title: LSD1cKO preosteoclast S6

source_name: bone marrow

value: bone marrow

value: osteoclast

value: conditional knockout

value: M-CSF and RANKL


title: HBO_JAGGED_3

status: Public on Oct 11 2024

type: SRA

city: Atlanta

first: Steven

middle: L

last: Goudy

state: GA

address: 2174 N Druid Hills Rd, 1st Floor

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
Sequencing and data processing was perfomed by the Molecular Evolution core at the Georgia Institute of Technology. Paired-end 150 base pairs (PE150) sequencing was performed on the Illumina NovaSeq 6000 instrument to obtain a sequencing depth of 30 million reads per sample. The transcripts obtained were aligned using the hg38 genome reference database along with elimination of duplicate reads, using the DNAStar Lasergene 17.3 application. The RNA levels were calculated in reads per kilobase per million mapped reads (RPKM). Genes expressed at > 1.5 RPKM were retained for further analyses.
Assembly: hg38 genome reference database
Supplementary files format and content: processed raw count matrix in comma separated value (.csv) file

molecule: polyA RNA

organism: Homo sapiens

source_name: Human bone-derived osteoblast-like

extract_protocol:
RNA was extracted using Qiagen Rneasy kit (Qiagen, 74106) according to manufacturer's protocols.
The samples were submitted to the Molecular Evolution core at the Georgia Institute of Technology for sequencing. Quality Control (QC) was performed using an Agilent Bioanalyzer 2100 to determine the RNA Integrity Number (RIN) of the samples. mRNA was enriched using the New England Biolab’s (NEB) NEBNext Poly(A) mRNA isolation module for samples with RINs greater than 7 and libraries were prepared using the NEBNext Ultra II directional RNA library preparation kit (NEB, E7760). QC was then performed on these libraries using an Agilent Bioanalyzer 2100 and the libraries were quantified using fluorometric methods.

tag: cell line

value: Human bone-derived osteoblast-like

tag: genotype

value: WT


title: LSD1WT preosteoclast S1

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38 v94) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed between WT and conditional KO were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: mouse (GRCm38 v94)
Supplementary files format and content: raw_counts.txt

molecule: total RNA

organism: Mus musculus

growth_protocol: Bone marrow macrophages were isolated from 3 month old mice

extract_protocol:
RNA was isolated using RNA Plus Mini kit (Qiagen)
Libraries were constructed by UMN Genomic center

treatment_protocol: Cells were grown in alpha MEM without phenol red in the presence of M-CSF and RANKL for 48 hours

tag: tissue

tag: cell type

value: wild type

tag: treatment


title: HBO_JAGGED_2


title: MOC_1430:gent:6.00000uM:30min:PA14:MOC_1430_1:r3

city: Boston

first: Keith

last: Romano

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

description:
moc1430_1779_0066_0110_2kd_counts_manuscript.csv
moc1430_1779_0066_0110_2kd_modzscore_ref_set.csv

data_processing:
BWA to align reads to reference
QC & filter samples with low counts and genes with low counts
DESeq2 to identify weak and robust transcriptional signals
VST function from DESeq2 for variance stabilization of counts
Calculate moderated z-scores using custom scripts, based on previously published scripts (Subramanian, A. et al. Cell. 2017. https://doi.org/10.1016/j.cell.2017.10.049)
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample
Supplementary files format and content: comma separated file with moderated z-score values for each treatment condition (replicates collapsed)

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: Bacterial cultures were grown with shaking (37°C, 250rpm) to mid-log phase, and 30uL of cultures were mixed with equal volume of 2X compound working solution, yielding final conditions containing 1x108 CFU/mL bacteria and with compounds (or vehicle) in 0.5% (v/v) DMSO or water in LB.

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

treatment_protocol: Cells were treated at 37°C without shaking in a humidity chamber.  In the case of the RNA-Seq Time Trial, cells were treated for 30, 60, 90, and 120 minutes. In the case of all other RNA-Seq experiments, cells were treated for 90 minutes.

tag: pert id

value: gent

tag: pert iname

value: Gentamicin

tag: pert dose

tag: pert dose_unit

value: uM

tag: pert idose

tag: pert time

tag: pert time_unit

value: min

tag: pert itime

tag: pert type

value: poscon

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well

tag: strain id

value: FALSE


title: HBO_JAGGED_1

tag: cell line

tag: genotype


title: LSD1WT preosteoclast S2

tag: tissue

tag: cell type

tag: treatment


title: HCI018_IL6expt_IL6_2

city: Edinburgh

first: Esme

last: Bullock

address: Edinburgh Cancer Research Centre, IGC, Western General Hospital, Crewe Road

country: United Kingdom

institute: University of Edinburgh

data_processing:
For the SUM44PE + CAF CM experiment (samples with CMexpt in library name), alignment and counting was carried out using the Lexogen Illumina Bluebee pipeline and all other data (IL6expt in library name) were analysed using Lexogen QuantSeq FWD data analysis pipeline. Both Bluebee and Lexogen QuantSeq FWD pipelines used Bbduk from the bbmap suite trimming, STAR alignment with modified ENCODE settings and gene counts using HTSeq-count with QuantSeq FWD-specific options.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw counts

source_name: breast

extract_protocol:
Qiagen RNeasy Mini kit
QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015)

treatment_protocol: Cells were grown in phenol-red free media for 24 hours (SUM44PE and MDA-MB-134VI) or 48 hours (HCI-013 and HCI-018) before stimulation with recombinant human IL-6 (10 ng/ml, Biolegend 570804) for 24 hours. For CAF CM experiment, SUM44PE cells were grown in phenol-red free media for 24 hours and then stimulated with ED26 CAF conditioned media (characterised here:https://doi.org/10.3390/cancers14040904) +/- anti-IL-6 (1 μg/ml, Biolegend 501125). CAF conditioned media was generated by growing ED26 ILC CAFs on collagen coated T75 flasks in DMEM/F12 + 10% FBS until confluent, then replacing media with phenol-red free and FBS-free media for 72 hours. Media was centrifuged at 1000xg to remove debris then filtered through a 0.22μm filter and stored at -80°C until used. Conditioned media was diluted 1:1 in phenol-red free growth factor free SUM44PE media for stimulation.

value: breast

value: Invasive lobular carcinoma

value: IL-6 24 hr


title: MOC_1430:gent:6.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert iname

tag: pert dose


title: HCI018_IL6expt_IL6_1


title: HCI018_IL6expt_IL6_3


title: HBO_DAPT_3


title: MOC_1430:gent:6.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert dose_unit

tag: pert idose

tag: pert time


title: HCI018_IL6expt_ctrl_3

value: Control


title: HCI018_IL6expt_ctrl_2


title: HBO_DAPT_2


title: HBO_DAPT_1


title: HCI013_IL6expt_IL624hr_1


title: HCI013_IL6expt_IL624hr_3


title: MOC_1430:gent:6.00000uM:120min:PA14:MOC_1430_1:r3

tag: pert time_unit

tag: pert itime

tag: pert type


title: HBO_Veh_2


title: MOC_1430:gent:6.00000uM:120min:PA14:MOC_1430_1:r1

tag: category

tag: project id

tag: replicate id


title: HCI013_IL6expt_IL624hr_5

tag: cell line


title: MOC_1430:gent:6.00000uM:120min:PA14:MOC_1430_1:r2

tag: project plate_id_384well

tag: strain id


title: MOC_1430:gent:6.00000uM:60min:PA14:MOC_1430_1:r1


title: HBO_Veh_3

tag: genotype


title: MOC_1430:fosfo:600.00000uM:90min:PA14:MOC_1430_1:r3

value: fosfo

value: Fosfomycin


title: HCI013_IL6expt_ctrl24hr_5

tag: tissue

tag: cell type

tag: treatment


title: HCI013_IL6expt_IL624hr_2


title: HCI013_IL6expt_ctrl24hr_2


title: HCI013_IL6expt_ctrl24hr_3


title: MOC_1430:fosfo:600.00000uM:90min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert iname

tag: pert dose


title: HBO_Veh_1


title: HCI013_IL6expt_ctrl24hr_1


title: MM134_IL6expt_IL6week_4

value: IL-6 1 week


title: MM134_IL6expt_IL6week_3


title: Tumor, Responder Progressed patient208

city: Los Angeles

first: Yiqian

last: Gu

state: CA

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

data_processing:
Utilizing STAR-2.7.11a, reads were aligned to the reference genome hg38. The "mappedReadsPerGene.out.tab" files were utilized for quantifying normalized expression values in Counts per Million (CPM)
Assembly: hg38
Supplementary files format and content: Tab seperated value files

source_name: tumor

extract_protocol:
The Tempus xT-RNA Assay employs TNA extraction methods for FFPE biopsy (tumor) from which total RNA is isolated through the digestion of DNA.
xT-RNA library preparation is performed using IDT unique dual-index adapters, followed by hybrid capture with custom the IDT xGen Lockdown probes.

value: tumor

tag: group

value: Responder Progressed


title: MOC_1430:fosfo:600.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert dose_unit

tag: pert idose

tag: pert time

tag: pert time_unit


title: HCI018_IL6expt_ctrl_1


title: Tumor, Responder Progressed patient204


title: MOC_1430:fosfo:600.00000uM:60min:PA14:MOC_1430_1:r3

tag: pert itime

tag: pert type

tag: category

tag: project id


title: Tumor, Responder Progressed patient203


title: MM134_IL6expt_ctrlweek_4

tag: cell line


title: MM134_IL6expt_ctrlweek_3


title: MOC_1430:fosfo:600.00000uM:60min:PA14:MOC_1430_1:r2

tag: replicate id

tag: project plate_id_384well

tag: strain id


title: MM134_IL6expt_ctrlweek_2

tag: tissue

tag: cell type

tag: treatment


title: Tumor, Responder Progressed patient202


title: MM134_IL6expt_ctrlweek_1


title: MOC_1430:fosfo:600.00000uM:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert iname

tag: pert dose


title: MOC_1430:fosfo:600.00000uM:120min:PA14:MOC_1430_1:r3

tag: pert dose_unit

tag: pert idose


title: MM134_IL6expt_IL624hr_3


title: Tumor, Responder patient107

tag: group

value: Responder


title: MOC_1430:fosfo:600.00000uM:120min:PA14:MOC_1430_1:r2

tag: pert time

tag: pert time_unit

tag: pert itime


title: Tumor, Responder patient106


title: Tumor, Responder patient105


title: MM134_IL6expt_ctrl24hr_4


title: MOC_1430:fosfo:600.00000uM:120min:PA14:MOC_1430_1:r1

tag: pert type

tag: category

tag: project id


title: MM134_IL6expt_ctrl24hr_2

tag: cell line


title: MM134_IL6expt_ctrl24hr_1


title: MM134_IL6expt_ctrl24hr_3


title: Tumor, Progressor patient102


title: MM134_IL6expt_IL6week_2


title: MM134_IL6expt_IL6week_1


title: SUM44PE_IL6expt_IL6week_4


title: MOC_1430:erythro:300.00000uM:90min:PA14:MOC_1430_1:r3

value: erythro

value: Erythromycin

tag: replicate id

tag: project plate_id_384well

tag: strain id


title: MOC_1430:erythro:300.00000uM:90min:PA14:MOC_1430_1:r2


title: MM134_IL6expt_IL624hr_1

tag: tissue

tag: cell type

tag: treatment


title: Tumor, Responder patient101


title: MM134_IL6expt_IL624hr_4


title: MM134_IL6expt_IL624hr_2


title: MOC_1430:erythro:300.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert iname

tag: pert dose


title: MOC_1430:erythro:300.00000uM:60min:PA14:MOC_1430_1:r3

tag: pert dose_unit

tag: pert idose


title: SMIS-WT cells, STM2457 treatment, input

city: Shenzhen

first: Qin

last: Peng

address: Gaoke Innovation Center

country: China

institute: Shenzhen Bay Laboratory

description: input sample

data_processing:
Cutadapt v3.7;Bowtie2 v2.2.5
Fastq sequences were first filtered for a quality score of 20, then trimmed of 5′ and 3′ adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC.
The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed.
Reads were mapped to the methylated spike-in (rUrCrUrCrCrUrUrArGrUrArGrCrUrCrCrUrArArGm6ArUrCrGrUrCrGrArGrUrUrArCrArCrGrArCrGrArCrArUrUrGrUrUrCrCrGrArCrUrGrArCrG) or to the mMaroon1 reporter gene sequence using Bowtie2 2.2.5 -q -N 1 –no-mixed –no-discordant.
Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates. To calculate the relative methylation level (m6ACE/input) of each site, the read-start counts at the middle of each of the 22 ‘GGACU’ m6ACE library were divided by the read-start counts at the same site in the input library.
Assembly: custom sequence
Supplementary files format and content: bedgraph includes read counts for each sample

source_name: HeLa

growth_protocol: HeLa cells overexpressing SMIS-WT system were cultured in DMEM supplemented with 10% Australian fetal bovine serum (AFBS) and 1% penicillin‒streptomycin solution in a sterile 37°C incubator with 5% CO2.

extract_protocol:
total RNA was extracted from cells using total RNA kit I (omega, R6834) according to manufacturer’s instructions. Then, Poly(A) RNA was purified by VAHTS mRNA Capture Beads 2.0 (Vazyme, N403-01).
RNA libriaries for RNA seq was prepared accroding to our previous publication (Koh et al. Nat Commun, 2019, PMID: 31822664)

treatment_protocol: SMIS-WT cells were preteated with DMSO or STM2457 for 3 hours and incubated with DMSO or STM2457 (60μM) and DOX (1μg/mL) for 12 hours.

value: HeLa

tag: genotype

value: SMIS-WT overexpression


title: SUM44PE_IL6expt_IL624hr_4


title: SUM44PE_IL6expt_ctrlweek_1


title: SMIS-WT cells, DMSO treatment, m6ACE

description: m6ACE sample

value: DMSO


title: SUM44PE_IL6expt_ctrlweek_2


title: Tumor, Responder patient104

tag: group


title: MOC_1430:erythro:300.00000uM:60min:PA14:MOC_1430_1:r2

value: uM

tag: pert time

tag: pert time_unit

value: min

tag: pert itime

tag: pert type

value: poscon


title: SUM44PE_IL6expt_IL6week_3

value: breast

tag: cell line

value: Invasive lobular carcinoma


title: MOC_1430:erythro:300.00000uM:60min:PA14:MOC_1430_1:r1

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well

value: FALSE


title: SUM44PE_IL6expt_IL624hr_3

tag: tissue

tag: cell type

tag: treatment

value: IL-6 24 hr


title: SUM44PE_IL6expt_IL6week_2


title: SUM44PE_IL6expt_IL624hr_1


title: SMIS-WT cells, DMSO treatment, input

description: input sample


title: MOC_1430:erythro:300.00000uM:30min:PA14:MOC_1430_1:r3

tag: pert id

tag: pert iname

tag: pert dose

tag: strain id


title: SUM44PE_IL6expt_IL6week_1


title: SUM44PE_IL6expt_ctrl24hr_4

value: Control


title: SUM44PE_IL6expt_IL624hr_2


title: BMSCs, si3

city: Guangzhou , Guangdong

first: ning

last: qing

address: Sun Yat sen University Sun Yat sen Memorial Hospital, No. 107 Yanjiang West Road, Yuexiu District

institute: Sun Yat-sen Memorial Hospital

data_processing:
The raw data was handled by Skewer v0.2.2 (https://sourceforge.net/projects/skewer/files/?source=navbar)and data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Theread length was 2×150 bp. Clean reads were aligned to thehuman genome (GRCh38) from ensmbleusing STAR (https://github.com/alexdobin/STAR), with one mismatch allowed. StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression was analysed by DESeq2 (v1.16.1) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) . The thresholds for determining DEGs areP< 0.05 and |log2FoldChange|>=1.Then DEGs were chosen for function and signaling pathway enrichmentanalysis using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KEGG database (https://www.genome.jp/kegg/pathway.html).The significantly enriched pathways were determined whenP< 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: BMSCs

growth_protocol: Cells were cultured in a medium consisting of 90% Dulbecco's Modified Eagle's Medium (DMEM, Gibco, New York, USA) with 1g/L D-Glucose and 10% Fetal Bovine Serum (FBS, TIANHANG, Zhejiang, China). The culture bottles were placed in an incubator set at 37 degrees Celsius with 5% carbon dioxide and 20% oxygen.

extract_protocol:
Total RNA was extracted from BMSCs with the TRIzol according to the manufacturer’s instructions. RNA quantity was analysed using Qubit 4.0 (Invitrogen) and quality examined by electrophoresis on a denaturing agarose gel.
RNA libraries were prepared using the NGSeUltima Dual-mode mRNA Library Prep Kit for Illumina (NR605-0, Vazyme), followed sequencing using the Illumina NovaSeq 6000 platform with the 150 paired-end sequencing strategy.Enrichment of mRNA, library construction, sequencing and data analysis were performed by Shanghai Xu Ran Biotechnology Co., Ltd (http://www.xurangene.com）.

treatment_protocol: After treatment with siRNA, induce bone differentiation for three days.Osteogenic induction is carried out using a medium consisting of 10% Fetal Bovine Serum (FBS), 50 μg/mL of ascorbic acid, 10 mmol/L of β-glycerophosphate, and 0.1 mM of dexamethasone in 90% Dulbecco's Modified Eagle Medium (DMEM) with 1 g/L of D-Glucose.

value: BMSCs

tag: genotype

value: lncRNA MRF knockdown


title: SUM44PE_IL6expt_ctrl24hr_3


title: SUM44PE_IL6expt_ctrl24hr_2


title: SMIS-WT cells, STM2457 treatment, m6ACE

description: m6ACE sample


title: BMSCs, si2


title: MOC_1430:erythro:300.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert dose_unit

tag: pert idose

tag: pert time


title: BMSCs, si1


title: SUM44PE_IL6expt_ctrlweek_3


title: SUM44PE_IL6expt_ctrl24hr_1


title: SUM44PE_IL6expt_ctrlweek_4


title: HCCLM3_DMSO_3

city: lianyungang

first: He

last: Jingliang

address: tongguan

institute: Jiangsu Ocean University

description:
HCCLM3_DMSO_3
D3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample

growth_protocol: HCCLM3 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without CC-885 for 24 hr with or without CC-885, respectively, and incubated in 5% CO2 at 37oC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver disease

value: Human Liver Cancer Cells


title: HCCLM3_DMSO_2

description:
HCCLM3_DMSO_2
D2


title: HCCLM3_DMSO_1

description:
HCCLM3_DMSO_1
D1


title: BMSCs, nc3

value: control


title: HCCLM3_CC_885_2

description:
HCCLM3_CC_885_2
C2


title: HCCLM3_CC_885_3

description:
HCCLM3_CC_885_3
C3


title: MOC_1430:erythro:300.00000uM:120min:PA14:MOC_1430_1:r2

value: erythro

value: Erythromycin

tag: pert time_unit

tag: pert itime

tag: pert type


title: BMSCs, nc2


title: HCCLM3_CC_885_1

description:
HCCLM3_CC_885_1
C1

tag: cell line


title: MOC_1430:erythro:300.00000uM:120min:PA14:MOC_1430_1:r1

tag: category

tag: project id

tag: replicate id


title: BMSCs, nc1

tag: cell type


title: MOC_1430:dmso:0.50000%:90min:PA14:MOC_1430_1:r3

value: dmso

value: negcon

tag: project plate_id_384well


title: MOC_1430:erythro:300.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert id

value: uM


title: MOC_1430:dmso:0.50000%:90min:PA14:MOC_1430_1:r2

tag: pert iname

value: min


title: d23_kidney_organoids_PPARa_agonists

city: Kobe

first: Yoshiki

last: Sahara

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing,  barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger).
The supplementary files named "d15-d31_kidney_organoids" were created by Cell Ranger aggregation command combined with "d15_kidney_organoids", "d19_kidney_organoids", "d23_kidney_organoids", "d27_kidney_organoids" and "d31_kidney_organoids".
The supplementary files named "d23_control-treatment_kidney_organoids" were created by Cell Ranger aggregation command combined with "d23_kidney_organoids_control" and "d23_kidney_organoids_PPARa_agonists".
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and matrix files

source_name: kidney organoids

growth_protocol: Organoid differentiation protocol: hiPSCs were treated with 8 μM CHIR99021 (TOCRIS, 4423) in APEL2 (StemCell Technologies, ST-05275) supplemented with 1% Protein Free Hybridoma Medium II (PFHM II, GIBCO, 12040077) (basal medium) for 5 days, followed by treatment with FGF9 (200 ng/ml, R&D, 273-F9) and heparin (1 μg/ml, Sigma, H4784) for another 3 days. At day 8, the cells were then collected and dissociated into single cells using TryPLE select (GIBCO, 12563011). One x 10^5 collected cells were seeded into PrimeSurface® 96M plates (Sumitomo Bakelite) and were cultivated for 1 day in a CO2 incubator to make spheroids. On the following day (day 9), these spheroids were transferred onto transwells with a 0.4 μm pore polyester membrane (Corning, 3450) and cultured at the liquid-air interface. Spheroids were treated with 10 μM CHIR99021 in basal medium for 3 h, and then cultured with FGF9 (200 ng/ml) and heparin (1 μg/ml) for another 6 days, followed by another 16 days (until day 31) in basal medium with changing the medium every other day.

extract_protocol:
Kidney organoids were incubated for 30 min at 6oC in cold active protease (DPBS(+), 5 mg/mL Bacillus Licheniformis Protease, 125 U/mL DNase) . Each cell suspension was diluted with fluorescence-activated cell sorting (FACS) buffer (DPBS(-), 0.5% FBS, 2 mM EDTA) + 125 U/mL DNase, centrifuged at 300 x g for 10 min at 4oC after which the supernatant was removed. This step was repeated twice after which the suspension was passed through a 35 μm filtered tube (Falcon) to prepare a cell suspension containing single cells.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics). Cells from kidney organoids 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 appropriated 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.

treatment_protocol: For the PPARα agonists treatment, kidney organoids were treated with 0.3 μM CP775146 (PPARα agonist, TOCRIS, 4190) and 1 μM 9-cis-retinoic acid (RXRα agonist, Abcam, ab141023) from day 15 in basal medium with changing the medium every other day.

tag: tissue

value: kidney organoids

value: hiPSCs

tag: treatment

value: PPARa agonists


title: d23_kidney_organoids_control

description: 10x Genomics

value: vehicle


title: KO-heart 4

type: RNA

first: Jennifer

middle: Q.

last: Kwong

address: 1750 Haygood Dr. NE N423

institute: Emory University School of Medicine

description: KO E17.5 Heart

hyb_protocol: According to manufacturer's instructions

data_processing: Data normalization was performed in nDolver 4.0 (NanoString)

source_name: E17.5 Heart

extract_protocol: Total RNA was extracted from E17.5 hearts using a RNeasy Micro kit (Qiagen), following the manufacturer's protocol.

value: Heart

tag: genotype

value: Slc25a1 KO


title: KO-heart 3

description: KO E17.5 Heart

scan_protocol: According to manufacturer's instructions


title: MOC_1430:dmso:0.50000%:90min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

tag: strain id

value: FALSE


title: MOC_1430:dmso:0.50000%:60min:PA14:MOC_1430_1:r3

tag: pert idose

tag: pert time

tag: pert time_unit


title: d31_kidney_organoids

description: 10x Genomics

tag: cell line


title: KO-heart 2

description: KO E17.5 Heart


title: d27_kidney_organoids

description: 10x Genomics


title: KO-heart 1

description: KO E17.5 Heart


title: WT-heart 4

description: WT E17.5 Heart

value: Slc25a1 WT


title: HET-heart 3

description: HET E17.5 Heart

value: Slc25a1 HET


title: MOC_1430:dmso:0.50000%:60min:PA14:MOC_1430_1:r2

tag: pert itime

tag: pert type

tag: category


title: HET-heart 1

description: HET E17.5 Heart


title: MOC_1430:erythro:300.00000uM:120min:PA14:MOC_1430_1:r3

value: poscon

tag: project id

tag: replicate id


title: MOC_1430:dmso:0.50000%:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: project plate_id_384well


title: d23_kidney_organoids

description: 10x Genomics

tag: tissue


title: WT-heart 3

description: WT E17.5 Heart


title: 10d leaf stimulus_240_rep4

city: Salt Lake City

first: Leslie

middle: Ellen

last: Sieburth

state: UT

address: 257 South 1400 East

department: Biology

institute: University of Utah

data_processing:
Reads were trimmed of adaptor sequences and aligned to the TAIR10 genome sequence using tophat2 and bowtie2.
Assembly: TAIR10
Supplementary files format and content: matrix of read counts for all genes in all samples.
Supplementary files format and content: comma separated values. Matrix of counts by gene.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Seeds were sown on moistened soil (Sungro Redi-Earth Plug and Seedling propagation mix) and imbibed in the dark at 4oC. After 2-4 d, pots were grown under continuous illumination with 75 µE m-2 s-1  at 21oC for 10 d. Leaves 1 and 2 were used.

extract_protocol:
Total RNA was extracted using the Quick-RNA Plant mini-prep kit (Zymo) and Treated with DNase I.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Plant to substantially deplete cytoplasmic, mitochondrial and chlorpoplast rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2401 and RS-122-2402).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis. HiSeq 50 Cycle Single-Read Sequencing version 4 Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

treatment_protocol: Whole detached leaves (~18-20/sample) were floated on distilled water during collection, followed by incubation in 10% bleach 0.1% Silwet L-77 for 3-5 min, and rinsing 3 times in sterile distilled water to surface sterilize. Sterile leaves were transferred to incubation buffer (0.22% Murashigie and Skoog salts [pH 5.7], 5.0% glucose, 0.2% dimethyl sulfoxide) with (stimulus) or without (mock) 20 µM bikinin, 2.5 µg mL-1 2,4-Dichlorophenoxyacetic acid, and 0.5 µg mL-1 kinetin. After 8 h, 1 mM cordycepin was added and samples were collected after an additional 0, 15, 60, or 240 min. Samples were treated at 21oC with shaking (120 RPM) and collected by flash freezing in liquid nitrogen.

value: leaf

tag: ecotype

tag: treatment


title: 10d leaf stimulus_060_rep4


title: MOC_1430:dmso:0.50000%:30min:PA14:MOC_1430_1:r3

tag: pert iname

tag: pert dose


title: HET-heart 2

description: HET E17.5 Heart

tag: genotype


title: d19_kidney_organoids

description: 10x Genomics


title: WT-heart 2

description: WT E17.5 Heart


title: 10d leaf stimulus_015_rep4


title: 10d leaf stimulus_000_rep4


title: MOC_1430:dmso:0.50000%:30min:PA14:MOC_1430_1:r2

tag: pert dose_unit

tag: pert idose

tag: strain id


title: WT-heart 1

description: WT E17.5 Heart


title: d15_kidney_organoids

description: 10x Genomics

tag: cell line


title: 10d leaf mock_060_rep4


title: 10d leaf mock_240_rep4


title: MOC_1430:dmso:0.50000%:30min:PA14:MOC_1430_1:r1

tag: pert time

tag: pert time_unit

tag: pert itime


title: 3552

city: Duesseldorf

first: Christopher

last: Nelke

state: NRW

address: UKD, Moorenstraße 5

country: Germany

institute: University Hospital Düsseldorf

description:
DYS
3552

data_processing:
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.
Assembly: Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. Genome GRCh38 Human Genome.
Supplementary files format and content: Processed data is in xlsx format with each gene counts for each sample.

source_name: Skeletal muscle

extract_protocol:
Total RNA was extracted from tissue samples using Qiagen RNeasy Mini kit following manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions.
Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: Skeletal muscle


title: 10d leaf mock_000_rep4


title: 10d leaf mock_015_rep4


title: 10d leaf stimulus_240_rep3


title: MOC_1430:dmso:0.50000%:120min:PA14:MOC_1430_1:r3

tag: pert type

tag: category

tag: project id


title: 3636

description:
DYS
3636


title: P20

description:
DM
P20


title: P19

description:
IMNM
P19


title: 10d leaf stimulus_060_rep3


title: 10d leaf stimulus_015_rep3


title: 10d leaf stimulus_000_rep3


title: C7

description:
Control
C7


title: 10d leaf mock_060_rep3


title: MOC_1430:dmso:0.50000%:120min:PA14:MOC_1430_1:r1

tag: pert id

tag: replicate id

tag: project plate_id_384well


title: 10d leaf mock_240_rep3

tag: tissue

tag: ecotype

tag: treatment


title: 10d leaf mock_015_rep3


title: HET-heart 4

description: HET E17.5 Heart

tag: genotype


title: MOC_1430:col:3.00000uM:90min:PA14:MOC_1430_1:r3

value: col

tag: pert iname

value: Colistin

tag: pert dose

tag: pert dose_unit


title: P18

description:
IMNM
P18


title: 10d leaf stimulus_060_rep2


title: 10d leaf stimulus_240_rep2


title: MOC_1430:col:3.00000uM:90min:PA14:MOC_1430_1:r2

tag: cell line

tag: pert idose

tag: strain id


title: MOC_1430:col:3.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert time

tag: pert time_unit

tag: pert itime


title: C5

description:
Control
C5


title: P5

description:
ASYS
P5


title: 10d leaf stimulus_015_rep2


title: MOC_1430:col:3.00000uM:60min:PA14:MOC_1430_1:r3

tag: pert type

tag: category

tag: project id


title: 10d leaf mock_060_rep2


title: P9

description:
DM
P9


title: 10d leaf mock_240_rep2


title: 10d leaf stimulus_000_rep2


title: MOC_1430:col:3.00000uM:60min:PA14:MOC_1430_1:r2

tag: pert id

tag: replicate id

tag: project plate_id_384well


title: P4

description:
NDC
P4

tag: tissue


title: 10d leaf mock_000_rep2

tag: ecotype

tag: treatment


title: MOC_1430:dmso:0.50000%:120min:PA14:MOC_1430_1:r2

value: dmso

tag: pert iname

tag: pert dose

value: negcon


title: 10d leaf mock_000_rep3


title: 10d leaf mock_015_rep2


title: Lung, ILC2, BLEO-HPS1

city: Providence

first: Yang

last: Zhou

state: Rhode Island

address: 171 Meeting St, BMC 624

department: Molecular Microbiology and Immunology

institute: Brown University

data_processing:
CLC Genomics Workbench
Assembly: NCBI
Supplementary files format and content: Differential gene expression results presented between different groups. Positive fold changes indicate the Treatment has a higher expression.

source_name: Lung

extract_protocol:
Total cellular RNA was extracted by Qiagen RNeasy kit per manufacturer’s instructions and used for RNA-Sequencing and gene expression analyses. The number of ILC2s used in sequencing are: WT PBS, 22,405 cells; HPS PBS, 38,873 cells; WT Bleomycin, 84,166 cells; HPS Bleomycin, 128,647 cells.
SMARTER mRNA-Seq Library Prep Kit

value: Lung

tag: cell type

tag: genotype

value: Bleomycin


title: MOC_1430:col:3.00000uM:60min:PA14:MOC_1430_1:r1

tag: cell line

tag: pert dose_unit

value: uM

tag: pert idose

value: min

tag: strain id


title: Lung, ILC2, BLEO-WT

value: WT


title: MOC_1430:col:3.00000uM:30min:PA14:MOC_1430_1:r3

tag: pert time

tag: pert time_unit

tag: pert itime

tag: pert type


title: P38

description:
DYS
P38


title: Lung, ILC2, PBS-HPS1

value: PBS


title: P452

description:
COVID
P452


title: MOC_1430:col:3.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert id

tag: category

tag: project id

tag: replicate id


title: P451

description:
COVID
P451

tag: tissue


title: MOC_1430:col:3.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert iname

tag: project plate_id_384well


title: Lung, ILC2, PBS-WT

tag: cell type

tag: treatment


title: MOC_1430:col:3.00000uM:120min:PA14:MOC_1430_1:r3

tag: cell line

tag: pert dose


title: JKZ230_MBD9_ChIP_rep1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

library_source: genomic

data_processing:
Reads were mapped to TAIR10 by Bowtie2 with parameter "-k 10 --very-sensitive --no-unal --no-mixed --no-discordant", duplicated reads were removed using samtools markdup -r.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bg -pc

molecule: genomic DNA

source_name: seedlings

growth_protocol: Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose and were harvested at 14-days old.

extract_protocol:
ChIP was performed according to a previously published protocol (Wierzbicki et al., 2008).
ChIP samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.

treatment_protocol: no treatment

tag: cultivar


title: JKZ230_MBD9_Input


title: JKZ230_MBD9_ChIP_rep2


title: MOC_1430:col:3.00000uM:120min:PA14:MOC_1430_1:r2

tag: pert dose_unit

tag: pert idose

tag: strain id


title: P2

description:
ASYS
P2


title: EAhy926_sgLRRC34_infected_rep1

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol. 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: replicate


title: EAhy926_uninfected_rep1

value: uninfected


title: P23

description:
IBM
P23


title: JKZ230_Col0_Input


title: JKZ230_Col0_ChIP_rep3


title: MOC_1430:col:3.00000uM:120min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert time

tag: pert time_unit

tag: pert itime

tag: pert type

value: FALSE


title: P40

description:
COVID
P40

tag: tissue


title: EAhy926_sgGRK4_infected_rep2


title: MOC_1430:clari:300.00000uM:90min:PA14:MOC_1430_1:r3

value: clari

tag: pert iname

value: Clarithromycin

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well


title: JKZ230_Col0_ChIP_rep2

tag: cultivar


title: JKZ230_MBD9_ChIP_rep3


title: C6

description:
Control
C6


title: EAhy926_uninfected_rep2

tag: cell line

tag: treatment


title: JKZ230_Col0_ChIP_rep1


title: MOC_1430:clari:300.00000uM:90min:PA14:MOC_1430_1:r2

tag: pert dose

tag: pert dose_unit

tag: pert idose

value: poscon

tag: strain id


title: EAhy926_sgLRRC34_infected_rep2

tag: genotype

tag: replicate


title: P25

description:
IBM
P25


title: MOC_1430:clari:300.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert time

tag: pert time_unit

tag: pert itime


title: pie1-7_BS

description: treated with bisulfite

data_processing:
MethylC-Seq： For data analysis, data were trimmed using trimmomatic with  parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP with parameter "-m 0 -x 1000  -w 2", and python script of BSMAP was used to remove potential PCR duplicates and extract methylation ratios.
Genome_build: TAIR10
Supplementary_files_format_and_content: The methratio files were generated by methratio.py with parameter "-z -r -m 4".

growth_protocol: Seedlings were grown on 1/2 MS medium with 1% Glucose and 0.8% agar

extract_protocol: Genomic DNA was extracted from 14-day-old seedlings using the DNeasy Plant Maxi Kit (Qiagen, 68163) and sent to the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) for bisulfite treatment. Libraries were prepared for sequencing according to the manufacturer’s (Illumina) instructions and sequenced on an Illumina Hiseq 2500 platform.

tag: tissue

value: seedlings


title: B50

description:
Neurogen
B50

value: Skeletal muscle


title: P1

description:
ASYS
P1


title: arp6-5_BS

description: treated with bisulfite


title: Jurkat_uninfected_rep1

source_name: Jurkat

value: Jurkat


title: P49

description:
Neurogen
P49


title: P10

description:
DM
P10


title: Jurkat_sgADAT1_infected_rep1


title: P48

description:
Neurogen
P48


title: MOC_1430:clari:300.00000uM:60min:PA14:MOC_1430_1:r2

tag: pert iname

tag: pert type

tag: category

tag: project id


title: arp6-5-H2A.Z

data_processing:
The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with BWA(0.7.10-r789) with default parameter
To remove potential PCR duplicates, rmdup from SAMtools (Li et al., 2009) was used
Mapped reads extended to the average length of the genomin fragments and counting the number of reads at each position  in the genome by genome CoverageBed of BEDTools， and then was normalized to the average base-pair count number
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files that represent the number  of reads at each position in genome normalized to the average base-pair count number

source_name: Seedlings

growth_protocol: Plants were grown at 23°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 1% glucose.

tag: chip antibody

value: seedling


title: pie1-7-H2A.Z


title: P21

description:
Neurogen
P21


title: Jurkat_uninfected_rep2

tag: cell line

tag: treatment


title: idm1-9-H2A.Z


title: MOC_1430:clari:300.00000uM:60min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

tag: replicate id

tag: project plate_id_384well


title: MOC_1430:clari:300.00000uM:30min:PA14:MOC_1430_1:r3

tag: pert idose

tag: strain id


title: Jurkat_uninfected_rep3

tag: genotype

tag: replicate


title: MOC_1430:clari:300.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert time

tag: pert time_unit

tag: pert itime


title: ros1-14-H2A.Z

tag: tissue


title: WT-H2A.Z


title: MOC_1430:clari:300.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert iname

tag: pert type

tag: category

tag: project id


title: P39

description:
COVID
P39


title: h2a.z-2_MethylC-Seq

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BSMAP 2.87 with parameters -r 1 -g 1
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for  total Cs. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China)  for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.


title: Jurkat_sgHMGB1_infected_rep3

tag: cell line

tag: treatment


title: Jurkat_sgHMGB1_infected_rep1


title: EAhy926_sgGRK4_infected_rep1


title: Jurkat_sgADAT1_infected_rep3


title: P12

description:
DM
P12


title: MOC_1430:clari:300.00000uM:60min:PA14:MOC_1430_1:r3

tag: pert dose

tag: pert dose_unit

tag: replicate id


title: pie1-7_MethylC-Seq

description: treated with bisulfite


title: P46

description:
Neurogen
P46


title: Jurkat_sgADAT1_infected_rep2


title: Jurkat_sgHMGB1_infected_rep2


title: P28

description:
IBM
P28


title: MOC_1430:cip:0.75000uM:90min:PA14:MOC_1430_1:r2

value: cip

value: Ciprofloxacin

tag: pert idose

tag: project plate_id_384well

tag: strain id


title: MOC_1430:cip:0.75000uM:90min:PA14:MOC_1430_1:r3

tag: pert id


title: Brain, E5

city: Chongqing

first: Zhai

last: Xuan

address: Chongqing 400010, China

department: Department of Neurosurgery

institute: Children’s Hospital of Chongqing Medical University

description: Brain epilepsy rep5

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
DESeq2 (v1.26.0) was applied for the detection of differentially expressed mRNAs and lncRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and FPKM values for each sample

source_name: Brain epilepsy

extract_protocol:
Brain tissues were collected, flash frozen on dry ice, and total RNA was extracted using TRIzol method.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Brain

tag: disease state

value: epilepsy


title: ros1-14_MethylC-Seq

description: treated with bisulfite

tag: genotype


title: Brain, E4

description: Brain epilepsy rep4


title: MOC_1430:clari:300.00000uM:120min:PA14:MOC_1430_1:r3

data_processing:
BWA to align reads to reference
QC & filter samples with low counts and genes with low counts
DESeq2 to identify weak and robust transcriptional signals
VST function from DESeq2 for variance stabilization of counts
Calculate moderated z-scores using custom scripts, based on previously published scripts (Subramanian, A. et al. Cell. 2017. https://doi.org/10.1016/j.cell.2017.10.049)
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample
Supplementary files format and content: comma separated file with moderated z-score values for each treatment condition (replicates collapsed)

value: uM

tag: pert time

tag: pert time_unit

tag: pert itime


title: WT_MethylC-Seq

description: treated with bisulfite

tag: tissue


title: Trabectedin-treated A673 in nude mouse, CD45- fraction

city: Columbus

first: Emily

middle: M.

last: Ringwalt

state: OH

address: 575 Children's Xrd

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

data_processing:
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/oHSV-trabectedin)
Assembly: The reference genome was built from mm10, hg19, and HSV-1 strain 17 (concatenated into one reference genome).
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

source_name: flank tumor (subQ)

extract_protocol:
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10XGenomics, PN-1000120) according to the manufacturer's instructions.
Libraries were constructed per 10x protocols

treatment_protocol: The Ewing sarcoma human xenografts were treated with either oHSV (1e7 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Osteosarcoma mouse models were treated with either oHSV (1e8 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Tumors were harvested on Day 3.

value: flank tumor (subQ)

tag: cell type

value: Ewing sarcoma

value: Trabectedin


title: oHSV-treated A673 in nude mouse, CD45- fraction

value: oHSV


title: sgADAT1_infected_rep2

data_processing:
Raw reads were aligned to the human reference (GRCh38) using BWA. Reads were filtered to include only uniquely mapped reads. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed. MACS2 was used to call peaks.
Assembly: GRCh38/hg38
Supplementary files format and content: Peak calls in narrowPeak format relative to the input per sample

extract_protocol: Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: T lymphocyte

tag: chip antibody

value: Active Motif 61757, Lot 10216001


title: P22

description:
IMNM
P22


title: Combination-treated A673 in nude mouse, CD45- fraction

tag: cell line

value: oHSV+Trabectedin


title: MOC_1430:cip:0.75000uM:90min:PA14:MOC_1430_1:r1

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

tag: pert iname

value: min

tag: pert type

value: poscon

tag: category

tag: project id

value: FALSE


title: Brain, E3

description: Brain epilepsy rep3


title: sgADAT1_infected_rep1

value: Jurkat


title: PBS-treated A673 in nude mouse, CD45- fraction

tag: treatment

value: PBS (control)


title: MOC_1430:cip:0.75000uM:60min:PA14:MOC_1430_1:r2

value: cip

tag: pert dose

tag: pert dose_unit

tag: pert idose

tag: replicate id

tag: project plate_id_384well


title: Brain, E2

description: Brain epilepsy rep2

tag: disease state


title: Brain, E1

description: Brain epilepsy rep1


title: RT112 siNUMB rep2

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

data_processing:
Sequenced raw reads were processed with NF-CORE RNASeq pipeline, using the human GRCh38 and mouse GRCm39 as reference genomes. Transcript abundances were quantified using the Salmon pseudo-aligner.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text file containing Salmongene-level quantification for each sample, including feature length, effective length, TPM, and number of reads.

extract_protocol:
Total RNA was extracted with QIAzol™ Reagentand then purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Goldkit according to the manufacturer’s protocol

value: urothelial bladder cancer

value: siNUMB


title: MOC_1430:clari:300.00000uM:120min:PA14:MOC_1430_1:r2

tag: pert id

value: clari

value: Clarithromycin

tag: pert time

tag: pert time_unit

tag: strain id


title: arp6-5_MethylC-Seq

description: treated with bisulfite

tag: genotype

tag: tissue

value: seedling


title: MOC_1430:clari:300.00000uM:120min:PA14:MOC_1430_1:r1

tag: cell line

tag: pert iname

value: uM

tag: pert itime


title: sgHMGB1_infected_rep2

tag: cell type

tag: chip antibody


title: idm1-9_MethylC-Seq

description: treated with bisulfite


title: Brain, C2

description: Brain normal rep2

source_name: Brain normal

value: Brain

value: normal


title: sgHMGB1_infected_rep1

value: T lymphocyte


title: Brain, C1

description: Brain normal rep1


title: RT112 siCTRL rep2

tag: treatment

value: siCTRL


title: MOC_1430:cip:0.75000uM:30min:PA14:MOC_1430_1:r2

value: Ciprofloxacin

tag: pert dose

tag: pert dose_unit

tag: pert type

tag: category

tag: project id


title: MOC_1430:cip:0.75000uM:60min:PA14:MOC_1430_1:r3

tag: pert id

tag: pert idose

value: min

tag: replicate id

tag: project plate_id_384well


title: RT112 siCTRL rep1


title: sgLRRC34_infected_rep2

value: somatic cell hybrid

value: Active Motif 61757, Lot 10216001


title: 10h_stimulus_biorep3

data_processing:
Reads were trimmed of adaptor sequences and aligned to the TAIR10 genome sequence using BWA.
Assembly: TAIR10
Supplementary files format and content: matrix of read counts for all genes in all samples.

source_name: leaf numbers 1 and 2

growth_protocol: Seeds were sown on moistened soil (Sungro Redi-Earth Plug and Seedling propagation mix) and imbibed in the dark at 4oC. After 2-4 d, pots were grown under continuous illumination with 75 µE m-2 s-1  at 21oC for 10 d. Leaves 1 and 2 were used

extract_protocol:
Total RNA was extracted using the Quick-RNA Plant mini-prep kit (Zymo) and Treated with DNase I.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Plant to substantially deplete cytoplasmic, mitochondrial and chlorpoplast rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2401 and RS-122-2402).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis. NovaSeq 150x150 bp Sequencing:  Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 151 x 151 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).

treatment_protocol: Whole detached leaves (~18-20/sample) were floated on distilled water during collection, followed by incubation in 10% bleach 0.1% Silwet L-77 for 3-5 min, and rinsing 3 times in sterile distilled water to surface sterilize. Sterile leaves were transferred to incubation buffer (0.22% Murashigie and Skoog salts [pH 5.7], 5.0% glucose, 0.2% dimethyl sulfoxide) with (stimulus) or without (mock) 20 µM bikinin, 2.5 µg mL-1 2,4-Dichlorophenoxyacetic acid, and 0.5 µg mL-1 kinetin. Samples were incubated at 21oC with shaking (120 RPM) for designated times and collected by flash freezing in liquid nitrogen.

value: leaf numbers 1 and 2

tag: ecotype

value: 10h stimulus


title: 10h_stimulus_biorep2

tag: tissue


title: MOC_1430:cip:0.75000uM:120min:PA14:MOC_1430_1:r3

tag: cell line

value: cip

tag: pert time

tag: pert time_unit

value: poscon

tag: strain id

value: FALSE


title: sgLRRC34_infected_rep1

tag: cell type

tag: chip antibody


title: 10h_stimulus_biorep1

tag: treatment


title: KK47 siNUMB rep2

value: urothelial bladder cancer

value: siNUMB


title: MOC_1430:cip:0.75000uM:120min:PA14:MOC_1430_1:r2

tag: pert iname

tag: pert dose

tag: pert dose_unit

tag: pert itime


title: sgGRK4_infected_rep1


title: sgGRK4_infected_rep2


title: 10h_mock_biorep3

value: 10 h mock


title: KK47 siCTRL rep2


title: KK47 siNUMB rep1


title: NK-K562-BR3

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
Differential expression analysis with DESeq2 v1.18.1 was utilized to identify differentially expressed genes
Genome_build: GRCh38

source_name: peripheral blood mononuclear cells

extract_protocol:
Isolation of RNA from liver was performed using NucleoSpin RNA Kit from Macherey-Nagel.
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

tag: donor

value: healthy volunteer

value: peripheral blood


title: 10h_mock_biorep2


title: RT112 siNUMB rep1


title: MOC_1430:cip:0.75000uM:120min:PA14:MOC_1430_1:r1

first: Keith

last: Romano

address: 185 Cambridge St.

institute: Massachusetts General Hospital

tag: pert id

value: uM

tag: pert idose

tag: pert type

tag: category

tag: project id


title: MOC_1430:ceftaz:24.00000uM:90min:PA14:MOC_1430_1:r3

tag: cell line

value: ceftaz

value: Ceftazidime

tag: replicate id

tag: project plate_id_384well


title: NK-K562-BR2

tag: tissue


title: KK47 siCTRL rep1

tag: cell type

value: siCTRL


title: 10h_mock_biorep1

tag: ecotype


title: NK-K562-BR1

tag: treatment


title: MOC_1430:cip:0.75000uM:30min:PA14:MOC_1430_1:r1

tag: pert iname

value: Ciprofloxacin

tag: pert time

tag: pert time_unit

value: min

tag: strain id


title: MOC_1430:ceftaz:24.00000uM:90min:PA14:MOC_1430_1:r2

tag: pert dose

tag: pert dose_unit

tag: pert itime


title: 9h_stimulus_biorep3

value: 9 h stimulus


title: RT4 siNUMB rep2


title: MOC_1430:cip:0.75000uM:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert idose

tag: pert type


title: 9h_stimulus_biorep2

value: leaf numbers 1 and 2


title: RT4 siCTRL rep2

tag: cell line


title: NK-Blasts-K562-BR2

tag: donor

value: AML blasts + K562


title: RT4 siNUMB rep1


title: MOC_1430:ceftaz:24.00000uM:90min:PA14:MOC_1430_1:r1

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well


title: MOC_1430:cip:0.75000uM:30min:PA14:MOC_1430_1:r3

value: cip


title: NK-Blasts-K562-BR3

tag: tissue

tag: treatment


title: RT4 siCTRL rep1

tag: cell type


title: NK-Blasts-K562-BR1


title: NK-Blasts-BR3

value: AML blasts


title: CLS439 rep2


title: MOC_1430:ceftaz:24.00000uM:120min:PA14:MOC_1430_1:r3

tag: pert iname

tag: pert time

tag: pert time_unit

value: poscon

value: FALSE


title: 9h_stimulus_biorep1

tag: ecotype


title: MOC_1430:ceftaz:24.00000uM:120min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

tag: pert itime

tag: strain id


title: 9h_mock_biorep2

value: 9 h mock


title: 9h_mock_biorep3


title: MOC_1430:carb:600.00000uM:90min:PA14:MOC_1430_1:r3

tag: cell line

tag: pert id

value: carb

value: Carbenicillin

tag: pert idose

tag: pert type


title: CLS439 rep1

value: urothelial bladder cancer


title: NK-Blasts-BR2

tag: donor

value: healthy volunteer

value: peripheral blood


title: 9h_mock_biorep1


title: MOC_1430:carb:600.00000uM:90min:PA14:MOC_1430_1:r2

value: uM

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well


title: 8h_stimulus_biorep3

tag: tissue

tag: treatment

value: 8 h stimulus


title: HT1376 rep2

tag: cell type


title: HT1376 rep1


title: MOC_1430:carb:600.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert iname

tag: pert time

tag: pert time_unit


title: 8h_stimulus_biorep2

tag: ecotype


title: NK-Blasts-BR1


title: NK-PGE2-BR3


title: NK-PGE2-BR1


title: NK-PGE2-BR2


title: MOC_1430:ceftaz:24.00000uM:120min:PA14:MOC_1430_1:r2

value: ceftaz

value: Ceftazidime

tag: pert dose

tag: pert dose_unit

tag: pert itime

tag: strain id


title: RT112 rep1

tag: cell line


title: MOC_1430:carb:600.00000uM:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert idose

value: min

tag: pert type


title: 8h_mock_biorep2

value: leaf numbers 1 and 2

value: 8 h mock


title: MOC_1430:carb:600.00000uM:60min:PA14:MOC_1430_1:r3

tag: category

tag: project id

tag: replicate id


title: 8h_stimulus_biorep1

tag: tissue

tag: treatment


title: 8h_mock_biorep1


title: 5637 rep1

tag: cell type


title: MOC_1430:carb:600.00000uM:60min:PA14:MOC_1430_1:r2

tag: pert iname

tag: pert time

tag: project plate_id_384well


title: KK47 rep2


title: 8h_mock_biorep3

tag: ecotype


title: 5637 rep2


title: NK-only-BR1

tag: donor


title: RT112 rep2


title: NK-only-BR3


title: MOC_1430:carb:600.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

tag: pert time_unit

tag: pert itime


title: MOC_1430:carb:600.00000uM:120min:PA14:MOC_1430_1:r3

tag: cell line

tag: pert id

tag: pert idose

tag: strain id


title: MOC_1430:carb:600.00000uM:30min:PA14:MOC_1430_1:r3

tag: pert type

tag: category

tag: project id

tag: replicate id


title: MOC_1430:carb:600.00000uM:120min:PA14:MOC_1430_1:r2

tag: pert iname


title: 7h_mock_biorep3

tag: tissue

tag: treatment

value: 7 h mock


title: 7h_stimulus_biorep3

tag: ecotype

value: 7 h stimulus


title: KK47 rep1

tag: cell type


title: MOC_1430:carb:600.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert dose

tag: pert time

value: poscon

tag: project plate_id_384well


title: 7h_stimulus_biorep2


title: 7h_mock_biorep1


title: CD8+ T cell, CMV stimulated, Dextramer, GEX, rep1

city: Philadelphia

first: Siwei

last: Luo

state: Pennsylvania

address: 3401 Civic Center Blvd.

institute: Children’s Hospital of Philadelphia

description:
DEX_GEX_1
10X 5' Single Cell GEX Library

data_processing:
The barcoded processing, V(D)J clonotye analysis, gene counting and aggregation from 10X Single Cell V(D)J libraries and 5' Single Cell GEX libraries were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/pipelines-overview)
Assembly: GRCh38
Supplementary files format and content: csv files contain single-cell V(D)J clonotype annotations
Supplementary files format and content: tsv and mtx.gz files contain filtered feature-barcode matrices of single-cell gene expressions

source_name: Blood

extract_protocol:
After the cell sorting in ATLAS-seq or Dextramer staining, collected T cell suspension was transferred to laminar wash plate (~80μl in each well) and incubated at room temperature for 30min, followed by washing 5 times with DPBS in Laminar Wash HT2000. Then, the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits were used to resuspend T cells into a proper concentration to achieve targeted cell recovery and prepare the V(D)J library for single-cell TCR sequencing and GEx library for single-cell mRNA sequencing.
Followed the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits

value: Blood

value: CD8+ T cell

value: CMV stimulated

tag: staining

value: Dextramer

tag: library type

value: GEX


title: RT4 rep2

tag: cell line

value: urothelial bladder cancer


title: 7h_stimulus_biorep1


title: X01sh1_2

city: HENAN

first: ZHENG

last: YUAN

address: Jinming Campus, Henan University, Minglun Street, Longting District, Kaifeng, Henan, China

institute: HENAN University

data_processing:
Raw data (raw reads) of fastq format processing
Reference genome mapping, Index of the reference genome was built using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: table-delimited text file of raw counts for each samples

growth_protocol: maintained in DMEM/F-12 supplemented with B27, EGF , bFGF.

extract_protocol:
Total RNA was extracted from X01 sh1/4 cells using the TRIzol Reagent
RNA sequencing libraries were prepared from 1 µg of total RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina

value: Glioblastoma stem cell


title: RT4 rep1


title: NK-only-BR2

tag: donor

value: healthy volunteer

value: peripheral blood


title: MOC_1430:carb:600.00000uM:120min:PA14:MOC_1430_1:r1

city: Boston

tag: pert id

value: carb

value: Carbenicillin

tag: pert dose_unit

value: uM

tag: pert idose

tag: pert time_unit

tag: pert itime

tag: strain id

value: FALSE


title: Mouse_Klf5OE_ES_clone2

city: Otsu

first: Masatsugu

last: Ema

state: Shiga

address: Seta, Tsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

description: Affymetrix GeneChip Expression Analysis  Technical manual Rev 3

data_processing: Transcriptome Analysis Console Software (Thermo Fisher Scientific)

label: biotin

growth_protocol: ES medium + 15% FBS　＋LIF

extract_protocol: Total RNA was extracted from the two clones of  Klf5 overexpression ES cells using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using Agilent bioanalyser (Agilent Technologies).

value: Mouse_E14 ES cell_Undifferentialted


title: CD8+ T cell, CMV stimulated, ATLAS, GEX, rep2

description:
ATLAS_GEX_2
10X 5' Single Cell GEX Library

tag: tissue

value: ATLAS


title: X01sh4_1


title: MOC_1430:ami:4.50000uM:90min:PA14:MOC_1430_1:r3

value: ami

tag: pert iname

value: Amikacin

value: min

tag: pert type

tag: category

tag: project id

tag: replicate id


title: 7h_mock_biorep2

value: leaf numbers 1 and 2

tag: ecotype

tag: treatment

value: 7 h mock


title: X01sh1_1

tag: cell type


title: MOC_1430:ami:4.50000uM:60min:PA14:MOC_1430_1:r3

tag: cell line

tag: pert dose

tag: pert time

value: poscon

tag: project plate_id_384well


title: Mouse_Klf5OE_ES_clone1

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical manual Rev 3


title: CD8+ T cell, CMV stimulated, Dextramer, V(D)J, rep2

description:
DEX_VDJ_2
10X Single Cell V(D)J Library

data_processing:
The barcoded processing, V(D)J clonotye analysis, gene counting and aggregation from 10X Single Cell V(D)J libraries and 5' Single Cell GEX libraries were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/pipelines-overview)
Assembly: GRCh38
Supplementary files format and content: csv files contain single-cell V(D)J clonotype annotations
Supplementary files format and content: tsv and mtx.gz files contain filtered feature-barcode matrices of single-cell gene expressions
Library strategy: scTCR-seq

value: Blood

value: CD8+ T cell

value: CMV stimulated

tag: staining

value: Dextramer

tag: library type

value: V(D)J


title: X01sh1_3

value: Glioblastoma stem cell


title: X01PK3


title: MOC_1430:ami:4.50000uM:90min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert dose_unit

tag: pert idose

tag: pert time_unit

tag: pert itime


title: X01sh4_3


title: MOC_1430:ami:4.50000uM:60min:PA14:MOC_1430_1:r2

tag: pert iname

tag: pert type

tag: category

tag: strain id


title: 6h_stimulus_biorep3

tag: tissue

tag: ecotype

tag: treatment

value: 6 h stimulus


title: CD8+ T cell, CMV stimulated, ATLAS, V(D)J, rep2

description:
ATLAS_VDJ_2
10X Single Cell V(D)J Library

tag: cell line

tag: cell type


title: CD8+ T cell, CMV stimulated, Dextramer, V(D)J, rep1

description:
DEX_VDJ_1
10X Single Cell V(D)J Library


title: MOC_1430:ami:4.50000uM:90min:PA14:MOC_1430_1:r1

tag: pert dose

value: uM

tag: pert time

tag: project id

tag: replicate id

tag: project plate_id_384well


title: MOC_1430:ami:4.50000uM:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert dose_unit

tag: pert idose

value: FALSE


title: 6h_stimulus_biorep2


title: X01PK1


title: X01sh4_2


title: MOC_1430:ami:4.50000uM:30min:PA14:MOC_1430_1:r3

tag: pert iname

tag: pert time_unit

tag: pert itime


title: MOC_1430:ami:4.50000uM:30min:PA14:MOC_1430_1:r2

tag: pert type

tag: category

tag: strain id


title: CD8+ T cell, CMV stimulated, Dextramer, GEX, rep2

description:
DEX_GEX_2
10X 5' Single Cell GEX Library

tag: tissue

tag: treatment

tag: staining

tag: library type

value: GEX


title: 6h_stimulus_biorep1

tag: ecotype


title: CD8+ T cell, CMV stimulated, ATLAS, GEX, rep1

description:
ATLAS_GEX_1
10X 5' Single Cell GEX Library

tag: cell line

tag: cell type

value: ATLAS


title: X01PK2


title: Combination-treated A673 flank tumor

description: Combination-treated A673 flank tumor

organism:
Homo sapiens
Mus musculus

value: flank tumor (subQ)

value: Ewing sarcoma (and infiltrating mouse cells)

value: oHSV+Trabectedin


title: CD8+ T cell, unstimulated, V(D)J

description:
Input_VDJ
10X Single Cell V(D)J Library

value: unstimulated


title: oHSV-treated A673 flank tumor

description: oHSV-treated A673 flank tumor

value: oHSV


title: MOC_1430:ami:4.50000uM:120min:PA14:MOC_1430_1:r3

value: ami

value: Amikacin

tag: pert dose

tag: pert time

value: min

value: poscon

tag: project id

tag: replicate id

tag: project plate_id_384well


title: PBS-treated A673 flank tumor

description: PBS-treated A673 flank tumor

value: PBS (control)


title: CD8+ T cell, unstimulated, GEX

description:
Input_GEX
10X 5' Single Cell GEX Library

value: Blood

value: CD8+ T cell


title: 6h_mock_biorep2

value: leaf numbers 1 and 2

value: 6 h mock


title: MOC_1430:ami:4.50000uM:120min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert iname

tag: pert dose_unit

value: uM

tag: pert idose

tag: pert time_unit

value: FALSE


title: K562 cells, imatinib, miR-92a mimic, biol rep 3

city: Woluwe-Saint-Lambert

first: Joanne

last: Peters

state: Brussels

address: Av. Hippocrate 75

department: MEXP

country: Belgium

institute: De Duve Institute

data_processing:
Sequencing reads were aligned with Kallisto software
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files giving raw counts for each sample

growth_protocol: K562 cells were cultured in RPMI medium supplemented with 10% FBS and 50 U/mL penicillin and 50 mg/mL streptomycin in humidified atmosphere at 37)C 5% CO2.

extract_protocol:
RNA was extracted using TriPure isolation reagent (Sigma-Aldrich) followed by a chloroform/isopropanol/ethanol purification step.
RNA was extracted and sent to Macrogen for RNA- sequencing. A paired-end sequencing was performed with an average sequencing coverage of 62 M. Results obtained were quantified using the Kallisto software.

treatment_protocol: 5E6 cells were transfected with  nucleoporated using Amaxa Nucleofector Technology (Lonza) with 500 pmol of hsa-miR-92a-1-5p synthetic miRVana mimic (#4464066) or  miRVana miRNA Mimic, Negative Control #1(#4464058) (Thermo Fisher Scientific). 4h after transfection, cells were treated with 1 µM of Imatinib. 24h later, RNA was extracted.

value: Myeloblast

tag: genotype

value: miR-92a overexpression

value: 1 µM Imatinib


title: Post-NACT Sample7_TCR

city: London

first: Samar

last: Elorbany

address: Barbican

department: Tumour Microenvironment

institute: Queen Mary University of London

description:
Post-NACT
10x Genomics,5' prime V1 kit

data_processing:
Cell ranger multi software Suite (version 6.0.1) was used for de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification, TCR/BCR  assembly, alignment, annotation and quantification of the reads.
Filtered feature barcode files were then imported in R for further processing using Seurat V4 and scRepertoire V1.7
Assembly: GRCh38-2020-A  and vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: For each patient sample, 3 libraries exit, GEX, BCR and TCR. For GEX library, processed data include 3 files, barcode.tsv, features.tsv and matrix.mtx.  For BCR and TCR libraries, one filtered_contig_annotation.csv file is submitted for each

source_name: Omentum

growth_protocol: Tumours were used immediately and cells were not grown

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and DNAse to obtain single-cell suspensions. Resulting cell suspensions were used enriched for live cells using Dead cell removal kit from Meltyni and CD45 positive cells using CD45 positive selection kit from Meltyni.
For all the samples, single cell 10X chromium 5' prime V1.0.0 kit with immunoprofiling(TCR and BCR) was used except for sample3, 10X chromium 5' prime V2 kit with immunprofiling was used

treatment_protocol: Fresh tissue was collected and placed in PBS on ice and immediately processed

value: HGSOC

tag: tissue

value: Omentum


title: CD8+ T cell, CMV stimulated, ATLAS, V(D)J, rep1

description:
ATLAS_VDJ_1
10X Single Cell V(D)J Library

tag: treatment

value: CMV stimulated

tag: staining

value: ATLAS

value: V(D)J


title: 6h_mock_biorep3

tag: ecotype


title: Trabectedin-treated A673 flank tumor

description: Trabectedin-treated A673 flank tumor

value: flank tumor (subQ)

tag: cell line

value: Ewing sarcoma (and infiltrating mouse cells)

value: Trabectedin


title: Post-NACT Sample7_BCR

description:
Post-NACT
10x Genomics,5' prime V1 kit

tag: cell type


title: 6h_mock_biorep1


title: K562 cells, imatinib, scramble mimic, biol rep 3

value: Control


title: Post-NACT Sample7_GEX

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: K562 cells, imatinib, scramble mimic, biol rep 1


title: Post-NACT Sample6_TCR

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: K562 cells, imatinib, miR-92a mimic, biol rep 2


title: K562 cells, imatinib, scramble mimic, biol rep 2


title: Post-NACT Sample6_BCR

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: K562 cells, imatinib, miR-92a mimic, biol rep 1


title: Post-NACT Sample6_GEX

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: 549High-2

city: Worcester

first: Yong-Xu

last: Wang

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Chan Medical School

data_processing:
Reads were aligned to hg38 with STAR.
Aligned reads were annotated with gencode.v34.primary_assembly.
Aligned exonic reads were counted with featureCounts using default settings except for ‘-Q 20 --minOverlap 1  --fracOverlap 0 -p -B -C’.
Differiental expresssion analysis was performed with DESeq2.
TPM was calculated with in-house R script.
Assembly: hg38
Supplementary files format and content: Tab-delimited Excel file including raw counts for each sample.
Supplementary files format and content: Tab-delimited Excel file including TPM/FPKM values for each sample .

extract_protocol:
RNA was harvested using EZ-10 DNAaway RNA mini-preps kit. 250ng of total RNA was used for library preparation.
RNA library was prepared using KAPA Stranded mRNA Hyper prep polyA selected kit and following the manufacturer's instructions

value: TNBC Cell line


title: 549Low-2


title: 549High-1


title: T24_CCNC_sg1_2

city: Shanghai

first: Shiyu

last: Mao

address: 301 Middle Yan Chang Road, Shanghai

institute: Shanghai Tenth People's Hospital of Tongji University; School of Medicine; Tongji University

data_processing:
Raw data (raw reads) were processed using Trimmomatic
Assembly: The clean reads were mapped to the human genome (GRCh38) using HISAT2
Supplementary files format and content: xls file includes raw counts for each sample
Supplementary files format and content: xls file includes FPKM for each sample

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

value: CCNC knockout

value: no


title: MOC_1430:ami:4.50000uM:30min:PA14:MOC_1430_1:r1

value: ami

value: Amikacin

tag: pert dose

value: uM

value: min

tag: pert itime

tag: pert type

value: poscon

tag: category

tag: strain id


title: ML uRNA 3

city: Gainesville

first: Sadeem

last: Qdaisat

address: 1333 Center Dr.

institute: University of Florida

hyb_protocol: Nanostring NS_Mm_CancerImm_C3400 kit protocol nCounter, NS_Mm_Glial_v1.0

scan_protocol: nCounter FLEX High sensitivity scan

data_processing: Rosalind

source_name: Osteosarcoma tumors in Balb/c

label_protocol: Nanostring NS_Mm_CancerImm_C3400 kit on a BIO-RAD T100 Thermal Cycler, NS_Mm_Glial_v1.0

growth_protocol: In vivo

extract_protocol: TriZol followed by RNA purification

tag: strain

value: Balb/c

value: Osteosarcoma tumors

value: ML uRNA


title: T24_CCNC_sg1_3


title: Post-NACT Sample5_BCR

description:
Post-NACT
10x Genomics,5' prime V1 kit

value: HGSOC

value: Omentum


title: MOC_1430:ami:4.50000uM:120min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert iname

tag: pert time

tag: project id

tag: replicate id

tag: project plate_id_384well

value: FALSE


title: 549Low-1


title: ML uRNA 2

tag: tissue

tag: treatment


title: Post-NACT Sample5_TCR

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: T24_sgNC_3

tag: genotype

value: WT


title: UT 2

value: UT


title: TD006634-8515

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
We initiated our analysis by aligning the raw fastq files to the customized mouse genome reference mm10, which included the Rfp sequence. This alignment process was executed using CellRanger v5.0.0 by 10X Genomics. Following alignment, we used the CellRanges algorithm to filter count matrices. Cells with less than 400 genes, fewer than 1000 UMI (unique molecular identifier), or over 25% mitochondrial gene expression were excluded. Subsequent data processing and analysis were conducted using the Seurat v4.2.2 R package. The data was normalized using the NormalizeData function, utilizing the normalization.method = 'LogNormalize' parameter. For dimensionality reduction, we focused on the top 2,000 variable features, using functions such as FindVariableFeatures, ScaleData, and RunPCA. Ultimately, we generated UMAPs based on the top 15 principal components (PCs).
To subcluster the immune compartment, we employed the R package Harmony to address batch effects stemming from technical variations across replicates. De novo clustering was carried out using the Louvain algorithm at multiple resolutions (0.2, 0.4, 0.8, 2, 3, 5, 8) within the KNN graph space. For high-level cell type annotation, we iteratively and semi-supervisedly assigned de novo discovered clusters to cell types based on the expression of established marker genes defining each cluster. The annotation of cell subtypes at a lower level followed a similar approach to the high-level annotation, with additional assistance from de novo marker discovery utilizing the Seurat FindMarkers function and Wilcoxon Rank Sum test.
To identify clusters enriched with doublets, we searched for cell clusters that exhibited the expression of canonical markers for two or more distinct cell types and a higher count of genes/UMI. These identified clusters were subsequently excluded from further analysis.
Cell-level proliferation analysis was performed using the Seurat function CellCycleScoring, which utilized a curated list of murine cell cycle genes. Subsequently, cells were categorized as 'cycling' or 'non-cycling' based on whether their S-phase score or G2M-score exceeded a threshold of 0.10 for the tumor compartment and immune compartment.
To identify modules of co-expressed genes, we employed the R package scWGCNA (https://github.com/smorabit/scWGCNA). Initially, we computed metacells, each comprising 100 cells (k=100), utilizing the construct_metacells function. For module identification, we utilized the blockwiseConsensusModules function with the following parameter settings: softPower=14, deepSplit=1, and mergeCutHeight=0.20 for the tumor analysis, and softPower=12, deepSplit=4, and mergeCutHeight = 0.20 for the microglia analysis. It's important to note that only the top 10,000 variable genes were included in this analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors were dissected from the brain, minced into pieces < 1 mm3, and digested with an enzymatic mixture that includes papain (0.94 mg/ml, Worthington, LS003120), EDTA (0.18 mg/ml, Sigma, E6758), cysteine (0.18 mg/ml, Sigma, A8199), and DNase I (60 μg/ml, Roche, 11284932001) in 2 ml HBSS (Gibco, 14175-095). Tumor tissues were kept at 37°C for 15 minutes with occasional agitation. The digestion was terminated with the addition of 2 ml Ovomucoid (0.7 mg/ml, Worthington, LS003086). Following digestion, single cells were passed through a 70 μm cell strainer, centrifuged, and resuspended in 30% Percoll (GE Healthcare, 17-0891-01) solution containing 10% FBS (Hyclone SH30396.03). Cells were separated by centrifugation at 800g for 15 minutes at 4°C. The pellet was resuspended in RBC lysis buffer (BioLegend, 420301) for 1 min at 37°C before they were centrifuged at 450g for 5 min. The pellet was resuspend in PBS and immediately dilvered for GEM preparation.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (ThermoFisher) analyses

value: brain tumor


title: Post-NACT Sample5_GEX

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: TD006637-8519

description: 10x Genomics


title: Post-NACT Sample4_BCR

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: T24_CCNC_sg1_1

tag: cell line


title: UT 3


title: T24_sgNC_1


title: Post-NACT Sample4_TCR

description:
Post-NACT
10x Genomics,5' prime V1 kit

tag: cell type


title: BJ_senescent_3

city: Sherbrooke

first: Mathieu

last: Deschênes

state: Québec

address: 3201, rue Jean-Mignault

department: Microbiologie et Infectiologie

country: Canada

institute: Université de Sherbrooke

description:
RNAseq_expression_TPM.xlsx
RNAseq_PSI.xlsx

data_processing:
Raw RNAseq data was trimmed using Trimmomatic and reads were aligned to the transcriptome reference genome database using Bowtie2. Relative transcripts abundance was quantified using RSEM and converted to transcripts per million (TPM).
PSI was calculated using the relative expression level (TPM) of long and short splicing variants involved in each identified/annotated alternative splicing event.
Assembly: GRCh38.p12
Supplementary files format and content: Excel file (.xlsx) containing normalized expression level (TPM) of every annotated poly-adenylated transcript. Also contains relative expression of genes in senescent BJ cells vs. young BJ cells and diverse information related to transcripts.
Supplementary files format and content: Excel file (.xlsx) containing percent spliced-in (PSI) of every annotated alternative splicing event. Also contains relative splicing change (delta-PSI) between senescent BJ cells and young BJ cells. Various information such as event types (e.g. exon skipping) is also included.

source_name: Foreskin

growth_protocol: BJ cells were cultured in AMEM (Wisent Bio-product) + 10% FBS and incubated at 37C with 5% CO2

extract_protocol:
RNA was extracted using TRIzol Lysis Reagent (Invitrogen) following manufacturer's instructions
800 ng per sample was used as input for the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs) for library prep.
Poly-adenylated mRNA isolation

value: Foreskin

value: BJ

value: Fibroblasts

value: 63 population doublings


title: UT 1


title: Pre-NACT Sample3_BCR

description:
Pre-NACT
10x Genomics, 5' prime V2 kit


title: BJ_senescent_1


title: NM UT 1

source_name: Glioma tumors in C57Bl/6

value: Glioma tumors


title: BS-5784-20210824

description: 10x Genomics


title: NM PD-1 2


title: BJ_young_3

value: 19 population doublings


title: Pre-NACT Sample3_TCR

description:
Pre-NACT
10x Genomics, 5' prime V2 kit


title: ML uRNA 1


title: T24_sgNC_2

value: no


title: Post-NACT Sample4_GEX

description:
Post-NACT
10x Genomics,5' prime V1 kit


title: BJ_young_1


title: BS-5765

description: 10x Genomics


title: TD006629-8493

description: 10x Genomics


title: BS-5764

description: 10x Genomics


title: NM PD-1 1


title: Pre-NACT Sample3_GEX

description:
Pre-NACT
10x Genomics, 5' prime V2 kit


title: IFNg KO UT 2


title: BS-5307-06162021

description: 10x Genomics


title: NM UT 2


title: Pre-NACT Sample2_BCR

description:
Pre-NACT
10x Genomics,5' prime V1 kit


title: IFNg KO UT 1


title: Pre-NACT Sample2_TCR

description:
Pre-NACT
10x Genomics,5' prime V1 kit


title: HK2 cells, AdCtrl+TGF 1

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (v0.21.0) software to filter the sequencing data to get high quality sequence （ Clean Data ） for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.1.0.
We used StringTie(v2.1.5) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 (v1.30.1) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant padj≤0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after the total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop spectrophotometer (Thermo Scientific) and Qubit 4.0; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative .
The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: Kidney

value: HK2 cells

value: Tubular epithelial cells

value: TGF-beta1 stimulation


title: IFNg KO PD-1 1


title: IFNg KO PD-1 2


title: Pre-NACT Sample2_GEX

description:
Pre-NACT
10x Genomics,5' prime V1 kit

value: HGSOC


title: hdp1-1_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

institute: Purdue University

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs (three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / (converted_C + unconverted_C )).

extract_protocol: The bisulfite treatment, library preparation, and sequencing was done in BGI (Shenzhan, China). Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype/variation

value: hdp1-1 mutant

tag: tag

value: seedling


title: hdp2-1_MethylC-Seq

value: hdp2-1 mutant


title: BS-21-06082021

description: 10x Genomics


title: MDA-LA-CB1-2

city: lianyungang

first: He

last: Jingliang

address: tongguan

institute: Jiangsu Ocean University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: mammary gland disease

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without LA-CB1 for 24 hr with or without LA-CB1, respectively, and incubated in 5% CO2 at 37oC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: mammary gland disease

value: Human breast cancer cells


title: CTX-5453-20210630

description: 10x Genomics

value: brain tumor


title: Pre-NACT Sample1_BCR

description:
Pre-NACT
10x Genomics,5' prime V1 kit

value: Omentum


title: MDA-LA-CB1-1


title: Pre-NACT Sample1_TCR

description:
Pre-NACT
10x Genomics,5' prime V1 kit


title: Pre-NACT Sample1_GEX

description:
Pre-NACT
10x Genomics,5' prime V1 kit


title: CTX-5454-20210630

description: 10x Genomics


title: pilocytic astrocytoma [203546000053_R07C01]

status: Public on Oct 10 2024

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: We analyzed the 950 independent test samples using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer's instructions. In summary, DNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue using the Maxwell® Clinical Sample Concentrator system (Promega, Madison, WI). Following extraction, DNA was quantified using a Qubit fluorometer and quantitation reagents (Thermo Fisher Scientific, Waltham, MA), and bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA). The overall DNA input amount was approximately 250 ng. All methylation dta were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.

scan_protocol: DNA methylation profiling was carried out with the Infinium HumanMethylationEPIC BeadChip (850K) array (Illumina Inc., San Diego, CA) on the Illumina iScan platform.

data_processing:
All methylation data were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.
Average beta values that were normalized by functional normalization from minfi R package

label: Cy5 and Cy3

source_name: FFPE

label_protocol: Illumina

growth_protocol: FFPE or frozen tumor samples representing pediatric patient samples encountered on the typical pathology service were evaluated.  The samples represented 650 samples expected to be present in the reference series and 300, true negative samples representative of non-brain solid tumors known to be absent from the reference series

treatment_protocol: Standard Illumina protocol

value: FFPE

tag: Sex

value: Male


title: MDA-DMSO-2

value: MDA-DMSO


title: Medulloblastoma, non-WNT/non-SHH [203548860057_R08C01]

extract_protocol: We analyzed the 950 independent test samples using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer's instructions. In summary, DNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue using the Maxwell® Clinical Sample Concentrator system (Promega, Madison, WI).

value: Female


title: IFNa KO UT 2

value: Glioma tumors

value: UT


title: Medulloblastoma, SHH-activated [203546000053_R03C01]


title: CTX-5384-20210623

description: 10x Genomics


title: MDA-DMSO-1


title: Medulloblastoma, non-WNT/non-SHH [203546000053_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [203546000037_R08C01]


title: Medulloblastoma, SHH-activated [203546000037_R05C01]


title: IFNa KO PD-1 2


title: Medulloblastoma, SHH-activated [203546000037_R07C01]


title: BS-5298-06152021

description: 10x Genomics


title: Medulloblastoma, non-WNT/non-SHH [203548860002_R08C01]


title: choroid plexus papilloma [203546000037_R04C01]


title: IFNa KO PD-1 1


title: Medulloblastoma, non-WNT/non-SHH [203546000037_R01C01]


title: Medulloblastoma, SHH-activated [203546000037_R02C01]


title: IFNa KO UT 1


title: Posterior fossa group A (PFA) ependyoma [203546000053_R02C01]


title: atypical teratoid/rhabdoid tumor [203546000019_R04C01]


title: Medulloblastoma, SHH-activated [203546000037_R03C01]


title: Pineoblastoma [203546000019_R03C01]


title: atypical teratoid/rhabdoid tumor [203546000019_R01C01]


title: Posterior fossa group A (PFA) ependyoma [203504440122_R06C01]


title: pilocytic astrocytoma [203504440122_R03C01]


title: CNS tumor with BCOR-ITD [203546000053_R06C01]


title: Medulloblastoma, SHH-activated [203504440122_R07C01]


title: Posterior fossa group A (PFA) ependyoma [203504440122_R01C01]


title: Embryonal tumor with multilayered rosettes [203504440122_R02C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [203504440080_R06C01]


title: dysembryoplastic neuroepithelial tumor [203504440080_R07C01]


title: atypical teratoid/rhabdoid tumor [203504440080_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [203504440080_R05C01]


title: diffuse hemispheric glioma, H3 G34-mutant [203504440079_R04C01]


title: Adamantinomatous craniopharyngioma [203504440079_R03C01]


title: diffuse hemispheric glioma, H3 G34-mutant [203504440079_R07C01]


title: Adamantinomatous craniopharyngioma [203504440079_R06C01]


title: Adamantinomatous craniopharyngioma [203504440079_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [203504440080_R02C01]


title: CIC-rearranged sarcoma [203504440079_R02C01]


title: pilocytic astrocytoma [203504440035_R06C01]


title: pilocytic astrocytoma [203504440035_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [203504440079_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [203504440035_R01C01]


title: pilocytic astrocytoma [203504440035_R03C01]


title: posterior fossa group B (PFB) ependymoma [203504440035_R04C01]


title: Posterior fossa group A (PFA) ependyoma [203504440035_R05C01]


title: Medulloblastoma, SHH-activated [203504440035_R02C01]


title: meningioma [203496240108_R04C01]


title: atypical teratoid/rhabdoid tumor [203496240108_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [203496240108_R03C01]


title: choroid plexus carcinoma [203496240071_R07C01]


title: pilocytic astrocytoma [203504440080_R04C01]


title: diffuse hemispheric glioma, H3 G34-mutant [203496240108_R06C01]


title: pilocytic astrocytoma [203496240108_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [203504440080_R01C01]


title: myoepithelial tumor [203496240011_R04C01]


title: Posterior fossa group A (PFA) ependyoma [203496240071_R03C01]


title: Angiomatoid Fibrous Histiocytoma [203496240011_R01C01]


title: Angiomatoid Fibrous Histiocytoma [203496240011_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [203496240008_R06C01]


title: Posterior fossa group A (PFA) ependyoma [203496240071_R02C01]


title: Papillary thryoid carcinoma [203496240008_R07C01]


title: Medulloblastoma, SHH-activated [203496240063_R05C01]