title: C2_8 [16_P01_H02]

description:
each of the clonal sublines (C1-C24) was derived from B2905 mouse melanoma cell line (Nature Med. 2020, 26:781)
Expression_CountValue.tsv, Expression_FPKM.tsv, Expression_TPM.tsv, Mutations.tsv

source_name: Clonal subline C2


title: C2_7 [15_P01_G02]

status: Public on Oct 25 2024

type: SRA

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

library_source: transcriptomic single cell

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

molecule: total RNA

organism: Mus musculus

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

tag: cell type

value: Melanoma cell line

tag: strain

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: single cells sorted from homogeneous culture


title: ML336_EIDD1931_0uM_1_HTB7386_O14

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

description: TC-83 nsP2-4

library_source: genomic

data_processing:
Basecalling was done using Nanopore Guppy (ver. 5.1.12)
Sequencing reads were checked for read quality and de-multiplexed using 9 nt-long barcode sequence plus adjacent 10 nt primer sequence
Reads were aligned to Venezuelan equine encephalitis virus genome L01443.1 using Minimap2 (version 2.17-r941)
VCF for each sample was generated by SAMtools mpileup function using mapped BAM file.
Assembly: L01443.1
Supplementary files format and content: vcf format

molecule: genomic DNA

organism: Venezuelan equine encephalitis virus (strain TC-83)

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.

tag: cell line

tag: treatment

value: 1uM ML336 + DMSO


title: ML336_EIDD1931_0uM_1_HTB7386_L15

description: TC-83 nsP2-4


title: SOX_REP2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

library_source: transcriptomic

data_processing:
Mapping and quantification were perfromed with STAR and Salmon (nf-core/rnaseq version 3.9) on the human genome hg38 with reverse strand-specificity setting and default parameters.
Raw counts were normalized in 3 batches of 6 samples each (batch1 MB157R-EV+MB157R-NICD; batch2 MB157-EV+MB157-SOX2; batch3 MB157R-EV+MB157-EV) using TMM method from EdgeR (v.3.42.4) and voom from limma (v.3.56.2).
Genes were filtered out if average TPM < 2 or average counts < 5 per sample. Uncharacterized, predicted and pseudogenes were also filtered out.
Differential expression was computed with limma. Gene set enrichment analysis was performed with clusterProfiler (v.4.8.3) applying GSEA with default parameters, 100’000 permutations to obtain P-values.
Assembly: hg38
Supplementary files format and content: tab separated normalized and raw counts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MB157 cells were obtained from the American Type Culture Collection and were cultured in DMEM supplemented with 10% foetal bovine serum and antibiotics at 37°C in a 5% CO2humidified atmosphere. MB157R are GSI-resistant MB157. Drug resistant cells were generated by treating the MB157 cells for 25 weeks with 1µM GSI (Spirochem, LY3039478), replenishing the inhibitor every 3-4 days. Cells were maintained at a minimal density of 2.5-3 × 106 cells/10-cm dish.

extract_protocol:
RNA was extracted from cell lines using Qiagen, RNAeasy kit (QIAGEN, Cat#74104).
We performed a "Illumina stranded mRNA ligation" (ISML) prep starting from 800ng of RNA, according to Illumina protocol 1000000124518 v01. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation TS4200.

treatment_protocol: Expression of SOX2 or N1-ICD was induced with 1µg/ml doxycycline (Merck, Cat #D9891) for 72h.

value: Triple Negative Breast Cancer

tag: genotype

value: Wild type


title: ML336_EIDD1931_1uM_1_HTB7375_A10

description: TC-83 nsP2-4


title: EV1_HA

description:
EV_HA_NEG_IP.bigWig
EV_HA_NEG_IP_peaks.narrowPeak
EV_HA_NEG_IP_treat_pileup.bdg

data_processing:
Reads were trimmed to remove NEBNext Ultra II DNA (TruSeq) adaptors with bclconvert (v 00.000.000.3.9.3).
Mapping and peak calling were perfromed with BWA and MACS2 (nf-core/chipseq version 2.0.0) on the human genome hg38 with the following parameters: macs_gsize = 2.7e9, macs_fdr = 0.05, narrow_peak = true, all other parameters were left to default.
Peak calling was performed with MACS2 on pooled replicates.
Assembly: hg38
Supplementary files format and content: bedgragh, narrowPeak (except for input samples)

extract_protocol:
Adherent cells were directly fixed into the dishes with 2mM DSG (Santa Cruz, Cat# sc-285455) + 1mM MgCl2 in 8ml 1X PBS for 45min at room temperature. Then cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies, Cat# 28906) and quenched with 0.125 M glycine. Cells were lysed with lysis buffer LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100, Protease inhibitor cocktail (Sigma, Cat # P8340)) twice during 10 minutes at 4 °C. Nuclear lysis was performed using LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, Protease inhibitor cocktail (Sigma, Cat # P8340)) for 10 minutes at 4°C. The cell pellet was rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS, Protease inhibitor cocktail), resuspended in 1ml SDS shearing buffer and transferred to a milliTUBE 1 ml AFA fiber. Chromatin was sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 18 min, 200 cycles, 5% duty, 140W. The IP reactions were performed following the protocols of the Diagenode iDeal ChIP-seq kit for Transcription Factors (Diagenode, Cat# C01010170). For each IP reaction, 4 million cells were used. Sheared chromatin was immunoprecipitated overnight at 4°C with HA (Abcam Cat #ab9110, 2µg), RBPJ (CST Cat #5313, 1:50) or SOX2 (CST Cat #23064, 1:50) antibodies. Eluted DNA was quantified with Qubit (Thermo Fisher) and Agilent Fragment Analyzer (Advanced Analytical).
We performed a "NEBNext Ultra II DNA" library prep starting from 3 ng of DNA for 'Chip' samples and 10ng of DNA for 'input' samples (see table below), according to New England Biolabs' protocol NEBNext Ultra™ II DNA Library Prep Kit, Version 6.1_5/20 (internal exp code RPX030). We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation TS4200.

treatment_protocol: Expression of SOX2-HA or N1-ICD was induced with 1µg/ml doxycycline (Merck, Cat #D9891) for 72h.

value: Dox-EV

tag: chip antibody

value: HA


title: C2_2 [10_P01_B02]


title: C2_5 [13_P01_E02]


title: Fn14 KO ATACseq rep2

city: Cold Spring Harbor

first: Lucas

last: Cheadle

state: NY

address: 1 Bungtown Rd

department: Neuroscience

institute: Cold Spring Harbor Laboratory

data_processing:
Fastq files were processed using the ENCODE ATAC-seq pipeline with default parameters.
Bigwig files generated using DeepTools version 3.5.0, bin size 1, normalize CPM
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

source_name: Brain (Cortex, dLGN, Hippocampus)

growth_protocol: P27 Fn14 KO and WT littermates. C57Bl/6J P32 mice.

extract_protocol:
Fn14: Mice were euthanised and their brains flash frozen. At the time of processing, coronal sections including both the hippocampus and dLGN were dissected. PLX: dLGNs were microdissected. Fn14 & PLX: Samples were homoginsed in a dounce and tight pestel 40x with ATAC buffer (AB (in mM): 10 Tris-HCl pH 7.4, 10 NaCl, 3 MgCl2, .5 Spermidine, .15 Spermine, 1 DTT, and .1 % Igepal, 1X Phosphatase inhibitors, 1X Protease inhibitors). The samples were then spun at 500 rcf for 10 minutes. The pellet was resuspended in 1.4 mL fresh AB and dounced once again 12 times. Next, the nuclei were washed by spinning for 5 minutes and resuspending in fresh AB. 50,000 nuclei were aliquoted according to the nuclei concentration obtained using the Countess II FL Automated Cell Counter. Aliquots were spun once more at 500 rcf, and then resuspended in 20 µL of DNAse free water.
Nextera DNA Library Prep Kit

treatment_protocol: No treatment for Fn14 KO/WT mice. C57Bl/6J mice were fed either PLX5562 formulated chow to depleate microglia, or control chow manufactured in parallel from P20 until euthanasia at P32.

tag: strain background

value: Fn14 KO

tag: age

tag: tissue/cell type

value: Brain (Cortex, dLGN, Hippocampus)


title: ML336_EIDD1931_0uM_1_HTB7386_I3

description: TC-83 nsP2-4


title: C2_4 [12_P01_D02]


title: C2_6 [14_P01_F02]


title: PLX ATACseq rep1

source_name: dLGN

value: PLX

value: dorsal lateral geniculate nuclei (dLGNs)


title: SOX_REP1


title: ML336_EIDD1931_0uM_1_HTB7386_K3

description: TC-83 nsP2-4


title: dLGN - Fn14 WT and KO multiplexed

data_processing:
BCL files were downloaded from Illumina BaseSpace platform after sequencing on an Illumina Next-Seq 500
BCL files were converted into FastQ format.
Files were filtered and demultiplexed using .yaml files specifying the indices used for each sample, .yaml files are provided in this upload.
Raw counts files were generated for each sample then used as input for downstream analyses in R.
Putative doublets were identified and removed using Doublet Finder in R.
QC was performed, data were normalized, and cells were clustered using Seurat version 3 in R.
Differential gene expression analysis was performed using Monocle version 2 in R.
Genome_build: Custom transcriptome was built from Ensemble GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1.
Supplementary_files_format_and_content: Raw counts tables (.tsv) files for each sample are provided. These files can be fed directly into Seurat for re-analysis.
Index identities for demultiplexing: Yaml files (Sample 1 Cheadle_Fn14snRNAseq.yaml . Sample 2: Cheadle_TWEAKsnRNAseq.yaml)

growth_protocol: P27 Fn14 KO WT littermates and P27 Tweak KO WT littermates.

extract_protocol:
Single-nuclear RNA-sequencing was performed using the inDrops strategy on nuclei from the dLGNs micro-dissected from Fn14 KO/WT and TWEAK KO/WT mice.
Library was constructed by single-cell core facility at Harvard Medical School.

value: Fn14 WT

value: Postnatal day 27

tag: sample type


title: Px_REP2

value: GSI-resistant MB157R


title: Fn14 KO ATACseq rep1


title: dLGN - TWEAK WT and KO multiplexed

value: TWEAK WT


title: C2_3 [11_P01_C02]


title: C1_8 [8_P01_H01]

source_name: Clonal subline C1


title: ML336_EIDD1931_0uM_1_HTB7386_C1

description: TC-83 nsP2-4


title: C2_1 [9_P01_A02]


title: NFE2L1DC-2

city: Zhengzhou

first: Lu

last: Qiu

state: Henan

address: No.1 East Jianshe Road, Erqi District

country: China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
The raw image data files obtained by Illumina Hiseq are converted into raw sequencing sequences (Sequenced Reads) through CASAVA base calling analysis, which we refer to as Raw Data or Raw Reads. The results are stored in FASTQ (abbreviated as fq) file format, which includes the sequence information of the sequencing sequences (reads) and their corresponding sequencing quality information.
Assembly: Homo sapiens genome GRCh38

source_name: HepG2 cell line

growth_protocol: The experimental cells were cultured in high glucose DMEM containing 10% FBS.

extract_protocol:
After cells were lysed with Trizol, they were shipped to Sangon Biotech (Shanghai, China)  in dry ice.
Total RNA transcriptomic sequencing of HepG2-pLVX, HepG2-NFE2L1, and HepG2-NFE2L1ΔC cells was performed by Sangon Biotech (Shanghai, China) on the HiseqNOVA platform (contract No.: MRNA193522ZZ).

value: HepG2 cell line

value: NFE2L1DC overexpression


title: NFE2L1DC-3


title: SOX_REP3


title: ML336_EIDD1931_0uM_1_HTB7386_D1

description: TC-83 nsP2-4


title: Px_REP3


title: C1_7 [7_P01_G01]

value: Melanoma cell line

value: HGF-tg C57BL6


title: ML336_EIDD1931_0uM_1_HTB7386_B8

description: TC-83 nsP2-4

value: 1uM ML336 + DMSO


title: Px_REP1

value: Triple Negative Breast Cancer


title: ML336_EIDD1931_0uM_1_HTB7386_L9

description: TC-83 nsP2-4


title: NFE2L1DC-1


title: C1_6 [6_P01_F01]

value: single cells sorted from homogeneous culture


title: NFE2L1-3

value: NFE2L1 overexpression


title: N_REP3

value: Dox-NICD


title: N_REP2


title: N_REP1


title: EV_REP3

value: Wild type

value: Dox-EV


title: ML336_EIDD1931_0uM_1_HTB7386_B1

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7386_A23

description: TC-83 nsP2-4


title: EV_REP2


title: HepG2-2

value: WT


title: EV_REP1


title: NFE2L1-1


title: C1_4 [4_P01_D01]


title: HepG2-3


title: HepG2-1


title: ML336_EIDD1931_0uM_1_HTB7386_A6

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7386_B14

description: TC-83 nsP2-4


title: C1_1 [1_P01_A01]


title: C1_2 [2_P01_B01]


title: Control THP-1 cells at 24 hours, biological replicate 3

status: Public on Oct 24 2024

type: RNA

city: Davis

first: Loubna

last: Tazi

state: CA

address: 451 Health Science Drive

department: Medical Microbiology & Immunology

institute: UC Davis School of Medicine

description: Gene expression data from non-infected THP-1 cells (control cells) at 24 hours.

hyb_protocol: Samples were hybridized to separate arrays using the GeneChip Human Exon 1.0 ST Array, according to the manufacturer's instructions. Triplicate hybridization assays were performed in these microarray experiments.

scan_protocol: Quality control of the hybridized arrays was carried out for each sample. A visual inspection of the scanned images was conducted looking for any defects, areas of high background, or areas of low signal. The spike-in controls were checked as well to examine for hybridization uniformity.

data_processing: Data from all samples were preprocessed, summarized at the transcript-cluster (gene) level and RMA normalized using Affymetrix Power tools. Differential expression analyses were conducted using the R/Bioconductor package limma.

label: Biotin

source_name: Control THP-1 cells (no infection, 24 hours)

label_protocol: Total RNA was reverse-transcribed to cDNA, amplified and labeled, according to the standard Affymetrix instructions.

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated FBS at 37∘C and 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was extracted from control and infected cells using Trizol, according to the manufacturer's protocol.

treatment_protocol: THP-1 cells were differentiated for 48 hours with 10 ng/ml PMA prior to infection with four different reference Mycobacterium tuberculosis (drug-sensitive H37Ra, drug-sensitive H37Rv, isoniazid-resistant H37Rv, rifampin-resistant H37Rv). Two time points, 4 hours and 24 hours, were used for infecting the cells. We also included control non-infected cells (mock-infected with PBS) as negative controls.

tag: tissue

value: Peripheral blood

value: Monocytic cell line

tag: infection

value: no infection

tag: time

value: 24 hours


title: Control THP-1 cells at 24 hours, biological replicate 2


title: C1_3 [3_P01_C01]


title: ML336_EIDD1931_0uM_1_HTB7386_A10

description: TC-83 nsP2-4


title: Control THP-1 cells at 24 hours, biological replicate 1


title: NFE2L1-2


title: C1_5 [5_P01_E01]


title: THP-1 cells infected with drug-sensitive H37Ra at 24 hours, biological replicate 1

description: Gene expression data from THP-1 cells infected with a drug-sensitive H37Ra Mycobacterium tuberculosis strain at 24 hours.

source_name: Infected THP-1 cells (drug-sensitive H37Ra, 24 hours)

value: drug-sensitive H37Ra


title: THP-1 cells infected with drug-sensitive H37Rv at 24 hours, biological replicate 3

description: Gene expression data from THP-1 cells infected with a drug-sensitive H37Rv Mycobacterium tuberculosis strain at 24 hours.

source_name: Infected THP-1 cells (drug-sensitive H37Rv, 24 hours)

value: drug-sensitive H37Rv


title: THP-1 cells infected with rifampin-resistant H37Rv at 24 hours, biological replicate 2

description: Gene expression data from THP-1 cells infected with a rifampin-resistant H37Rv Mycobacterium tuberculosis strain at 24 hours.

source_name: Infected THP-1 cells (rifampin-resistant H37Rv, 24 hours)

value: rifampin-resistant H37Rv


title: THP-1 cells infected with rifampin-resistant H37Rv at 24 hours, biological replicate 3


title: THP-1 cells infected with rifampin-resistant H37Rv at 24 hours, biological replicate 1


title: THP-1 cells infected with drug-sensitive H37Ra at 24 hours, biological replicate 2


title: THP-1 cells infected with rifampin-resistant H37Rv at 4 hours, biological replicate 2

description: Gene expression data from THP-1 cells infected with a rifampin-resistant H37Rv Mycobacterium tuberculosis strain at 4 hours.

source_name: Infected THP-1 cells (rifampin-resistant H37Rv, 4 hours)

value: 4 hours


title: THP-1 cells infected with rifampin-resistant H37Rv at 4 hours, biological replicate 1


title: THP-1 cells infected with drug-sensitive H37Rv at 24 hours, biological replicate 1


title: THP-1 cells infected with drug-sensitive H37Ra at 4 hours, biological replicate 2

description: Gene expression data from THP-1 cells infected with a drug-sensitive H37Ra Mycobacterium tuberculosis strain at 4 hours.

source_name: Infected THP-1 cells (drug-sensitive H37Ra, 4 hours)


title: THP-1 cells infected with drug-sensitive H37Ra at 4 hours, biological replicate 3


title: THP-1 cells infected with drug-sensitive H37Rv at 24 hours, biological replicate 2


title: THP-1 cells infected with isoniazid-resistant H37Rv at 4 hours, biological replicate 3

description: Gene expression data from THP-1 cells infected with an isoniazid-resistant H37Rv Mycobacterium tuberculosis strain at 4 hours.

source_name: Infected THP-1 cells (isoniazid-resistant H37Rv, 4 hours)

value: isoniazid-resistant H37Rv


title: THP-1 cells infected with drug-sensitive H37Ra at 24 hours, biological replicate 3


title: TP57-8_WT-3ppm

city: Leuven

first: Lehua

last: Chen

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Adapters, polyA/T tails, and bad quality reads (Phred score > 20) were trimmed using Trim Galore! (v0.6.4_dev) with default parameters. Reads were aligned to the transcriptome and quantified using Salmon (v0.14.1) (Patro et al. 2017) with default parameters using GENCODE release 23 of the mouse reference transcriptome sequences and gene annotation. Subsequently, the counts were imported into R (v4.0.2) using tximport (v1.18.0). Differentially expressed genes were defined using DEseq2 (v1.30.0) (Love et al. 2014) (FDR adjusted p.val < 0.05) and log fold changes corrected using “ashr” method (Stephens 2017). GO term enrichment was performed using Cluster Profiler (3.18.1). TPM values were calculated using tximport.
Assembly: mm10
Supplementary files format and content: tab separated file with raw counts per sample
Supplementary files format and content: tab separated file with TPM normalized counts per sample

source_name: embryonic brain

extract_protocol:
RNA was extracted from embryonic brainsusing RNeasy plus mini kit (Qiagen, 74136) according to the manufacturer's instructions.
Libraries were prepared from 1 µg of total RNA using the KAPA Stranded mRNA Hyperprep Kit (96rxn) (Roche, KK8581) according to manufacturer’s specifications. 7 µM KAPA-single index adapters (Roche, KK8700d) were added to A-tailed cDNA, and libraries were amplified for 10 cycles. Finally, 1x library clean-up was performed using Agencourt AMPure XP beads (Beckman Coulter, A63881). Library fragment size was assessed using Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). Each library was diluted to 4 nM and pooled for sequencing on an Illumina Hiseq4000 at KU Leuven Genomics Core (Belgium), aiming at 15-20 million SE50 reads per sample (19 million reads on average).

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain


title: TP54-3_HET-01ppm

value: HET


title: TP57-6_KO-3ppm

value: KO


title: THP-1 cells infected with isoniazid-resistant H37Rv at 24 hours, biological replicate 2

description: Gene expression data from THP-1 cells infected with an isoniazid-resistant H37Rv Mycobacterium tuberculosis strain at 24 hours.

source_name: Infected THP-1 cells (isoniazid-resistant H37Rv, 24 hours)


title: THP-1 cells infected with isoniazid-resistant H37Rv at 24 hours, biological replicate 1


title: TP54-2_HET-01ppm


title: TP54-1_KO-01ppm


title: THP-1 cells infected with isoniazid-resistant H37Rv at 24 hours, biological replicate 3


title: THP-1 cells infected with rifampin-resistant H37Rv at 4 hours, biological replicate 3


title: Control THP-1 cells at 4 hours, biological replicate 1

description: Gene expression data from non-infected THP-1 cells (control cells) at 4 hours.

source_name: Control THP-1 cells (no infection, 4 hours)


title: THP-1 cells infected with drug-sensitive H37Rv at 4 hours, biological replicate 1

description: Gene expression data from THP-1 cells infected with a drug-sensitive H37Rv Mycobacterium tuberculosis strain at 4 hours.

source_name: Infected THP-1 cells (drug-sensitive H37Rv, 4 hours)


title: Control THP-1 cells at 4 hours, biological replicate 3


title: THP-1 cells infected with isoniazid-resistant H37Rv at 4 hours, biological replicate 2


title: Control THP-1 cells at 4 hours, biological replicate 2


title: THP-1 cells infected with drug-sensitive H37Rv at 4 hours, biological replicate 2


title: TP52-5_KO-01ppm


title: THP-1 cells infected with isoniazid-resistant H37Rv at 4 hours, biological replicate 1


title: THP-1 cells infected with drug-sensitive H37Ra at 4 hours, biological replicate 1


title: THP-1 cells infected with drug-sensitive H37Rv at 4 hours, biological replicate 3


title: TP53-1_KO-3ppm


title: TP52-1_WT-01ppm


title: TP52-3_WT-01ppm


title: TP52-2_WT-01ppm


title: TP51-6_KO-3ppm


title: TP51-2_HET-3ppm


title: TP50-6_KO-01ppm


title: TP49-2_KO-30ppm


title: TP53-2_WT-3ppm


title: TP48-1_KO-01ppm


title: TP53-4_HET-3ppm


title: TP49-1_WT-30ppm


title: TP48-5_HET-01ppm


title: TP47-5_HET-30ppm


title: TP47-3_KO-30ppm


title: TP46-8_HET-30ppm


title: TP43-2_WT-30ppm


title: TP46-7_HET-30ppm


title: TP47-1_WT-30ppm


title: TP35-1_HET-01ppm


title: TP45-4_HET-3ppm


title: TP38-4_HET-30ppm


title: TP46-4_KO-30ppm


title: TP43-3_HET-30ppm


title: TP35-5_KO-01ppm


title: TP51-9_WT-3ppm


title: TP34-2_HET-01ppm


title: TP46-3_WT-30ppm


title: TP45-1_KO-3ppm


title: TP38-1_WT-30ppm


title: Fibroblasts from Fibrosis patient 10

city: Evry

first: Nicolas

last: FORTUNEL

address: 2 Rue Gaston Cremieux

country: France

institute: CEA

description: Sample F10

data_processing:
Read Quality: For patients RNA-seq: reads were preprocessed by trimming the adapters using cutadapt v. 1.134  and quality filtered (QV > 15) check on fastqc tool v. 0.11.7.5 For VIM-AS1 knockdown: reads were trimmed with TrimGalore v0.6.7, and the overall quality of raw sequencing data was checked using FastQC v0.11.9.5
Pseudoaligment and quantification: The clean Fastq files were used as an input of Salmon tool v 1.6.0.6 The human transcriptome GRCh37 v32 (for RNA-seq from patients) and  GRCh38.p13 v43 (for RNA-seq from VIM-AS1 KD) fasta files from GENCODE were used to generate the Salmon index. Transcript expression quantification was performed for each sample using Salmon tool (parameters: --numBootstraps, --validateMappings).
Gene filtering: batch effects were adjusted using the ComBat function from the R package sva version 3.36.0,7 all genes lowly expressed were removed using filterByExpr function on edgeR package version 3.30.3  (Patients RNA-seq) and 3.42.4 (VIM-AS1 KD).
Normalization: We applied normalisation by the method of trimmed mean of M-values (TMM). This method is performed using the calcNormFactors function from edgeR package version 3.30.3 (Patients RNA-seq) and 3.42.4 (VIM-AS1 KD).
Differential expression analysis: Mean-variance relationship was estimated using the estimateDisp function from the EdgeR package. Moderated p values were calculated by fitting a quasi-likelihood negative binomial generalized log-linear model to the count data using the empirical Bayes method (glmQLFit function from the EdgeR package). RNAs satisfying the following criteria were tagged as differentially expressed (DE): |fold-change| > 1.5 and Pvalue < 0.05.
Assembly: GRCh37 v32 (for RNA-seq from patients) and GRCh38.p13 v43 (for RNA-seq from VIM-AS1 KD)
Supplementary files format and content: TXT files includes raw counts (raw_counts)  and cpm values (norm_counts) for each sample from patients and VIM-AS1 KD sets

source_name: skin

growth_protocol: For patients RNA-seq: Fibroblasts were derived from skin explants issued from patient forearm after local anesthesia with a standardized dermatologic punch. For VIM-AS1 KD: A strain of primary dermal fibroblasts from a healthy female donor  (skin fibroblasts) was obtained at CEA from a breast skin surgical sample. All fibroblasts were cultured in Dulbecco’s Modified Eagle Medium – Glutamax medium (Thermo Fisher Scientific Inc) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific Inc) and 1% penicillin/streptomycin (Thermo Fisher Scientific Inc) in a 5% CO2 humid 37°C incubator.

extract_protocol:
Total RNA from fibroblast strains was isolated and purified using the RNeasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions. Total amount and integrity of RNA samples were evaluated by NanoDrop One (Thermo Fisher Scientific) and Bioanalyzer System (Agilent technologies). The integrity criteria were values between 1.8 and 2.2 (A 260/280), >1.8 (A260/230), and RIN ≥ 8.
RNA sequencing of patient fibroblasts was performed at the CEA Genomic Center (CNRGH, Evry, France). RNA libraries were prepared using the Illumina Truseq RNA Library Preparation Kit V2 according to the manufacturer's instructions. Paired-end RNA sequencing was performed on HiSeq4000 (Illumina) with an input of 1 µg, with 100 bp paired-end reads. A single sequencing run was performed per patient. For sequencing after VIM-AS1 knockdown, RNA sequencing was performed at the Curie Institute NGS/Bioinformatics core facilities. An Illumina Stranded mRNA Prep Kit was used for library preparation, followed by paired-end RNA sequencing on an Illumina NovaSeq System, with an input of 1 µg, with 100 bp paired-end reads.  A single sequencing run was performed per biological replicate.

treatment_protocol: For VIM-AS1 KD: Primary skin fibroblasts obtained from a healthy donor were cultured in a DMEM complete medium containing 10% FBS and treated with 25 nM of custom-designed Antisense LNA GapmeRs-ASOs or scramble LNA-GapmeRs (Qiagen) using Lipofectamine 3000 (Thermo Fisher Scientific Inc) at a final concentration of 1 µL/mL and incubated for 24 hours. Cells were then starved in a DMEM medium containing 1% FBS for another 24 hours, and stimulated with TGFB1 10 ng/mL for another 72 hours, for a total of 120 hours of treatment

value: skin

value: Fibroblasts

value: Fibrosis


title: Fibroblasts from Fibrosis patient 11

description: Sample F11


title: TP34-7_KO-01ppm


title: TP47-6_KO-30ppm


title: Fibroblasts from Fibrosis patient 08

description: Sample F08


title: Fibroblasts from No Fibrosis patient 09

description: Sample NF09

value: Non Fibrosis


title: TP43-6_KO-30ppm


title: Fibroblasts from No Fibrosis patient 07

description: Sample NF07


title: Fibroblasts from No Fibrosis patient 08

description: Sample NF08


title: Fibroblasts from Fibrosis patient 05


title: TP34-4_HET-01ppm


title: Fibroblasts from Fibrosis patient 03


title: Fibroblasts from Fibrosis patient 04


title: Fibroblasts from Fibrosis patient 02


title: Fibroblasts from No Fibrosis patient 06


title: Fibroblasts from No Fibrosis patient 05


title: Fibroblasts from No Fibrosis patient 04


title: Fibroblasts from Fibrosis patient 01


title: Fibroblasts from No Fibrosis patient 03


title: Fibroblasts from No Fibrosis patient 01


title: Fibroblasts from Fibrosis patient 07

description: Sample F07


title: Ab_12

city: Shenzhen

first: Wenxiang

last: Cheng

state: Guangdong

institute: Shenzhen Institutes Of Advanced Technology, Chinese Academy Of Sciences,

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 file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPkM values for each Sample

organism: Rattus norvegicus

source_name: Synovial tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
CON: The control group was comprised of rats that did not undergo any treatment
AIA: A volume of 100   uL of Complete Freund's Adjuvant (Chondrex, USA) was injected intradermally into the tail of each rat to establish the AIA animal model.
Ab: Anti-cANGPTL4 antibody was administered intraperitoneally twice per week for AIA rat model.

value: Synovial tissue

value: WT

value: Anti-cANGPTL4 antibody treatment for AIA model


title: Ab_10


title: Fibroblasts from No Fibrosis patient 02


title: Ab_9


title: AIA_18

value: injected with adjuvant for AIA model


title: Ab_3


title: Ab_21_8


title: AIA_23


title: AIA_19


title: Fibroblasts from Fibrosis patient 06


title: AIA_5


title: CON_17

value: control (no treatment)


title: AIA_13


title: CON_14


title: CON_11


title: CON_2


title: CSN48-2_03_P24

city: Dresden

first: Mohammad

middle: Nadeem

last: Akhtar

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TU Dresden

data_processing:
bcl2fastq2 2.19.1
Alignment with GSNAP (v2019-06-10) to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites (gsnap.sse42 -d GRCz11 --gunzip -A sam -t 20 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-95.ss.GRCz11.iit -N 0)
Counts were created with featureCounts (v2.0.1; featureCounts -a EnsemblGene-95.GRCz11.TR.gtf -s 0 -p -o  bfx1391.GRCz11.e95.tsv -Q 1 -T 8)
Assembly: GRCz11
Supplementary files format and content: tab separated file with the output of featurecounts, where each column represent either a sample or gene information (start, end, strand, geneid) and each row is a gene. Cells countain fragments per gene per sample.

organism: Danio rerio

source_name: beta cells

extract_protocol:
The cells are sorted with an Aria III FACS into a 384 well plate pre-loaded with 0.5 µl freshly prepared lysis buffer (0.2 % Tween-20 solution with 4 U/µl murine RNase inhibitor (NEB)). After the sort, the plate is shortly centrifuged and lysed cells stored at -80°C.After thawing the plate, the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP (Invitrogen), 0.5 µM dT-primer*, 2 U RNase Inhibitor (NEB), ERCC spike in mix with a final dilution of 1:2*107. RNA is denatured for 3 minutes at 72 °C, followed by reverse transcription at 42 °C for 90 min after filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 2.3 U RNase Inhibitor and 25 U Superscript II. After synthesis, the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium)
For library preparation up to 700 pg cDNA (maximal 2 µl) is desiccated and rehydrated in 1 ul Tagmentation mix (1x TTBL buffer, 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and size selected with 0.6x(right)/0.9x (left) volume of rebuffered Sera-Mag SpeedBeads. This is followed by Illumina sequencing on a Novaseq6000 (50 bp PE, S1 flowcell) aiming at an average sequencing depth of 0.6 mio reads per cell. dT-primer: C6-aminolinkerAAGCAGTGGTATCAACGCAGAGTCGAC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, where N represents a random base and V any base beside thymidine; TSO-primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, where rG stands for ribo-guanosine; UP-primer: C6-aminolinker- AAGCAGTGGTATCAACGCAGAGT

value: beta cells


title: CON_7


title: CSN48-2_03_P23


title: CSN48-2_03_P22


title: CSN48-2_03_P21


title: CSN48-2_03_P19


title: RNA_03_P18


title: CSN48-2_03_O23


title: CSN48-2_03_O21


title: CSN48-2_03_O19


title: CSN48-2_03_O18


title: CSN48-2_03_O16


title: CSN48-2_03_O12


title: CSN48-2_03_O17


title: CSN48-2_03_O20


title: CSN48-2_03_O14


title: CSN48-2_03_O10


title: CSN48-2_03_O09


title: CSN48-2_03_O13


title: CSN48-2_03_O11


title: CSN48-2_03_O07


title: CSN48-2_03_O04


title: CSN48-2_03_O08


title: CSN48-2_03_O03


title: CSN48-2_03_O05


title: CSN48-2_03_P20


title: CSN48-2_03_N24


title: CSN48-2_03_N23


title: CSN48-2_03_N22


title: CSN48-2_03_O01


title: CSN48-2_03_N21


title: CSN48-2_03_O22


title: CSN48-2_03_O15


title: CSN48-2_03_N19


title: CSN48-2_03_N20


title: CSN48-2_03_N18


title: CSN48-2_03_N16


title: CSN48-2_03_O06


title: CSN48-2_03_N13


title: CSN48-2_03_N10


title: CSN48-2_03_N14


title: CSN48-2_03_N12


title: CSN48-2_03_N11


title: CSN48-2_03_N09


title: CSN48-2_03_N08


title: CSN48-2_03_O02


title: CSN48-2_03_O24


title: CSN48-2_03_N06


title: CSN48-2_03_N05


title: CSN48-2_03_N01


title: CSN48-2_03_M23


title: CSN48-2_03_N04


title: CSN48-2_03_M22


title: CSN48-2_03_M21


title: CSN48-2_03_N03


title: CSN48-2_03_N02


title: CSN48-2_03_N15


title: CSN48-2_03_M24


title: CSN48-2_03_M19


title: CSN48-2_03_M18


title: CSN48-2_03_M17


title: CSN48-2_03_M16


title: CSN48-2_03_M14


title: CSN48-2_03_N07


title: CSN48-2_03_M12


title: CSN48-2_03_M11


title: CSN48-2_03_M10


title: CSN48-2_03_M08


title: CSN48-2_03_M13


title: CSN48-2_03_M07


title: CSN48-2_03_M06


title: CSN48-2_03_M05


title: CSN48-2_03_M02


title: CSN48-2_03_M20


title: CSN48-2_03_M04


title: CSN48-2_03_M01


title: CSN48-2_03_L23


title: CSN48-2_03_M03


title: CSN48-2_03_L22


title: CSN48-2_03_L19


title: CSN48-2_03_M15


title: CSN48-2_03_L16


title: CSN48-2_03_L21


title: CSN48-2_03_L24


title: CSN48-2_03_L20


title: CSN48-2_03_L15


title: CSN48-2_03_L18


title: CSN48-2_03_L17


title: CSN48-2_03_L12


title: CSN48-2_03_L13


title: CSN48-2_03_L11


title: CSN48-2_03_M09


title: CSN48-2_03_L14


title: CSN48-2_03_L09


title: CSN48-2_03_L05


title: CSN48-2_03_L10


title: CSN48-2_03_L06


title: CSN48-2_03_L04


title: CSN48-2_03_L08


title: CSN48-2_03_L01


title: CSN48-2_03_L03


title: CSN48-2_03_L02


title: CSN48-2_03_N17


title: CSN48-2_03_K21


title: CSN48-2_03_K22


title: CSN48-2_03_K23


title: CSN48-2_03_K20


title: CSN48-2_03_K18


title: CSN48-2_03_K17


title: CSN48-2_03_K19


title: CSN48-2_03_K16


title: CSN48-2_03_K13


title: CSN48-2_03_K24


title: CSN48-2_03_K11


title: CSN48-2_03_K12


title: CSN48-2_03_K15


title: CSN48-2_03_K14


title: CSN48-2_03_K08


title: CSN48-2_03_K09


title: CSN48-2_03_K07


title: CSN48-2_03_K05


title: CSN48-2_03_K06


title: CSN48-2_03_L07


title: CSN48-2_03_K04


title: CSN48-2_03_K03


title: CSN48-2_03_K01


title: CSN48-2_03_K02


title: CSN48-2_03_J21


title: CSN48-2_03_J23


title: CSN48-2_03_J24


title: CSN48-2_03_J22


title: CSN48-2_03_J20


title: CSN48-2_03_J19


title: CSN48-2_03_J17


title: CSN48-2_03_J18


title: CSN48-2_03_J13


title: CSN48-2_03_J15


title: CSN48-2_03_K10


title: CSN48-2_03_J14


title: CSN48-2_03_J12


title: CSN48-2_03_J11


title: CSN48-2_03_J10


title: CSN48-2_03_J06


title: CSN48-2_03_J07


title: CSN48-2_03_J09


title: CSN48-2_03_J05


title: CSN48-2_03_J04


title: CSN48-2_03_J08


title: CSN48-2_03_J02


title: CSN48-2_03_I24


title: CSN48-2_03_I22


title: CSN48-2_03_J01


title: CSN48-2_03_I21


title: CSN48-2_03_J03


title: CSN48-2_03_I20


title: CSN48-2_03_I23


title: CSN48-2_03_J16


title: CSN48-2_03_I14


title: CSN48-2_03_I17


title: CSN48-2_03_I13


title: CSN48-2_03_I19


title: CSN48-2_03_I18


title: CSN48-2_03_I15


title: CSN48-2_03_I16


title: CSN48-2_03_I05


title: CSN48-2_03_I06


title: CSN48-2_03_I04


title: CSN48-2_03_I09


title: CSN48-2_03_I10


title: CSN48-2_03_I07


title: CSN48-2_03_I08


title: CSN48-2_03_I02


title: CSN48-2_03_I01


title: CSN48-2_03_I03


title: CSN48-2_03_H23


title: CSN48-2_03_H20


title: CSN48-2_03_H17


title: CSN48-2_03_H21


title: CSN48-2_03_H18


title: CSN48-2_03_H16


title: CSN48-2_03_H22


title: CSN48-2_03_I12


title: CSN48-2_03_H15


title: CSN48-2_03_H14


title: CSN48-2_03_I11


title: CSN48-2_03_H08


title: CSN48-2_03_H13


title: CSN48-2_03_H12


title: CSN48-2_03_H11


title: CSN48-2_03_H09


title: CSN48-2_03_H24


title: CSN48-2_03_H06


title: CSN48-2_03_H10


title: CSN48-2_03_H04


title: CSN48-2_03_H07


title: CSN48-2_03_H02


title: CSN48-2_03_H01


title: CSN48-2_03_G24


title: CSN48-2_03_H05


title: CSN48-2_03_G21


title: CSN48-2_03_G19


title: CSN48-2_03_H03


title: CSN48-2_03_H19


title: CSN48-2_03_G20


title: CSN48-2_03_G22


title: CSN48-2_03_G18


title: CSN48-2_03_G17


title: CSN48-2_03_G13


title: CSN48-2_03_G15


title: CSN48-2_03_G12


title: CSN48-2_03_G11


title: CSN48-2_03_G09


title: CSN48-2_03_G06


title: CSN48-2_03_G08


title: CSN48-2_03_G04


title: CSN48-2_03_G02


title: CSN48-2_03_G10


title: CSN48-2_03_G03


title: CSN48-1_03_F23


title: CSN48-2_03_G05


title: CSN48-2_03_G01


title: CSN48-2_03_G23


title: CSN48-1_03_F20


title: CSN48-1_03_F22


title: CSN48-1_03_F21


title: CSN48-2_03_G16


title: CSN48-2_03_G14


title: CSN48-1_03_F14


title: CSN48-1_03_F18


title: CSN48-1_03_F19


title: CSN48-1_03_F11


title: CSN48-1_03_F15


title: CSN48-1_03_F17


title: CSN48-1_03_F16


title: CSN48-1_03_F10


title: CSN48-1_03_F12


title: CSN48-2_03_G07


title: CSN48-1_03_F07


title: CSN48-1_03_F09


title: CSN48-1_03_F24


title: CSN48-1_03_F13


title: CSN48-1_03_F06


title: CSN48-1_03_F08


title: CSN48-1_03_F05


title: CSN48-2_03_F01


title: CSN48-1_03_E24


title: CSN48-1_03_F04


title: CSN48-1_03_F02


title: CSN48-1_03_E23


title: CSN48-1_03_E20


title: CSN48-1_03_E18


title: CSN48-1_03_E17


title: CSN48-1_03_E19


title: CSN48-1_03_E15


title: CSN48-1_03_E21


title: CSN48-1_03_E16


title: CSN48-1_03_E12


title: CSN48-1_03_E10


title: CSN48-1_03_E11


title: CSN48-1_03_E08


title: CSN48-1_03_E09


title: CSN48-1_03_E07


title: CSN48-1_03_E04


title: CSN48-1_03_E06


title: CSN48-1_03_E05


title: CSN48-1_03_F03


title: CSN48-1_03_E02


title: CSN48-1_03_E03


title: CSN48-1_03_D24


title: CSN48-1_03_E01


title: CSN48-1_03_E22


title: CSN48-1_03_D22


title: CSN48-1_03_D20


title: CSN48-1_03_D19


title: CSN48-1_03_D17


title: CSN48-1_03_D21


title: CSN48-1_03_D18


title: CSN48-1_03_D16


title: CSN48-1_03_D15


title: CSN48-1_03_E14


title: CSN48-1_03_D09


title: CSN48-1_03_D07


title: CSN48-1_03_D12


title: CSN48-1_03_D13


title: CSN48-1_03_D06


title: CSN48-1_03_D08


title: CSN48-1_03_D10


title: CSN48-1_03_D11


title: CSN48-1_03_D23


title: CSN48-1_03_D01


title: CSN48-1_03_D03


title: CSN48-1_03_C23


title: CSN48-1_03_C22


title: CSN48-1_03_D02


title: CSN48-1_03_C21


title: CSN48-1_03_C19


title: CSN48-1_03_C20


title: CSN48-1_03_E13


title: CSN48-1_03_C24


title: CSN48-1_03_D14


title: CSN48-1_03_C18


title: CSN48-1_03_C15


title: CSN48-1_03_C14


title: CSN48-1_03_C17


title: CSN48-1_03_C13


title: CSN48-1_03_D04


title: CSN48-1_03_C16


title: CSN48-1_03_C12


title: CSN48-1_03_C08


title: CSN48-1_03_C04


title: CSN48-1_03_C10


title: CSN48-1_03_C07


title: CSN48-1_03_C06


title: CSN48-1_03_C02


title: CSN48-1_03_C03


title: CSN48-1_03_C09


title: CSN48-1_03_C11


title: CSN48-1_03_B23


title: CSN48-1_03_C01


title: CSN48-1_03_B24


title: CSN48-1_03_C05


title: CSN48-1_03_B22


title: CSN48-1_03_B21


title: CSN48-1_03_B19


title: CSN48-1_03_B18


title: CSN48-1_03_B15


title: CSN48-1_03_B11


title: CSN48-1_03_B14


title: CSN48-1_03_B12


title: CSN48-1_03_B13


title: CSN48-1_03_B09


title: CSN48-1_03_B07


title: CSN48-1_03_B16


title: CSN48-1_03_B05


title: CSN48-1_03_B06


title: CSN48-1_03_B03


title: CSN48-1_03_B02


title: CSN48-1_03_B20


title: CSN48-1_03_A24


title: CSN48-1_03_A21


title: CSN48-1_03_B01


title: CSN48-1_03_B04


title: CSN48-1_03_B17


title: CSN48-1_03_A22


title: CSN48-1_03_A19


title: CSN48-1_03_A20


title: CSN48-1_03_A18


title: CSN48-1_03_A17


title: CSN48-1_03_A14


title: CSN48-1_03_B10


title: CSN48-1_03_B08


title: CSN48-1_03_A13


title: CSN48-1_03_A09


title: CSN48-1_03_A12


title: CSN48-1_03_A10


title: CSN48-1_03_A08


title: CSN48-1_03_A11


title: CSN48-1_03_A07


title: CSN48-1_03_A23


title: CSN48-1_03_A06


title: CSN48-1_03_D05


title: CSN48-1_03_A05


title: CSN48-1_03_A04


title: CSN48-1_03_A02


title: CSN48-1_03_A15


title: CSN48-1_03_A16


title: CSN24_02_G07


title: CSN48-1_03_A01


title: CSN24_02_G09


title: RNA_02_G11


title: CSN24_02_G10


title: CSN24_02_G08


title: CSN24_02_G02


title: CSN24_02_G05


title: CSN24_02_G06


title: CSN24_02_G04


title: CSN24_02_F24


title: CSN24_02_F23


title: CSN24_02_F22


title: CSN24_02_G01


title: CSN24_02_F20


title: CSN24_02_F18


title: CSN24_02_F17


title: CSN24_02_F16


title: CSN48-1_03_A03


title: CSN24_02_F15


title: CSN24_02_F14


title: CSN24_02_F12


title: CSN24_02_F11


title: CSN24_02_F09


title: CSN24_02_F10


title: CSN24_02_F13


title: CSN24_02_F08


title: CSN24_02_F04


title: CSN24_02_G03


title: CSN24_02_E22


title: CSN24_02_F07


title: CSN24_02_E24


title: CSN24_02_F02


title: CSN24_02_F05


title: CSN24_02_F06


title: CSN24_02_F03


title: CSN24_02_F21


title: CSN24_02_F01


title: CSN24_02_F19


title: CSN24_02_E21


title: CSN24_02_E20


title: CSN24_02_E23


title: CSN24_02_E18


title: CSN24_02_E19


title: CSN24_02_E15


title: CSN24_02_E16


title: CSN24_02_E14


title: CSN24_02_E13


title: CSN24_02_E17


title: CSN24_02_E12


title: CSN24_02_E07


title: CSN24_02_E10


title: CSN24_02_E06


title: CSN24_02_E08


title: CSN24_02_E05


title: CSN24_02_E09


title: CSN24_02_E04


title: CSN24_02_E03


title: CSN24_02_D24


title: CSN24_02_E01


title: CSN24_02_D23


title: CSN24_02_D22


title: CSN24_02_D20


title: CSN24_02_D15


title: CSN24_02_D16


title: CSN24_02_D19


title: CSN24_02_E02


title: CSN24_02_D14


title: CSN24_02_D18


title: CSN24_02_D21


title: CSN24_02_D13


title: CSN24_02_D11


title: CSN24_02_D17


title: CSN24_02_D12


title: CSN24_02_D09


title: CSN24_02_D08


title: CSN24_02_D07


title: CSN24_02_D10


title: CSN24_02_D06


title: CSN24_02_E11


title: CSN24_02_D04


title: CSN24_02_D05


title: CSN24_02_D01


title: CSN24_02_D03


title: CSN24_02_D02


title: CSN24_02_C24


title: CSN24_02_C23


title: CSN24_02_C22


title: CSN24_02_C21


title: CSN24_02_C20


title: CSN24_02_C18


title: CSN24_02_C13


title: CSN24_02_C16


title: CSN24_02_C10


title: CSN24_02_C17


title: CSN24_02_C09


title: CSN24_02_C08


title: CSN24_02_C15


title: CSN24_02_C12


title: CSN24_02_C06


title: CSN24_02_C07


title: CSN24_02_C14


title: CSN24_02_C05


title: CSN24_02_C04


title: CSN24_02_C01


title: CSN24_02_C03


title: CSN24_02_C02


title: CSN24_02_B24


title: CSN24_02_B19


title: CSN24_02_B22


title: CSN24_02_B20


title: CSN24_02_B18


title: CSN24_02_B21


title: CSN24_02_C19


title: CSN24_02_B16


title: CSN24_02_B14


title: CSN24_02_B17


title: CSN24_02_B15


title: CSN24_02_B08


title: CSN24_02_B10


title: CSN24_02_B12


title: CSN24_02_C11


title: CSN24_02_B01


title: CSN24_02_B03


title: CSN24_02_B06


title: CSN24_02_B09


title: CSN24_02_B13


title: CSN24_02_B02


title: CSN24_02_A24


title: CSN24_02_B05


title: CSN24_02_B04


title: CSN24_02_B11


title: CSN24_02_A21


title: CSN24_02_B23


title: CSN24_02_A20


title: CSN24_02_A23


title: CSN24_02_A16


title: CSN24_02_A19


title: CSN24_02_A14


title: CSN24_02_A13


title: CSN24_02_A15


title: CSN24_02_B07


title: CSN24_02_A12


title: CSN24_02_A11


title: CSN24_02_A09


title: CSN24_02_A07


title: CSN24_02_A08


title: CSN24_02_A10


title: CSN24_02_A03


title: Ctrl_01_H23

value: Ctrl


title: CSN24_02_A02


title: CSN24_02_A01


title: CSN24_02_A06


title: Ctrl_01_H24


title: CSN24_02_A22


title: RNA_01_H19


title: CSN24_02_A04


title: NC_01_H18

value: NC


title: Ctrl_01_H22


title: CSN24_02_A17


title: Ctrl_01_H20


title: Ctrl_01_H21


title: CSN24_02_A18


title: Ctrl_01_G24


title: Ctrl_01_G21


title: Ctrl_01_G23


title: Ctrl_01_G20


title: Ctrl_01_G18


title: Ctrl_01_G19


title: Ctrl_01_G17


title: CSN24_02_A05


title: Ctrl_01_G16


title: Ctrl_01_G13


title: Ctrl_01_G14


title: Ctrl_01_G11


title: T3_3

city: Qingdao

first: Yanjing

last: Shi

state: Shandong

address: 53# Zhengzhou Road

institute: Qingdao university of Science & Technology

data_processing:
clean data (clean reads) were obtained by removing reads containing adapter, reads
containing ploy-N and low quality reads from raw data
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two
conditions/groups (two biological replicates per condition) was performed using the DESeq2
R package (1.20.0)
Supplementary files format and content: tab-delimited text file of FKPM

organism: Malus spectabilis

source_name: receptacle of WB_3 grafted on M. robusta

extract_protocol:
Total RNA was isolated from each sample using a previously reported method modified by the addition of a purification step, and cDNA was synthesized as previously described (Xia et al., 2012).Xia, R., Zhu, H., An, Y. Q., Beers, E. P., and Liu, Z. (2012). Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol. 13:R47. doi: 10.1186/ gb-2012-13-6-r47
After treatment with DNase I to eliminate contaminating DNA, mRNA was purified from total RNA extracts using magnetic oligo (dT) beads. The mRNA was mixed with fragmentation buffer and cleaved into short fragments for use as templates for cDNA synthesis. Short fragments were purified, resolved with buffer for end reparation and single adenine nucleotide addition and connected with adapters. After agarose gel electrophoresis, suitable fragments were selected as templates for PCR amplification. An Agilent 2100 Bioanalyzer and an ABI StepOnePlusTM Real-Time PCR system were used for quantification and quality assessment of sample libraries. The constructed libraries were sequenced using an Illumina HiSeqTM 2000 system (BGI, Shenzhen, China).

value: flower

value: multibranching (MB)


title: MB_1_2

source_name: leaves of  WB_2  grafted on M. robusta

value: leaves


title: MB_1_3

source_name: leaves of  WB_3  grafted on M. robusta


title: Ctrl_01_G10


title: Ctrl_01_G08


title: T3_1

source_name: receptacle of WB_1 grafted on M. robusta


title: Ctrl_01_G22


title: Ctrl_01_G07


title: T3_2

source_name: receptacle of WB_2 grafted on M. robusta


title: MS_2

source_name: stem of  WB_2  grafted on M. robusta

value: stem


title: W3_3

source_name: receptacle of Malus spectabilis ‘Bly116’  grafted on M. robusta


title: MS_1

source_name: stem of  WB_1  grafted on M. robusta


title: Ctrl_01_G06


title: Ctrl_01_G09


title: Ctrl_01_G04


title: Ctrl_01_G05


title: MS_3

source_name: stem of  WB_3  grafted on M. robusta


title: Ctrl_01_G15


title: Ctrl_01_G02


title: Ctrl_01_G01


title: W3_1


title: WL_3

source_name: leaves of  Malus spectabilis ‘Bly114’  grafted on M. robusta

value: leave


title: Ctrl_01_G03


title: W3_2


title: Ctrl_01_G12


title: MB_1_1

source_name: leaves of  WB_1  grafted on M. robusta


title: Ctrl_01_F24


title: WS_3

source_name: stem of  Malus spectabilis ‘Bly114’  grafted on M. robusta


title: WL_1


title: Ctrl_01_F21


title: Ctrl_01_F22


title: Ctrl_01_F20


title: Ctrl_01_F19


title: Ctrl_01_F16


title: WS_1


title: Ctrl_01_F18


title: WS_2


title: Ctrl_01_F17


title: Ctrl_01_F15


title: Ctrl_01_F13


title: Ctrl_01_F09


title: Ctrl_01_F12


title: Ctrl_01_F08


title: Ctrl_01_F10


title: Ctrl_01_F14


title: Ctrl_01_F04


title: Ctrl_01_F07


title: Ctrl_01_F05


title: Ctrl_01_F06


title: WL_2


title: Ctrl_01_F02


title: Ctrl_01_F23


title: Ctrl_01_F03


title: Ctrl_01_F01


title: Ctrl_01_E23


title: Ctrl_01_E24


title: Ctrl_01_E22


title: Ctrl_01_E20


title: Ctrl_01_E21


title: Ctrl_01_E17


title: Ctrl_01_E16


title: Ctrl_01_E19


title: Ctrl_01_E12


title: Ctrl_01_E15


title: Ctrl_01_E10


title: Ctrl_01_E08


title: Ctrl_01_E14


title: Ctrl_01_E11


title: Ctrl_01_E07


title: Ctrl_01_E03


title: Ctrl_01_E04


title: Ctrl_01_E01


title: Ctrl_01_D24


title: Ctrl_01_E05


title: Ctrl_01_E02


title: Ctrl_01_D23


title: Ctrl_01_D22


title: Ctrl_01_E18


title: Ctrl_01_D17


title: Ctrl_01_D16


title: Ctrl_01_E13


title: Ctrl_01_D20


title: Ctrl_01_D15


title: Ctrl_01_D21


title: Ctrl_01_D19


title: Ctrl_01_D18


title: Ctrl_01_D12


title: Ctrl_01_D10


title: Ctrl_01_D09


title: Ctrl_01_D14


title: Ctrl_01_D07


title: Ctrl_01_E09


title: Ctrl_01_D06


title: Ctrl_01_D13


title: Ctrl_01_D08


title: Ctrl_01_D03


title: Ctrl_01_C22


title: Ctrl_01_C24


title: Ctrl_01_D01


title: Ctrl_01_E06


title: Ctrl_01_D11


title: Ctrl_01_C21


title: Ctrl_01_D05


title: Ctrl_01_D02


title: Ctrl_01_C23


title: Ctrl_01_C20


title: Ctrl_01_D04


title: ADAR CRISPR-KO screen teratoma 3

city: La Jolla

first: Prashant

last: Mali

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description: feature_reference.csv file available on series record

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger count with default parameters
Assembly: hg38_and_mm10
Supplementary files format and content: Files ending in "_matrix.mtx.gz" are counts matrices output by 10X CellRanger in sparse matrix format
Supplementary files format and content: Files ending in "_barcode.tsv.gz" are cell barcodes output by 10X CellRanger
Supplementary files format and content: Files ending in "_features.tsv.gz" are gene features output by 10X CellRanger
Library strategy: CRISPR screen

molecule: cytoplasmic RNA

growth_protocol: H1, H9, HUES62, and PGP1 PSC cell lines were maintained under feeder-free conditions in mTeSR1 medium (Stem Cell Technologies 85850). Prior to passaging, tissue-culture plates were coated with growth factor-reduced Matrigel (Corning 356230) diluted in DMEM/F-12 medium (Thermo Fisher Scientific 11320033) and incubated for 30 minutes at 37 ⁰C, 5% CO2. Cells were dissociated and passaged using the dissociation reagent Versene (Thermo Fisher Scientific 15040066).

extract_protocol:
Mice were euthanized by slow release of CO2 followed by secondary means via cervical dislocation. Tumor area was shaved, sprayed with 70% ethanol, and then extracted via surgical excision using scissors and forceps. Tumor was rinsed with PBS, weighed, and photographed. Tumor was then cut into small 1 inch pieces in a semi-random fashion and frozen in OCT for sectioning and H&E staining courtesy of the Moore’s Cancer Center Histology Core. Remaining tumor was cut into small pieces 1–2 mm in diameter and subjected to standard GentleMACS (Miltenyi) protocols: Human Tumor Dissociation Kit (medium tumor settings) and Red Blood Cell Lysis Kit. For single cell RNA-seq, samples were also processed with the Dead Cell Removal Kit (Miltenyi). Single cells were then resuspended in PBS + 0.04% BSA for processing on the 10X Genomics Chromium 58 platform and downstream sequencing on an Illumina NovaSeq platform. For bulk processing, after red blood cell removal, cells were divided into multiple tubes and pelleted for 5 minutes at 300g. Supernatant was then removed and cells were either directly frozen at −80°C or resuspended in RNALater (Thermo Fisher Scientific AM7021), incubated overnight at 4°C, RNALater removed and then frozen at −80°C.
Cells were passed through a 40 𝜇m filter, spun down at 300 rcf for 5 minutes, and resuspended in 0.04% BSA solution. Cells were then loaded into the Chromium Chip B (10x Genomics) and single cell libraries were made using Chromium Single Cell 3ʹ Reagent Kits v3 workflow (10x Genomics). Fastq files were aligned to a hg38 reference and expression matrices were generated using the count command in cellranger v3.0.1 (10X Genomics).

value: PGP1 cells had Cas9 knocked in


title: Ctrl_01_C18


title: Ctrl_01_C16


title: ADAR CRISPR-KO screen teratoma 2


title: ADAR CRISPR-KO screen teratoma 1


title: 204228990026_R06C01: T47D_KO2_no_transfection_Arsenic

type: genomic

city: PETALING JAYA

first: Felicia

last: Chung

state: Selangor

address: Sunway University, 5, Jalan Universiti, Bandar Sunway, 47500 Petaling Jaya, Selangor

country: Malaysia

institute: Sunway University

description:
Arsenic-treated, p53-knockout T47D
T47D_KO2_no_transfection_Arsenic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Chips were scanned using Illumina iScan with standard recommended Illumina scanner settings to produce two-color raw data files (.idat format)

data_processing: The data was analyzed using the methylkey pipeline developed by the Epigenomics and Mechanisms Branch at the International Agency for Research on Cancer (https://github.com/IARCbioinfo/methylkey)

label: Cy5 and Cy3

source_name: genomic DNA from arsenic-treated, p53-knockout T47D

label_protocol: Standard Illumina Protocol

growth_protocol: Parental and knockout human breast carcinoma cell lines MCF7 and T47D were maintained in RPMI (Gibco) containing 10% fetal bovine serum (Gibco), 100 IU/mL penicillin (Gibco), and 100 μg/mL streptomycin (Gibco). All cells were maintained in a 37°C environment containing 5% CO2.

extract_protocol: Total DNA and RNA were extracted using the Qiagen AllPrep® DNA/RNA Kit from cell pellets stored in -80°C.

treatment_protocol: Sodium arsenite (S7400, Sigma-Aldrich) was prepared in dimethyl sulfoxide (DMSO), and cells were treated with a final concentration of 3 μM sodium arsenite for 72 hours. The DMSO-only treatment served as the negative control.

tag: p53 status

value: Arsenic


title: Ctrl_01_C15


title: 204228990017_R08C01: T47D_KO1_no_transfection_Arsenic

description:
Arsenic-treated, p53-knockout T47D
T47D_KO1_no_transfection_Arsenic


title: 204228990026_R01C01: T47D_parental_no_transfection_Arsenic

description:
Arsenic-treated, parental T47D
T47D_parental_no_transfection_Arsenic

source_name: genomic DNA from arsenic-treated, parental T47D


title: 204228990006_R02C01: T47D_KO2_no_transfection_Control

description:
Untreated, p53-knockout T47D
T47D_KO2_no_transfection_Control

source_name: genomic DNA from untreated, p53-knockout T47D

value: Control


title: 204228990017_R02C01: T47D_KO1_no_transfection_Control

description:
Untreated, p53-knockout T47D
T47D_KO1_no_transfection_Control


title: 204228990017_R01C01: T47D_KO1_no_transfection_Arsenic


title: 204228990026_R05C01: T47D_KO1_no_transfection_Control


title: Ctrl_01_C19


title: 204228990026_R02C01: T47D_KO2_no_transfection_Control


title: Ctrl_01_C13


title: Ctrl_01_C12


title: 204228990017_R04C01: T47D_KO2_no_transfection_Arsenic

description:
Arsenic-treated,  p53-knockout T47D
T47D_KO2_no_transfection_Arsenic

source_name: genomic DNA from arsenic-treated,  p53-knockout T47D


title: Ctrl_01_C11

source_name: beta cells


title: Ctrl_01_C10


title: 204228990006_R01C01: MCF7_KO2_pcDNA_Arsenic

description:
Arsenic-treated, p53-knockout MCF7 cells transfected with pcDNA
MCF7_KO2_pcDNA_Arsenic

source_name: genomic DNA from arsenic-treated, p53-knockout MCF7 cells transfected with pcDNA

value: pcDNA


title: 204228990006_R07C01: MCF7_KO2_pcDNA_Control

description:
Untreated, p53-knockout MCF7 cells transfected with pcDNA
MCF7_KO2_pcDNA_Control

source_name: genomic DNA from untreated, p53-knockout MCF7 cells transfected with pcDNA


title: ADAR CRISPR-KO screen teratoma 4


title: Ctrl_01_C17


title: 204228980151_R01C01: MCF7_WT_WToe_Control

description:
Untreated, parental MCF7 cells transfected with pcDNA-p53
MCF7_WT_WToe_Control

source_name: genomic DNA from untreated, parental MCF7 cells transfected with pcDNA-p53


title: 204228990026_R03C01: T47D_parental_no_transfection_Control

description:
Untreated, parental T47D
T47D_parental_no_transfection_Control

source_name: genomic DNA from untreated, parental T47D


title: 204228990017_R03C01: T47D_parental_no_transfection_Control


title: Ctrl_01_C09


title: 204228990017_R07C01: T47D_parental_no_transfection_Arsenic


title: 204228980151_R03C01: MCF7_WT_pcDNA_Arsenic

description:
Arsenic-treated, parental MCF7 cells transfected with pcDNA
MCF7_WT_pcDNA_Arsenic

source_name: genomic DNA from arsenic-treated, parental MCF7 cells transfected with pcDNA


title: Ctrl_01_C14


title: 204228990006_R08C01: MCF7_KO2_WToe_Control

description:
Untreated, p53-knockout MCF7 cells transfected with pcDNA-p53
MCF7_KO2_WToe_Control

source_name: genomic DNA from untreated, p53-knockout MCF7 cells transfected with pcDNA-p53


title: Ctrl_01_C07


title: 204228980055_R01C01: MCF7_KO2_pcDNA_Arsenic


title: 204228980055_R07C01: MCF7_KO2_pcDNA_Control


title: 204228980083_R08C01: MCF7_WT_WToe_Control


title: 204228980055_R05C01: MCF7_WT_pcDNA_Arsenic


title: 204228980083_R06C01: MCF7_WT_WToe_Arsenic

description:
Arsenic-treated, parental MCF7 cells transfected with pcDNA-p53
MCF7_WT_WToe_Arsenic

source_name: genomic DNA from arsenic-treated, parental MCF7 cells transfected with pcDNA-p53


title: Ctrl_01_C06


title: 204228980151_R02C01: MCF7_WT_WToe_Arsenic


title: 204228980083_R07C01: MCF7_KO2_WToe_Arsenic

description:
Arsenic-treated, p53-knockout MCF7 cells transfected with pcDNA-p53
MCF7_KO2_WToe_Arsenic

source_name: genomic DNA from arsenic-treated, p53-knockout MCF7 cells transfected with pcDNA-p53


title: 204228980055_R06C01: MCF7_WT_pcDNA_Control

description:
Untreated, parental MCF7 cells transfected with pcDNA
MCF7_WT_pcDNA_Control

source_name: genomic DNA from untreated, parental MCF7 cells transfected with pcDNA


title: 204228980083_R04C01: MCF7_KO2_WToe_Control


title: Ctrl_01_C05


title: Ctrl_01_C04


title: Ctrl_01_C02


title: Ctrl_01_C01


title: 01-130_Normal - GEX

city: Baltimore

first: Kellie

last: Smith

address: 1550 Orleans St

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Cell Ranger v7.1.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
Assembly: Hg38
Supplementary files format and content: Tab-separated values, matrix files and comma separated values

source_name: adjacent normal lung

growth_protocol: Cells were thawed and washed twice with pre-warmed RPMI with 20% FBS and gentamicin before preparing for single cell RNA/TCR sequencing.

extract_protocol:
In brief, cryobanked T cells were thawed and washed twice with pre-warmed RPMI with 20% FBS and gentamicin. Cells were resuspended in PBS and incubated with Fc block for 15 min on ice. Surface staining with antibody against CD3 (BV421, clone SK7 or APC, clone SK7) was performed for 30 min on ice. Viability was stained using LIVE/DEAD Fixable Near-IR (ThermoFisher) or Propidium Iodide (PI) according to manufacturer's protocol. After staining, highly viable CD3+ T cells were sorted into 0.04% bovine serum albumin in PBS using a BD FACSAria II Cell Sorter or MoFlo XDP sorter. Sorted cells were manually counted and prepared at a  desired cell concentration of 1000 cells/uL, when possible.
The Single-Cell 5′ V(D)J and 5′ digital gene expression (DGE) kits (10X Genomics) were used to capture immune repertoire information and gene expression from the same cell in an emulsion-based protocol at the single-cell level. Cells and barcoded gel beads were partitioned into nanoliter-scale droplets using the 10X Genomics Chromium platform to partition up to 10,000 cells per sample followed by RNA capture and cell-barcoded cDNA synthesis using the manufacturer’s standard protocols. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2 × 150-bp paired end sequencing. The 5′ VDJ libraries were sequenced to a depth of ~5000 reads per cell, for a total of 5 million to 25 million reads. The 5′ DGE libraries were sequenced to a target depth of ~50,000 reads per cell.

treatment_protocol: All resected tissue specimens are derived from neoadjuvant-ICB-treated NSCLC patients, see above.

value: adjacent normal lung

value: cryopreserved dissociated tissue

value: Sorted T cells

value: nivolumab


title: 01-130_Normal - TCR

description: 10x Genomics

data_processing:
Cell Ranger v7.1.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
Assembly: Hg38
Supplementary files format and content: Tab-separated values, matrix files and comma separated values
Library strategy: scTCR-seq


title: 01-130_Tumor - TCR

description: 10x Genomics

source_name: lung tumor

value: lung tumor


title: Ctrl_01_C08

value: beta cells


title: MD043-132_tumor_1 - TCR

description: 10x Genomics

value: freshly dissociated tissue

value: Mixed CD45 positive and negative

value: nivolumab+chemotherapy


title: 204228990006_R04C01: MCF7_KO2_WToe_Arsenic


title: 204228980151_R05C01: MCF7_WT_pcDNA_Control

value: WT


title: MD043-132_tumor_1 - GEX

description: 10x Genomics


title: 25-BSL

city: Washington, DC

first: Max

last: Stevenson

state: DC

address: 3970 Reservoir Rd. NW

institute: Georgetown University

description:
NILAD-SCRN-047-SCRN
NILAD-SCRN-047-SCRN

data_processing:
Data analysis was performed using Partek Flow software to identify differentially expressed microRNAs. An optimized workflow was used to perform quality assessment, alignment, quantification, normalization, and different analysis. Quality assessment of data in fastq format was performed in Partek flow and reads containing the adapters or low-quality bases (Qscore ≤5) were removed. The trimmed reads were then aligned to the hg38 reference genome using the Bowtie method. The aligned reads were then quantified to the miRBase reference to obtain the total miRNA read count for each sample.
Assembly: hg38
Supplementary files format and content: Excel

source_name: CSF

extract_protocol:
Cell-free total RNA was isolated from 200 μl of CSF using the Qiagen miRNAeasy extraction kit
Samples were normalized to an input volume of 5 μl RNA eluate to prepare miRNAseq libraries using Qiagen QiaSeq miRNA-seq library preparation kit

treatment_protocol: AD patients were randomized to placebo for 12 months or nilotinib,150 mg for 6 months followed by nilotinib, 300 mg, for another 6 months

value: CSF

tag: disease

value: AD

tag: time point

value: Placebo


title: Ctrl_01_C03

tag: cell type

value: Ctrl


title: 34-BSL

description:
NILAD-SCRN-057-SCRN
NILAD-SCRN-057-SCRN


title: MD043-132_normal_2 - TCR

description: 10x Genomics


title: MD043-132_tumor_2 - TCR

description: 10x Genomics


title: Ctrl_01_B22


title: 23-BSL

description:
NILAD-SCRN-040-SCRN
NILAD-SCRN-040-SCRN


title: 18-BSL

description:
NILAD-SCRN-033-SCRN
NILAD-SCRN-033-SCRN


title: MD043-132_normal_2 - GEX

description: 10x Genomics


title: MD043-132_normal_1 - TCR

description: 10x Genomics


title: Ctrl_01_B21


title: 01-130_Tumor - GEX

description: 10x Genomics


title: 17-BSL

description:
NILAD-SCRN-030-SCRN
NILAD-SCRN-030-SCRN

value: Nilotinib


title: Ctrl_01_B24


title: Ctrl_01_B20


title: MD043-132_normal_1 - GEX

description: 10x Genomics


title: 11318-145_tumor - GEX

description: 10x Genomics


title: 16-BSL

description:
NILAD-SCRN-029-SCRN
NILAD-SCRN-029-SCRN


title: 11318-143_tumor - TCR

description: 10x Genomics


title: 11318-139_tumor - TCR

description: 10x Genomics


title: 11318-139_tumor - GEX

description: 10x Genomics


title: 19-BSL

description:
NILAD-SCRN-028-SCRN
NILAD-SCRN-028-SCRN


title: 11318-143_tumor - GEX

description: 10x Genomics


title: Ctrl_01_B18


title: 11318-141_tumor - TCR

description: 10x Genomics


title: Ctrl_01_B19


title: Ctrl_01_B17


title: 13-BSL

description:
NILAD-SCRN-027-SCRN
NILAD-SCRN-027-SCRN


title: MD043-118_tumor - TCR

description: 10x Genomics


title: Ctrl_01_B16


title: 11318-141_tumor - GEX

description: 10x Genomics


title: Ctrl_01_F11


title: 14-BSL

description:
NILAD-SCRN-022-SCRN
NILAD-SCRN-022-SCRN


title: 11318-145_tumor - TCR

description: 10x Genomics


title: MD043-118_normal - TCR

description: 10x Genomics


title: 11-BSL

description:
NILAD-SCRN-021-SCRN
NILAD-SCRN-021-SCRN


title: MD043-118_normal - GEX

description: 10x Genomics


title: MD043-118_tumor - GEX

description: 10x Genomics


title: 01-110_tumor - TCR

description: 10x Genomics


title: 15-BSL

description:
NILAD-SCRN-019-SCRN
NILAD-SCRN-019-SCRN


title: Ctrl_01_B15


title: 01-110_normal - TCR

description: 10x Genomics


title: 01-110_normal - GEX

description: 10x Genomics


title: Ctrl_01_B13


title: 07-BSL

description:
NILAD-SCRN-014-SCRN
NILAD-SCRN-014-SCRN


title: 01-110_tumor - GEX

description: 10x Genomics


title: Ctrl_01_B14


title: 08-BSL

description:
NILAD-SCRN-007-SCRN
NILAD-SCRN-007-SCRN


title: Ctrl_01_B12


title: 01-105_tumor - TCR

description: 10x Genomics

value: nivolumab and ipilimumab


title: 01-103_tumor - GEX

description: 10x Genomics


title: 01-103_tumor - TCR

description: 10x Genomics


title: 33-BSL

description:
NILAD-SCR-054-SCR
NILAD-SCR-054-SCR


title: 01-105_tumor - GEX

description: 10x Genomics


title: Ctrl_01_B11


title: 01-103_normal - TCR

description: 10x Genomics


title: MD043-102_tumor - TCR

description: 10x Genomics


title: MD043-102_tumor - GEX

description: 10x Genomics


title: Ctrl_01_B10


title: 31-BSL

description:
NILAD-SCR-050-SCR
NILAD-SCR-050-SCR


title: 01-103_normal - GEX

description: 10x Genomics


title: 30-BSL

description:
NILAD-SCR-049-SCR
NILAD-SCR-049-SCR


title: MD043-102_normal - TCR

description: 10x Genomics


title: Ctrl_01_B09


title: Ctrl_01_B08


title: MD043-102_normal - GEX

description: 10x Genomics


title: 24-BSL

description:
NILAD-SCR-044-SCRN
NILAD-SCR-044-SCRN


title: 29-BSL

description:
NILAD-SCR-045-SCR
NILAD-SCR-045-SCR


title: MD043-100_tumor - TCR

description: 10x Genomics


title: MD043-132_tumor_2 - GEX

description: 10x Genomics


title: MD043-100_normal - TCR

description: 10x Genomics


title: Ctrl_01_B06


title: 22-BSL

description:
NILAD-SCR-038-SCR
NILAD-SCR-038-SCR


title: Ctrl_01_B07


title: 20-BSL

description:
NILAD-SCR-035-SCRN
NILAD-SCR-035-SCRN


title: CD34-CRS, tucidinostat, mouse IgG, CUT&Tag

city: Suzhou

first: meng

last: shan

address: shizi street

institute: Soochow university

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: CD34+ cells

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: CD34+ cells

value: hematopoietic stem and progenitor cell

value: CRS overexpression

value: 0.1 μM tucidinostat for 9 days

tag: antibody

value: mouse IgG (Millipore, #12-371)


title: MD043-100_normal - GEX

description: 10x Genomics

value: adjacent normal lung

value: cryopreserved dissociated tissue

value: Sorted T cells


title: CD34-CRL, tucidinostat, flag antibody, CUT&Tag

value: CRL overexpression

value: flag (Sigma, #F1804)


title: CD34-CRS, tucidinostat, flag antibody, CUT&Tag


title: CD34-CRL, tucidinostat, mouse IgG, CUT&Tag


title: Ctrl_01_B04

value: beta cells


title: Ctrl_01_B05


title: CD34-CRS, RGFP966, mouse IgG, CUT&Tag

value: 2 μM RGFP966 for 9 days


title: 34-12

description:
NILAD-034-M12
NILAD-034-M12

value: CSF

value: AD


title: 33-6

description:
NILAD-033-M6
NILAD-033-M6

value: Placebo


title: CD34-CRL, RGFP966, flag antibody, CUT&Tag


title: CD34-CRS, RGFP966, flag antibody, CUT&Tag


title: MD043-100_tumor - GEX

description: 10x Genomics

value: lung tumor


title: CD34-CRL, RGFP966, mouse IgG, CUT&Tag


title: Ctrl_01_B03

value: Ctrl


title: 33-12

description:
NILAD-033-M12
NILAD-033-M12


title: 31-6

description:
NILAD-031-V6
NILAD-031-V6


title: CD34-CRS, rabbit IgG, CUT&Tag

value: CD34+ cells

value: rabbit IgG (Millipore, #12-370)


title: 31-12

description:
NILAD-031-M12
NILAD-031-M12


title: CD34-CRL, rabbit IgG, CUT&Tag

value: hematopoietic stem and progenitor cell


title: Ctrl_01_B01


title: CD34-CRL, HDAC3 antibody, CUT&Tag

value: HDAC3 (Abcam, #ab32369)


title: CD34-CRS, HDAC3 antibody, CUT&Tag

value: CRS overexpression


title: Ctrl_01_A24


title: CD34-RARG, rabblit IgG (H3K27me3), CUT&Tag

value: RARG overexpressio


title: CD34-RARG, H3K27me3  antibody, CUT&Tag


title: 30-6

description:
NILAD-030-V6
NILAD-030-V6

value: Nilotinib


title: 30-12

description:
NILAD-030-M12
NILAD-030-M12


title: Ctrl_01_A23


title: Ctrl_01_B02


title: 29-6

description:
NILAD-029-V6
NILAD-029-V6


title: Ctrl_01_A21


title: Ctrl_01_A22


title: Ctrl_01_B23


title: CD34-CRS, H3K27me3 antibody, CUT&Tag


title: CD34-CRS, rabblit IgG (H3K27me3), CUT&Tag


title: 29-12

description:
NILAD-029-M12
NILAD-029-M12


title: Ctrl_01_A20


title: 25-12

description:
NILAD-025-M12
NILAD-025-M12


title: Ctrl_01_A19


title: W3 PBMCs, lanes 1-4, TCR-derived cDNA

city: New York

first: Ramin

last: Herati

state: New York

address: 430 E. 29th Street, 1st floor, room 135A-C

institute: NYU School of Medicine

description:
10X Genomics
W3_GEX_barcodes.tsv.gz
W3_GEX_features.tsv.gz
W3_GEX_matrix.mtx.gz
W3_GEX_vdj_b_filtered_contig_annotations.csv
W3_GEX_vdj_t_filtered_contig_annotations.csv
20230723_HTO_taglist.csv

data_processing:
Cellranger software v7 (10X Genomics) was used to align FASTQ files to the human genome (GRCh38), evaluate gene and protein expression, and exclude empty droplets via the Barcode Rank Plot. Seurat v5.0.3 was used for single cell library processing and assay integration. HTO demultiplexing was conducted using CLR normalization (via NormalizeData()) and HTODemux(). Cells were filtered out and excluded based on high mitochondrial counts, and low and high UMI counts, which were tailored to the batch being processed. Additional batch processing included normalizing and scaling. Souporcell software was used as an additional metric for demultiplexing and ambient RNA removal. For doublet detection, scDblFinder() was used, with an estimated doublet rate of 0.4% per 1000 cells. HTODemux() negatives and scDblFinder() doublets were removed. scRepertoire v1.11.0 was used for TCR and BCR sequence processing. Seurat allowed for integration, via SCTransform for normalization, SelectIntegrationFeatures() (utilizing 5000 features), and FindIntegrationAnchors() (utilizing the first 20 dimensions, rpca reduction, and 20 k.anchors). limma v3.56.2 was used to remove batch effect for PCA visualization. SCPA v1.6.1 was used for pathway analysis and enrichment evaluation.
Assembly: GRCh38 ensemble
Supplementary files format and content: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz, vdj_t_filtered_contig_annotations.csv, vdj_b_filtered_contig_annotations.csv
Library strategy: CITE-seq

source_name: Peripheral blood mononuclear cells

extract_protocol:
After one hour rest, cells being used for cellular indexing of transcriptomics and epitopes by sequencing (CITEseq) were blocked at 1:20 with TruStain FcX (BioLegend) and FCR Blocking Reagent (Miltenyi Biotec) in staining buffer (PBS, 2% BSA, 0.01% Tween) for 10 minutes at room temperature. Following this, cells were stained with hashtag oligos (Biolegend) for 30 minutes at room temperature. Cells were then pooled, loaded onto Chromium HT Chips from the Chromium Next GEM Single Cell 5’ HT Kit v2 and run on a Chromium controller (10X Genomics).
Gene expression and V(D)J libraries were constructed with the 5’ Feature Barcode Kit, Chromium Single Cell V(D)J Amplification Kit, and Chromium Next GEM Single Cell 5’ Library Kit (10X Genomics) as recommended by the manufacturer. Libraries were pooled and sequenced using the NovaSeq 6000.

treatment_protocol: Patient samples were collected under the Checkmate-238 clinical trial in which patients with resected stage III or IV melanoma were treated with adjuvant Nivolumab or Ipilimumab. Blood samples were collected on the same day as the first immunotherapy infusion (Week 1) and again three weeks after the start of treatment (Week 3). Peripheral blood mononuclear cells (PBMCs) were isolated from the blood samples and cryopreserved. Cryopreserved PBMCs were thawed into RPMI 1640 with L-glutamine (Fischer) containing 10% FBS (Fisher), 2 mM L-glutamine (Fisher) and supplemented with 10 units DNaseI and 5mM MgCl2. The cells rested for one hour at 37°C before use in flow cytometry and CITEseq. After one hour rest, cells being used for flow cytometry were blocked at 1:100 with Human TruStain FcX (BioLegend) and NovaBlock (Thermo Fischer Scientific) in FACS buffer for 10 minutes at room temperature. Following this, cells were stained with fluorescently-labeled anti-human surface antibodies (see Reagent Table) for 20 minutes at room temperature in the dark. Cells were then permeabilized using the eBioscience Foxp3/Transcription Factor Staining Buffer Set (ThermoFisher) for 20 minutes at room temperature in the dark. After permeabilization, cells were stained with intracellular antibodies for 1 hour at room temperature in the dark. Cells were then resuspended in 1% para-formaldehyde (Electron Microscopy Sciences). All samples were acquired on a five-laser Aurora cytometer (Cytek Biosciences).

value: Peripheral blood mononuclear cells


title: KYSE30 cells, GPRC5A Overexpression

city: Hong Kong

first: Hongyu

last: Zhou

address: L10-51, No. 21 Sassoon Rd, Hong Kong

department: Clinical Oncology

institute: The university of Hong Kong

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes FPKM values for each sample

source_name: Esophagus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Esophagus

value: esophageal squamous cell carcinoma

value: GPRC5A overexpression


title: KYSE520 cells, ShGPRC5A#1

value: GPRC5A knockdown#1


title: KYSE520 cells, ShControl

value: ShControl


title: Ctrl_01_A18

value: beta cells


title: 24-6

description:
NILAD-024-M6
NILAD-024-M6

value: CSF

value: AD


title: W3 PBMCs, lanes 1-4, BCR-derived cDNA


title: Ctrl_01_A17

value: Ctrl


title: W2 PBMCs, lanes 1-4, TCR-derived cDNA

description:
10X Genomics
W2_GEX_barcodes.tsv.gz
W2_GEX_features.tsv.gz
W2_GEX_matrix.mtx.gz
W2_GEX_vdj_b_filtered_contig_annotations.csv
W2_GEX_vdj_t_filtered_contig_annotations.csv
20230723_HTO_taglist.csv


title: W3 PBMCs, lanes 1-4, mRNA-derived cDNA


title: 24-12

description:
NILAD-024-EOT
NILAD-024-EOT


title: CD34-CRL, H3K27me3 antibody, CUT&Tag

value: CD34+ cells

value: CRL overexpression


title: Ctrl_01_A16


title: CD34-CRL, rabblit IgG (H3K27me3), CUT&Tag

value: hematopoietic stem and progenitor cell

value: rabbit IgG (Millipore, #12-370)


title: KYSE520 cells, ShGPRC5A#2

value: GPRC5A knockdown#2


title: 23-6

description:
NILAD-023-M6
NILAD-023-M6

value: Placebo


title: W2 PBMCs, lanes 1-4, mRNA-derived cDNA


title: W2 PBMCs, lanes 1-4, ADT-derived cDNA

library_source: other

molecule: protein


title: Ctrl_01_A15


title: Ctrl_01_A14


title: W1 PBMCs, lanes 1-4, TCR-derived cDNA

description:
10X Genomics
W1_GEX_barcodes.tsv.gz
W1_GEX_features.tsv.gz
W1_GEX_matrix.mtx.gz
W1_GEX_vdj_b_filtered_contig_annotations.csv
W1_GEX_vdj_t_filtered_contig_annotations.csv
20230723_HTO_taglist.csv


title: 23-12

description:
NILAD-023-M12
NILAD-023-M12


title: W2 PBMCs, lanes 1-4, BCR-derived cDNA


title: 25-6

description:
NILAD-025-V6
NILAD-025-V6


title: W1 PBMCs, lanes 1-4, BCR-derived cDNA


title: 22-6

description:
NILAD-022-M6
NILAD-022-M6


title: W1 PBMCs, lanes 1-4, ADT-derived cDNA


title: W3 PBMCs, lanes 1-4, ADT-derived cDNA


title: 22-12

description:
NILAD-022-EOT
NILAD-022-EOT


title: ER1 PBMCs, lanes 1-4, TCR-derived cDNA

description:
10X Genomics
ER1_GEX_barcodes.tsv.gz
ER1_GEX_features.tsv.gz
ER1_GEX_matrix.mtx.gz
ER1_GEX_vdj_b_filtered_contig_annotations.csv
ER1_GEX_vdj_t_filtered_contig_annotations.csv
20230723_HTO_taglist.csv


title: 20-6

description:
NILAD-020-M6
NILAD-020-M6

value: Nilotinib


title: ER1 PBMCs, lanes 1-4, BCR-derived cDNA

value: Peripheral blood mononuclear cells


title: Ctrl_01_A12


title: W1 PBMCs, lanes 1-4, mRNA-derived cDNA


title: 20-12

description:
NILAD-020-M12
NILAD-020-M12


title: ER1 PBMCs, lanes 1-4, mRNA-derived cDNA


title: Ctrl_01_A11


title: L34 PBMCs, lanes 1-2, TCR-derived cDNA

description:
10X Genomics
L34_GEX_barcodes.tsv.gz
L34_GEX_features.tsv.gz
L34_GEX_matrix.mtx.gz
L34_GEX_vdj_b_filtered_contig_annotations.csv
L34_GEX_vdj_t_filtered_contig_annotations.csv
20220822_HTO_taglist.csv


title: Ctrl_01_A10


title: Ctrl_01_A09


title: 19-6

description:
NILAD-019-M6
NILAD-019-M6


title: L34 PBMCs, lanes 1-2, BCR-derived cDNA


title: L34 PBMCs, lanes 1-2, ADT-derived cDNA


title: Ctrl_01_A08


title: Ctrl_01_A13


title: L12 PBMCs, lanes 1-2, mRNA-derived cDNA

description:
10X Genomics
L12_GEX_barcodes.tsv.gz
L12_GEX_features.tsv.gz
L12_GEX_matrix.mtx.gz
L12_GEX_vdj_b_filtered_contig_annotations.csv
L12_GEX_vdj_t_filtered_contig_annotations.csv
20220822_HTO_taglist.csv


title: 10-BSL

description:
NILAD-018-SCRN
NILAD-018-SCRN


title: L12 PBMCs, lanes 1-2, BCR-derived cDNA


title: Ctrl_01_A07


title: 18-6

description:
NILAD-018-M6
NILAD-018-M6


title: L12 PBMCs, lanes 1-2, ADT-derived cDNA


title: L34 PBMCs, lanes 1-2, mRNA-derived cDNA


title: Ctrl_01_A06


title: 18-12

description:
NILAD-018-M12
NILAD-018-M12


title: ER1 PBMCs, lanes 1-4, ADT-derived cDNA


title: HepG2_H3K27me3_siEZH2_1, CUT&Tag

city: Cheongju-si

first: Jaehyun

last: Lee

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological Science and Biotechnology

country: South Korea

institute: Chungbuk National University

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
To ensure data quality, the raw files were trimmed using Trim Galore (version 0.6.6, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
These trimmed reads were then aligned to the human genome (hg38 assembly) using Bowtie2 (version 2.3.5.1) with the following parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
To identify peaks over background signals, the makeTagDirectory and findPeaks commands from HOMER (version 4.11.1) were utilized.
A FDR cutoff of 0.05 was employed. The total number of mapped reads for each sample was normalized to 10 million mapped reads. Differential peak analysis for the CUT&Tag data was performed using the getDifferentialPeaks command.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peaks.txt
Library strategy: CUT&Tag

source_name: Liver

growth_protocol: HepG2 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HepG2 cells were washed with PBS and resuspended in NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol, 1x protease inhibitors). After incubation on ice for 10 min, nuclei were centrifuged and washed once with PBS. Nuclei were then fixed with 0.1% formaldehyde for 2 min at room temperature, and the reaction was quenched with glycine. Fixed nuclei were resuspended in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease inhibitors) and counted. 1 × 10^5 nuclei were used per CUT&Tag reaction. Nuclei were bound to activated concanavalin A-coated magnetic beads (catalog no. 21-1401; Epicypher) and incubated with an H3K27me3 antibody (catalog no. C36B11; Cell Signaling Technology) in antibody buffer overnight at 4°C. After washing in wash buffer, samples were incubated with a goat anti-rabbit secondary antibody (catalog no. ab182016; Abcam) in wash buffer for 30 min at room temperature, followed by an additional wash. After further wash in 300-wash buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x protease inhibitors), samples were incubated with pAG-Tn5 (catalog no. 15-1017; Epicypher) for 1 hour at room temperature. After additional washes, tagmentation was carried out in 300-wash buffer containing 10 mM MgCl2 for 1 hour at 37°C. To release pA-Tn5 and cleaved chromatin fragments, samples were resuspended in 0.1% SDS release solution, incubated at 58°C for 1 hour, and neutralized by the addition of 0.67% Triton-X100.
PCR was performed by directly adding NEBNext HiFi PCR Master Mix (catalog no. M0541L; NEB) and sample-specific barcoded adapters to the tagmented fragments. After amplification, libraries were cleaned up using AMPure beads (catalog no. A63880; Beckman Coulter). The prepared libraries were sequenced using 150-base pair paired-end sequencing on an Illumina Novaseq platform.

treatment_protocol: HepG2 cells were stabilized for 24 h and 5 μM Tazemetostat (MCE) dissolved in DMSO was treated for 48 h. For EZH2 knockdown, siEZH2 or siNC were treated for 24 h. The EZH2 gene was knocked down with SMART pool ON‐TARGETplus siRNA (catalog no. L‐015700‐00‐0005; Dharmacon Inc., Lafayette, CO, USA). The ON‐TARGETplus Non‐targeting Pool was used as a negative control (catalog no. D‐001810‐10‐05; Dharmacon Inc.). The cells were then transfected with the RNA duplex and LipofectamineTM RNAi‐MAX (catalog no. 13778075, Invitrogen) in Opti‐MEM I reduced serum medium (catalog no. 31985-062; Thermo Fisher Scientific) without antibiotics, according to the manufacturer’s instructions. After 24 hours, the medium was replaced with complete medium containing antibiotics, and the cells were harvested for subsequent experiments after an additional 24-hour incubation at 37 °C in a humidified 5% CO2 incubator.

value: Liver

value: Epithelial cell

value: WT

value: siEZH2 treatment


title: HepG2_H3K27me3_siEZH2_3, CUT&Tag


title: 17-12

description:
NILAD-017-V12
NILAD-017-V12


title: HepG2_H3K27me3_siNC_3, CUT&Tag

value: siNon-targeting control treatment


title: HepG2_H3K27me3_siEZH2_2, CUT&Tag


title: Ctrl_01_A04

source_name: beta cells

value: beta cells


title: KYSE30 cells, Control

value: Esophagus

value: esophageal squamous cell carcinoma

value: Control


title: L12 PBMCs, lanes 1-2, TCR-derived cDNA


title: HepG2_H3K27me3_Taze_3, CUT&Tag

value: Tazemetostat treatment


title: HepG2_H3K27me3_siNC_1, CUT&Tag


title: HepG2_H3K27me3_siNC_2, CUT&Tag


title: HepG2_H3K27me3_Taze_2, CUT&Tag


title: Ctrl_01_A03

value: Ctrl


title: 17-6

description:
NILAD-017-M6
NILAD-017-M6

value: CSF

value: AD


title: 09-BSL

description:
NILAD-017-SCRN
NILAD-017-SCRN


title: HepG2_H3K27me3_Taze_1, CUT&Tag


title: 19-12

description:
NILAD-019-EOT
NILAD-019-EOT


title: Ctrl_01_A02


title: NGP cells, OTSSP167-3

city: Washington

first: Yang

last: Yu

address: 111 Michigan Ave NW

institute: Children's national hospital

data_processing:
RNA-Seq experiments were conducted by using Illumina paired-end sequencing technology.
Raw reads were adaptor removed, and sequencing quality was assessed with the bioinformatics software FastQC (version 0.11.2).
Reads were mapped against the human reference genome (GRCh38.p13 assembly) using the aligner, HISAT2 (v2.1.0).
The mapped reads were subsequently assembled into transcripts or genes using the assembler, StringTie (v1.3.5).
Assembly: Homo_sapiens.GRCh38.dna. primary_assembly.fa.gz
Supplementary files format and content: ReadCounts.xlsx

source_name: neuroblastoma

growth_protocol: NGP cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Thermo Fisher). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: NGP cells were treated with OTSSP167 at 60 nmol/L for 12 hours, same volum DMSO were used as the control.

value: neuroblastoma

value: NGP

value: neuroblastoma cells


title: HepG2_siEZH2_2, RNA-seq

data_processing:
Sequenced reads were mapped to the reference human genome (hg38 assembly) using STAR aligner (v 2.7.1a) with default parameters
The expression levels of genes in each sample were normalized by means of transcript per million (TPM).
Differentially expressed genes (DEGs) were identified using edgeR with raw read counts.
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 file includes TPM values for each sample.

extract_protocol:
Total RNA was extracted from cells using the Ribospin II kit (GeneAll). 1 μg of total RNA was used  for the construction of sequencing libraries.
RNA libraries for sequencing were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were stabilized for 24 h and siEZH2 or siNC were treated for 24 h. The EZH2 gene was knocked down with SMART pool ON‐TARGETplus siRNA (catalog no. L‐015700‐00‐0005; Dharmacon Inc., Lafayette, CO, USA). The ON‐TARGETplus Non‐targeting Pool was used as a negative control (catalog no. D‐001810‐10‐05; Dharmacon Inc.). The cells were then transfected with the RNA duplex and LipofectamineTM RNAi‐MAX (catalog no. 13778075, Invitrogen) in Opti‐MEM I reduced serum medium (catalog no. 31985-062; Thermo Fisher Scientific) without antibiotics, according to the manufacturer’s instructions. After 24 hours, the medium was replaced with complete medium containing antibiotics, and the cells were harvested for subsequent experiments after an additional 24-hour incubation at 37 °C in a humidified 5% CO2 incubator.


title: HepG2_H3K27me3_Ctrl_3, CUT&Tag

value: Untreated


title: HepG2_H3K27me3_Ctrl_2, CUT&Tag

value: Liver


title: Ctrl_01_A01


title: HepG2_H3K27me3_Ctrl_1, CUT&Tag

value: Epithelial cell


title: 16-6

description:
NILAD-016-M6
NILAD-016-M6

value: Placebo


title: HepG2_siEZH2_1, RNA-seq

value: WT

value: siEZH2 treatment


title: Ctrl_01_A05

value: beta cells


title: HepG2_siNC_1, RNA-seq

value: siNon-targeting control treatment


title: HepG2_siNC_2, RNA-seq


title: 15-12

description:
NILAD-015-M12
NILAD-015-M12

value: Nilotinib


title: Gammadelta MF, P202, scTCR-seq

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids); filtered_contig_annotations.csv and clonotypes.csv (information about TCR sequencing)
Supplementary files format and content: *filtered_contig_annotations.csv (TCR alpha beta clonotypes file )
Supplementary files format and content: *clonotypes.csv (TCR alpha beta clonotypes file )
Supplementary files format and content: *filtered_contig_annotations_gd.csv (TCR gamma delta clonotypes file )
Supplementary files format and content: *clonotypes_gd.csv (TCR gamma delta clonotypes file )

source_name: Skin

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 and v2 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin

value: mixture of skin cells

tag: condition

value: Gammadelta MF


title: NGP cells, OTSSP167-1

tag: cell line


title: Gammadelta MF, P124, scTCR-seq


title: 14-12

description:
NILAD-014-M12
NILAD-014-M12

value: CSF

tag: treatment


title: Gammadelta MF, P97, scTCR-seq


title: 14-6

description:
NILAD-014-M6
NILAD-014-M6

value: AD


title: NGP cells, DMSO-3

value: neuroblastoma

value: DMSO


title: NGP cells, DMSO-2

value: NGP

value: neuroblastoma cells


title: 16-12

description:
NILAD-016-V12
NILAD-016-V12


title: Gammadelta MF, P318B, scTCR-seq


title: Gammadelta MF, P71, scTCR-seq


title: Gammadelta MF, P318A, scTCR-seq


title: NGP cells, DMSO-1


title: Gammadelta MF, P127, scTCR-seq


title: Berti’s Lymphoma, P95, scTCR-seq

value: Berti’s Lymphoma


title: Berti’s Lymphoma, P195, scTCR-seq


title: NGP cells, CAMKV-KD-3

source_name: Neuroblastoma

growth_protocol: NGP with CAMKV knockdown or the control  cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

value: Neuroblastoma

tag: genotype

value: CAMKV-KD


title: Berti’s Lymphoma, P230, scTCR-seq


title: 15-6

description:
NILAD-015-V6
NILAD-015-V6


title: 13-12

description:
NILAD-013-M12
NILAD-013-M12


title: NGP cells, OTSSP167-2


title: 11-6

description:
NILAD-011-M6
NILAD-011-M6


title: Berti’s Lymphoma, P218, scTCR-seq


title: 11-12

description:
NILAD-011-M12
NILAD-011-M12


title: NGP cells, CAMKV-KD-2


title: CD4 MF, P311, scTCR-seq

value: CD4 MF


title: CD4 MF, P303, scTCR-seq


title: 10-6

description:
NILAD-010-M6
NILAD-010-M6


title: NGP cells, CAMKV-KD-1


title: 13-6

description:
NILAD-013-V6
NILAD-013-V6


title: CD4 MF, P171, scTCR-seq


title: CD4 MF, PGS, scTCR-seq


title: NGP cells, Control-2

value: Control


title: 10-12

description:
NILAD-010-M12
NILAD-010-M12


title: CD4 MF, P204, scTCR-seq


title: CD4 MF, P76, scTCR-seq


title: Healthy control skin, P121, scTCR-seq

value: Healthy control skin


title: 9-6

description:
NILAD-009-M6
NILAD-009-M6


title: Healthy control skin, P116, scTCR-seq


title: 9-12

description:
NILAD-009-M12
NILAD-009-M12


title: NGP cells, Control-1


title: Healthy control skin, P115, scTCR-seq


title: Healthy control skin, P112, scTCR-seq


title: healthy gingiva 3

city: Hefei

first: Tingyue

address: Huangshan road

institute: USTC

data_processing:
RNA-Seq fastq files were first processed by fastp
aligned to the GRCh38 human genome assembly by STAR (v2.5.3a), followed by quantification with HT-seq (v0.9.0)
first quantile-adjusted, using a conditional maximum likelihood (qCML) model (estimate Common Disp function of EdgeR version v3.29.2).
differentially expressed genes between the experimental groups were identified by edgeR (v3.29.2), and further filtered for at least 1.5-fold changes.
Assembly: STAR (v2.5.3a)

source_name: gingiva

extract_protocol:
RNA-Seq fastq files were first processed by fastp, to remove adaptor and low-quality reads, and then aligned to the GRCh38 human genome assembly by STAR (v2.5.3a), followed by quantification with HT-seq (v0.9.0). The resulting gene count data were first quantile-adjusted, using a conditional maximum likelihood (qCML) model (estimate Common Disp function of EdgeR version v3.29.2). Then, differentially expressed genes between the experimental groups were identified by edgeR (v3.29.2), and further filtered for at least 1.5-fold changes. Gene ontology (GO) analysis was performed using Metascape (http://metascape.org/gp/index.html#/main/step1).
STAR (v2.5.3a)

value: gingiva


title: 8-6

description:
NILAD-008-M6
NILAD-008-M6

value: Placebo


title: Gammadelta MF, P202, scRNA-seq

value: Skin


title: Gammadelta MF, P97, scRNA-seq

value: mixture of skin cells


title: Gammadelta MF, P124, scRNA-seq

value: Gammadelta MF


title: CD4 MF, P312, scTCR-seq


title: 8-12

description:
NILAD-008-M12
NILAD-008-M12

value: CSF


title: Gammadelta MF, P318B, scRNA-seq


title: healthy gingiva 2


title: 7-6

description:
NILAD-007-M6
NILAD-007-M6

value: AD


title: healthy gingiva 1


title: periapical lesion 2

source_name: periapical inflammatory tissue

value: periapical inflammatory tissue


title: Gammadelta MF, P71, scRNA-seq


title: 7-12

description:
NILAD-007-M12
NILAD-007-M12


title: NGP cells, Control-3


title: Berti’s Lymphoma, P95, scRNA-seq


title: Gammadelta MF, P127, scRNA-seq


title: periapical lesion 1


title: 6-6

description:
NILAD-006-M6
NILAD-006-M6