title: donor 2, HTO

city: New York

first: Oriana

last: Miltiadous

address: 1275 York Ave

institute: Memorial Sloan Kettering

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.1.0)
Assembly: GRCh38-2020-A
Supplementary files format and content: in_vitro_human.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

source_name: peripheral blood mononuclear cells

extract_protocol:
In brief, human T cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 1,000 cells per ul. Live cells were enriched applying the LeviCell v1 system following the user guide manual (20’ incubation time in Levitation Buffer with concentration of 150mM Levitation Agent). The viability of cells after enrichment was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. A total of 30,000 cells were targeted for each sample.
Samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO) following the previously published protocol73. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package73. Viable cells were identified based on library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. Hashing of isolated T cells: For scRNA-seq seq, individual cell suspension were incubated for 30 min with hashtag oligonucleotide-conjugated antibodies (Extended Data Table 9) in addition to FACS antibodies

value: peripheral blood mononuclear cells

tag: subject id

value: donor 2

value: CD3 T cells

value: unknown

value: primary T cells treated with DMSO or FXR ligands


title: 12_H3K27ac_r3_D2PRNBSA

status: Public on Feb 09 2024

type: SRA

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

country: USA

institute: Fred Hutch Cancer Research

library_source: genomic

data_processing:
Peak calls for ASCL1, H3K4me1, H3K4me3 and H3K27ac from CUT&RUN data at different timepoints were performed using SEACR (v1.3)
Assembly: hg38
Supplementary files format and content: bed files
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: C4-2B cells were maintained in Advanced DMEM/F12 medium supplemented with 1X serum-free B27, 10 ng/mL recombinant human basic FGF (bFGF), 10 ng/mL recombinant human EGF, 100 U/mL penicillin and 100 μg/mL streptomycin, and 4 mmol/L GlutaMAX in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cut-and-Run_extract_protocol.rtf PMID 25827087
Libraries were prepared using the AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1)

tag: cell line

tag: cell type

value: Prostate cancer cells

tag: chip antibody

value: H3K27ac (EMD, MABE647)


title: 11_H3K27ac_r2_D2PRNBSA


title: WT_scRNAseq

city: Shanghai

first: Yijie

last: Huang

state: Shanghai

address: 上海市徐汇区淮海西路241号

department: Cardiology

country: China

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.0.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Cell Ranger output

molecule: total RNA

organism: Mus musculus

source_name: duodenum tissues

extract_protocol:
Tissues were cut into 0.5mm3 pieces, and digested in HBSS containing 0.2% collagenase type II in 37°C with a shaking speed of 50rpm for about 40min. The digested suspension was subsequently filtered through a 40-µm cell strainer and washed with pre-warmed Dulbecco's Modified Eagle’s Medium (DMEM)/F-12 50/50 supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, and 100U/ml streptomycin, and centrifuged at 300 x g for 5min.
Library was performed according to the manufacturer’s instructions  (single cell 3’ v3 protocol, 10x Genomics).

tag: tissue

value: duodenum tissues

tag: genotype

value: WT


title: Knockout sample 2755 Liver

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (UCSC, GRCm39) using the alignment tool STAR (v2.7.10b). Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0). HTSeq (v.0.2.0) and python (v.2.7) was used for counting mapped sequencing reads. RSeQC (v5.0.1) was used to further quality control mapped sequenced reads.
Quantified read counts were normalized and analyzed using DESeq2 (v1.12.3) to determine differential expression between groups, within the R statistical computing environment (v4.2.2)
Pairwise differential expression analysis were performed with DESeq2. Identical read filtering parameters were used for different organs, and genes with read counts < 5 in at least half of the samples per treatment group were removed.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Liver

extract_protocol:
Total RNA from tissue was isolated using the PureLink RNA mini kit using manufacturer’s instructions (Invitrogen). Genomic DNA was removed using RapidOut DNA Removal Kit (ThermoFisher).
Sequencing libraries were constructed using a 3’ Tag-based approach (TagSeq), targeting the 3’ end of mRNA fragments.
3’ TagSeq was performed by the University of Texas Genomic Sequencing and Analysis Facility (RRID#: SCR_021713) . Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550bp on a 2% gel using the Blue Pippin (Sage Science). The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were then sequenced on the NovaSeq 6000 (Illumina) instrument with single-end, 100-bp reads.

value: Liver

tag: chow

value: Low Mn Chow

value: total homogenate

tag: mouse background

value: hybrid C57BL/6 × 129S

value: KO

tag: treatment

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: Control sample 2544 Liver

value: Ctl


title: 10_H3K27ac_r1_D2PRNBSA


title: 9_H3K4me1_r3_D2PRNBSA

value: H3K4me1 (Abcam, #ab8895)


title: donor 2, GEX

state: NY

department: Pediatrics

molecule: polyA RNA

value: peripheral blood mononuclear cells

value: wild type

tag: age


title: donor 1, HTO

value: donor 1

value: CD3 T cells


title: 8_H3K4me1_r2_D2PRNBSA


title: Knockout sample 2543 Liver


title: 7_H3K4me1_r1_D2PRNBSA


title: 5_H3K4me3_r2_D2PRNBSA


title: 6_H3K4me3_r3_D2PRNBSA


title: Control sample 2534 Liver


title: Control sample 2535 Liver


title: 4_H3K4me3_r1_D2PRNBSA


title: 3_ASCL1_r3_D2PRNBSA

value: ASCL1 (Abcam, #ab74065)


title: Knockout sample 2533 Liver


title: HEK 293T, RPB1_26xCTD, RNA, replicate 2

first: Qian

last: Zhang

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

data_processing:
Quality of raw reads was assessed using FastQC read quality reports (Galaxy).
Adapter Illumina sequences (--illumina) were trimmed off by TrimGalore! v.0.6.7 with default parameters.
Reads were aligned to human reference genome, GRCh38 version, using HISAT2 fast aligner v.2.2.1 with default parameters, except Reverse (RF) --rna-strandedness. Gencode v38 gtf file was used as annotation gtf.
Mapped fragments were quantified by featureCounts v.2.0.1 in Galaxy.
Assembly: GRCh38
Supplementary files format and content: bam files outputted from HISAT2 fast aligner v.2.2.1.
Supplementary files format and content: featureCounts outputted from featureCounts v.2.0.1 in Galaxy.

source_name: HEK 293T

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated using DirectZol RNA Miniprep kit (Zymo Research). 1 ug RNA per sample was used for library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library.

treatment_protocol: We transfected RPB1_52xCTD and RPB1_26xCTD plasmids in HEK 293T cells separately, after 24 h of transfection, α-amanitin 2.5 μg/mL was added in the culture media for extra 72 h.

value: HEK 293T

value: embryonic kidney cells

value: alpha--amanitin


title: HEK 293T, RPB1_26xCTD, RNA, replicate 1

value: WT


title: 2_ASCL1_r2_D2PRNBSA

value: Prostate cancer cells


title: HEK 293T, RPB1_52xCTD, RNA, replicate 2


title: 1_ASCL1_r1_D2PRNBSA


title: P5_Well8_measurements

type: RNA

city: Leuven

first: Elia

last: Micoli

address: Herestraat 49

department: VIB - Center for Brain and Disease Research

country: Belgium

institute: VIB - KU Leuven

description:
P5_Well8_measurements
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 16_P5_W8

hyb_protocol: Resolve Biosciences Molecular Cartography custom platform (94 genes)

data_processing: The final image analysis was performed  using Genexyz Polylux tool plugin from Resolve Bioscience to examine specific Molecular Cartography signals

source_name: Fixed tissue

extract_protocol: P5 brain tissue sections were dissected, fresh frozen and placen on Resolve BioScience slides.After fixation the sections were used for Molecular Cartography. Tissue were primed, followed by overnight hybridization of all the probes specific for the trarget genes.The excess of probes was removed and color development, imaging and decolorization were repeated for multiple cycles to build a unique combinatorial code for every target gene derived from raw images. Samples were imaged on a Zeiss Celldiscoverer 7.

value: P5 Brain


title: E8.5 embryo, Cdca7G305V/G305V, ONT adaptive sampling

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

country: Netherlands

institute: Leiden Univeristy Medica Center

data_processing:
The basecalling with modification was done after the Adaptive Sampling run was completed using Guppy version 6.3.9 with model dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_sup_prom.cfg. The BAM file containing the fastq reads and the modifications were mapped against mm10 using samtools (version 1.13) with operation fastq and flags -TMM,ML and piped to Minimap2 (version 2.24) were no secondary mapping was allowed. The output results in a sam file which also contains the modification information. The sam files were converted to bam file, sorted and indexed using samtools.  The sam files were converted to bam file, sorted and indexed using samtools.
Assembly: mm10
Supplementary files format and content: bw, bed (input for ONT adaptive sampling)
Library strategy: ONT adaptive sampling

source_name: E8.5 embryo

extract_protocol:
Genomic DNA (gDNA) was isolated using the salt-extraction method. Briefly, tissues were lysed in cell lysis buffer (50 mM Tris-HCl (pH 8), 4 mM EDTA (pH 8), 2% SDS) plus Proteinase K (390973P, VWR), and incubated at 55°C overnight. Cell lysate was treated with RNaseA (EN0531, Thermo) at 37°C for 1 h. Saturated NaCl buffer was added, followed by addition of isopropanol to precipitate gDNA and washing with 70% EtOH. gDNA was dissolved in water. DNA concentration was determined by Qubit using the Qubit High Sensitivity Kit and size was determined on a Femto Pulse System (Agilent Technologies).
ONT sequencing libraries were prepared using the Genomic DNA ligation kit (SQK-LSK114) and sequenced using the vendors instructions. Briefly, 600ng gDNA was used as input and yielded approximately 20fmol of library to load on a PromethION Flowcell (FLO-PRO114M) and sequenced on a PromethION 24 device (A100). Adaptive Sampling in MinKNOW (v22.10.7) was enabled during the sequencing of these samples using fast basecalling and a BED file was provided for the regions of interest while mm10 of the mouse genome was used as a reference for the enrichment. After 20h the run yielded around 400k reads which accounts for 3.53Gb with a N50 of 28kb.

tag: strain

value: FVB

value: E8.5 embryo


title: HEK 293T, RPB1_52xCTD, RNA, replicate 1


title: Knockout sample 2529 Liver

value: Liver

value: Low Mn Chow

value: total homogenate

value: hybrid C57BL/6 × 129S

value: KO


title: Control sample 2467 Liver

value: Ctl

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: E8.5 embryo, WT, ONT adaptive sampling


title: P5_Well8_Index_Region

description:
P5_Well8_index_region_layer
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 15_P5_W8


title: P5_Well8_DAPI

description:
Well8_DAPI
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 14_P5_W8


title: Knockout sample 2466 Liver


title: donor 1, GEX

value: peripheral blood mononuclear cells

value: donor 1

value: CD3 T cells

value: wild type

value: unknown

value: primary T cells treated with DMSO or FXR ligands


title: HEK 293T, IgG, replicate 2

data_processing:
Base-calling was performed by Novogene Inc. with the latest Illumina software.
Quality of raw reads was assessed using FastQC read quality reports (Galaxy).
Adapter Illumina sequences (--illumina) were trimmed off by TrimGalore! v.0.6.7 with default parameters.
Reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS v2.2.7.1 with the default significance cut-off q-value <=0.1 for broad peaks, bigWig files were generated using the bedGraph files of scores outputted from MACS2.
Assembly: hg38
Supplementary files format and content: bigWig files outputted from MACS2 (except for input files).

extract_protocol:
Cells were fixed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorupter UCD-200, and then GFP antibody was used for immunoprecipitation (IP).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina with barcode primers from NEBNext® Multiplex Oligos. 5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 11 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: We transfected RPB1_52xCTD, RPB1_26xCTD or RPB1_26xCTD T4E/S7E mutants with YFP tag  plasmids in HEK 293T cells separately, after 24 h of transfection, cells were collected for Chip experiment.

value: HEK 293T

value: embryonic kidney cells

value: WT


title: P5_Well7_measurements

description:
P5_Well7_measurements
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 12_P5_W7

value: P5 Brain


title: HEK 293T, IgG, replicate 1


title: RAS_day21_CD11c-_rep2

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

department: Immunology

country: Australia

institute: The Australian National University

data_processing:
The generated single-end 75bp reads were processed under the Galaxy project online platform following standard protocol to generate mapped count files.
Assembly: GRCm38
Supplementary files format and content: The processed file: raw_count_files.tar.gz contains raw counts files for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Qiagen) following the recommended protocol.
Library preparation was completed using NEBNext® Single Cell/Low Input RNA Library Prep Kit following the recommended protocol.

value: Spleen

value: B cell


title: RAS_day21_CD11c+_rep1


title: RAS_day21_CD11c-_rep1


title: Knockout sample 2755 Globus Pallidus

source_name: Globus Pallidus

value: Globus Pallidus

value: Low Mn Chow

value: total homogenate


title: Control sample 2544 Globus Pallidus

value: hybrid C57BL/6 × 129S

value: Ctl


title: Knockout sample 2543 Globus Pallidus

value: KO

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: RAS_day10_CD11c+_rep3


title: Longissimus dorsi muscle of Suhuai pig

city: NanJing

first: Wei

last: Xiao

state: JiangSu

address: No. 1,Weigang Road,Xuanwu District

institute: NanJing Agricultural University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: sscrofa11.1/susScr11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Longissimus dorsi

extract_protocol:
The 1-day-old Suhuai boar was anaesthetized before the trial started. Then, the skin of the back was disinfected, and the longest dorsal muscle tissue was taken for cell suspension preparation using a sterile scalpel (1 cm3).The collected tissues were washed 3 times with PBS, the appropriate amount of PBS was added, and the tissues were cut with ophthalmic scissors (<1 mm). Add 5 ml of tissue lysate and incubate at 37°C. The tissue digest contained 4 mg/ml papain (Sigma‒Aldrich, cat# 9001-73-4), 20 mg/ml collagenase II (Sigma‒Aldrich, cat# 9001-12-1), and 20 mg/ml collagenase IV (Sigma‒Aldrich, sku# C4-22-1G). The digestion reactions were shaken vigorously for 30 s and further incubated at 37°C for 30 to 40 min in an incubator with general shaking every 6 min to release cells. The released cells were passed through a 70-μm cell strainer (BD, 352350) and collected in 15-mL tubes. Sample viability was assessed via Trypan Blue (Thermo Fisher) and an automatic cell counter (Countstar).
GEMs are generated by combining barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction.P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

value: Longissimus dorsi


title: P5_Well7_DAPI

description:
Well7_DAPI
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 10_P5_W7


title: Control sample 2530 Liver

value: Liver


title: Control sample 2535 Globus Pallidus


title: HEK 293T, RPB1_T4E_sp, replicate 2


title: HEK 293T, RPB1_T4E_sp, replicate 1


title: RAS_day10_CD11c+_rep2


title: RAS_day21_CD11c+_rep2


title: HEK 293T, RPB1_T4E_all, replicate 2


title: Knockout sample 2533 Globus Pallidus


title: RAS_day10_CD11c+_rep1


title: P5_Well4_measurements

description:
P5_Well4_measurements
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 8_P5_W4


title: P5_Well8_Raw

description:
Well8_raw
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 13_P5_W8


title: P5_Well4_Index_Region

description:
P5_Well4_index_region_layer
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 7_P5_W4


title: RAS_day10_CD11c-_rep3


title: HEK 293T, RPB1_T4E_all, replicate 1


title: Control sample 2530 Globus Pallidus


title: Knockout sample 2529 Globus Pallidus


title: HEK 293T, RPB1_26xCTD, replicate 2


title: P5_Well4_DAPI

description:
Well4_DAPI
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 6_P5_W4


title: RAS_day10_CD11c-_rep1


title: HEK 293T, RPB1_52xCTD, replicate 2


title: Control sample 2467 Globus Pallidus


title: P5_Well7_Index_Region

description:
P5_Well7_index_region_layer
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 11_P5_W7


title: HEK 293T, RPB1_26xCTD, replicate 1


title: RAS_day10_CD11c-_rep2


title: P5_Well4_Raw

description:
Well4_raw
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 5_P5_W4


title: P5_Well3_measurements

description:
P5_Well3_measurements
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 4_P5_W3


title: RAS_day4_CD11c+_rep1


title: P5_Well7_Raw

description:
Well7_raw
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 9_P5_W7


title: RAS_day4_CD11c+_rep2


title: HEK 293T, RPB1_52xCTD, replicate 1


title: Control sample 2534 Globus Pallidus


title: Knockout sample 2466 Globus Pallidus


title: Knockout sample 2755 Caudate Putamen

source_name: Caudate Putamen

value: Caudate Putamen


title: RAS_day4_CD11c-_rep2


title: AORB_2

city: Atlanta

first: Shuichi

last: Takayama

state: GA

address: 950 Atlantic Dr NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description: AORB replicate 2

data_processing:
FASTQ files provided by Georgia Tech Molecular Evolution Core were deposited onto BaseSapce, then downloaded to Georgia Tech’s high-performance computing cluster called Partnership for an Advanced Computing Environment (PACE). Quality control was then performed using FastQC.
Slurm scheduler was used to run pipseeker software. pipseeker outputs UMAP, cluster information, differential expressions, as well as feature plots.
Assembly: GRCh38.p14
Supplementary files format and content: barcodes, features, matrix

source_name: Bronchi

extract_protocol:
Organoids were dissociated in TrypLE to collect single cell suspension. A cell purification kit was to enrich live cells to improve cell viability. Purified cell suspension was dilluted according to PIPSeq recommendation. PIPSeq T2 v4.0 kit was used to capture cells, isolate mRNA, synthesize cDNA, and prepare library.
The cDNA was synthesized using the kits included in PIPseq-T2-v4 kits (Fluent BioSciences). Library preparation kits were also inlcuded in the same PIPseq kits. Libraries with a passing QC score were then used for sequencing on a 100-cycle NovaSeq SP kit with read lengths as specified by Fluent BioSciences.

value: Bronchi

value: NHBE

value: Epithelial

tag: organoid type

value: AORBs


title: P5_Well3_Raw

description:
Well3_raw
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 1_P5_W3

value: P5 Brain


title: Knockout sample 2543 Caudate Putamen


title: Control sample 2544 Caudate Putamen


title: AORB_1

description: AORB replicate 1


title: OB023_SVF_PD1_PLUS_2

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.32)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts. Only reads mapped to exons were considered in the counting procedure.
Genomic features were annotated according to the Gencode basic annotations (Gencode version 28)
Assembly: UCSC hg38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: stromal vascular fraction

extract_protocol:
RNA extraction was carried out with Qiagen Micro RNeasy kit
cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

treatment_protocol: Peripheral blood samples were processed to isolate PBMC using Lympholyte Cell Separation density gradient centrifugation media . Visceral adipose tissue samples were minced and enzimatically digested to isolate stromal vascular fraction (SVF). PBMC and SVF samples were FACS-stained to sort PD-1+ CD4 Tconv cells

value: stromal vascular fraction

tag: cell subset

value: PD-1+ CD4 Tconv cells

value: primary CD4 T lymphocytes

tag: disease state

value: obese dysglycemic

tag: patient of_origin


title: pchabaudi_infection_CD11c+_rep3

value: Spleen

value: B cell


title: Pa, hard, sup, 17h, rep2

city: Bethesda

first: Anupama

last: Khare

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

data_processing:
Reads were cut with Cutadapt. Sequence AGATCGGAAGAGC was removed.
Reads were trimmed with Trimmomatic for single end using leading (3), trailing (3), sliding window (4-15), and minimum length of 10.
Rockhopper was run to match reads to P. aeruginosa UCBPP-PA14 genome and compare expression levels.
Assembly: RefSeq GCF_000014625.1
Supplementary files format and content: txt files were generated using Rockhopper

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa was grown on semisolid (0.5% agar) or hard (1.5% agar) plates containing a modified M63 medium at 37C

extract_protocol:
RNA Purification Plus Kit (Norgen)
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: The plates contained either 25% of media salts control or S. aureus supernatant and were incubated for 17 h

value: bacterial

value: WT

value: S. aureus supernatant


title: pchabaudi_infection_CD11c+_rep2


title: Hela Cells,  1 μmol/L concentration of JQ1 treated for 72h [JQ-1-3]

city: Quanzhou

first: Jianqing

last: Zheng

state: Fujian

address: No. 950, Donghai Street, Fengze District, Quanzhou 362000, Fujian Province, P.R.

institute: The Second Affiliated Hospital of Fujian Medical University

data_processing:
Using Fastp software to filter Raw Data
The rRNA sequences were remove from the sequencing data using bowtie2 software.
Reference Sequence mapping analysis
Quality evaluation of Transcriptome data using RSeQC software
Read count extraction and normalization were performed
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The HeLa-cell lines were cultured in DMEM medium (GIBCO) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in 5.0% CO2 at 37 °C.

extract_protocol:
Total cellular RNA was extracted according to the kit instructions, and the RNA purity and concentration were determined using a spectrophotometer and the Qubit RNA assay kit in the Invitrogen Qubit 3.0. Agarose gel electrophoresis (NanoDrop 2000) and Agilent 2100 Bioanalyzer were used to assess the RNA integrity.
RNA sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit. The constructed libraries were sequenced using the Illumina Novaseq 6000 sequencing platform.

treatment_protocol: Based on the CCK-8 assay results, 1 μmol/L concentration of JQ1 treated for 72h was applied to inhibit HeLa cells.

value: Hela Cells

value: Human cervical cancer cells


title: Pa, hard, sup, 17h, rep1


title: pchabaudi_infection_CD11c+_rep1


title: Pa, hard, salts, 17h, rep2

value: media salts


title: Control sample 2534 Caudate Putamen

value: Caudate Putamen

value: Low Mn Chow

value: total homogenate

value: hybrid C57BL/6 × 129S

value: Ctl

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: P5_Well3_Index_Region

description:
P5_Well3_index_region_layer
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 3_P5_W3

value: P5 Brain


title: Hela Cells,  1 μmol/L concentration of JQ1 treated for 72h [JQ-1-2]


title: Knockout sample 2533 Caudate Putamen

value: KO


title: Hela Cells,  1 μmol/L concentration of JQ1 treated for 72h [JQ-1-1]


title: pchabaudi_infection_CD11c-_rep3


title: P5_Well3_DAPI

description:
Well3_DAPI
Probe based
94 probe based hybridization for spatial transcriptomic
SAMPLE 2_P5_W3


title: Pa, hard, salts, 17h, rep1


title: pchabaudi_infection_CD11c-_rep2


title: Pa, swarm, sup, 17h, rep2


title: Hela Cells, control [CTL-2]

source_name: Hela Cells, control

value: incubated with a drug-free medium for 72 h


title: Control sample 2530 Caudate Putamen


title: RAS_day4_CD11c-_rep1

value: Spleen


title: Pa, swarm, sup, 17h, rep1


title: Hela Cells, control [CTL-1]


title: Knockout sample 2466 Caudate Putamen


title: pchabaudi_infection_CD11c-_rep1

value: B cell


title: Control sample 2467 Caudate Putamen


title: In_vitro_no_cytokine_rep3


title: Knockout sample 2529 Caudate Putamen


title: Pa, swarm, salts, 17h, rep2

value: bacterial


title: In_vitro_no_cytokine_rep2


title: Control sample 2535 Caudate Putamen


title: Pa, swarm, salts, 17h, rep1

value: WT


title: Knockout sample 2755 Substantia Nigra

source_name: Substantia Nigra

value: Substantia Nigra


title: Hela Cells, control [CTL-3]

value: Hela Cells


title: In_vitro_no_cytokine_rep1


title: NHBE_3D_O-3

data_processing:
FASTQ files provided by Emory Integrated Genomics Core were first downloaded to Georgia Tech’s high-performance computing cluster called Partnership for an Advanced Computing Environment (PACE). Quality control was then performed using FastQC.
Upon passing quality requirements, the reads were aligned using STAR version 2.7.10a. A custom Python script was written to generate a gene count matrix.
Genes with less than 0.5 CPM in at least 3 samples were eliminated. Differential gene expression analysis was conducted using the EdgeR package in R. PCA analysis was performed to examine the samples for possible outliers prior to further analysis. The counts were normalized based on library size using the default TMM method from EdgeR. A comparison was run between the two groups through GLM, and LRT to identified statistically significant differential expressions. The cutoff for significance was set at under an alpha value of 0.05 for the adjusted p-value, and the log2 fold change of ±1.
Assembly: GRCh38.p14
Supplementary files format and content: AORB_normalized_count.csv

extract_protocol:
Cells/organoids were lysed in RLT buffer, then processed for RNA extraction, or flash frozen, and stored in -80oC until future extraction. RNA was isolated using the Quick-RNA Microprep Kit (Zymo Research)
The cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio). The final sequencing library was made using the Nextera XT kit (Illumina). The library construction used Nextera XT chemistry which tagmented 200pg of DNA and added adapters in one step. The fragmented and tagged DNA was then PCR amplified for 12 cycles to incorporate dual-indexing sequencing adapters to generate the final library. A combination of both concentration and library size patterning was used as QC metrics to determine the success of the assay. The UV Qubit fluorometer quantitation step determined the concentration of the library. The Bio/Fragment Analyzer trace revealed the size distribution and concentration of the final sequencing library. Based on these three parameters we assigned library scores to each library. Libraries with a pass score were then used for sequencing in NextSeq 550.

value: Bronchi

value: NHBE

value: Epithelial

value: Infection with Omicron SARS-CoV-2

tag: organoid status

value: Organoid+Omicron SARS-CoV-2


title: Knockout sample 2543 Substantia Nigra

value: Low Mn Chow

value: total homogenate

value: hybrid C57BL/6 × 129S


title: OE_FOXO3A_2

city: Urumqi

first: Zhuo

last: Chen

institute: The First Affiliated Hospital of Xinjiang Medical University

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling. Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
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.
Clean reads were aligned to the GRCh38 genome by HISAT2 allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: FOXO3A overexpressed  in HUVEC cell

growth_protocol: The HUVEC cells line (Angio-Proteomie, Boston, MA, USA) were cultured at 37℃ with 5% CO2 in Ham's F-12K with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.. HUVEC cells were infected by lentivirus with MOI=35.

extract_protocol:
Total RNAs were extracted from HUVEC cells using TRIzol Reagent (Invitrogen, cat. NO 15596026 ） following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Infected cells were harvested after 48h for RT-qPCR and Western blotting analysis.

value: Umbilical Vein

value: HUVEC

value: FOXO3A overexpressed


title: Control sample 2544 Substantia Nigra

value: Ctl

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: NHBE_3D_O-2


title: OE_FOXO3A_1


title: Control sample 2535 Substantia Nigra


title: In_vitro_IL21+TGFb_rep1

value: Spleen

value: B cell


title: NHBE_3D_O-1


title: NC_3

source_name: HUVEC  cell (control plasmid)

value: control


title: NC_2


title: In_vitro_IL21+antiTGFb_rep2


title: OE_FOXO3A_3


title: NC_1


title: Control sample 2534 Substantia Nigra

value: Substantia Nigra


title: Knockout sample 2533 Substantia Nigra

value: KO


title: NHBE_3D_D-3

value: Bronchi

value: NHBE

value: Infection with Delta SARS-CoV-2

value: Organoid+Delta SARS-CoV-2


title: i3Neuron, BORCS5-KO neuron, biological rep 3

first: Raffaella

last: De Pace

state: Maryland

address: 9000 Rockville Pike Bethesda 35A 2F242 20892

department: NICHD

institute: NIH/NICHD

description:
BORCS5_Neuron_3
featurecounts.txt

data_processing:
Sequenced reads were aligned to GRCh38 human reference GENCODE release 28 using STAR (1-pass) v2.7.8a.
Aligned reads were quantitated using the featureCounts of the subread package v2.0.1 with GRCh38 human reference GENCODE release 28.
Assembly: GRCh38
Supplementary files format and content: tab-separated read count table with columns for samples and rows for genes

source_name: neuron

growth_protocol:
Human-induced pluripotent stem cells (iPSCs) expressing doxycycline-inducible NGN2 (neurogenin) were cultured on Matrigel-coated dishes in Essential 8 Flex Medium (E8Flex) (Thermo Fisher Scientific) according to the manufacturer’s instructions.
iPSCs were seeded on day 0 in induction medium containing DMEM/F12 (Gibco, Thermo Fisher Scientific) with 1 x non-essential amino acids (NEAA) (Gibco, Thermo Fisher Scientific), 1× GlutaMAX (Gibco, Thermo Fisher Scientific), 1 x N2A supplement (Gibco, Thermo Fisher Scientific), 2 μg/mL doxycycline (Millipore Sigma), and 10 μM Y-27632 dihydrochloride ROCK inhibitor (Selleckchem).
The induction medium was changed every day for three days. Cells were then lifted with Accutase, counted and plated in neuronal culture medium consisting of BrainPhys medium (Stem Cell Technology) supplemented with 10 ng/mL neurotrophin-3 (Peprotech, Thermo Fisher Scientific), 10 ng/mL BDNF (Peprotech, Thermo Fisher Scientific), 1 x B-27™ Supplement serum free (Gibco, Thermo Fisher Scientific), 2 μg/mL doxycycline (Millipore Sigma), and 1 μg/mL mouse laminin (Gibco, Thermo Fisher Scientific).
The coverslips for i3Neurons growth were pre-treated with poly-lysine and laminin. Every three days, half of the medium was removed, and an equal volume of fresh medium was added to maintain neuronal health

extract_protocol:
RNA from three axonal or neuronal compartments was extracted using a total of 100 μl of the kit’s extraction buffer.
No carrier RNA was used for the extraction. On-column DNase digestion was performed. The RNA was eluted from the columns with 10 μl RNase-free water.
5 μl for axon samples and 1 μl for neuron samples were used for synthesizing cDNAs using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara). Nextera XT DNA Library Preparation Kit (Illumina) was used to prepare libraries from the cDNA samples using 1 ng cDNA.
Libraries were run on the NovaSeq (SP Kit v1.5 – 200 cycles). Approximately 1 billion 2x100 bp reads were obtained with sequencing.

value: neuron

value: iPSC

value: neuronal differentiation


title: NHBE_3D_D-2

value: Epithelial


title: In_vitro_IL21_rep2


title: In_vitro_IL21+antiTGFb_rep1


title: Control sample 2530 Substantia Nigra

value: Low Mn Chow

value: total homogenate

value: hybrid C57BL/6 × 129S


title: In_vitro_IL21+TGFb_rep2


title: In_vitro_IL21_rep1


title: Knockout sample 2529 Substantia Nigra

value: Slc30a10 genotype with low Mn rodent chow (~11 µg Mn/g chow)


title: NHBE_3D_W-3

value: Infection with Washington SARS-CoV-2

value: Organoid+Washington SARS-CoV-2


title: i3Neuron, BORCS5-KO neuron, biological rep 2

description:
BORCS5_Neuron_2
featurecounts.txt


title: i3Neuron, BORCS5-KO neuron, biological rep 1

description:
BORCS5_Neuron_1
featurecounts.txt


title: Control sample 2467 Substantia Nigra

value: Ctl


title: NHBE_3D_W-2


title: NHBE_3D_W-1


title: Knockout sample 2466 Substantia Nigra

value: Substantia Nigra


title: i3Neuron, BORCS5-KO axon, biological rep 3

description:
BORCS5_Axon_3
featurecounts.txt

source_name: axon

value: axon


title: i3Neuron, BORCS5-KO axon, biological rep 2

description:
BORCS5_Axon_2
featurecounts.txt


title: i3Neuron, BORCS5-KO axon, biological rep 1

description:
BORCS5_Axon_1
featurecounts.txt


title: Knockout sample 2379 Liver

value: Liver

value: Regular Chow

value: KO

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: Control sample 2363 Liver


title: i3Neuron, WT neuron, biological rep 2

description:
WT_Neuron_2
featurecounts.txt

value: neuron

value: WT


title: NHBE_3D_IL-13-3

value: Bronchi

value: NHBE


title: NHBE_3D_IL-13-2

value: Epithelial


title: NHBE_3D-6

value: Organoid


title: Control sample 2354 Liver

value: total homogenate

value: hybrid C57BL/6 × 129S


title: NHBE_3D_IL-13-1


title: i3Neuron, WT neuron, biological rep 1

description:
WT_Neuron_1
featurecounts.txt

value: iPSC

value: neuronal differentiation


title: NHBE_3D_D-1

value: Infection with Delta SARS-CoV-2

value: Organoid+Delta SARS-CoV-2


title: Control sample 2353 Liver

value: Ctl


title: NHBE_3D-5


title: i3Neuron, WT axon, biological rep 2

description:
WT_Axon_2
featurecounts.txt

value: axon


title: Knockout sample 2352 Liver

value: Liver

value: Regular Chow


title: NHBE_3D-4


title: TFH_PGD_5

city: Toulouse

first: Marie

last: Tosolini

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

description: Gene expression data from T follicular helper cells cohort 4

hyb_protocol: cRNA was fragmented and hybridized to Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: the chips were then washed, scanned on the Affymetrix Fluidics Station 400

data_processing: Raw data were normalized using RMA method and log (base 2)-transformed

label: biotin

source_name: Biopsie

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted of about 1 million NLC using TRIzolTM reagent (Invitrogen), according to the manufacturer’s instructions.

tag: type

value: TFH PGD


title: TFH_PGD_3


title: TFH_PGD_4


title: PRNBSN_R2, scATAC-seq

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
N/A
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: prostate cancer cell line

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: i3Neuron, WT axon, biological rep 1

description:
WT_Axon_1
featurecounts.txt

value: WT


title: NHBE_3D-3

value: Bronchi

value: NHBE


title: Knockout sample 2351 Liver

source_name: Liver

value: KO

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: TFH_PGD_1


title: Knockout sample 2350 Liver

value: total homogenate

value: hybrid C57BL/6 × 129S


title: PRNBSN_R1, scATAC-seq

description: 10x Genomics


title: TFH_KTE_5

description: Gene expression data from T follicular helper cells cohort 3

value: TFH KTE


title: PRNBSA_R2, scATAC-seq

description: 10x Genomics

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: Control sample 1333 Liver


title: NHBE_3D-2

value: Epithelial

value: Organoid


title: PRNBSA_R1, scATAC-seq

description: 10x Genomics


title: Control sample 1104 Liver

value: Ctl


title: NHBE_3D-1


title: Knockout sample 1103 Liver

value: Liver


title: NHBE_2D-6


title: TFH_KTE_7


title: NHBE_2D-5


title: PRNBS_R1, scATAC-seq

description: 10x Genomics

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: PRNBS_R2, scATAC-seq

description: 10x Genomics


title: TFH_KTE_6


title: Knockout sample 2379 Substantia Nigra

value: Substantia Nigra

value: Regular Chow


title: TFH_KTE_4


title: TFH_PGD_2

value: TFH PGD


title: TFH_KTE_3


title: NHBE_2D-4


title: TFH_KTE_2


title: TFH_KTE_1


title: PRNB_R2, scATAC-seq

description: 10x Genomics

value: prostate cancer cell line

value: shRB1, TP53(DN), MYCN, BCL2


title: Knockout sample 2379 Globus Pallidus

value: Globus Pallidus


title: NHBE_2D-2

value: Bronchi

value: NHBE


title: Knockout sample 2379 Caudate Putamen

value: Caudate Putamen

value: total homogenate

value: KO

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: PRNBSN_R2, scRNA-seq

description: 10x Genomics

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: Control sample 2363 Substantia Nigra

value: hybrid C57BL/6 × 129S


title: NHBE_2D-1

value: Epithelial


title: Knockout sample 1086 Liver

value: Liver


title: PRNBSN_R1, scRNA-seq

description: 10x Genomics


title: PRNBSA_R2, scRNA-seq

description: 10x Genomics

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: HCC1806 Cells, Platinum treated 10 days post treatment, R3

city: Lund

first: Christopher

middle: Paul

last: Carroll

state: Skåne

address: BMC, B11

department: Experimental Medical Science

country: Sweden

institute: Lund University

data_processing:
Genomic regions with high levels of transposition/tagging events are determined using the MACS2 peak calling algorithm
Assembly: Hg38
Supplementary files format and content: Tab deliminated text file

source_name: Breast

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS in humidified atomosphere 5% CO2 and 37C

extract_protocol:
100k nuclei were treated with T5n transposase and they underwent PCR amplification and libary preparation
atac-seq kit (Active Motif) was used according to manufcaters instruction

treatment_protocol: Drug resilient cells were produced by the addition of cisplatin at LD50 for 72h

value: Breast

value: Cancer cell line

value: WT

value: Cisplatin

tag: time point

value: 10 days


title: AITL_PGD_4

description: Gene expression data from Angioimmunoblastic T-cell lymphoma cohort 2

value: AITL PGD


title: Control sample 2363 Globus Pallidus

data_processing:
Reads were mapped to the mouse reference genome (UCSC, GRCm39) using the alignment tool STAR (v2.7.10b). Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0). HTSeq (v.0.2.0) and python (v.2.7) was used for counting mapped sequencing reads. RSeQC (v5.0.1) was used to further quality control mapped sequenced reads.
Quantified read counts were normalized and analyzed using DESeq2 (v1.12.3) to determine differential expression between groups, within the R statistical computing environment (v4.2.2)
Pairwise differential expression analysis were performed with DESeq2. Identical read filtering parameters were used for different organs, and genes with read counts < 5 in at least half of the samples per treatment group were removed.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

extract_protocol:
Total RNA from tissue was isolated using the PureLink RNA mini kit using manufacturer’s instructions (Invitrogen). Genomic DNA was removed using RapidOut DNA Removal Kit (ThermoFisher).
Sequencing libraries were constructed using a 3’ Tag-based approach (TagSeq), targeting the 3’ end of mRNA fragments.
3’ TagSeq was performed by the University of Texas Genomic Sequencing and Analysis Facility (RRID#: SCR_021713) . Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550bp on a 2% gel using the Blue Pippin (Sage Science). The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were then sequenced on the NovaSeq 6000 (Illumina) instrument with single-end, 100-bp reads.

value: Globus Pallidus

value: Regular Chow

value: Ctl


title: HCC1806 Cells, Platinum treated 10 days post treatment, R2

tag: cell line


title: NHBE_2D-3

value: Bronchi

value: NHBE

tag: cell type


title: PRNB_R1, scATAC-seq

description: 10x Genomics

value: prostate cancer cell line

value: shRB1, TP53(DN), MYCN, BCL2


title: PRNBSA_R1, scRNA-seq

description: 10x Genomics


title: PRNBS_R2, scRNA-seq

description: 10x Genomics

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: HCC1806 Cells, Platinum treated 10 days post treatment, R1


title: Control sample 2354 Substantia Nigra

value: Substantia Nigra

value: total homogenate

value: hybrid C57BL/6 × 129S

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: 6wk_kaku4-3

city: Beijing

first: Zhen

last: Su

address: #2 Yuanmingyuan Xilu

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
RNA-seq data with 3 biological replicates were generated. The paired-end clean reads of RNA-seq were aligned to the reference genome (TAIR10) by TopHat2 v2.0.9 software. FPKM values were calculated using Cufflinks.
Assembly: Arabidopsis reference genome (TAIR10)
Supplementary files format and content: RNA-seq_FPKM_matrix

organism: Arabidopsis thaliana

source_name: 6-week-old leaves

extract_protocol:
Total RNA was isolated using TRIZOL® reagent (Invitrogen, CA, USA) and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Sequencing libraries were constructed by the Beijing Genomics Institute and sequenced using an IlluminaHiSeq™ 2000 with 150-bp pair-end reads.

value: 6-week-old leaves


title: Control sample 2354 Globus Pallidus


title: AITL_PGD_3


title: HCC1806 Cells, Platinum treated 0 days post treatment, R3

value: Breast

value: Cancer cell line

value: WT

value: 0 day


title: AITL_PGD_5

value: AITL PGD


title: AITL_PGD_1


title: PRNBS_R1, scRNA-seq

first: John

last: Lee

institute: Fred Hutch Cancer Research

description: 10x Genomics


title: AITL_PGD_6


title: 6wk_kaku4-2


title: Control sample 2354 Caudate Putamen

value: Caudate Putamen

value: Regular Chow


title: HCC1806 Cells, Platinum treated 0 days post treatment, R2

value: Cisplatin


title: AITL_PG_2

description: Gene expression data from Angioimmunoblastic T-cell lymphoma cohort 1

value: AITL PG


title: 6wk_kaku4-1


title: AITL_PG_1


title: Control sample 2353 Substantia Nigra

value: Ctl


title: PRNB_R2, scRNA-seq

description: 10x Genomics

value: prostate cancer cell line

value: shRB1, TP53(DN), MYCN, BCL2


title: HCC1806 Cells, Platinum treated 0 days post treatment, R1


title: AITL_PGD_2


title: Control sample 2353 Globus Pallidus

value: Globus Pallidus


title: HCC1806 Cells, Control, R3

value: Vehicle


title: 6wkWT-2

value: col


title: 6wkWT-3


title: D14_PRNB_SRRM4_ASCL1_R2

data_processing:
UCSC TOIL processing pipeline was used to align the reads to the reference genome and generating count matrix files.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

extract_protocol:
RNA was harvested using PurelinkTM RNA mini kit (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep Kit following manufacturer's protocols.

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1

tag: time

value: Day 14


title: HCC1806 Cells, Control, R2

tag: tissue

value: Breast

value: Cancer cell line


title: Control sample 2353 Caudate Putamen

value: total homogenate

value: hybrid C57BL/6 × 129S

tag: genotype

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: D14_PRNB_SRRM4_ASCL1_R1


title: HCC1806 Cells, Control, R1

value: WT


title: Knockout sample 2352 Substantia Nigra

value: Substantia Nigra

tag: chow

value: Regular Chow

value: KO


title: D14_PRNB_SRRM4_NEUROD1_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: 6wkWT-1

value: 6-week-old leaves


title: HSV-ZFP189-VPR, 4d, Bio Rep 8

city: Richmond

first: Peter

last: Hamilton

state: VA

address: 1217 E Marshall St

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genomes using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 Only unique reads within exon regions were counted.
Assembly: Mus musculus GRCm38 reference genome

source_name: microdissected prefrontal cortex

extract_protocol:
Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelectTM−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were multiplexed and clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

value: microdissected prefrontal cortex


title: HN07

city: CHANDIGARH

first: KHEM

last: RAJ

state: Chandigarh

address: Deparment of Microbiology, BMS Block-I, PANJAB UNI, PANJAB UNIVERSITY, SECTOR -25

department: Microbiology

country: India

institute: PANJAB UNIVERSITY

data_processing:
Read quality check: Raw reads fastq files generated from Illumina HiSeqX were checked for quality assurance using the Fastq tool for parameters such as base quality score distribution, sequence quality score distribution, average base content per read, GC distribution in the reads, PCR amplification issues, checks for over-represented sequences and adapter trimming. Based on the quality report of fastq files the sequence reads were trimmed where necessary to only retain high-quality sequences for further analysis. In addition, the low-quality sequence reads were excluded from the analysis. The adapter trimming was performed using Trimmomatic software (v-0.36).
Contamination removal: For the RNA-Seq analysis, the unwanted sequences such as non-polyA-tailed RNAs were removed from the samples (assuming that poly-A-tailed RNAs are sequenced). Other unwanted sequences such as mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, and adapter sequences were also removed. Contamination removal was performed using Trimmomatic software.
Read quality check: Raw reads fastq files generated from Illumina HiSeqX were checked for quality assurance using the Fastq tool for parameters such as base quality score distribution, sequence quality score distribution, average base content per read, GC distribution in the reads, PCR amplification issues, checks for over-represented sequences and adapter trimming. Based on the quality report of fastq files the sequence reads were trimmed where necessary to only retain high-quality sequences for further analysis. In addition, the low-quality sequence reads were excluded from the analysis. The adapter trimming was performed using Trimmomatic software (v-0.36).
Contamination removal: For the RNA-Seq analysis, the unwanted sequences such as non-polyA-tailed RNAs were removed from the samples (assuming that poly-A-tailed RNAs are sequenced). Other unwanted sequences such as mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, and adapter sequences were also removed. Contamination removal was performed using Trimmomatic software.
Expression estimation: The aligned reads were used for estimating the expression of the genes. The raw read counts were estimated using Feature Count (v-1.5.2). Read count data were normalized using DESeq2.Differential expression analysis: The raw read counts were normalized using DESeq2. The ratio of normalized read counts or fold change was calculated for disease groups over healthy controls. The distribution of these log2 (foldchange) values was found to be normally distributed. Those genes which were found to have -2 <= log2(foldchange) >= 2 with p-value (<=0.05) were considered as statistically significant.  software.
Assembly: The paired-end reads were aligned to the reference human genome (hg19). Alignment was performed using HISAT2 (v-2.1.0).

source_name: Human Granulocytes

extract_protocol:
Isolated monocytes and neutrophils were kept in RLT buffer (Qiagen) at -80°C till RNA isolation. Total RNA was isolated using the RNeasy@ Mini kit (Qiagen) as per the manufacturer’s instructions . The purity of RNA was assessed in-house by a Nanodrop (Thermo Scientific) spectrophotometric measurement. The samples with a 260/280 ratio between 1.9 and 2.0 were processed for RNA sequencing. A
NEB Ultra II Directional RNA-Seq Library Prep kit protocol was used to prepare libraries for total RNA sequencing (NEB, Cat# E7760L). An initial Concentration of 200ng of total RNA was taken for the assay. First, the ribosomal RNA (rRNA) which constitutes ~95% of the total RNA population was removed using biotinylated, target-specific oligos combined with Ribo-Cop rRNA removal beads. Following purification, the ribodepleted RNA was fragmented using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase. Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H enzyme. The cDNA fragments were then subjected to a series of enzymatic steps that repair the ends, tails the 3’ end with a single ‘A’ base, followed by ligation of the adapters. The adapter-ligated products were then purified and enriched using the following thermal conditions: initial denaturation of 98°C for 30sec; 13 cycles of - 98°C for 10sec, 65°C for 75sec; final extension of 65°C for 5mins. PCR products were then purified and checked for fragment size distribution on Fragment Analyzer using HS NGS Fragment Kit (1- 6000bp) (Agilent, Cat# DNF-474-1000) and a few samples were checked for fragment size distribution on TapeStation using D1000 DNA ScreenTapes (Agilent, Cat# 5067-5582).
The libraries for all the samples were prepared with paired-end chemistry and a length of 150 bp. Quantification of all libraries was carried out using Qubit High Sensitivity Assay (Invitrogen, Cat# Q32854). The obtained libraries were pooled and diluted to the final optimal loading concentration before cluster amplification on the Illumina flow cell. Once the cluster generation was completed, the clustered flow cell was loaded on the Illumina HiSeqX instrument to generate a minimum of 100M raw reads per sample

value: Human Granulocytes

value: Human control granulocytes


title: D14_PRNB_SRRM4_NEUROD1_R1

city: Seattle

address: 1100 Fairview Ave N, E2-112

value: prostate cancer cells


title: HN08


title: D14_PRNB_SRRM4_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: Knockout sample 2352 Caudate Putamen

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

value: Caudate Putamen

tag: mouse background


title: HSV-ZFP189-VPR, 4d, Bio Rep 6

tag: treatment


title: Knockout sample 2351 Substantia Nigra


title: HN06


title: D14_PRNB_SRRM4_R1

value: Day 14


title: PRNB_R1, scRNA-seq

description: 10x Genomics

value: prostate cancer cell line

value: shRB1, TP53(DN), MYCN, BCL2


title: HSV-ZFP189-VPR, 4d, Bio Rep 5


title: HN05


title: D8_PRNB_SRRM4_NEUROD1_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1

value: Day 8


title: Knockout sample 2351 Caudate Putamen

value: total homogenate

value: hybrid C57BL/6 × 129S

value: Slc30a10 genotype with regular rodent chow (~84 µg Mn/g chow)


title: HSV-ZFP189-VPR, 4d, Bio Rep 4


title: HSV-ZFP189-VPR, 4d, Bio Rep 3


title: HN02_R


title: HM04

source_name: Human Monocytes

value: Human Monocytes

value: Human control monocytes


title: Knockout sample 2350 Substantia Nigra

value: Substantia Nigra

value: Regular Chow

value: KO


title: D8_PRNB_SRRM4_ASCL1_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: HSV-ZFP189-VPR, 4d, Bio Rep 2

value: microdissected prefrontal cortex


title: HM03


title: Knockout sample 2350 Globus Pallidus

source_name: Globus Pallidus

value: Globus Pallidus


title: D8_PRNB_SRRM4_ASCL1_R1

value: prostate cancer cells


title: Knockout sample 2352 Globus Pallidus


title: HSV-ZFP189-VPR, 4d, Bio Rep 7


title: HSV-ZFP189-VPR, 4d, Bio Rep 1


title: Knockout sample 2350 Caudate Putamen

source_name: Caudate Putamen

value: Caudate Putamen


title: HM06_R


title: Control sample 2363 Caudate Putamen

value: Ctl


title: Knockout sample 2351 Globus Pallidus


title: HSV-ZFP189-WT, 4d, Bio Rep 5


title: Control sample 1333 Caudate Putamen


title: HSV-ZFP189-WT, 4d, Bio Rep 4


title: Control sample 1333 Substantia Nigra


title: HM05


title: D8_PRNB_SRRM4_R1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: D8_PRNB_SRRM4_NEUROD1_R1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: D5_PRNB_SRRM4_ASCL1_R2

value: Day 5


title: HM02


title: HSV-ZFP189-WT, 4d, Bio Rep 3


title: SN11

value: Human Granulocytes

value: Covid-19 positive human granulocytes


title: D5_PRNB_SRRM4_ASCL1_R1


title: LysM-Cre IL10R fl/fl #2

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
Sequencing quality was assessed with FastQC v. 0.11.5, followed by trimming of low quality bases with Trimmomatic v. 0.33 and alignment to the Mus musculus genome draft GRCm38.84 using STAR v. 2.5.0.
Assembly: GRCm38.84
Supplementary files format and content: Raw counts summarized per gene for each sample after alignment with STAR

source_name: liver

extract_protocol:
Murine livers were harvested after PBS perfusion and gallbladder removal, cut into small pieces and digested in HBSS (with Ca2+ and Mg2+) containing 10 U/ml DNase and 1 mg/ml Collagenase, in a shaking incubator at 37°C for 25 minutes. After digestion, the livers were smashed and washed using PBS (1% FBS) through a cell strainer to a single cell resolution, and the pellet was collected after centrifugation at 400 g for 8 minutes. Immune cells were then enriched from the pellet by Percoll gradient centrifugation (GE Healthcare, Chicago, IL). Immune cells were then FACS sorted, with myeloid cells being gated as CD45+ CD3- CD11c- CD11b+. RNA was isolated from sorted cells using Trizol (Invitrogen).
libraries were constructed using polyA enrichment

value: liver

value: sorted myeloid cells

value: LysM-Cre IL10R fl/fl


title: LysM-Cre IL10R fl/fl #1


title: SN06_R


title: HSV-ZFP189-WT, 4d, Bio Rep 2


title: LysM-Cre IL10R wt/wt #2

value: LysM-Cre IL10R wt/wt


title: HSV-ZFP189-WT, 4d, Bio Rep 1


title: SN05_R


title: LysM-Cre IL10R wt/wt #1


title: HSV-ZFP189-NFD, 4d, Bio Rep 5


title: D8_PRNB_SRRM4_R2

value: Day 8


title: D5_PRNB_SRRM4_NEUROD1_R1


title: D5_PRNB_SRRM4_R2


title: HSV-ZFP189-NFD, 4d, Bio Rep 4


title: SN02_R


title: D5_PRNB_SRRM4_R1


title: HSV-ZFP189-NFD, 4d, Bio Rep 3


title: D4_PRNB_SRRM4_ASCL1_R2

value: Day 4


title: HSV-ZFP189-NFD, 4d, Bio Rep 2


title: Cerebrum, input, H3K27me3

first: Lucia

last: Daxinger

institute: Leiden Univeristy Medica Center

data_processing:
After preprocessing with TrimGalore to remove low quality reads, reads were aligned to the mouse genome (mm10) using bowtie2 v2.3.4.2 (Langmead and Salzberg, 2012) with parameters -very sensitive.
Peaks were called using SICER (Xu et al, 2014) parameters – W 1000, G 4000. For ChIP-seq peaks were called using input fractions as control.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig,broadPeak (except for Input sample)

source_name: Cerebrum E14.5

extract_protocol:
Nuclei were isolated as previously described (Krishnaswami et al, 2016). Briefly, tissue was chopped, flash frozen and stored at -80 ºC. The Dounce homogenizer (2 ml one), pestles and all the buffers (NIM1 – 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris pH 8; NIM2 – NIM1, 1 µM DTT, protease inhibitor; Homogenization buffer – NIM2, 0,4 U/µl RiboLock (ThermoFisher, EO0384)) were precooled. The tissue was homogenized in 1 ml homogenization buffer with five strokes of the loose pestle, followed by 15 strokes of the tight pestle. Homogenate was filtered through a BD Falcon tube with a 35-μm nylon cell strainer cap (352235, Corning). The number of nuclei was counted by staining an aliquot with trypan blue and using TC10 Automated Cell Counter (BioRad). The nuclei were resuspended in 1 ml NIM2 buffer and sample was centrifugated (500 g, 5 min, 4 ºC). The washing step was repeated 2-3 times. Further ULI-ChIP-seq protocol was followed (Brind'Amour, 2015). Briefly, around 1 million nuclei per IP were diluted in 50 µl Nuclear storage buffer (15% sucrose, 10 mM Tris pH 7,2, 70 mM KCl, 2 mM MgCl2 and proteinase inhibitors) and fragmented using MNase at 37 ºC for 7,5 min. Upon fragmentation reaction was stopped with 6,6 µl 100 mM EDTA and 6,6 µl 1% Triton/1% DOC. The samples were then diluted up to 200 µl with Complete immunoprecipitation buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 15 mM NaCl, 0.1% Triton X-100, 1x EDTA-free protease inhibitor cocktail, 1mM PMSF).
The eluted DNA was purified by phenol–chloroform, precipitated with EtOH, and resuspended in 20 µl MQ. For library preparation the Kapa Hyper Prep Kit (Roche, KK8504, 07962363001) was used, following the manufacturer’s instructions.

value: FVB

value: Cerebrum E14.5

tag: chip antibody

value: Millipore 17-622


title: SM11_R

value: Human Monocytes

value: Covid-19 positive human monocytes


title: D4_PRNB_SRRM4_ASCL1_R1

value: prostate cancer cells


title: SM06


title: Cerebrum, WT, H3K27me3

tag: strain


title: SN01_R


title: HSV-ZFP189-NFD, 4d, Bio Rep 1

value: microdissected prefrontal cortex


title: SM05


title: BMDMS, VPA treatment,  replicate 3 [T3]

city: wuhan

first: Xudong

last: Xie

address: wuhan, 1277, Jiefang avenue

institute: wuhan union hospital

data_processing:
The VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) was used to generate the stranded mRNA-seq libraries.
The libraries were quantified with a Qubit and sequenced on an Ilumina Novaseq 6000 platform to generate 150 bp paired-end reads.
Skewer (V0.2.2) was used to eliminate low-quality reads to obtain clean reads, and FastQC was used to conduct quality control analyses (V0.11.5).
The clean reads were mapped to the reference genome using STAR (2.5.3a), and StringTie was used to obtain the read counts for each gene (V1.3.1c).
DESeq2 was utilized to perform differential expression analysis (V1.16.1). A P value 0.05, a foldchange > 2 or a foldchange -2 was set as the cutoff for differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Processed data xks file includes raw counts for each sample

source_name: Bone marrow

growth_protocol: BMDMs were incubated at 37°C in 5% CO2

extract_protocol:
Cells were extracted from the femurs and tibias of mice aged five weeks. After red blood cells (RBC) lysis buffer (Servicebio) was used to get rid of the RBC, the cells were cultured in medium overnight. Nonadherent cells grew into osteoclast precursors by incubation with 30 ng/ml M-CSF for five days.
The VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) was used to generate the stranded mRNA-seq libraries. The libraries were quantified with a Qubit and sequenced on an Ilumina Novaseq 6000 platform to generate 150 bp paired-end reads. Skewer (V0.2.2) was used to eliminate low-quality reads to obtain clean reads, and FastQC was used to conduct quality control analyses (V0.11.5). The clean reads were mapped to the reference genome using STAR (2.5.3a), and StringTie was used to obtain the read counts for each gene (V1.3.1c). DESeq2 was utilized to perform differential expression analysis (V1.16.1). A P value 0.05, a foldchange > 2 or a foldchange -2 was set as the cutoff for differentially expressed genes (DEGs).

treatment_protocol: Bone Marrow cells were cultured in 6-well plates in the presence of 30 ng/ml M-CSF for 5 days. And then the BMDMs were treatment with 20 μM VPA or vihicle for 48 hours, and totol RNA was collected.

value: Bone marrow

value: Bone marrow derived-macrophages (BMDMs)

value: Wild type

value: VPA treatment for 48 hours


title: D5_PRNB_SRRM4_NEUROD1_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1

value: Day 5


title: D4_PRNB_SRRM4_NEUROD1_R2


title: BMDMS, VPA treatment,  replicate 2 [T2]


title: SM02


title: HSV-ZFP189-WT, 24h, Bio Rep 5


title: BMDMS, VPA treatment,  replicate 1 [T1]


title: SM01


title: D4_PRNB_SRRM4_NEUROD1_R1


title: D4_PRNB_SRRM4_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: D4_PRNB_SRRM4_R1


title: BMDMS, control,  replicate 3 [C3]

value: Vehicle treatment for 48 hours


title: HSV-ZFP189-WT, 24h, Bio Rep 3


title: HSV-ZFP189-WT, 24h, Bio Rep 2


title: Cerebrum, Cdca7G305V/G305V, H3K27me3

address: Albinusdreef 2


title: RN07

value: Human Granulocytes

value: Mucormycosis positive human granulocytes


title: BMDMS, control,  replicate 2 [C2]


title: D3_PRNB_SRRM4_ASCL1_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1

value: Day 3


title: BMDMS, control,  replicate 1 [C1]


title: RN04


title: HSV-ZFP189-WT, 24h, Bio Rep 1


title: D3_PRNB_SRRM4_ASCL1_R1


title: RN03


title: 23039Pol_9

city: College Station

first: Michael

last: Polymenis

state: Texas

address: 2128 TAMU

department: Biochemistry and Biophysics

institute: Texas A&M Univ

description: Fresh frozen transcriptome sequencing

data_processing:
Bases were trimmed based on quality (min quality of 24 ) and adapters (Stringency of 5).
The resulting reads were mapped to the Mouse Build 39 Jun 2020, GCA_000001635.9, with the DRAGEN Bio-IT platform using default parameters.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes per gene and per sample raw counts
Supplementary files format and content: tab-delimited text files include per transcript and per sample raw counts

extract_protocol:
Fresh liver tissue (~20mg) was stored in DNA/RNA ShieldTM (Zymo Research) at 4 C until processed. RNA was extracted with a Quick-RNATM Miniprep Plus Kit (Zymo Research) using Proteinase K digestion and subsequent steps according to the manufacturerâ€™s protocol.
mRNA was isolated from 150ng total RNA using a Nextflex Poly-A Selection kit (Perkin Elmer, Waltham, MA, USA). cDNA libraries were prepared using a Nextflex Rapid Directional RNA 2.0 kit, miniaturized to 2/5 reaction volume and automated on a Sciclone NGSx liquid handler

value: liver

value: female

value: F/C-


title: D3_PRNB_SRRM4_NEUROD1_R2

value: prostate cancer cells


title: HSV-ZFP189-VPR, 24h, Bio Rep 5

value: microdissected prefrontal cortex


title: HSV-ZFP189-VPR, 24h, Bio Rep 4


title: RN02


title: HSV-ZFP189-VPR, 24h, Bio Rep 3


title: RN01


title: D3_PRNB_SRRM4_NEUROD1_R1


title: HSV-ZFP189-WT, 24h, Bio Rep 4


title: 23039Pol_7

description: Fresh frozen transcriptome sequencing


title: D3_PRNB_SRRM4_R2


title: RM07

value: Human Monocytes

value: Mucormycosis positive human monocytes


title: HSV-ZFP189-VPR, 24h, Bio Rep 2


title: RM04


title: D3_PRNB_SRRM4_R1


title: 23039Pol_5

description: Fresh frozen transcriptome sequencing

value: F/C+


title: 23039Pol_4

description: Fresh frozen transcriptome sequencing


title: HSV-ZFP189-NFD, 24h, Bio Rep 5


title: RM02


title: D2_PRNB_SRRM4_ASCL1_R2

value: Day 2


title: D2_PRNB_SRRM4_ASCL1_R1


title: RM01


title: 23039Pol_39

description: Fresh frozen transcriptome sequencing

value: male


title: HSV-ZFP189-NFD, 24h,  Bio Rep 4


title: 23039Pol_8

description: Fresh frozen transcriptome sequencing


title: HSV-ZFP189-NFD, 24h,  Bio Rep 3


title: 23039Pol_38

description: Fresh frozen transcriptome sequencing


title: HSV-ZFP189-NFD, 24h, Bio Rep 1


title: 23039Pol_36

description: Fresh frozen transcriptome sequencing


title: D2_PRNB_SRRM4_NEUROD1_R1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: 23039Pol_37

description: Fresh frozen transcriptome sequencing


title: CMN06

value: Covid-19 associated mucormycosis positive human granulocytes


title: D2_PRNB_SRRM4_R1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: HSV-ZFP189-NFD, 24h,  Bio Rep 2


title: CMN02

value: Human Granulocytes


title: CMN04


title: HSV-ZFP189-VPR, 24h, Bio Rep 1


title: RM03


title: 23039Pol_6

description: Fresh frozen transcriptome sequencing


title: U1690 Cells, Platinum treated, Replicate3

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Hg38
Supplementary files format and content: tab deliminated text file

source_name: Lung

extract_protocol:
RNA was exctracted using Trizol (Merck). 1 μg RNA per sample was used as input material
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Lung

value: Cancer cell line

value: WT

value: Cisplatin


title: GFP_4

treatment_protocol:
N/A
N/A

value: Day 14


title: CMN01


title: 23039Pol_34

description: Fresh frozen transcriptome sequencing

value: liver

value: F/C-


title: PRNB_ASCL1_4

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2, ASCL1


title: U1690 Cells, Platinum treated, Replicate1


title: D2_PRNB_SRRM4_NEUROD1_R2


title: PRNB_NEUROD1_4

value: shRB1, TP53(DN), MYCN, BCL2, NEUROD1


title: U1690 Cells, Platinum treated, Replicate2


title: CMM06

value: Human Monocytes

value: Covid-19 associated mucormycosis positive human monocytes


title: 23039Pol_33

description: Fresh frozen transcriptome sequencing

value: male


title: U1690 Cells, Control, Replicate3

value: Vehicle


title: 23039Pol_32

description: Fresh frozen transcriptome sequencing


title: CMN05

value: Covid-19 associated mucormycosis positive human granulocytes


title: PRNB_SRRM4_ASCL1_4

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: CMM05


title: 23039Pol_35

description: Fresh frozen transcriptome sequencing


title: U1690 Cells, Control, Replicate2


title: 23039Pol_31

description: Fresh frozen transcriptome sequencing


title: D2_PRNB_SRRM4_R2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4

value: Day 2


title: CMM04


title: U1690 Cells, Control, Replicate1

value: Lung

value: Cancer cell line


title: PRNB_SRRM4_4


title: CMM02


title: 23039Pol_3

description: Fresh frozen transcriptome sequencing

value: female

value: F/C+


title: HCT116 Cells, Platinum treated, Replicate3

source_name: Colon

value: Colon

value: WT

value: Cisplatin


title: PRNB_4

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2

value: Day 14


title: 23039Pol_30

description: Fresh frozen transcriptome sequencing

value: liver

value: F/C-


title: CMM01

value: Human Monocytes

value: Covid-19 associated mucormycosis positive human monocytes


title: HCT116 Cells, Platinum treated, Replicate2


title: LP, warm,  28d,  rep3

city: Kearneysville

first: Jianyang

last: Liu

state: WV

address: 2217 Wiltshire Road

institute: USDA-ARS

data_processing:
Illumina paired-end bisulfite sequences were evaluated for quality using FastQC (version 0.11.9)
Trim reads with Trimmomatic to remove adapter sequence or poor quality sequence from raw reads
FASTQ files were aligned to Prunus persica NCBIv2 genome (Cheng et al. 2017) using the STAR (v2.6.0) software
Mapped read counts were transformed to Counts per Million (CPM) using the Bioconductor package edgeR (Robinson et al., 2010
Differentially expressed genes (DEGs) were identified on genes with false discovery rate (FDR) < 0.05 and log fold-changes (logFC) > 1.5 between LFP and JB at each time point.

organism: Prunus persica

source_name: Floral bud

growth_protocol: Peach cuttings (shoots with floral buds attached) were kept with the base submersed in water, which was changed periodically.

extract_protocol:
RNA was extract from the floral buds using a RNA Isolation Kit (Norgen BiotecK Corp, Ontario, Canada)
Truseq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Peach cuttings were kept in chilling condition (4℃) for 1000 h, and then moved to warm condition (22℃) for 20 d for JB and 28 for LFP until they started to bloom.

value: Floral bud

value: Warm (22 C)


title: HCT116 Cells, Platinum treated, Replicate1


title: GFP_3


title: HCT116 Cells, Control, Replicate3

value: Vehicle


title: PRNB_ASCL1_3

value: shRB1, TP53(DN), MYCN, BCL2, ASCL1


title: LP, warm,  28d,  rep2


title: HCT116 Cells, Control, Replicate2

value: Cancer cell line


title: 23039Pol_29

description: Fresh frozen transcriptome sequencing

value: male


title: 23039Pol_28

description: Fresh frozen transcriptome sequencing


title: 23039Pol_27

description: Fresh frozen transcriptome sequencing


title: LP, warm,  24d,  rep3


title: PRNB_SRRM4_ASCL1_3

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: PRNB_SRRM4_NEUROD1_4

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: 23039Pol_25

description: Fresh frozen transcriptome sequencing

value: F/C+


title: HCT116 Cells, Control, Replicate1

value: Colon

value: WT


title: 23039Pol_26

description: Fresh frozen transcriptome sequencing


title: LP, warm,  24d,  rep2


title: 786-0 Cells, Platinum treated, Replicate3

source_name: Kidney

value: Kidney

value: Cisplatin


title: 23039Pol_23

description: Fresh frozen transcriptome sequencing

value: liver


title: 786-0 Cells, Platinum treated, Replicate2


title: PRNB_SRRM4_3

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4

value: Day 14


title: LP, warm,  20d,  rep3

value: Floral bud


title: 23039Pol_24

description: Fresh frozen transcriptome sequencing


title: PRNB_3

value: shRB1, TP53(DN), MYCN, BCL2


title: 786-0 Cells, Platinum treated, Replicate1


title: 23039Pol_22

description: Fresh frozen transcriptome sequencing


title: 786-0 Cells, Control, Replicate1

value: Vehicle


title: LP, warm,  20d,  rep1

value: Warm (22 C)


title: PRNB_NEUROD1_2

value: shRB1, TP53(DN), MYCN, BCL2, NEUROD1


title: LP, warm,  20d,  rep2


title: 23039Pol_2

description: Fresh frozen transcriptome sequencing

value: female


title: GFP_2


title: 786-0 Cells, Control, Replicate3

value: Cancer cell line


title: 23039Pol_20

description: Fresh frozen transcriptome sequencing

value: male


title: PRNB_ASCL1_2

value: shRB1, TP53(DN), MYCN, BCL2, ASCL1


title: 23039Pol_21

description: Fresh frozen transcriptome sequencing

value: F/C+


title: LP, warm,  28d,  rep1


title: PRNB_NEUROD1_3


title: LP, warm,  16d,  rep2


title: HCC1806 Cells, Platinum treated, Replicate3

value: Breast

value: WT


title: PRNB_SRRM4_ASCL1_2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1


title: 786-0 Cells, Control, Replicate2

value: Kidney


title: 23039Pol_19

description: Fresh frozen transcriptome sequencing

value: liver


title: LP, warm,  16d,  rep1


title: PRNB_SRRM4_NEUROD1_3

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: PRNB_SRRM4_NEUROD1_2

value: Day 14


title: HCC1806 Cells, Platinum treated, Replicate2

value: Cisplatin


title: PRNB_2

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: LP, warm,  12d,  rep3

value: Floral bud

value: Warm (22 C)


title: LP, warm,  24d,  rep1


title: 23039Pol_18

description: Fresh frozen transcriptome sequencing


title: HCC1806 Cells, Platinum treated, Replicate1


title: LP, warm,  12d,  rep2


title: LP, warm,  16d,  rep3


title: 23039Pol_17

description: Fresh frozen transcriptome sequencing


title: PRNB_SRRM4_2

value: shRB1, TP53(DN), MYCN, BCL2


title: GFP_1


title: 23039Pol_16

description: Fresh frozen transcriptome sequencing


title: HCC1806 Cells, Control, Replicate3

value: Cancer cell line

value: Vehicle


title: PRNB_NEUROD1_1

value: shRB1, TP53(DN), MYCN, BCL2, NEUROD1


title: LP, warm,  8d,  rep2


title: HCT116 Cells, Control, R2

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Hg38
Supplementary files format and content: tab deliminated text file
Supplementary files format and content: gene_count


title: 23039Pol_14

description: Fresh frozen transcriptome sequencing

value: female

value: F/C-


title: LP, warm,  8d,  rep3


title: PRNB_ASCL1_1

value: shRB1, TP53(DN), MYCN, BCL2, ASCL1


title: HCC1806 Cells, Control, Replicate1

value: Breast

value: WT


title: HCT116 Cells, Control, R3


title: 23039Pol_15

description: Fresh frozen transcriptome sequencing

value: liver

value: male

value: F/C+


title: 23039Pol_13

description: Fresh frozen transcriptome sequencing


title: 23039Pol_12

description: Fresh frozen transcriptome sequencing


title: PRNB_SRRM4_ASCL1_1

value: prostate cancer cells

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1

value: Day 14


title: HCC1806 Cells, Platinum treated 10 days post treatment, R3

value: Cisplatin

value: 10 days


title: LP, warm,  8d,  rep1

value: Floral bud

value: Warm (22 C)


title: HCT116 Cells, Control, R1

value: Cancer cell line


title: LP, warm,  4d,  rep3


title: 23039Pol_10

description: Fresh frozen transcriptome sequencing


title: PRNB_SRRM4_1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4


title: HCC1806 Cells, Platinum treated 10 days post treatment, R2


title: 23039Pol_11

description: Fresh frozen transcriptome sequencing

value: female


title: LP, warm,  4d,  rep2


title: 23039Pol_1

description: Fresh frozen transcriptome sequencing


title: PRNB_SRRM4_NEUROD1_1

value: shRB1, TP53(DN), MYCN, BCL2, SRRM4, NEUROD1


title: LP, warm,  4d,  rep1


title: LP, warm,  12d,  rep1


title: HCC1806 Cells, Control, Replicate2

value: Vehicle


title: PRNB_1

value: shRB1, TP53(DN), MYCN, BCL2


title: LP, warm,  1d,  rep3


title: LP, warm,  1d,  rep2


title: RNA_Proargdrop_DFMO_5825

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: RNA Sequencing

data_processing:
Fastq files were adaptor stripped using cutadapt with a minimum length of 15 and a quality cutoff of 2 (parameters: -a CTGTAGGCACCATCAAT –minimum-length = 15 –quality-cutoff = 2).
Resulting reads were mapped, using default parameters, with HISAT2 (PMID: 25751142), using a GRCm38, release 101 genome and index. Ribosome profiling: reads were removed if they mapped to rRNA or tRNA according to GRCm38 RepeatMasker definitions from UCSC. A full set of transcript and CDS sequences for Ensembl release 101 was then established. Only canonical transcripts [defined by knownCanonical table, downloaded from UCSC] were retained with their corresponding CDS. Reads were then mapped to the canonical transcriptome with bowtie2 using default parameters.
Assembly: GRCm38, release 101

source_name: Tumor tissue

extract_protocol:
Mouse tumors were mechanically disrupted in liquid nitrogen and homogenized in a lysis buffer (LB, 50 mM Tris, pH 7.4, 100 mM KCl, 1.5 mM MgCl2, 1.0% Triton X-100, 0.5% Na-Deoxycholate, 25 U/ml Turbo DNase I, 1mM DTT, 100 µg/ml cycloheximide, and Protease inhibitors) 3 ml of LB per 1 g of tissue. Ribosome profiling: Mouse tumors were mechanically disrupted in liquid nitrogen and homogenized in a lysis buffer (LB, 50 mM Tris, pH 7.4, 100 mM KCl, 1.5 mM MgCl2, 1.0% Triton X-100, 0.5% Na-Deoxycholate, 25 U/ml Turbo DNase I, 1mM DTT, 100 µg/ml cycloheximide, and Protease inhibitors) 3 ml of LB per 1 g of tissue. To obtain ribosome footprints 0.12 ml of total extracts containing 300 µg of total RNA were treated with RNAse I (Epicentre) (25U/1 mg of total RNA), for 45 min at 20ºC with slow agitation. 10 ml SUPERaseIn RNase inhibitor was added to stop nuclease digestion. Monosomes were isolated using S-400 columns. For isolation of mRNA protected fragments (RPF) 3 volumes of QIAzol® were added to the S-400 eluate, mixed thoroughly and proceed to RNA purification with Direct-Zol RNA Mini Prep Plus kit. RNA-seq: Total RNA were isolated from the same extracts, that were used to obtain RPF (bellow, RiboSeq). 3 volumes of QIAzol® (Qiagen, Cat. No. 79306) were added to 80 µl of cell extracts, mixed thoroughly and proceed to RNA purification with Direct-Zol RNA Mini Prep Plus kit.
Ribosome Profiling: RPF libraries were prepared as described (PMID: 28579404, PMID: 19213877). Briefly, RPFs (25-34 nt) were size-selected by electrophoresis using a 15% TBE-Urea polyacrylamide gel electrophoresis (PAGE) and two RNA markers, 25-mer (5’ AUGUACACGGAGUCGAGCACCCGCA 3’) and 34-mer (5’AUGUACACGGAGUCGAGCACCCGCAACGCGAAUG 3’). After dephosphorylation with T4 Polynucleotide Kinase (NEB, #M0201S) the adapter Linker-1 (5' rAppCTGTAGGCACCATCAAT/3ddC/ 3') was ligated to the 3′ end of the RPF using T4 RNA Ligase 2. Ligated products were purified using 10% TBE-Urea PAGE. Ribosomal RNA was subtracted using RiboCop rRNA Depletion Kit V2 H/M/R. The adapter Linker-1 was used for priming reverse transcription (RT) with the RT primer Ni-Ni-9 (5’AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC5CACTCA5TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG 3’) using ProtoScript® II Reverse Transcriptase. RT products were purified using 10% TBE-Urea PAGE. The cDNA was circularized with CircLigase™ II ssDNA Ligase. The final libraries were generated by PCR using forward index primer NI-N-2 (5’ AATGATACGGCGACCACCGAGATCTACAC 3’) and one of the reverse index primers. Amplified libraries were purified using 8% TBE-PAGE and analyzed by Qubit and TapeStation. RNAseq: RNA were sent to Genomic Platform (UNIGE) for stranded mRNA libraries preparation. Libraries were sequenced on an Illumina NovaSeq 6000, SR 100 bp, 10 libraries in 1 pool.

treatment_protocol: Pharmalogical (treament with/wihtout difluoromethylornithine DFMO) and dietary intervention (with/without proline and arginine in the diet)

value: Tumor tissue

value: neuroblastoma cancer cells

value: Neuroblast

value: MYCN Amplified

value: Proline Arginine Dropout Diet with DFMO Treatment(ProArg DFMO)


title: RS243_CD32+_DLL4-

first: Monah

last: Abou Alezz

address: Via Olgettina 60

institute: SR-TIGET

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR v2.7.6a (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts of mapped reads for each Sample

source_name: H1 human embryonic stem cells

growth_protocol: H1 human embryonic stem cells were expanded and differentiated as reported in Ditadi et al., 2015 (doi.org/10.1038/ncb3161); Ditadi et al, 2016 (doi.org/10.1016/j.ymeth.2015.10.001)

extract_protocol:
On day 8 of culture, embryoid bodies were dissociated with 0.25% Trypsin-EDTA for 8 minutes and Collagenase II for 30 minutes, immunolabled at 4C for 25 minutes. CD34+CD32+CD43–CD184–CD73– and CD34+CD184+CD73+DLL4+CD43neg  cells were then FACS sorted using a BD FACS Aria Fusion II and stored on ice until ready for RNA extraction. We extracted total RNA using the ReliaPrep RNA Cell Miniprep System (Promega). We quantified RNA concentration using Qubit RNA HS Assay Kit using Qubit 3.0 and we evaluated RNA integrity with Agilent RNA 6000 Pico Kit using Bionalyzer (Agilent).
RNA-Seq libraries were generated using the Smart-seq2 method (Picelli et al., 2014) starting from 0,876 ng of RNA. Retro-transcription was performed using SuperScript II Reverse Transcriptase, cDNA was PCR-amplified (16 cycles) with KAPA HiFi HotStart and purified with AMPure XP beads. After purification, we determined cDNA concentration using Qubit dsDNA HS Assay Kit at Qubit 3.0 and we assessed size distribution at Agilent 4200 TapeStation system. We performed the tagmentation reaction starting from 0.5 ng of cDNA for 30 minutes at 55°C and we performed enrichment PCR using 12 cycles. Libraries were purified with AMPure XP beads, quantified using Qubit 3.0, assessed for fragment size distribution on an Agilent 4200 TapeStation system.

treatment_protocol: Samples were incubated with antibody mixes for 15-30’ at 4°C then sorted at BD FACSAria Fusion Class II Type A2 Biosafety Cabinet.

value: isolated cells of Wnt dependent heamtopoietic culture

value: Day 8

tag: sorted fraction

value: CD34+CD32+CD43-CD184-CD73-DLL4- cells


title: HCC1806 Cells, Platinum treated 10 days post treatment, R1

value: Breast

value: WT

value: Cisplatin

value: 10 days


title: LP, warm,  1d,  rep1

value: Floral bud

value: Warm (22 C)


title: HCC1806 Cells, Platinum treated 5 days post treatment, R2

value: Cancer cell line

value: 5 days


title: LP, chill,  1000h,  rep3

value: Chilling (4 C)


title: RNA_Proargdrop_DFMO_5746

description: RNA Sequencing

value: Tumor tissue


title: HCC1806 Cells, Platinum treated 5 days post treatment, R3


title: RS242_CD32+_DLL4-


title: HCC1806 Cells, Platinum treated 5 days post treatment, R1


title: RS242_CD184+_DLL4+

value: CD34+CD184+CD73+DLL4+CD43- cells


title: LP, chill,  1000h,  rep2


title: HCC1806 Cells, Platinum treated 0 days post treatment, R2

value: 0 days


title: RS243_CD184+_DLL4+


title: RS227_CD184+_DLL4+


title: LP, chill,  1000h,  rep1


title: RNA_Proargdrop_DFMO_5736

description: RNA Sequencing

value: neuroblastoma cancer cells

value: Neuroblast

value: MYCN Amplified


title: HCC1806 Cells, Platinum treated 0 days post treatment, R1


title: HCC1806 Cells, Platinum treated 0 days post treatment, R3


title: RNA_CD_DFMO_5823

description: RNA Sequencing

value: DFMO Treatment (CD DFMO)


title: RNA_CD_DFMO_135

description: RNA Sequencing


title: LP, chill,  800h,  rep2


title: RNA_Proargdrop_DFMO_5805

description: RNA Sequencing

value: Proline Arginine Dropout Diet with DFMO Treatment(ProArg DFMO)


title: Ab_2

city: Canberra

first: Xin

last: Gao

address: 131 Garran Rd

institute: The Australian National University

description: 10X Gemonics

data_processing:
The data was processed by Cell Ranger software under default settings (10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Cellranger output contains two folders, one includes matrix file for gene expression and CITE-seq antibody expression and the other for VDJ information

source_name: Tonsil

extract_protocol:
Sorted cells were incubated with Totalseq-C antibodies (1:50 dilution) on ice for 30 min, washed 3 times, counted and mixed at 1:1:1 ratio. 10000 mixed cells were loaded onto each lane of the 10X Chromium platform (10X Genomics)
Library was performed according to the manufacter’s instructions (Chromium Single Cell 5' Reagent Kits by 10x Genomics)

value: Tonsil

value: B cell


title: RS227_CD32+_DLL4-

value: isolated cells of Wnt dependent heamtopoietic culture

value: Day 8

value: CD34+CD32+CD43-CD184-CD73-DLL4- cells


title: HCC1806 Cells, Control, R3

source_name: Breast

value: Breast

value: WT

value: Vehicle


title: GEX_2

description: 10X Gemonics


title: HCC1806 Cells, Control, R2

value: Cancer cell line


title: RNA_CD_DFMO_5806

description: RNA Sequencing

value: Tumor tissue


title: LP, chill,  800h,  rep1

value: Floral bud

value: Chilling (4 C)


title: LP, chill,  800h,  rep3


title: RNA_CD_DFMO_5747

description: RNA Sequencing

value: neuroblastoma cancer cells


title: VDJ_2

description: 10X Gemonics


title: HCC1806 Cells, Control, R1


title: Ab_1

description: 10X Gemonics


title: LP, chill,  600h,  rep2


title: LP, chill,  600h,  rep3


title: E4 ACE+

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR v2.7.6a (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts of mapped reads for each Sample

source_name: AGM tissue

extract_protocol: Full length cDNA were generated directly from 10 to 140 cells/tissues frozen in PBS buffer containing RNAses inhibitor using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 15 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: hemogenic endothelial cells

tag: sorted cells

value: AGM tissue

tag: Stage

value: 32 day-old embryo


title: VDJ_1

description: 10X Gemonics


title: RNA_CD_DFMO_5802

description: RNA Sequencing

value: Neuroblast

value: MYCN Amplified

value: DFMO Treatment (CD DFMO)


title: LP, chill,  600h,  rep1


title: GEX_1

description: 10X Gemonics

value: Tonsil

value: B cell


title: RNA_Proargdrop_5828

description: RNA Sequencing

value: Proline Arginine Dropout Diet (ProArg)


title: LP, chill,  400h,  rep3


title: E3 ACE+

value: 30 day-old embryo


title: RNA_Proargdrop_5785

description: RNA Sequencing


title: LP, chill,  400h,  rep2


title: RNA_Proargdrop_5784

description: RNA Sequencing


title: SIC_97_Colon_318_TST_Nuclei_5p_GEX

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

data_processing:
We used Cell Ranger v3.1.0 for generating gene count matrices from sequencing reads (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). We used R scripts to analyze the count matrices.
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 files, anndata h5ad files, HTML files, CSV files

source_name: Colon mucosal biopsy

extract_protocol:
Please see the methods in the associated publication.
Please see the methods in the associated publication.

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: channel

tag: pcr primer

tag: chemistry


title: SIC_89_Colon_310_TST_Nuclei_5p_GEX

tag: tissue

value: Prednisone 2.5mg


title: SIC_53_Colon_182_TST_Nuclei_5p_GEX

value: Control - On ICI Therapy


title: LP, chill,  400h,  rep1

value: Floral bud

tag: genotype


title: RNA_Proargdrop_5705

description: RNA Sequencing

value: Tumor tissue

tag: cell line

tag: cell type


title: E2 ACEneg

city: Milan

value: endothelial cells


title: E3 ACEneg


title: RNA_Proargdrop_5702

description: RNA Sequencing

value: neuroblastoma cancer cells

tag: treatment


title: LP, chill,  200h,  rep3

value: Chilling (4 C)


title: SIC_43_RectosigmoidColon_157_TST_Nuclei_5p_GEX


title: RNA_CD_5812

description: RNA Sequencing

value: Control Diet (CD)


title: E4 ACEneg

value: AGM tissue

value: 32 day-old embryo


title: E1 ACE+

value: hemogenic endothelial cells

value: 28 day-old embryo


title: RNA_CD_5781

description: RNA Sequencing

value: Neuroblast

value: MYCN Amplified


title: SIC_40_Colon_155_TST_Nuclei_5p_GEX_B


title: E2 ACE+


title: LP, chill,  100h,  rep3


title: E1 ACEneg


title: RNA_CD_5778

description: RNA Sequencing


title: LP, chill,  200h,  rep1


title: SIC_40_Colon_155_TST_Nuclei_5p_GEX_A


title: LP, chill,  200h,  rep2


title: RNA_CD_5696

description: RNA Sequencing


title: SIC_36_Colon_140_TST_Nuclei_5p_GEX


title: SIC_33_Colon_132_TST_Nuclei_5p_GEX

value: Prednisone 10mg