We fragmented chromatin using Micrococcal nuclease and destroyed nuclei by sonication.

value: pupal

value: whole brain

value: none (input)


title: ATAC-Seq Wild type#1

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

state: PA

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

description: ATAC-seq

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25 for Chip-seq and >=1 for ATAC seq) were used for further analysis
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with signal calling

source_name: islets

extract_protocol:
islets were isolated after collagenase digestion and density gradient purification and then hand picked for purity, flash frozen in liquid nitrogen. For Chip-seq they were fixed with formaldehyde and then after sonication (300-500bp), IP was performed on 10 micrograms of chromatin with Anti-Tead1 antibody or the IgG isotype control. For ATAC-seq 100,000 of the frozen nuclei  were used.
Chip-Seq - Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). ATAC-seq - 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).
Chip-seq and ATAC-seq

value: islets

tag: age

value: 12 weeks

value: Wild type


title: Ovarian Clear Cell Carcinoma 17

value: no


title: U937-PR9 Control rep1 omni ATAC-seq


title: SPECTRUM-OV-007_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Ovarian Clear Cell Carcinoma 16


title: Pupal whole brain cells - Mblk-1_inputDNA_rep1


title: SPECTRUM-OV-007_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: Ovarian Clear Cell Carcinoma 15

value: yes


title: W517NAZ3

city: 广州市

first: Linxuan

last: Wu

state: 广东省

address: 广东省广州市天河区五山路483号华南农业大学科技楼713

country: China

institute: South China Agricultural University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the RGAP(MSU7) using HISAT2.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: RGAP(MSU7)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: non-abscission zone

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: sample group

value: easy to shattering  (W517)

value: non-abscission zone

value: WT

tag: time point

value: after flowering

value: Day 10


title: SPECTRUM-OV-007_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: Ovarian Clear Cell Carcinoma 14


title: Pupal whole brain cells - Mblk-1_immunoprecipitated_rep1

tag: chip antibody


title: SPECTRUM-OV-007_S1_CD45N_ANTERIOR_ABDOMINAL_WALL

description:
matrix.h5
GEO_cells.tsv

source_name: Other


title: W517NAZ1

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: W517NAZ2

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: Pupal whole brain cells - Mblk-1_immunoprecipitated_rep2


title: Ovarian Clear Cell Carcinoma 13

source_name: primary Ovarian Clear Cell Carcinoma


title: Adult MB Kenyon cells - Mblk-1_inputDNA_rep2

source_name: Adult MBs

value: adult

value: mushroom bodies(MBs)


title: Ovarian Clear Cell Carcinoma 12


title: W517AZ2

address: 广东省广州市天河区五山路483号华南农业大学科技楼713

source_name: abscission zone

value: abscission zone


title: Adult MB Kenyon cells - Mblk-1_inputDNA_rep1


title: Ovarian Clear Cell Carcinoma 11


title: W517AZ3

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: SPECTRUM-OV-003_S1_UNSORTED_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

source_name: UQ

value: U


title: W517AZ1

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: Ovarian Clear Cell Carcinoma 10


title: Ovarian Clear Cell Carcinoma 9


title: DZ129NAZ3

address: 广东省广州市天河区五山路483号华南农业大学科技楼713

value: loss of shattering (DZ129)


title: SPECTRUM-OV-003_S1_UNSORTED_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-003_S1_UNSORTED_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Adult MB Kenyon cells - Mblk-1_immunoprecipitated_rep2


title: SPECTRUM-OV-003_S1_UNSORTED_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-003_S1_UNSORTED_LEFT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: Ovarian Clear Cell Carcinoma 8


title: ATAC-Seq Wild Type#2

description: ATAC-seq


title: DZ129NAZ2

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: DZ129NAZ1

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: ChIP-Seq Input Wild type#2

description: Input


title: ChIP-Seq Wild Type#2

description: ChIP-seq


title: Ovarian Clear Cell Carcinoma 4


title: SPECTRUM-OV-002_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: ChIP-Seq Input Wild type#1

description: Input


title: DZ129AZ3

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: Ovarian Clear Cell Carcinoma 7


title: Ovarian Clear Cell Carcinoma 1


title: SPECTRUM-OV-003_S1_UNSORTED_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: DZ129AZ2

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: SPECTRUM-OV-002_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: DZ129AZ1

address: 广东省广州市天河区五山路483号华南农业大学科技楼713


title: Adult MB Kenyon cells - Mblk-1_immunoprecipitated_rep1


title: Vero E6 HCoV-OC43 infected, treated with Remdesivir rep3

status: Public on Dec 13 2022

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed using cutadapt version 2.3.
Trimmed reads were aligned to Chlorocebus sabaeus genome version ChlSab1.1 and Ensembl gene annotations version 104 using STAR aligner version 2.7.0d_0221 and ENCODE long RNA-seq pipeline parameters (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM version 1.3.1.
Assembly: ChlSab1.1
Supplementary files format and content: Matrix table with normalized gene expression (TPM)

organism: Chlorocebus sabaeus

source_name: Vero E6 cell line

growth_protocol: Vero E6 cells were obtained from the American Type Culture Collection (ATCC) and maintained in high-glucose Dulbecco's modified Eagle's medium (HyClone) with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using a total RNA miniprep kit (Sigma) with the On-column DNase I digestion step included.
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 system using the High output V2.5 kit (Illumina Inc., San Diego, CA). Read data was processed and multiplexed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).

treatment_protocol: Cells were seeded in 6-well (2 x 105) or 96-well (1 x 104) plates. The next day, cells were incubated 1 h with a dilution of OC43 virus stock at a MOI of 0.1.  Media supplemented with 2% FBS and test compounds at various concentrations were then added to infected cells. Cells were collected for Western blotting analysis and RNA-seq (6-well plate) after 24 h or subjected to IF staining (96-well plate) after 48 h

tag: cell line

value: Vero E6 cell line

tag: infection

value: infected

value: Remdesivir

tag: treatment concentration

value: 5 uM


title: Vero E6 HCoV-OC43 infected, treated with Remdesivir rep2

tag: treatment


title: SPECTRUM-OV-002_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Vero E6 HCoV-OC43 infected, treated with SBI-756 rep3

value: 1 uM


title: Vero E6 HCoV-OC43 infected, treated with Remdesivir rep1


title: Vero E6 HCoV-OC43 infected, treated with SBI-756 rep1


title: ChIP-Seq Wild type#1

description: ChIP-seq

tag: strain

value: islets

value: 12 weeks

tag: genotype

value: Wild type


title: Vero E6 HCoV-OC43 infected, treated with SBI-0498 rep1

value: 10 uM


title: Vero E6 HCoV-OC43 infected, treated with SBI-0498 rep2


title: Vero E6 HCoV-OC43 infected rep1

value: untreated


title: Vero E6 HCoV-OC43 infected, treated with SBI-0498 rep3


title: Vero E6 HCoV-OC43 infected, treated with SBI-5844 rep2


title: Vero E6 HCoV-OC43 infected rep3


title: Vero E6 HCoV-OC43 infected rep2


title: Egg_Pellet_Rep 3

city: Urbana

first: Jing

last: Yang

state: Illinois

address: 2001 South Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois Urbana Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors were trimmed from the 3'-end of the reads. The quality-scores line in fastq files uses an ASCII offset of 33 known as Sanger scores.
Transcripts per million (TPM) were quantified using Kallisto (v 0.46.2) and the Xenopus laevis transcriptome (v 9.2) from the XenBase (http://www.xenbase.org) was used as the reference sequence.
TPM was converted to the absolute concentration by the regression estimation with five spike-in RNAs (egfp, mCherry, mRuby2, firefly, renilla).
Assembly: XENLA_9.2_genome.fa.gz (Xenopus laevis transcriptome)
Supplementary files format and content: tsv files were generated from Kallisto and included TPM values.
Supplementary files format and content: xlsx files contained the absolute concentration, FC, qvalue and proportion of all genes in each fraction.

organism: Xenopus laevis

source_name: Mature egg

growth_protocol: Defolliculated stage VI oocytes were cultured in the oocyte culture medium, or oocyte culture medium containing 2µM progesterone to induce oocyte maturation. All cells were incubated at 18 ℃.

extract_protocol:
Oocytes and mature eggs were fractionated into the cytosolic, ER, and pellet fractions. Spike mixture was added into each fraction. Total RNAs were extracted using the TRIzol reagent. Before library construction, Ribosomal RNAs was removed with the Ribozero HMR kit (Illumina).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Reads are 100 nt in length.

tag: developmental stage

value: Germinal Vesicle Breakdown (GVBD)

tag: cell fraction

value: Pellet

tag: cell type

value: Mature egg


title: Ovarian Clear Cell Carcinoma 2

value: no


title: Vero E6 HCoV-OC43 infected, treated with SBI-756 rep2


title: Vero E6 uninfected control rep2

value: uninfected


title: Vero E6 uninfected control rep1


title: Vero E6 HCoV-OC43 infected, treated with SBI-5844 rep3


title: Egg_Pellet_Rep 1


title: Egg_ER_Rep 2

value: Endoplasmic Reticulum (ER)


title: Egg_Pellet_Rep 2


title: Oocyte_Pellet_Rep 3

source_name: Oocyte

value: Stage VI Oocyte

value: Oocyte


title: Oocyte_ER_Rep 3


title: Oocyte_Pellet_Rep 2


title: Oocyte_ER_Rep 2


title: Oocyte_Cytosol_Rep 3

value: Cytosol


title: Egg_ER_Rep 3


title: Egg_ER_Rep 1


title: Egg_Cytosol_Rep 2


title: Egg_Cytosol_Rep 3


title: Vero E6 HCoV-OC43 infected, treated with SBI-5844 rep1

value: Vero E6 cell line

value: infected


title: 403C_4937_NB 403/+ M SvEv

city: Boston

first: Daniel

last: DeLaughter

state: MA

address: 7 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
403_NB_4937(norm)
Reichart_et_al_RPKM_2.txt

data_processing:
Reads were aligned to the mm10 mouse genome using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013).
Data were normalized to the total number of reads per kilobase of exon per million (RPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized read values for each Sample

source_name: Left Ventricular Apex

extract_protocol:
Total RNA (1 ug) underwent two rounds of mRNA purification (polyA-selection) using Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad, CA).
Double-stranded cDNA was generated using the Superscript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA). The cDNA products were used to construct libraries with the Nextera XT DNA Sample Preparation Kit (Illumina, Inc., San Diego, CA)

tag: tissue

value: Left Ventricular Apex

value: SvEv

tag: gender

value: male


title: 1096_LVa 403/+ M SvEv

description:
1096_LVa(norm),
Reichart_et_al_RPKM_1.txt


title: 403C_4942_NB 403/+ M SvEv

description:
403_NB_4942(norm)
Reichart_et_al_RPKM_2.txt


title: 2243_LV 403/+ M S4/SvEv

description:
2243_LVap(norm)
Reichart_et_al_RPKM_1.txt

value: BoostedABE


title: 2244_LV 403/+ M S4/SvEv

description:
2244_LVap(norm)
Reichart_et_al_RPKM_1.txt


title: 403C_4944_NB 403/+ M SvEv

description:
403_NB_4944(norm)
Reichart_et_al_RPKM_2.txt


title: Oocyte_ER_Rep 1


title: Hypothalamus; ABI3 KO rep 3

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

data_processing:
Base calling done by Illumina Real-Time Analysis v2
Adapters and polyA tails removed by bbduk from bbtools/38.72 using references files polyA/polyT (poly(A) sequence of 18 As, and a poly(T) sequence of 18 Ts) & truseq_rna.fa (from the BBTools suite: https://sourceforge.net/projects/bbmap/) and parameters k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
Alignment done by STAR/2.7.3a using parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Gene counts done by htseq-count from htseq/0.9.1-py13 using parameters htseq-count -m intersection-nonempty -s yes -f bam -r pos
Assembly: GRCm39
Supplementary files format and content: Matrix table of raw gene counts for each gene and each sample in experimental design

source_name: hypothalamus

extract_protocol:
RNA was extracted from the hypothalami and brown adipose tissue via a standard phenol/chloroform extraction using TRIzol reagent (MRC). The concentration and purity of the RNA samples were then assessed via Nanodrop 2000 spectrophotometer. The isolated RNA was then stored at -80 °C until further processing.
Isolated RNA was shipped to Lexogen for library preparation and sequencing. Libraries were prepared manually according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit (Lexogen, UG Version 015UG009V0252). Briefly, 50 ng total RNA was denatured for 3 minutes at 85°C with oligo(dT) primers containing an Illumina-compatible sequence at its 5’ end followed by reverse transcription at 42°C for 15 minutes. After RNA removal, the second strand of the cDNA was synthesized by a random primer containing an Illumina-compatible linker sequence at its 5’ end, and the end product was purified by a magnetic bead-based method to remove all reaction components. Finally, individual sample barcodes (dual indexing) for multiplexing were introduced via PCR (cycle number determined by qPCR) and the leftover reaction components were removed by a magnetic bead-based purification method. All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer System using the DNF-474 HS NGS Fragment kit (1-6,000 bp) (Agilent). After pooling the libraries in an equimolar ratio, the concentration and the size distribution of the lane mix was analyzed by Qubit dsDNA HS assay (Thermo Fisher Scientific) and by 2100 Bioanalyzer device using the HS-DNA assay (Agilent), respectively. A 2 nM dilution of the lane mix was denatured and diluted to loading concentration for sequencing on a NextSeq 500 instrument with SR75 High Output Kit (Illumina). Seventy-six-base-pair single-end reads were generated at Lexogen Services.

value: hypothalamus

value: ABI3 KO

tag: Sex


title: Oocyte_Cytosol_Rep 1


title: Oocyte_Cytosol_Rep 2


title: Hypothalamus; ABI3 WT rep 3

value: ABI3 WT


title: Hypothalamus; ABI3 KO rep 4


title: Egg_Cytosol_Rep 1

value: Germinal Vesicle Breakdown (GVBD)


title: 403C_4939_NB 403/+ M SvEv

description:
403_NB_4939(norm)
Reichart_et_al_RPKM_2.txt


title: Brown Adipose Tissue; ABI3 KO rep 4

source_name: brown adipose tissue from the sub-scapular depot


title: Brown Adipose Tissue; ABI3 KO rep 1

value: brown adipose tissue from the sub-scapular depot


title: Oocyte_Pellet_Rep 1

value: Pellet


title: Brown Adipose Tissue; ABI3 WT rep 3


title: Brown Adipose Tissue; ABI3 KO rep 2


title: Brown Adipose Tissue; ABI3 WT rep 2


title: ChIPSeq_H3K4me3_iMEF2_KO_HOT_minus

city: Aachen

first: Mirna

last: Barsoum

state: North Rhine Westphalia

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Biology

country: Germany

institute: Uniklinik RWTH Aachen

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm9

growth_protocol: For the generation of immoralized fibroblast cultures (iMEF) the cells were infected with a retrovirus encoding an shRNA against p19Arf and a Blasticidin resistance gene used for the initial selection of infected cells (10 µg/ml Blasticidin, Invivogen, ant-bl). MEF cells were cultivated in DMEM (ThermoFisher Scientific, 61965059) supplemented with 10% heat-inactivated fetal bovine serum (FBS, ThermoFisher Scientific, 10270106) and 1% penicillin/streptomycin (ThermoFisher Scientific, 15070063).

extract_protocol:
iMEF cells were treated with HOT or vehicle for 5 days and cross-linked with 1% formaldehyde in cell culture medium on a shaking platform for 10 min at room temperature (RT). The cross-linking reaction was quenched by adding glycine to 125 mM and incubation for another 5 min at RT. Adherent cells were washed with PBS twice and collected in PBS by scraping the cells from the dish. Cells were centrifuged at 380 x g for 5 min at 4°C and resuspended in 1 ml Lysis Buffer B (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 0.25% (v/v) Triton X-100) per 2 x 107 cells and centrifuged. To the pellet 1 ml Lysis Buffer C (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 200 mM NaCl) was added per 2 x 107 cells, followed by an incubation on ice for 10 min. After a further centrifugation step, disruption of the pelleted nuclei was performed in 200 μl lysis buffer D (50 mM Tris pH 8, 10 mM EDTA, 1% (w/v) SDS, protease inhibitor cocktail (1xPIC, Merck, P8340) per 5 x 106 MEF cells for 30 min at 15°C.  200 μl aliquots were sonicated for a minimum of 10 cycles using a Bioruptor Pico (Diagenode) with 30-second on-off-cycles to achieve DNA fragment lengths of about 800 bp or 300 bp for ChIP-qPCR or ChIP-seq, respectively. The size distribution of the resulting DNA fragments was assessed by agarose gel electrophoresis. To remove cell debris, lysates were centrifuged for 10 min at 10,000 x g (15°C), the supernatants pooled, and DNA concentrations were measured using a NanoDrop 1000 device (Peqlab). ChIP assays were performed using the OneDay ChIP Kit from Diagenode (C01010080) according to the manufacturer’s instructions. To capture protein-DNA complexes, 42 μl of Protein A beads per sample were pre-incubated in 1 x ChIP buffer for 2 hours at 4 °C with 2 μg of specific antibody or rabbit IgG (provided by the kit). The sheared chromatin (10 – 100 µg) was diluted 4.7-fold with 1 x ChIP buffer, setting aside 1/10 of the diluted chromatin for the input control, and mixed with the pre-incubated beads for 30 min at 4°C. Subsequently, the chromatin-antibody-bead complexes were washed three times with 1 x ChIP buffer and taken up in DNA purifying slurry. The diluted input control chromatin was precipitated by the addition of 5 volumes 100% ethanol and centrifuged at 16,000 x g, 4°C for 10 min. The dried pellets were resuspended in RNase-free H2O and mixed with DNA purifying slurry. The DNA of all samples was reverse crosslinked and further purified according to the manual.
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as single reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturers recommendations.

treatment_protocol: At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter cells were passaged when needed to maintain subconfluency or solely supplied with new medium with the addition of HOT or vehicle as before.

value: HOT minus


title: ChIPSeq_H3K4me3_iMEF2_KO_HOT_plus

value: HOT plus


title: ChIPSeq_H3K4me3_iMEF1_KO_HOT_minus


title: Hypothalamus; ABI3 KO rep 2


title: ChIPSeq_H3K4me3_iMEF1_WT_HOT_minus


title: Hypothalamus; ABI3 KO rep 1


title: 2245_LV 403/+ M S4/SvEv

description:
2245_LVap(norm)
Reichart_et_al_RPKM_1.txt


title: 403C_4939_NA 403/+ M SvEv

description:
403_NA_4939(norm)
Reichart_et_al_RPKM_2.txt


title: Brown Adipose Tissue; ABI3 KO rep 3


title: Hypothalamus; ABI3 WT rep 1


title: Hypothalamus; ABI3 WT rep 2


title: ChIPSeq_H3K4me3_iMEF1_input

value: untreated


title: Hypothalamus; ABI3 WT rep 4


title: 5_12_16_f

city: Cologne

first: Ludwig

last: Eichinger

state: NRW

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

institute: Centre for Biochemistry Medical Faculty University of Cologne

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline  version 1.2.7, based on Ensembl release 33
Sequenced reads mapped to Dictyostelium_discoideum
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Dictyostelium_discoideum 33
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample

organism: Dictyostelium discoideum

source_name: D. discoideum cells

growth_protocol: D. discoideum cells were grown to log phase and 1 x 107 cells were harvested (500 x g, 5 min, 4°C), followed by two washing steps with 10 ml Soerensen’s phosphate buffer

extract_protocol:
total RNA extraction was carried out using the Qiagen RNeasy® Mini Kit according to the manufacturer’s instructions
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Total RNA from vegetative D. discoideum cells was isolated

tag: condition

value: vegetative


title: 5_12_16_e


title: ChIPSeq_H3K4me1_iMEF2_KO_HOT_plus


title: 5_12_16_c


title: Brown Adipose Tissue; ABI3 WT rep 1


title: ChIPSeq_H3K4me3_iMEF2_WT_HOT_plus


title: ChIPSeq_H3K4me3_iMEF2_input


title: ChIPSeq_H3K4me3_iMEF1_KO_HOT_plus


title: 5_12_16_b


title: ChIPSeq_H3K4me1_iMEF1_KO_HOT_minus


title: 5_12_g

value: ATG5-/12- mutant


title: Brown Adipose Tissue; ABI3 WT rep 4


title: 5_12_16_g


title: ChIPSeq_H3K4me1_iMEF2_KO_HOT_minus


title: ChIPSeq_H3K4me3_iMEF1_WT_HOT_plus


title: ChIPSeq_H3K4me1_iMEF2_WT_HOT_minus


title: ChIPSeq_H3K4me1_iMEF2_WT_HOT_plus


title: ChIPSeq_H3K4me1_iMEF2_input


title: 5_12_d


title: 5_12_16_d


title: 5_f

value: ATG5- mutant


title: ChIPSeq_H3K4me3_iMEF2_WT_HOT_minus


title: ChIPSeq_H3K4me1_iMEF1_KO_HOT_plus


title: ChIPSeq_H3K4me1_iMEF1_WT_HOT_plus


title: ChIPSeq_H3K4me1_iMEF1_input


title: ChIPSeq_CTCF_R2_HOT_minus_input

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: For the generation of immortalized fibroblast cultures (iMEF) the cells were infected with a retrovirus encoding an shRNA against p19Arf and a Blasticidin resistance gene used for the initial selection of infected cells (10 µg/ml Blasticidin, Invivogen, ant-bl). MEF cells were cultivated in DMEM (ThermoFisher Scientific, 61965059) supplemented with 10% heat-inactivated fetal bovine serum (FBS, ThermoFisher Scientific, 10270106) and 1% penicillin/streptomycin (ThermoFisher Scientific, 15070063).

extract_protocol:
iMEF cells were treated with HOT or vehicle for 7 days and cross-linked with 1% formaldehyde in cell culture medium on a shaking platform for 10 min at room temperature (RT). The cross-linking reaction was quenched by adding glycine to 125 mM and incubation for another 5 min at RT. Adherent cells were washed with PBS twice and collected in PBS by scraping the cells from the dish. Cells were centrifuged at 380 x g for 5 min at 4°C and resuspended in 1 ml Lysis Buffer B (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 0.25% (v/v) Triton X-100) per  107 cells and centrifuged. To the pellet 1 ml Lysis Buffer C (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 200 mM NaCl) was added per 107 cells, followed by an incubation on ice for 10 min. After a further centrifugation step, disruption of the pelleted nuclei was performed in 100 μl lysis buffer D (50 mM Tris pH 8, 10 mM EDTA, 1% (w/v) SDS, protease inhibitor cocktail (1xPIC, Merck, P8340) per 107 MEF cells for 30 min at 15°C. 300 μl aliquots were sonicated for a minimum of 5 cycles using a Bioruptor Pico (Diagenode) with 30-second on-off-cycles to achieve DNA fragment lengths with a majority around 300 bp for  ChIP-seq, respectively. The size distribution of the resulting DNA fragments was assessed by agarose gel electrophoresis. To remove cell debris, lysates were centrifuged for 10 min at 10,000 x g (15°C), the supernatants pooled, and DNA concentrations were measured using a NanoDrop 1000 device (Peqlab). ChIP assays were performed using the OneDay ChIP Kit from Diagenode (C01010080) according to the manufacturer’s instructions. The sheared chromatin (100 µg) was diluted 4.7-fold with 1 x ChIP buffer, setting aside 1/10 of the diluted chromatin for the input control. The diluted chromatin was supplemented with 5 µg of CTCF-specific antibody. This immunoselection was done at 4°C in a rotator overnight. To capture the antibody-chromatin-complexes, 42 µl of Protein A beads per sample were washed with 1x ChIP buffer. After the washing, the supernatant of the beads were discarded and the pre-incubated antibody-chromatin-complexes were added to the beads. The IP was done for 90 min at 4°C. Subsequently, the chromatin-antibody-bead complexes were washed three times with 1 x ChIP. The diluted input control chromatin was precipitated by the addition of 5 volumes 100% ethanol and centrifuged at 16,000 x g, 4°C for 10 min. The dried pellets were resuspended in RNase-free. The DNA of all samples (including input) were reverse crosslinked and further purified with the QIAquick PCR purification Kit (28106).
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as single reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter, cells were passaged at day 3 and day 5 for vehicle treated cells. This was done to maintain subconfluency. The newly used medium was supplemented with vehicle. HOT treated cells were passaged at day 3, but only washed at day 5 and supplied with new medium, including the addition of HOT. This was done, because of the proliferation stop after day 3 of HOT-treatment.

value: HOT minus (EtOH)


title: ChIPSeq_CTCF_R2_HOT_plus

value: CTCF


title: ChIPSeq_CTCF_R2_HOT_plus_input


title: ChIPSeq_H3K4me1_iMEF1_WT_HOT_minus


title: 5_e


title: 5_d


title: 5_12_e


title: 5_12_f


title: AX2_f

value: AX2 wild-type


title: ChIPSeq_CTCF_R2_HOT_minus


title: 5_12_c


title: 5_12_b


title: AX2_e


title: AX2_d


title: 5_g


title: AX2_c


title: ChIPSeq_CTCF_R1_HOT_minus


title: ChIPSeq_CTCF_R1_HOT_plus


title: ATAC-seq_R1_HOT_plus

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
RGT-HINT for TF-footprinting
Assembly: mm9
Supplementary files format and content: BigWig files

extract_protocol:
iMEF cells were treated with HOT or vehicle for 7 days. Adherent cells were washed with PBS twice, trypsinized and collected in a 15 ml falcon. Cell count were measured using a Innovatis CASY Cell counter. 10^5 cells were transferred in 1.5 ml reaction tube. The cells were centrifuged at 500 x g for 5 min at 4°C and carefully re-suspended in ice-cold 1xPBS. Cell count were measured another time with Innovatis CASY cell counter. 5*10^4 cells per sample were aliquoted in fresh tubes. Cells were spin down at 500 x g for 5 min at 4°C and subsequently the supernatant removed. For ATAC-Seq basically the protocol of Corces et al., Nature Methods 14, 959-962 (2017) with adaptions of Thomas Look & Prof. Martin Zenke (Institute of Biomedical Engineering, Cell Biology, Aachen University Medical School, Germany can be found in Li et al., BMC Genome Biology 20, 45 (2019)) was employed.  Crude nulcei extracts were prepared by adding 50 µl of ice-cold ATAC-RSB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1 % NP40, 0.1% Tween-20, 0.01% Digitonin. Cells were incubated for 3 mins on ice. Cooled 1ml Wash buffer (ATAC-RSB + 0.1% Tween-20) was added, tubes inverted and centrifuged for at 500 x g for 10 min at 4°C afterwards. With the pellets of the crude nuclei extracts, transposition procedure was performed. 50 µl Transposition mix (1xTD buffer, Tagment DNA Enzyme TDE1 both part of the Nextera Rapid Capture Exome Kit #FC140-1000 by Illumina, PBS, 0.1% Tween-20, 0.01% Digitonin) was added to nuclei samples and incubated for 1h at 37°C while shaking in a thermoblock. Purification of transposed DNA was done with the Quiagen MinElute PCR Purification Kit (#28004).  Transposed DNA was barcoded using i5/i7 primers of the Nextera Rapid Capture Custom Enrichment Kit (FC-140-1007 by Illumina) and NEBNext Ultra II Q5 Master Mix (#M0544) by New England Labs. Amplification with barcoding primers was done for initial 5 cycles. After this an aliquote of PCR product was taken and supplemented with SYBR Green in DMSO (SYBR Gold Nucleic Acid Gel Stain #S11494, Thermo Fisher) together with the attributed set of primers per sample and fresh Q5 polymerase. Another 20 cycles on this aliquot were performed and the amplification was monitored in a real-time application (RotorGeneQ, Qiagen) to assess the progress of the library preparation after the initial 5 cycles in the thermocycler. Both +HOT treated and one –HOT treated sample 4 additional cycles and for the second –HOT replicate 3 additional amplification cycles were needed to perform to extend the initial 5 cycles of preparation. After library preparation was done, samples were purified with the Quiagen MinElute PCR Purification Kit (#28004).
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as pared-end reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter, cells were passaged when needed to maintain subconfluency or solely supplied with new medium with the addition of HOT or vehicle as before.


title: 5_c


title: ChIPSeq_CTCF_R1_HOT_plus_input


title: ChIPSeq_CTCF_R1_HOT_minus_input


title: 5_b


title: Beige, mRNA2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
MAPS_beige.gtf
STRINGTIE_beige.gtf

data_processing:
Raw sequencing data was quality assessed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
After trimming adapters with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), removal of mm10 rRNA and tRNA sequences, and alignment to the mm10 genome with STAR v2.53b (Dobin et. al., 2014)
Stringtie v2.1.4 (PMCID: PMC4643835) and MAPS v1.0(PMCID: PMC5870951) were run using default parameters on combined alignments from total and mRNA RNA-Seq libraries from BAT, beige, and WAT adipocytes, followed by 3-frame translated using a custom script GTFtoFasta (see PMC7085969 for details).
The resulting 3-frame translated ORF databases were then scored for translation using ribORF (PMCID: PMC6168376) with the pipeline described by Martinez et al (PMC7085969), which briefly included shifting reads of each length to obtain base-pair resolution, and then scoring each candidate smORF using ribORF, keeping only highly scoring (score ≥ 0.7), short (≤ 150 aa), and novel (not overlapped with known coding regions in RefSeq, and a maximum blastp alignment evalue  to SwissProt (Bairoch and Apweiler, 1997) of 100).
The resulting microproteins were then collated into a non-redundant table and were further annotated using HOMER (Heinz et al, PMID: 20513432; genomic location of their ORFs), and using PhyloCSF (Lin et al, 2014; conservation from a multi-way alignment of mammals) as described previously (PMC7085969).
Candidate microproteins were then split into categories based on the genomic location of their ORF with respect to genomic features: uORFs exist upstream of known genes, non-uORFs are all other ORFs, iORFs specifically exist in intergenic regions, while dORFs exist downstream of known genes. These categories of ORFs were then further tested for expression in RNA-Seq datasets and visualized using read pileup tracks.
The GTF files are assemblies created by combining the RNA-Seq files specified for each of the tissues: WAT, BAT, and Beige. We only used the RNA-seq for transcriptome assembly, but provide each raw RNA-Seq file separately in case GEO users would like to process them separately.
Genome_build: mm10
Supplementary_files_format_and_content: GTF files of assembled transcriptome

source_name: beige adipose tissue

growth_protocol: Twenty female C57Bl6/J mice aged 7 weeks old were sacrificed using an overdose of anaesthesia. Interscapular and subscapular BAT was excised with dissecting scissors, being careful to avoid surrounding muscle and white adipose tissue. For white adipose tissue, subcutaneous (scWAT) depots were excised bilaterally. Fat pads were placed collectively in a 50 mL falcon containing ice-cold DMEM.  DMEM was carefully decanted through a mesh filter, and the pads washed briefly in HBSS. Most of the HBSS was then decanted, before transferring each tube of fat pads to a single well of a 6-well culture plate. Dissecting scissors were then used to thoroughly mince each collection of pooled fat explants. Digests were performed in the following solutions (pre-warmed to 37 ºC): 1) for scWAT, 40 mg Collagenase Type I with 80 mg Collagenase Type II in 28 mL Hanks BSS and 12 mL 7.5% w/v BSA (Sigma); 2) for BAT, 80 mg Collagenase Type I with 80 mg Collagenase Type II in 28 mL Hanks BSS and 12 mL 7.5% w/v BSA (Sigma). Digests were incubated at 37 ºC for 15-20 mins with shaking (225 rpm), resulting in complete dissociation of adipose tissue. Digests were then filtered through a 100 μm mesh (yellow) into 50 ml falcon tubes and allowed to sit on ice for 20 minutes. Visible fat floating as a layer was carefully aspirated. Working from the top, the supernatant was pipetted into a clean 50 ml Falcon tube, leaving behind the lowest 10 ml of digested material. This fraction is enriched for pre-adipocytes and was mixed 1:1 with 10% newborn calf serum. Cells were spun down at 700 g for 15 minutes and resuspended in growth media consisting of: 1) for scWAT (“scWAT media”), DMEM plus 10% NCS with Pen/Strep, 4 mM Glutamax, 150 μM sodium ascorbate, 30 nM insulin, and 1 μM rosiglitazone; and 2) for BAT (“BAT media”) DMEM plus 10% NCS with Pen/Strep, 4 mM Glutamax, 150 μM sodium ascorbate, 4 nM insulin, and 2 nM T3. Cells were spun again for 10 minutes and resuspended ready for plating in the following volumes (based on 2 ml of media for each well seeded): 1) for scWAT, a ratio of 5 mice in 38 mL of plating media with suspended cells, and 2) for BAT, a ratio of 5 mice in 25 mL of plating media with suspended cells. Cells were plated into 6-well dishes with 2 mL of cell suspension per well. Cells cultured as the “Beige” phenotype represent the scWAT cultures that were switched to the BAT media 24 hours after plating in the scWAT media. Media was changed daily for days 1-4 and every other day from days 4-8. On day 6, media was changed to phenol red free DMEM and rosiglitazone was removed from the scWAT cultures to allow wash out before harvest. All cultures were treated or harvested or both on day 8

extract_protocol:
For sample collection of BAT/WAT/Beige cultures for Ribo-Seq and total mRNA-Seq used for smORF discovery, each culture was washed directly out of the incubators 3x with ice-cold PBS supplemented with 100μg/mL cyclohexamide (Fisher Scientific #AAJ66004X). After the last wash, liquid nitrogen was gently ladled onto the surfaces of the cells and plates were stored at -80 °C prior to Ribo-Seq analysis. Each biological replicate for Ribo-Seq in our experiments represents 11 wells of a 6-well dish leaving one well to be lysed with Trizol reagent (Thermo #15596026) for the bulk mRNA-Seq used int the de novo transcriptome assembly of the cells under analysis. Cells were lysed with 400 μl of ice-cold lysis buffer (20 mM Tris–HCl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, with 1 mM DTT, 25 U ml−1 Turbo DNase (Thermo Fisher, catalog no. AM2238) and 100 μg ml−1 CHX added fresh) was dripped onto the plate. Cells were incubated on ice in lysis buffer for 10 min with periodic vortexing and pipetting to disperse the cells. The lysate was then clarified by centrifugation at 15,000g for 10 min. Cell lysates were flash-frozen in liquid nitrogen and stored at −80 °C for up to 7 d before ribosome footprinting. For each cell type, ribosome footprinting was carried out by digesting 40-60 μg of RNA in 200-300 μL lysate with 0.375 U/μg−1 RNase I (Lucigen, N6901K) for 50 min at room temperature. Digestion reactions were quenched with 200 U Superase-In RNase I inhibitor (Thermo Fisher, AM2694) on ice. Following digestion, monosomes were purified from small RNA fragments using MicroSpin S-400 HR columns (GE Life Sciences), and ribosome protected RNA fragments (RPFs) were extracted by acid phenol chloroform and isopropanol precipitation.
TruSeq mRNA and Total RNA kits (Illumina) were used to prepare polyA and total RNA libraries.
total RNA and polyA mRNA paired end deep sequencing

value: adipose tissue

tag: tissue subtype

value: Beige adipose tissue

tag: replicate


title: ATAC-seq_R2_HOT_plus


title: BAT, totalRNA3

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf

source_name: brown adipose tissue

value: brown adipose tissue (BAT)


title: WAT, mRNA2

description:
MAPS_WAT.gtf
STRINGTIE_WAT.gtf

source_name: white adipose tissue

value: white adipose tissue (WAT)


title: BAT, mRNA3

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf


title: WAT, totalRNA2

description:
MAPS_WAT.gtf
STRINGTIE_WAT.gtf


title: WAT, totalRNA1

description:
MAPS_WAT.gtf
STRINGTIE_WAT.gtf


title: ATAC-seq_R2_HOT_minus


title: AX2_b


title: ATAC-seq_R1_HOT_minus


title: AX2_a


title: Beige, totalRNA2

description:
MAPS_beige.gtf
STRINGTIE_beige.gtf


title: BAT, totalRNA2

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf


title: Beige, mRNA1

description:
MAPS_beige.gtf
STRINGTIE_beige.gtf


title: Beige, totalRNA1

description:
MAPS_beige.gtf
STRINGTIE_beige.gtf


title: BAT, totalRNA1

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf


title: BAT, mRNA1

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf


title: Collagen replica 3 [UMC-AK3]

city: Utrecht

first: Antoine

middle: A

last: Khalil

address: Universiteitsweg 100

country: Netherlands

institute: UMC Utrecht

description: Single breast cancer cells were sorted and processed for mRNA sequencing

data_processing:
Paired-end reads were aligned to the transcriptome assembly mm10 including DTR-eGFP and tDimer2 reporter transcripts using the BWA-MEM algorithm.
Reads mapping to multiple loci were discarded.
Left reads contain barcodes and unique molecular identifiers (UMIs) (read length of 26 bp) and were not used for quantification.
Transcript counts were obtained by counting the number of UMIs for each cell barcode and each transcript and aggregating the number across all transcripts of the same locus.
Downstream analysis of processed data file in the linked study included: exclusion of spike-in RNAs, inclusion of cells with > 250 unique transcripts and < 10 % mitochondrial reads.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing transcript counts

source_name: 5 days invasion collagen I

growth_protocol: The murine breast cancer model of the MMTV-PyMT was a generous gift from Jacco van Rheenen and cultured in BME and growth media containing Advanced DMEM/F12 (Invitrogen) supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), and 2,5 nM FGF2 was refreshed every 2-3 days. Organoids isolated from teh BME gels using Dispase II and embedded in eithe BME or Collagen I for 5 days.

extract_protocol:
RNA isolation and library preparation was performed by the company SCdiscoveries (Utrecht, NL) according to their  published SORT-seq technique (Muraro et al., Cell Syst, 2016): using a FACS Aria II sorter, live single cells (based on DAPI exclusion and forward/side scatter properties) were sorted into 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100-200 nl of RT primers, dNTPs and synthetic mRNA Spike-Ins and immediately spun down and frozen to −80°C. Cells were lysed by 5 min at 65°C, after which RT and second strand mixes were dispersed with the Nanodrop II liquid handling platform (GC biotech). Aqueous phase was separated from the oil phase after pooling all cells in one library, followed by IVT transcription
Library preparation was performed according to the SORT-seq technique by Scdiscoveries: The CEL-Seq2 protocol was used for library prep. Primers consisted of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter. mRNA of each cell was then reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed for linear following the CEL-Seq 2 protocol (Hashimshony et al., 2016). Libraries were sequenced on an Illumina NextSeq using 75bp paired end sequencing.

treatment_protocol: MMTV-PyMT organoids growing in either 3D BME or collagen I were isolated using a combination of 20mg/mL Collagenase I (Cat# C0130, Sigma-Aldrich) and 1mg/mL Dispase II (Cat# 17105041, Life Technologies). Isolated organoids were dissociated into single cells using trypsin-EDTA. Single cell sorting into 384-well plate was performed by FACS.

value: Breast cancer cells

tag: model

value: MMTV-PyMT

tag: invasion status

value: invasion


title: Collagen replica 2 [UMC-AK2]


title: BAT, mRNA2

description:
MAPS_BAT.gtf
STRINGTIE_BAT.gtf


title: BME replica 3 [AK-CS3]

source_name: 5 days growing BME

value: no invasion


title: Collagen replica 1 [UMC-AK1]


title: 677_GFPneg

city: Paris

first: Isabelle

last: Leroux

address: 47 Boulevard de l'Hôpital

country: France

institute: Paris Brain Institute

data_processing:
Cell barcodes and UMIs were extracted with ddSeeker
Dropseq tools 2.0.0 has been used to trim starting sequence and polyA tail.
Then unaligned filtered bam were converted to fastq with picard tools.
STAR has been used to align reads on mm10 reference genome.
Finally, dropseq tools TagReadWithGeneExonFunction and DigitalExpression functions have been used to extract gene expression values for each gene, each cellular barcode.
Genome_build: mm10
Supplementary_files_format_and_content: DGE matrix, with a row for each gene, and a column for each cell

source_name: GBM_GFP- cell suspensions

growth_protocol: The lentivirus (1 µL, 6 x 108 PFU/mL) was stereotaxically injected in the right SVZ of brain mouse. From the next day, the mouse was injected i.p. with tamoxifen (TMX, 100 mg/kg) once per day for five consecutive days

extract_protocol:
GFP+ GBM was macrodissected, papain-based and mechanically dissociated. A debris removal step was performed, and blood cells were removed using a blood lysis buffer. Cells were labeled with eBiosciences Fixable Viability Dye Fluor 450 and sorted using the S3e cell sorter (Biorad). GFP+ and GFP- live cells were collected, centrifuged and resuspended in a final volume of HBSS-0,1%BSA to get a 3400 cells/µL solution.
Libraries were prepared according to Illumina's instructions accompanying the SureCell WTA 3′ Library Prep Kit. The cartridge was loaded with three GFP+ cell suspensions (GFP-1,2,3) and one GFP- cell suspension (GFPneg). Libraries were sequenced on the ddSEQ Single-Cell Isolator (Biorad) following the manufacturer's protocols.
paired-end. R1 contains the metadata, R2 mRNA

treatment_protocol: No treatment. The mouse was sacrificed at the endpoints.

tag: strain background

value: 129/SVJ x C57BL/6 x FVB

value: GlastCreERT2/+; Ptenfl/fl; p16-3MR/+

tag: injected lentivirus

tag: harvesting

value: end point


title: f3hrde-1_hypoxia_rep2 [small RNA-seq]

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
The illumine fastq files were assessed for quality with FastQC. The 3’ adaptors (TGGAATTCTCGGGTGCCAAGG) were removed and the 4 random bases at both 5’ and 3’ ends were trimmed with cutadapt (version 2.5).
The clipped reads were mapped to the C.elegans genome WS277 assembly with shortstack and allowing 1 mismatch.
Count tables were generated with featurecount and the differential analysis was performed with edgeR
Genome_build: WS277
Supplementary_files_format_and_content: Data matrix was generated with featurecount

growth_protocol: The worms were kept in 20 °C incubator with sufficient food supply for at least 3 generations before the hypoxic exposure experiments. For single exposure experiments, L4 stage worms were exposed at 0.1% oxygen level in a hypoxic chamber (Eppendorf Galaxy 48R incubator) for 16 hours at 20 °C, then they were returned to ambient oxygen level (~20 %).

extract_protocol:
The total RNA of worms in WT and hrde-1 mutants were extracted using mirVana miRNA Isolation kit (life technologies). 500 ng of total RNA was treated with RNA 5’ pyrophosphohydrolase (RppH) (NEB #M0356) at 37 °C for 30 min, to ensure 5’ monophosphate-independent capture of small RNAs. 500 mM EDTA was added to stop the reaction and was cleaned up in RNA Clean & Concentrator-5 (Zymo 11-352) and eluted in nuclease free water.
Around 100 -300 ng of total RNAs including small RNAs (larger than 17 nt) were used as starting materials for the library preparation using the Nextflex Small RNA-seq Kit v3 (NOVA-5132-06) for 32 libraries.

value: whole worm

tag: treatment

value: Hypoxia

tag: generation

tag: genotype/variation

tag: molecule subtype

value: small RNA


title: BME replica 2 [AK-CS2]


title: BME replica 1 [AK-CS1]


title: 677_GFP-1

source_name: GBM_GFP+ cell suspensions

tag: genotype


title: 677_GFP-3


title: f3hrde-1_hypoxia_rep1 [small RNA-seq]


title: JM8.N4 mESC, Triptolide 4hr, RNAPolIIXChIP, rep2

city: Cambridge

first: Viraat

middle: Y

last: Goel

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the a concatenation of the UCSC mm39 and hg38 genomes using bowtie2 v2.3.5.1 with --no-mixed --no-discordant.
Uniquely aligned reads were filtered for PCR duplicates using Sambamba markdup. Reads for each condition were randomly subsambled using normalization factors based on hg38 spike-in. Normalization factors were corrected using the ratio of human to mouse read counts in corresponding input samples.
Assembly: mm39; hg38
Supplementary files format and content: bigwig file with data based on all uniquely aligning non-duplicate reads

organism:
Homo sapiens
Mus musculus

growth_protocol: Mouse embryonic stem cells (JM8.N4 mESCs) were cultured on plates coated with 0.1% gelatin solution (Sigma-Aldrich) under feeder-free conditions in medium consisting of KnockOut DMEM (Thermofisher) with 15% FBS (HyClone, SH30396.03, Lot. No. AE28209315) and 1000U/mL LIF (home-made), 1 mM MEM Non-Essential Amino Acid Solution (Thermofisher), 2 mM GlutaMAX (Thermofisher), 100 μg/ml Penicillin-Streptomycin (Thermofisher), and 0.1 mM 2-mercapoethanol (Sigma) supplemented with 2i, 10 μM MEK inhibitor (Tocris) and 3 μM GSK inhibitor (Sigma). mESCs were fed daily by replacing half the medium and passaged every two days with 0.05% Trypsin-EDTA (Thermo Fisher Scientific). 1 day prior to harvesting, cells were swapped to medium as described above without 2i.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins. Following quenching, chromatin was sonicated. Chromatin crosslinked to RPB1 was immunoprecipitated and then reverse crosslinked. Naked DNA was further sonicated to the 400-800bp range.
DNA from RPB1 ChIP or input chromatin was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with a number of PCR cycles according to the manufacturer's protocol on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified twice using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR. Following qPCR quantification, libraries were submitted for sequencing.

treatment_protocol: Transcription inhibition was performed by adding triptolide to the media of confluent cells at 1 µM for 45 minutes.

tag: cell line

tag: cell type

value: Mouse embryonic stem cell

tag: spike-in reference_organism

value: Homo sapiens

tag: spike-in cell_line

tag: chip antibody

tag: antibody info

value: Cell Signaling Technology (#14958)

value: WT

value: Triptolide

tag: time

value: 4 hours


title: JM8.N4 mESC, Triptolide 4hr, RNAPolIIXChIP, rep1


title: JM8.N4 mESC, Triptolide 45min, RNAPolIIXChIP, rep2

value: 45 minutes


title: f3wt_hypoxia_rep2 [small RNA-seq]

tag: tissue


title: JM8.N4 mESC, WT, RNAPolIIXChIP, rep2


title: WAT, mRNA1

description:
MAPS_WAT.gtf
STRINGTIE_WAT.gtf

value: adipose tissue

tag: tissue subtype

value: white adipose tissue (WAT)

tag: replicate


title: f3wt_hypoxia_rep1 [small RNA-seq]


title: 677_GFP-2

tag: strain background

tag: injected lentivirus


title: f3wt_normoxia_rep2 [small RNA-seq]

tag: treatment

value: Normoxia


title: JM8.N4 mESC, Triptolide 4hr, XInput, rep1

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins. Following quenching, chromatin was sonicated and then reverse crosslinked. Naked DNA was further sonicated to the 400-800bp range.
DNA from RPB1 ChIP or input chromatin was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with a number of PCR cycles according to the manufacturer's protocol on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified twice using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR. Following qPCR quantification, libraries were submitted for sequencing.


title: f3wt_normoxia_rep1 [small RNA-seq]

tag: generation


title: f3hrde-1_normoxia_rep1 [small RNA-seq]

tag: genotype/variation


title: f3hrde-1_normoxia_rep2 [small RNA-seq]

tag: molecule subtype


title: JM8.N4 mESC, Triptolide 4hr, XInput, rep2

tag: genotype


title: f2hrde-1_hypoxia_rep2 [small RNA-seq]


title: 16HBE14o- ins-35kb #16 viewpoint_int1 [4C-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 4C-seq library with the CFTR intron 1 region as the viewpoint

data_processing:
library strategy: 4C-seq
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: Aligned 4C-seq of each clone and viewpoint in bigWig format

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925) with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per PMID: 31351925 for corresponding samples as listed in the treatment protocol section.

tag: cell line

value: human bronchial epithelial cells


title: JM8.N4 mESC, Triptolide 45min, XInput, rep2

tag: cell type


title: P7

city: Beijing

first: Jingtao

address: Dong Dan San Tiao Wu Hao

institute: Chinese Academy of Medical Sciences

description: polluted blood sample

hyb_protocol: Not provided

scan_protocol: The purity and concentration of DNA were estimated using Nanodrop 2000 (ThermoScietific).

data_processing: R (4.1.2) Bioconductor package

label: Cy5 and Cy3

source_name: genomic DNA from polution group sample 7

label_protocol: According to the sample group

growth_protocol: According to standard instructions

extract_protocol: A DNeasy Blood and Tissue Kit (Qiagen) was used to isolate DNA from whole blood.

treatment_protocol: According to standard instructions

tag: smoke status

value: yes

tag: alcohol status

tag: age

tag: gender

value: female

tag: cr concentration

tag: investigate year

tag: urine creatinine

value: whole blood


title: f2hrde-1_normoxia_rep1 [small RNA-seq]

tag: tissue

value: whole worm


title: f2hrde-1_hypoxia_rep1 [small RNA-seq]

value: Hypoxia


title: 16HBE14o- ins-35kb #16 viewpoint_-20.9kb [4C-seq]

description: 4C-seq library with the CFTR -20.9 kb region as the viewpoint


title: P8

description: polluted blood sample

source_name: genomic DNA from polution group sample 8

value: male


title: f2hrde-1_normoxia_rep2 [small RNA-seq]

value: small RNA


title: f2wt_normoxia_rep2 [small RNA-seq]


title: 16HBE14o- ins-35kb #65 rep 2

data_processing:
Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 or modified hg19 genomes using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: hg19 or '-35kb deletion/intron 1 insetion hg19 genome
Supplementary files format and content: hg19 aligned IDR ATAC-seq of each cell line in bigWig format
Supplementary files format and content: -35del/INSERTION Genome aligned IDR ATAC-seq of each cell line in bigWig format

growth_protocol: Cells were grown in DMEM + 10% FBS using standard protocols

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were construced using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion


title: P10

description: polluted blood sample

source_name: genomic DNA from polution group sample 10

value: no


title: 16HBE14o- del-35kb viewpoint_int1 [4C-seq]

value: del -35kb


title: 16HBE14o- WT viewpoint_-20.9kb [4C-seq]

value: WT


title: 16HBE14o- del-35kb viewpoint_-20.9kb [4C-seq]


title: C8

description: control blood sample

source_name: genomic DNA from control group sample 8


title: f2wt_hypoxia_rep2 [small RNA-seq]


title: 16HBE14o- ins-35kb #26 rep 2


title: f1hrde-1_hypoxia_rep2 [small RNA-seq]


title: f2wt_hypoxia_rep1 [small RNA-seq]


title: 16HBE14o- ins-35kb #26 rep 1


title: P9

description: polluted blood sample

source_name: genomic DNA from polution group sample 9


title: f1hrde-1_normoxia_rep2 [small RNA-seq]


title: f1hrde-1_hypoxia_rep1 [small RNA-seq]


title: 16HBE14o- ins-35kb #16 rep 2


title: C1

description: control blood sample

source_name: genomic DNA from control group sample 1


title: f2wt_normoxia_rep1 [small RNA-seq]


title: P2

description: polluted blood sample

source_name: genomic DNA from polution group sample 2


title: f1hrde-1_normoxia_rep1 [small RNA-seq]


title: C9

description: control blood sample

source_name: genomic DNA from control group sample 9


title: 16HBE14o- del-35kb rep 2


title: f1wt_hypoxia_rep2 [small RNA-seq]


title: 16HBE14o- del-35kb rep 1


title: f1wt_hypoxia_rep1 [small RNA-seq]


title: 16HBE14o- WT rep 2


title: C6

description: control blood sample

source_name: genomic DNA from control group sample 6


title: P3

description: polluted blood sample

source_name: genomic DNA from polution group sample 3


title: f1wt_normoxia_rep2 [small RNA-seq]


title: C5

description: control blood sample

source_name: genomic DNA from control group sample 5


title: C7

description: control blood sample

source_name: genomic DNA from control group sample 7


title: P1

description: polluted blood sample

source_name: genomic DNA from polution group sample 1


title: 16HBE14o- WT rep 1


title: 16HBE14o- ins-35kb #65 rep 1


title: 16HBE14o- ins-35kb #16 rep 1


title: P6

description: polluted blood sample

source_name: genomic DNA from polution group sample 6


title: C4

description: control blood sample

source_name: genomic DNA from control group sample 4


title: A549 HCoV-OC43 infected, treated with Remdesivir rep3

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed using cutadapt version 2.3.
Trimmed reads were aligned to human genome version hg38 and Ensembl gene annotations version 84 using STAR aligner version 2.7.0d_0221 and ENCODE long RNA-seq pipeline parameters (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM version 1.3.1.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene expression (TPM)

source_name: A549 cell line

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC) and maintained in high-glucose Dulbecco's modified Eagle's medium (HyClone) with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using a total RNA miniprep kit (Sigma) with the On-column DNase I digestion step included.
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 system using the High output V2.5 kit (Illumina Inc., San Diego, CA). Read data was processed and multiplexed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).

value: A549 cell line

tag: infection

value: infected

value: Remdesivir

tag: treatment concentration

value: 1 uM


title: p0hrde-1_hypoxia_rep2 [small RNA-seq]

tag: treatment


title: p0hrde-1_normoxia_rep2 [small RNA-seq]

tag: generation


title: A549 HCoV-OC43 infected, treated with Remdesivir rep1


title: p0hrde-1_hypoxia_rep1 [small RNA-seq]

tag: genotype/variation


title: A549 HCoV-OC43 infected, treated with Remdesivir rep2


title: C2

description: control blood sample

source_name: genomic DNA from control group sample 2


title: f1wt_normoxia_rep1 [small RNA-seq]

tag: molecule subtype


title: C3

description: control blood sample

source_name: genomic DNA from control group sample 3


title: p0hrde-1_normoxia_rep1 [small RNA-seq]


title: A549 HCoV-OC43 infected, treated with SBI-756 rep3


title: p0wt_hypoxia_rep1 [small RNA-seq]


title: p0wt_hypoxia_rep2 [small RNA-seq]


title: A549 HCoV-OC43 infected, treated with SBI-756 rep2


title: A549 HCoV-OC43 infected, treated with SBI-5844 rep2

value: 10 uM


title: A549 HCoV-OC43 infected, treated with SBI-5844 rep1


title: Sib4

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: rRNA-depleted

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM, Cufflinks (version 2.2.1) was used.
Assembly: GRcz10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Danio rerio

source_name: endothelial cells

extract_protocol:
kdrl-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo). Ribosomal RNA was depleted with Ribogone (Clontech).
Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA-Seq Kit (Clontech).

tag: time

value: 28 hours post fertilization


title: p0wt_normoxia_rep2 [small RNA-seq]

value: Normoxia


title: p0wt_normoxia_rep1 [small RNA-seq]


title: A549 HCoV-OC43 infected, treated with SBI-0498 rep3

tag: cell line


title: P5

description: polluted blood sample

source_name: genomic DNA from polution group sample 5

value: yes


title: P4

description: polluted blood sample

source_name: genomic DNA from polution group sample 4

value: female


title: A549 HCoV-OC43 infected, treated with SBI-0498 rep2


title: A549 HCoV-OC43 infected, treated with SBI-5844 rep3


title: A549 HCoV-OC43 infected, treated with SBI-0498 rep1


title: C10

description: control blood sample

source_name: genomic DNA from control group sample 10

value: whole blood


title: Sib3

description: rRNA-depleted


title: Sib2

description: rRNA-depleted


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P9-7]

city: New York

first: Ana

middle: S.

last: Gonzalez-Reiche

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: average read depth ~30 million pairs of 2 × 95 bp reads

data_processing:
Illumina’s Real-Time Analysis (RTA) software was used for base-calling and quality scoring of RNA-sequencing (RNA-seq) data.
Adapters were removed with cutadapt and base quality trimming to remove 3′ read sequences if more than 20 bases with Q ≥ 20 were present
QC-passed paired-end reads were mapped to the human hg38 reference genome using STAR
A combined matrix of mapped paired end read raw counts (genes x samples) was generated with featureCounts
Assembly: hg38 (Release 23 GRCh38.p3)
Supplementary files format and content: A single tab-delimited text file includes all FPKM values for each Sample

source_name: Blood

extract_protocol:
RNAdvance Blood Kit (Beckman Coulter)
Libraries were prepared from 300 ng of total RNA were using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States)

treatment_protocol: Blood samples collected with PAXgene tubes

value: Blood

tag: cell type

value: Blood cells

value: Male

value: Day 113


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P9-6]

value: Day 92


title: Sib1

description: rRNA-depleted


title: A549 HCoV-OC43 infected rep3

value: untreated


title: A549 HCoV-OC43 infected rep2


title: A549 uninfected control rep3

value: uninfected


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P9-5]

value: Day 85


title: Mut4

description: rRNA-depleted


title: A549 HCoV-OC43 infected rep1

value: A549 cell line

value: infected


title: A549 uninfected control rep2


title: Mut3

description: rRNA-depleted


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P9-3]

value: Day 7


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P9-4]

value: Day 29


title: A549 uninfected control rep1


title: Mut2

description: rRNA-depleted

value: 28 hours post fertilization


title: Group 2 LAIV8-IIV5 Day 113 [P8-7]


title: Mut1

description: rRNA-depleted