title: liver, TCPOBOP + SHAM, replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: sample 16
TCPOBOP_SHAM-4

data_processing:
Reads were quality checked with fastqc
Reads were aligned to the mm39 reference genome (GENCODE M30) with the STAR aligner (v2.7.11a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples

source_name: liver

extract_protocol:
Mouse livers were isolated 9h after surgery, thus 3h post-injection, and stored in RNA later. RNA was extracted using the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s-protocol
Per sample, an amount of 1000ng of total RNA was used as input. Using the Illumina Stranded mRNA Sample Prep Kit (protocol version: # 1000000124518 v03, June 2022), poly-A containing mRNA molecules were purified from the total RNA input using poly-dT oligo-attached magnetic beads. The purified mRNA was fragmented, and in a reverse transcription reaction using random primers and Actinomycin D, RNA was converted into first strand cDNA, and subsequently into double-stranded cDNA in a second strand cDNA synthesis reaction using dUTP to achieve strand specificity. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments, after which pre-index anchors were ligated preparing the fragments for dual indexing. Anchor-ligated fragments were then purified using magnetic beads. Finally, enrichment PCR was carried out to enrich those DNA fragments that have anchor-ligated DNA fragments and to add indexes and primer sequences for cluster generation. Purified dual-indexed sequence-libraries of each sample were equimolarly pooled and sequenced on Element Biosciences AVITI (2x75 Cloudbreak High kit, single read 100 (101-10-10-0)) at the VIB Nucleomics Core

treatment_protocol: Mice were subjected to SHAM or CLP surgery, 6h after surgery TCPOBOP (12.5 mg/kg, dissolved in 50% corn oil and 50% DMSO) or a control injection (vehicle) was given

value: liver

tag: treatment 1

value: TCPOBOP

tag: treatment 2

value: SHAM

tag: duration treatment_2


title: liver, TCPOBOP + SHAM, replicate 3

status: Public on Aug 31 2025

type: SRA

description:
Library name: sample 15
TCPOBOP_SHAM-3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: WES_Case3_post

city: Xiamen

first: Qing

last: Li

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

country: China

institute: xiamen university

library_source: genomic

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were mapped to the Hg38 human reference genomes using BWA (v0.7.17) and generated SAM files were converted to BAM files using Samtools (v.1.5) using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters.
Mapped reads were processed using GATK (v4.1.7) pipeline commands HaplotypeCaller, VariantFiltration, SelectVariants, BaseRecalibrator, ApplyBQSR, and HaplotypeCaller to identify variants. High quality SNPs were filtered using the filter expression: “QD < 2.0 || MQ < 40.0 || FS >60.0 || SOR> 3.0 || MQRankSum < −12.5 || ReadPosRankSum <−8.0”, High quality Indels were filtered using the filter expression: “QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0” (McKenna et al., 2010).
Variants were annotated with Annovar (table_annovar.pl; ensGene, cytoBand, genomicSuperDups, rmsk, exac03, esp6500siv2_all, avsnp147, ALL.sites.2015_08, clinvar_202). Putative SNVs were then filtered using the following parameters: 1000G_ALL < 0.01, ExAC_ALL < 0.01, ESP6500siv2_ALL < 0.01, genomicSuperDups score < 0.9. Only mutations with nonsynonymous, stop/gain and stop/loss in exonic and splicing regions were kept as final SNVs.
CNVkit (v0.9.3) was used to call copy number from sorted BAM files. Copy number was called using batch mode with the drop-low-coverage option against the GRCh38.97 reference. Copy numbers were reported in log2 scale. Thresholds for calling copy number changes for homozygous and amplification were log2(0.2/2) and log2(8/2).
Assembly: hg38
Supplementary files format and content: csv files include mutation data for each Sample,cns files include copy number data for each sample.
Library strategy: Whole-exome seq

molecule: genomic DNA

organism: Homo sapiens

source_name: ovarian cancer tissue

growth_protocol: OC316, HCC1937 cells were cultured in  RPMI1640 medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Genomic DNA samples were extracted by TIANamp Genomic DNA kit.
A total amount of 0.2 μg DNA per sample was used as input material for the DNA library preparations. Sequencing library was generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to each sample. Briefly, genomic DNA sample was fragmented by sonication to a size of 350 bp. Then DNA fragments were endpolished, A-tailed, and ligated with the full-length adapter for Illumina sequencing, followed by further PCR amplification. After PCR products were purified by AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by NGS3K/Caliper and quantified by real-time PCR (3 nM). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Illumina PE Cluster Kit (Illumina, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with indicated drugs.

value: ovarian cancer tissue

tag: treatment

value: PARPi-treatment (Niraparib)


title: Knee BALB/c_Healthy, biological rep3

type: RNA

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: Gene expression data from knees of healthy BALB/c mice

hyb_protocol: Following fragmentation, 5500 ng of fragmented and labeled ss-cDNA was hybridized for 16 or 18hr at 45°C on GeneChips Clariom™ D Assay, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Transcriptome Analysis Console (TAC) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: BALB/c mice Healthy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA according User Guide: GeneChip WT PLUS Reagent Kit Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays.

extract_protocol: RNeasy Lipid Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: BALB/c

tag: condition

value: Healthy

tag: age

value: 30 weeks

value: Knee


title: ΔlrhA replicate 1, sample 13

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

country: Germany

institute: University of Cologne

description: Library name: E.coli K12 strain U504 replicate 1

data_processing:
Galaxy platform was used for all data processing steps (https://usegalaxy.org/)
Sequences were aligned with Bowtie2 (Galaxy version 2.3.4.2) and default settings
Reads mapping to genes were counted with Htseq (Galaxy version 0.9.1) in union mode and a minimum alignment quality of 10 in addition to default settings
Differential expression of genes was tested using DESeq2 (Galaxy version 2.11.40.2) and default settings.
Assembly: GCA_000005845.2_ASM584v2
Supplementary files format and content: tab-delimited text file includes raw counts fo each sample

organism: Escherichia coli K-12

growth_protocol: For RNA extraction 10 ml of tryptone medium was inoculated to an OD600 of 0.05 using fresh overnight cultures, and grown at 37°C, while shaking, to OD600 of 0.8. 1.5 ml were harvested for RNA isolation.

extract_protocol:
Total RNA was extracted from 1.5 ml of culture using RNAprotect Bacteria Reagent (Qiagen, cat. No 76506) and RNeasy Mini Kit (Qiagen, cat. No 74134) with on column DNase I digestion (Qiagen, cat. No 79254), according to the manufacturer’s instructions (Qiagen, Germany).
Illumina TruSeq RNA Library Kit (with ribo-depletion, without Poly-A selection)

tag: cell line

tag: genotype

value: U4 delta-lrhA


title: WES_Case3_pre

value: PARPi-naive


title: Knee BALB/c_Healthy, biological rep2


title: liver, TCPOBOP + SHAM, replicate 2

description:
Library name: sample 14
TCPOBOP_SHAM-2


title: ΔyhaJ replicate 3, sample 22

description: Library name: E.coli K12 strain U458 replicate 3

value: U4 delta-yhaJ


title: WES_Case2_post

value: PARPi-treatment (Olaparib)


title: Knee BALB/c_Healthy, biological rep1


title: ΔyhaJ replicate 2, sample 17

description: Library name: E.coli K12 strain U458 replicate 2


title: ΔlrhA replicate 3, sample 23

description: Library name: E.coli K12 strain U504 replicate 3


title: Knee DBA/1_SpAD, biological rep3

description: Gene expression data from knees of DBA/1 mice with Spontaneous arthritis

source_name: DBA/1 mice with Spontaneous arthritis

value: Spontaneous arthritis


title: ΔyhaJ replicate 1, sample 12

description: Library name: E.coli K12 strain U458 replicate 1


title: WES_Case1_post


title: liver, TCPOBOP + CLP, replicate 4

description:
Library name: sample 12
TCPOBOP_CLP-4

value: CLP


title: ΔyafC replicate 3, sample 21

description: Library name: E.coli K12 strain U456 replicate 3

value: U4 delta-yafC


title: WES_Case2_pre


title: WES_Case1_pre


title: ΔyafC replicate 2, sample 16

description: Library name: E.coli K12 strain U456 replicate 2


title: liver, TCPOBOP + CLP, replicate 3

description:
Library name: sample 11
TCPOBOP_CLP-3


title: Knee DBA/1_SpAD, biological rep2


title: Knee DBA/1_SpAD, biological rep1


title: liver, TCPOBOP + CLP, replicate 2

description:
Library name: sample 10
TCPOBOP_CLP-2


title: ChIP_seq_FoxO1_HA_Olap

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v2.3.4.1) and generated SAM files were converted to BAM files using Samtools (v.1.9)  using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters which were converted to BigWig files using Deeptools. BigWig files were visualized using the Integrative Genomics Viewer (Broad Institute).
HOMER suit of tools was used. Aligned bam files were subjected to peak calling using findPeaks tools with the -style factor.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deeptools and were visualized using the Integrative Genomics Viewer (Broad Institute).

growth_protocol: SUM159 cells were cultured in Ham’s F12 medium supplemented with 10% FBS, 5 mg/mL insulin and 1 mg/mL hydrocortisone in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed once with cold PBS prior to cross-linking with 2 mM DSG for 45 minutes followed by 1% formaldehyde (28908, Thermo) for 15 min at room temperature (except for the etoposide ChIP of TOP2A, cells were treated with 100mM etoposide for 10min). To quench the cross-linking reaction, 2.5 M glycine dissolved in PBS was added and cells were incubated at room temperature for a further 5 minutes. Cells were washed twice with ice-cold PBS and lysed using cell lysis buffer (50 mM Tris pH 8.0, 0.5% NP40, 50 mM NaCl) to remove the cytoplasmic proteins. The pellet was resuspended in nuclear lysis buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 400 mM NaCl, 20 mM Tris pH 8.0, 0.1% SDS). Chromatin DNA was sheared to 300–500 bp average in size through sonication using a Bioruptor instrument (Diagenode). Fragmented chromatin was diluted 1:1 with dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100) and immunoprecipitated with IgG or indicated specific antibodies overnight at 4°C, followed by incubation with protein A/G magnetic Dynabeads for 4 h. Dynabeads were washed once each with ChIP wash buffer 1 (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and ChIP wash buffer 2 (20 mM Tris pH 8.0, 400 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and washed twice with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA pH 8.0). After washing and elution, the protein–DNA complex was reversed by heating overnight at 65°C. Immunoprecipitated DNA was purified by QIAquick spin columns. Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing.
Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing. Briefly, Chip DNA was end-blunted and added with an ‘A’ base. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Cells were infected with indicated lentivirus and/or treated with indicated drugs.

tag: cell type

value: breast cancer

tag: chip antibody

value: HA (abcam, ab9110)

value: WT

value: 10 uM Olaparib

tag: time

value: 3 days


title: ChIP_seq_FoxO1_HA_DMSO

value: DMSO


title: wildtype replicate 3, sample 20

description: Library name: E.coli K12 strain U4 replicate 3

value: U4, BW30270 ilvG+ delta-lacZ


title: liver, CTRL + SHAM, replicate 4

description:
Library name: sample 8
CTRL_SHAM-4

value: liver

value: control

value: SHAM


title: ΔyafC replicate 1, sample 11

description: Library name: E.coli K12 strain U456 replicate 1


title: liver, TCPOBOP + CLP, replicate 1

description:
Library name: sample 9
TCPOBOP_CLP-1

value: TCPOBOP


title: GFP::rde-1, dcr-1 RNAi, IP, rep2

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

country: USA

institute: Colorado State University

description:
Library name: Lib657
RNA from Argonaute-RNA-co-IP

data_processing:
End-to-end data processing was done using the default configuration in the tinyRNA pipeline v1.5.0 (https://github.com/MontgomeryLab/tinyRNA).
Assembly: WS279
Supplementary files format and content: GFP-RDE-1_coIP_dcr-1_RNAi_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown for 50 or 54 hours (L4) or 68 or 72 hours (adults) from synchronized L1 larvae at 20˚C on media containing E. coli (OP50 or HT115).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. Total RNA from cell lysates or Argonaute co-immunoprecipitates was isolated using trizol/chloroform and isopropanol precipitation.
Small RNA libraries were prepared according to the NEBNext Multiplex Small RNA kit or QIAseq miRNA Library Kit protocol, omitting the initial size selection step. PCR products corresponding to 16-30 nt small RNAs were size selected using 10% polyacrylamide gels.

value: rde-4(cmp320[rde-4::2xFLAG]) III; rde-1(cmp133[(gfp + loxP + 3xFLAG)::rde-1) V


title: GFP::rde-1, dcr-1 RNAi, IP, rep3

description:
Library name: Lib658
RNA from Argonaute-RNA-co-IP

value: gravid hermaphroditic adult whole animals


title: ChIP_seq_Vector_Olap


title: wildtype replicate 2, sample 15

description: Library name: E.coli K12 strain U4 replicate 2


title: liver, CTRL + SHAM, replicate 3

description:
Library name: sample 7
CTRL_SHAM-3


title: GFP::rde-1, dcr-1 RNAi, IP, rep1

description:
Library name: Lib656
RNA from Argonaute-RNA-co-IP


title: liver, CTRL + SHAM, replicate 2

description:
Library name: sample 6
CTRL_SHAM-2


title: RNA_Seq_FoxO1_SUM159_shFoxO1_Olap_REP2

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0)
Cufflinks (v2.2.1) was used to calculate the expression of RefSeq annotated genes
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values for each Sample

growth_protocol: OC316, HCC1937, HEY, DU145 cells were cultured in  RPMI1640 medium supplemented with 10% FBS; CAPAN2 cells were cultured in DMEM medium supplemented with 10% FBS; SUM159 cells were cultured in Ham’s F12 medium supplemented with 10% FBS, 5 mg/mL insulin and 1 mg/mL hydrocortisone in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were lyzed by trizol.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd  Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of NEBNext rRNA Depletion Kit (NEB E6310). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (NEB, E7760), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-Ten at Amogene (Xiamen, China) Biotech Co., Ltd following the vendor's recommended protocol.


title: liver, TCPOBOP + SHAM, replicate 1

description:
Library name: sample 13
TCPOBOP_SHAM-1


title: wildtype replicate 1, sample 10

description: Library name: E.coli K12 strain U4 replicate 1


title: GFP::rde-1,  L4440 RNAi, IP, rep3

description:
Library name: Lib655
RNA from Argonaute-RNA-co-IP


title: liver, CTRL + SHAM, replicate 1

description:
Library name: sample 5
CTRL_SHAM-1


title: RNA_Seq_FoxO1_SUM159_Con_Olap_REP2

value: shCon


title: RNA_Seq_FoxO1_SUM159_shFoxO1_Olap_REP1


title: GFP::rde-1,  L4440 RNAi, IP, rep1

description:
Library name: Lib653
RNA from Argonaute-RNA-co-IP


title: liver, CTRL + CLP, replicate 4

description:
Library name: sample 4
CTRL_CLP-4


title: GFP::rde-1,  L4440 RNAi, IP, rep2

description:
Library name: Lib654
RNA from Argonaute-RNA-co-IP


title: liver, CTRL + CLP, replicate 3

description:
Library name: sample 3
CTRL_CLP-3


title: RNA_Seq_FoxO1_SUM159_shFoxO1_DMSO_REP2


title: RNA_Seq_FoxO1_SUM159_Con_Olap_REP1


title: LP7 T cells cultured after 4 weeks cryopreservation

city: Baltimore

first: Isha

last: Gurumurthy

state: MD

address: 1650 Orleans Street, CRB1, 4M

department: Oncology

institute: Johns Hopkins University

description: Library name: LP7_4

data_processing:
MiXCR to align and trim CDR3 regions
Assembly: hg38
Supplementary files format and content: .txt files contain TCR Vbeta sequences and related information
Library strategy: TCR-Seq

source_name: Peripheral blood T cells

growth_protocol: T cells cultured for 10 days with relevant peptide or no peptide

extract_protocol:
Qiagen DNeasy Blood and Tissue Kit
AmpliSEQ for Illumina TCRb Short Read Assay

treatment_protocol: T cell-depleted PBMC from two donors (LP6 and LP7; Table 1) were loaded with a CEF peptide pool spanning MHC class I and class II epitopes in 5 replicate wells (except for the 1 week timepoint for the LP7 CD8 assay, which only had enough cells cryobanked for triplicate conditions), an HIV negative control peptide pool, or no peptide, and were cultured with either CD4+ or CD8+ T cells for 10 days. This assay was performed using fresh T cells (never cryopreserved), or those that had been cryobanked for 1, 2, or 4 weeks (Fig. 2). After 10 days of culture and bulk TCR sequencing, we compared the clonal overlap at each timepoint for the CEF-stimulated CD4+ and CD8+ T cell assays separately.

value: Peripheral blood T cells

value: Primary T cells

value: T cells

value: Cultured for 10 days


title: RNA_Seq_FoxO1_SUM159_shFoxO1_DMSO_REP1

value: breast cancer


title: GFP::rde-1, dcr-1 RNAi, input, rep3

description:
Library name: Lib652
RNA from cell lysate


title: LP7 T cells cultured after 2 weeks cryopreservation

description: Library name: LP7_2


title: liver, CTRL + CLP, replicate 1

description:
Library name: sample 1
CTRL_CLP-1

value: CLP


title: LP7 T cells cultured after 1 week cryopreservation

description: Library name: LP7_1


title: GFP::rde-1, dcr-1 RNAi, input, rep2

description:
Library name: Lib651
RNA from cell lysate


title: liver, CTRL + CLP, replicate 2

description:
Library name: sample 2
CTRL_CLP-2


title: GFP::rde-1, dcr-1 RNAi, input, rep1

description:
Library name: Lib650
RNA from cell lysate


title: RNA_Seq_FoxO1_SUM159_Con_DMSO_REP2


title: LP6 T cells cultured after 4 weeks cryopreservation

description: Library name: LP6_4


title: RNA_Seq_FoxO1_SUM159_Con_DMSO_REP1


title: GFP::rde-1, L4440 RNAi, input, rep3

description:
Library name: Lib649
RNA from cell lysate


title: LP7 T cells cultured fresh

description: Library name: LP7_0


title: GFP::rde-1, L4440 RNAi, input, rep2

description:
Library name: Lib648
RNA from cell lysate


title: A. caldus p-sscRAc-Flag, engineered strain, SscRAc (ChIP)

city: Wuxi

first: Xingyu

last: Huo

state: Jiangsu

address: No. 1800, Lihu Avenue

institute: Jiangnan University

description: Library name: SscR_ip

data_processing:
Basecalls were performed using fastp (version 0.23.1) for Novaseq output.
Remove adapter contamination by trimming adapter sequences from read ends and discarding reads shorter than 18 bp; Filter low-quality reads by removing those with >20% of bases having a Phred quality score <Q20; Exclude reads containing >5 ambiguous bases (N).
ChIP-seq reads were aligned to the Acidithiobacillus caldus ATCC51756 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS2 with the significance cut-off q-value <=0.01
Assembly: Acidithiobacillus caldus ATCC 51756
Supplementary files format and content: bigWig

organism: Acidithiobacillus caldus

source_name: Chemolithoautotrophic prokaryotic cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bio Scientific. 10 ng of DNA was used as starting material for input and ip samples.  Libraries were amplified using 13 cycles on the thermocycler.  Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.  Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Chemolithoautotrophic prokaryotic cells

value: ::p-sscRAc-Flag


title: ADAR1p110 KD, +MDA5

city: STANFORD

first: Jin

middle: Billy

state: CA

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford University

description:
ADAR1p110 kd with MDA5
s110MUT

data_processing:
Raw sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore 0.6.4
Preprocessed reads were then mapped to the reference genome (hg38) using STAR v2.5.2a with default parameters for paired-end mapping.
We then extracted reads mapped to the transcriptome from the STAR genome mapping data based on transcripts defined by GENCODE Release 34 and then used RSEM v1.3.2 to quantify the expression level of each transcripts.
Genome_build: hg38
Supplementary_files_format_and_content: Expression data of transcripts is provided in tsv file format for each sample. Expression level is estimated using reads counts (4th column) and TPM (5th column).

extract_protocol:
Approximately 2-5 million HEK293T wild type or mutant cells were collected and the RNA was extracted using the Zymo RNA miniprep kit following the manufacture’s manual. Genomic DNA was removed by on-column digestion of DNase I. Human embryonic stem cells (hESCs) and the differentiated neural progenitor cells (NPCs) were collected and the RNA was extracted using the Trizol method. Briefly, the cells were resuspended in 500ul-1000ul Trizol and incubated at room temperature for 5 minutes and debris was removed after centrifugation. 0.2 volume of chloroform was added to the supernatant. Aqueous phase was collected after centrifugation at 4C and mixed with 1 volume of isopropanol at -20C for more than 30 minutes. RNA was precipitated at 13,000 rpm 4C. 1-2ug RNA was used for cDNA synthesis using the iScript Advanced kit (Bio-Rad) following the manual.
rRNA was depleted from total RNA using RNase H-based protocols adopted from (Adiconis et al., 2013; Morlan et al., 2012). In brief, approximately 100-1000 ng of RNA was annealed with pooled rRNA antisense DNA oligo (gift from J. Salzman lab at Stanford) by heating at 94°C  and slowly cooling down to 45°C. Hybridase Thermostable RNase H (Epicenter, Madison, WI: Lucigen H39500) was added to the mix and incubated at 45°C on a thermocycler for 30 minutes to remove rRNA. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads (Beckman Coulter: A63987). Excessive DNA oligo was removed by treatment of TURBO DNase (Invitrogen: AM1907). The RNA was then purified with RNAClean XP beads again and was used as RNAseq library prep input using the KAPA HyperPrep RNA-seq Kit (Kapa Biosystems: KK8540).

value: HEK293T cell line

value: ADAR1p110 KD, +MDA5


title: LP6 T cells cultured after 2 weeks cryopreservation

description: Library name: LP6_2


title: GFP::rde-1, L4440 RNAi, input, rep1

description:
Library name: Lib647
RNA from cell lysate


title: LP6 T cells cultured after 1 week cryopreservation

description: Library name: LP6_1


title: LP6 T cells cultured fresh

description: Library name: LP6_0


title: WT_Nuclear

description:
WT nuclear RNA
WTNUC

molecule: nuclear RNA

value: WT


title: Sema4d-shRNA-tumor-2

city: Hefei

first: Jinguo

last: Zhang

state: Anhui Province

address: No. 17 Lujiang Road Luyang District Hefei Anhui Province

institute: University of Science and Technology of China

description: Library name: SH-2

library_source: transcriptomic single cell

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software ). Briefly, all samples were performed sample de-multiplexing, barcode processing, and single-cell 3' unique molecular identifier (UMI) counting with default parameters.
Processed reads were then aligned to GRCh38 genome reference using STAR (2.5.1b). Valid cells were automatically identified based on the UMI number distribution of each cell by using the “barcodeRanks()” function of the DropletUtils tool to remove background beads and the beads that had UMI counts less than the threshold value
Finally, we used PISA to calculate the gene expression of cells and create a gene x cell matrix for each library.
Assembly: mm10-1.2.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: transplanted tumor

extract_protocol:
Tissues were cut into approximately 0.5-mm3 pieces in the RPMI-1640 medium (Invitrogen) with 1% Penicillin/Streptomycin, and enzymatically digested with the MACS Tumour Dissociation Kit _mouse (Miltenyi Biotec) at 37 °C for 30 min with agitation, according to the manufacturer’s instructions. The dissociated cells were subsequently passed through a 70-μm and 40-µm cell-strainer (BD) and centrifuged at 300g for 10 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Thermo Fisher) and incubated on ice for 2 min to lyse red blood cells. After washing twice with PBS (Invitrogen), the cell pellets were re-suspended in PBS (containing 0.04%BSA).
DNBelab C Series High-throughput Single-Cell RNA Library Preparation Set (MGI, #940-001818-00 was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 300-500 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the DNBSEQ-T7 sequencing platform with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index

value: transplanted tumor

value: tumor cell


title: WT_Cytosolic

description:
WT cytoplasmic RNA
WTCYTO

molecule: cytoplasmic RNA


title: Sema4d-shRNA-tumor-1

description: Library name: SH-1


title: KJCXn4, xylose plus xylan, biol rep 1

city: Golden

first: Katherine

middle: J

last: Chou

address: 15013 Denver West Parkway

department: Biosciences Center

institute: NREL

data_processing:
Sequences were aligned to the reference genome (GCF_000184925.1_ASM18492v1_genomic) using bwa-mem2
samtools was used to fixmate, sort and index the bam files
The Rsubread package was used to count reads per feature based off the GCF_000184925.1_ASM18492v1_genomic.gtf
Assembly: GCF_000184925.1_ASM18492v1
Supplementary files format and content: bam file with both reads aligned to genome
Supplementary files format and content: .csv file with all read counts of all samples

organism: Acetivibrio thermocellus DSM 1313

growth_protocol: The seeding culture was a fresh overnight culture also grown in defined media to minimize yeast extract carryover, and the culture was at its late log phase at inoculation. No sodium bicarbonate was added in any of the tubes.

extract_protocol:
All cultures were harvested for total RNA purification at the mid-log phase (e.g., OD600 between 0.45 – 0.50).  To harvest the cells for total RNA purification, it was first chilled by swirling the anaerobic culture in dry ice/70% ethanol for 45 seconds and kept on ice for 5 minutes. The inactivated cells (1 – 1.5 mL) were then pelleted by centrifugation. The supernatant was discarded, and the cell pellets were lysed with lysozyme-EDTA using a Qiagen RNeasy Mini kit (Cat No./ID: 74104) following the manufacturer’s protocol. Each sample was treated with DNaseI (Qiagen, Cat No./ID: 79254) twice following the protocol to remove the genomic DNA in the total RNA completely.
Performed by commercial service through Genewiz

value: xylose plus xylan


title: WTMDA5

description:
WT with MDA5
WTMDA5

value: WT, +MDA5


title: NC-tumor-1

description: Library name: NC-1

value: control


title: KJCXn4, xylose plus xylan, biol rep 2


title: KJCXn4, xylose plus xylan, biol rep 3


title: NC-tumor-2

description: Library name: NC-2


title: RICWT

description:
WT with MDA5
RICWT


title: SAMPLE 10_Healthy

city: OTTAWA

first: Shirley

middle: H

last: Mei

state: ON

address: 501 Smythe Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Data analysis was performed using GeneGlobe (Qiagen), setting CT (cycle threshold) cut-off at 35.
The normalization was performed using automatic selection, software algorithm selection of optimum reference set of gene in the array panel.
Matrix Non-Normalized txt (Raw non-normalized data)

source_name: Healthy

label_protocol: RT² First Strand Kit (Qiagen)

growth_protocol: Human bone marrow derived MSC were cultured, characterized, and cryopreserved.Cryopreserved MSCs were thawed and plated overnight in the Nutristem complete media (Sartorius)

extract_protocol: Total RNA was extracted from cells using miRNeasy Mini Kit (Qiagen)

treatment_protocol: After 24hr co-culture with sepsis whole blood, MSCs were washed twice with PBS and dissociated using TrypLE select,  (Gibco), another two washes with PBS (Gibco), Human FC block added. After sorting (CD90-PE  and CD45-FITC), a portion of cells were pelleted.

value: Human bone marrow derived MSC

tag: sample group

value: Healthy


title: 150KO_MDA5

description:
ADAR1p150 ko with MDA5
RIC15


title: KJCXn4, xylose, biol rep 3

value: xylose


title: KJCXn4, xylose, biol rep 1


title: NPCWT29

description:
WT NPC day29
NPCWT29

source_name: Neural Progenitor Cell

value: Neural Progenitor Cell

tag: developmental stage

value: day 29


title: SAMPLE 9_Sepsis

source_name: Sepsis

value: Sepsis


title: SAMPLE 12_Healthy


title: KJCXn4, xylose, biol rep 2


title: SAMPLE 6_Sepsis


title: Lpr3

city: Hohhot

first: yong

last: jin

address: 1 North Passage Road, Hohhot, Inner Mongolia, China

institute: Inner Mongolia Medical University

description: Library name: SAMPLES 10

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
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 file includes FPKM values for each Sample

source_name: Kidney

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).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Kidney

value: MRL/lpr


title: SAMPLE 11_Healthy


title: Lpr4

description: Library name: SAMPLES 11


title: SAMPLE 8_Sepsis


title: Lpr2

description: Library name: SAMPLES 9


title: SAMPLE 5_Sepsis


title: KJC19-9, xylose, biol rep 3


title: NPCKO29

description:
ADAR1 KO NPC day29
NPCKO29


title: KJC19-9, xylose, biol rep 2


title: NPCKO15

description:
ADAR1 KO NPC day15
NPCKO15

value: day 15


title: Lpr1

description: Library name: SAMPLES 8


title: SAMPLE 4_CTRL

source_name: CTRL

value: CTRL


title: Dnase_3

description: Library name: SAMPLES 6

value: DNase I treatment


title: KJC19-9, xylose, biol rep 1


title: SAMPLE 3_CTRL


title: NPC110

description:
ADAR1KO_NPC with p110
NPC110


title: NPC150

description:
ADAR1KO_NPC with p110
NPC150


title: Dnase_2

description: Library name: SAMPLES 5


title: KJC335, cellobiose, biol rep 3

value: cellobiose


title: Dnase_1

description: Library name: SAMPLES 4


title: KJC335, cellobiose, biol rep 1


title: KJC335, cellobiose, biol rep 2


title: SAMPLE 1_CTRL


title: DI_ADAR150_MDA5

description:
di with p150 with MDA5
DI150

value: HEK293T cell line


title: SAMPLE 2_CTRL


title: shcyp2e1-2

city: Shenyang

first: LIN

last: QIN

address: PuHe Road 77

institute: China Medical University

data_processing:
Cutadapt V1.9.1
Assembly: GRCh38
Supplementary files format and content: counts and FPKM for each sample

source_name: primary human neural progenitor cells

extract_protocol:
The total RNA of each sample was extracted from the lentivirus infected, early differentiated HNPs with CYP2E1-shRNAs (n=3) or CYP2E1-shRNA (n=3) by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: primary human neural progenitor cells


title: DI_cytoADAR2_iMDA5

description:
DI with cytoADAR2 with inducible MDA5
IM5AD2CT

value: ADAR1 E912A/E912A/E912A, +MDA5, +ADAR2-NLS


title: shcyp2e1-3


title: KJC335, xylose, biol rep 3


title: Ctr2

description: Library name: SAMPLES 2


title: shcyp2e1-1


title: KJC335, xylose, biol rep 2


title: A. caldus WT, wild type strain (Input)

description: Library name: SscR_input

value: Chemolithoautotrophic prokaryotic cells

value: Wild type (CCTCC M 2018727) strain


title: DI_ADAR110_MDA5

description:
di with p110 with MDA5
DI110


title: Dnase_4

description: Library name: SAMPLES 7


title: shs-3

value: shs


title: ADAR2KO_MDA5

description:
ADAR2 KO with MDA5
AD2MUT

value: ADAR2-/-, +MDA5


title: shs-2


title: DI_ADAR2_iMDA5

description:
DI with ADAR2 with inducible MDA5
AD2MDA5


title: KJC335, xylose, biol rep 1

value: xylose


title: Hikeshi Cko

city: shanghai

first: Debao

last: Wu

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

description: Library name: Sample2

data_processing:
A total of 2 samples were tested using the DNBSEQ platform, with an average yield of 6.62G data per sample. The average alignment ratio of the sample comparison genome was 98.87%, which was comparative The average alignment of the gene set was 85.59%; a total of 15953 genes were detected.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

source_name: neural stem cell

extract_protocol:
Total RNA fraction was extracted using EastepSuper Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neural stem cell

value: Suspension culture


title: shs-1


title: ADAR1KO_MDA5

description:
ADAR1 KO with MDA5
AD1MUT


title: Opto-BMP4 edge

city: New York

first: Riccardo

last: De Santis

address: 1230 York Ave

institute: The Rockefeller univeristy

data_processing:
Demultiplexing followed allignment using CellRanger
Assembly: h38
Supplementary files format and content: Cell ranger output

source_name: Differentiated hESCs

growth_protocol: hESCs were maintained in pluripotency condition and the induced to differentiate upon BMP4-light induction

extract_protocol:
10X genomics GEM fomation according to manufacture's instruction
10X genomics 3 prime v3
polyA UMI

treatment_protocol: DOX treatment confers light sentitivity to hESCs which respond to light inducing LoxP recombination

value: Differentiated hESCs

tag: group

value: edge

value: Germ layers

value: Female XX

value: Light-induction


title: Opto-BMP4 center

value: center


title: Wild type

description: Library name: Sample1


title: Nicalin, IP, rep2

status: Public on Aug 30 2025

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

description: Library name: Sample 18

data_processing:
RNase footprinting reads were trimmed to remove the first 7 nucleotides and A-tail adaptor sequence using Cutadapt v4.1. Trimmed reads were aligned to ribosome RNA sequences (downloaded from Ensembl) using Bowtie v2.2.6, and matched reads were discarded. The remaining reads were then mapped to the human hg38 genome and transcriptome using TopHat v2.1.0, with transcriptome annotations based on RefSeq. Uniquely mapped reads were selected for calculating ribosome occupancy.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Ribo-Seq

source_name: Flp-In T-REx 293

growth_protocol: Flp-In T-REx 293 cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 0.1 mg/mL streptomycin mixture at 37 °C and 5% CO2.

extract_protocol:
Cells were lysed, and microsomes were isolated. After treatmnet with 10,000 U micrococcal nuclease for 30 min at 37 °C, microsomes were pelleted and solubilized. The cleared supernatant was used as input, after M2 Flag affinity beads binding, immunoprecipitated material was used as IP. To prepare RNase footprints, input and IP samples were digested with RNase 1 at 0.5 - 1 U/µl within a 90 µl reaction at RT for 1.5 h. RNase footprints were extracted by adding 400 µl TRIzol followed by 100 µl of chloroform. RNA in the aqueous layer was separated by centrifugation at 12000 g for 15 min at 4 ℃ and then precipitated overnight by adding 0.1 volume of 3 M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
Purified RNase footprints were used for library preparation. RNase footprints were resuspended in 5 µl TNK reaction mixture (1x PNK buffer, 10 U PNK (NEB), and 10 U SUPERase·In) and end-repaired at 37 ℃ for 1 h. The reaction was added with 5 µl of polyadenylation mix containing 10 U E. coli poly (A) polymerase (NEB), 2 µl of 5x first-strand buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2), 0.25 mM ATP, and 10 U SUPERase·In and incubated at 37 ℃ for 2 h. The resulting polyadenylated RNA was then reverse transcribed by a SMAT-RT reaction. The reaction mixture was first added with 2.5 µl of RT primer (10 µM, 5’-ACGTGTGCTCTTCCGATCTNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTVN-3’, where “N” is any base and “V” is either “A”, “C” or “G”) and annealed by heating to 72 °C for 5 min and cooled on ice, and then supplemented with SMAT-RT mixture (2.5 µl dNTP (10 mM), 400 U Superscript II reverse transcriptase (Invitrogen), 10 U SUPERase·In, 4 µl Superscript II first-strand buffer (5x), 1.5 µl DTT (100 mM), 6 µl Betaine (5 mM), 0.12 µl MgCl2 (1 M), 0.5 µl template-switching oligos (100 µM 5’-CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNrGrG+G-3’, where “N” is any base and “+G'' is a locked nucleic acid guanylate), and 0.5 µl nuclease-free water. Reverse transcription was carried out with incubation at 42 ℃ for 1 h, followed by 10 cycles of heating at 50 °C for 2 min and then incubating at 42 ℃ for 2 min. The reverse transcriptase was inactivated by heating at 70 ℃ for 10 min. RNA footprints hybridized to DNA were removed by incubating at 37 ℃ for 15 min with 5 U of RNase H. The resultant cDNA was then amplified by a first round of PCR with 7 cycles. Purified PCR1 products were amplified by a second round of PCR with 4 cycles. The DNA library was visualized and separated in a 4% agarose gel. DNA with 15-35 bp-insert was excised and recovered using a DNA gel recovery kit (Zymo). Equal amounts of barcoded libraries were pooled and then sequenced with Illumina NovoSeq.

treatment_protocol: Cells were seeded in ten 15-cm dishes, induced with 0.5-1.0 ng/mL doxycycline and harvested after 72 hours (~80% confluency) with ice-cold PBS containing 0.1 mg/mL CHX.

value: Flp-In T-REx 293

value: Embryonic kidney

value: Nicalin knockout, doxycycline-inducible 3Flag-Nicalin expressing

value: IP

tag: batch

value: replicate 2


title: Ctr3

description: Library name: SAMPLES 3

value: Kidney


title: Nicalin, IP, rep1

description: Library name: Sample 16

value: replicate 1


title: Nicalin, Input, rep2

description: Library name: Sample 17

value: Input


title: Nicalin, Input, rep1

description: Library name: Sample 15


title: CCDC47, Input, rep2

description: Library name: Sample 13

value: CCDC47 knockout, doxycycline-inducible 3Flag-CCDC47 expressing


title: CCDC47, IP, rep2

description: Library name: Sample 14


title: CCDC47, Input, rep1

description: Library name: Sample 11


title: TMCO1, IP, rep2

description: Library name: Sample 10

value: TMCO1 knockout, doxycycline-inducible 3Flag-TMCO1 expressing


title: CCDC47, IP, rep1

description: Library name: Sample 12


title: TMCO1, Input, rep2

description: Library name: Sample 9


title: RPN2, Input, rep1

description: Library name: Sample 5

value: 3Flag-RPN2 expressing


title: SAMPLE 7_Sepsis

value: Human bone marrow derived MSC

value: Sepsis


title: TMCO1, IP, rep1

description: Library name: Sample 8


title: OST48, IP, rep2

description: Library name: Sample 4

value: 3Flag-OST48 expressing


title: RPN2, IP, rep1

description: Library name: Sample 6


title: Ctr1

description: Library name: SAMPLES 1


title: TMCO1, Input, rep1

description: Library name: Sample 7


title: OST48, IP, rep1

description: Library name: Sample 2


title: OST48, Input, rep2

description: Library name: Sample 3


title: Tumour, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep3

city: Edinburgh

first: Alan

last: Serrels

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

description: Library name: CDKNZA_Smad4_NM

data_processing:
Data was processed using nf-core/rnaseq v3.15.1 (doi: https://doi.org/10.5281/zenodo.13769441) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
Assembly: Ensembl/GRCm38
Supplementary files format and content: A tab-separated text file with counts per Ensembl transcript (salmon quant format)
Supplementary files format and content: A tab-separated table of gene-level counts, for all samples, that have been corrected for effective gene length, generated by the tximport package from Salmon quantification files.

source_name: blood

growth_protocol: Tumours were established by intrapancreatic injection of 1x10e5 cells into the pancreas of a C57BL/6 mouse. Mice were euthanised 3 weeks post injection and pancreatic tumours removed into RNA later.

extract_protocol:
RNA was purified using a Qiagen RNEasy Mini kit, including DNAse digestion, as per the manufacturers protocol.
Libraries were prepared from total-RNA samples using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760) and rRNA Depletion according to the provided protocol.

value: blood

value: KrasG12D p53-/- Cdkn2a-/- Smad4-/-

value: Injection of tumour cells into the pancreas


title: medullart thymic epithelial cell, Aebp2-ko, replicate3, bulk RNAseq

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

institute: Westlake Laboratory of Life Sciences and Biomedicine

description: Library name: KO3 mTEC

data_processing:
For bulkRNAseq, raw reads were mapped to the Mus musculus (mm10) reference genome using HISAT2. HISAT was run in a 2-pass approach with options “--score-min L,0.0,-0.2” and known splice sites for the first pass, and novel splice sites detected across all samples for the second pass. Gene-level count data was obtained using featureCounts program (http://bioinf.wehi.edu.au/featureCounts/). For scRNAseq and scATACseq, barcode processing and mapping to the mouse genome was performed with Cell Ranger v3.0. For Cut&tag, all peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: Mouse mm10
Supplementary files format and content: Excel file, matrix files and bigwig files

molecule: polyA RNA

source_name: thymus

extract_protocol:
Thymi were isolated and cleaned to get rid of the residual fat and connective tissue, followed by a serial steps of enzymatic digestion with 0.15% mg/ml Liberase TM in RPMI 1640 at 37 °C. For adult thymi, CD45- cells were enriched with anti-CD45 beads and MACS LS columns (Miltenyi) followed by FACS sorting to harvest living CD45-Ter119-EpCAM+ thymic epithelial cells. The enriched total TECs or mTEChi (UEA1+MHCIIhi) were subjected to scRNA-seq, scATAC-seq, Cut&Tag, bulk RNA-seq.
Liraries for scRNAseq, scATACseq, Cut&tag, and bulkRNAseq were prepared following the manufactures' instructions described in the paper's method section.

value: thymus

value: thymic epithelial cell

value: medullary thymic epithelial cell

value: Aebp2-knock out

value: knock out


title: OST48, Input, rep1

description: Library name: Sample 1

value: Flp-In T-REx 293

value: Embryonic kidney


title: Tumour, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep2

description: Library name: CDKNZA_Smad4_M4


title: Tumour, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep1

description: Library name: CDKNZA_Smad4_M1


title: cortical thymic epithelial cell, Aebp2-knockout, replicate3, bulk RNAseq

description: Library name: KO3 cTEC

value: cortical thymic epithelial cell

value: Aebp2-wild type

value: wild type


title: Tumour, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep3

description: Library name: Smad_4_NM

value: KrasG12D p53-/- Smad4-/-


title: medullart thymic epithelial cell, Aebp2-ko, replicate2, bulk RNAseq

description: Library name: KO2 mTEC


title: Tumour, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep2

description: Library name: Smad_4_M4


title: cortical thymic epithelial cell, Aebp2-knockout, replicate2, bulk RNAseq

description: Library name: KO2 cTEC


title: medullart thymic epithelial cell, Aebp2-ko, replicate1, bulk RNAseq

description: Library name: KO1 mTEC


title: cortical thymic epithelial cell, Aebp2-knockout, replicate1, bulk RNAseq

description: Library name: KO1 cTEC


title: Tumour, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep1

description: Library name: Smad_4_M1


title: medullart thymic epithelial cell, Aebp2-wild type, replicate3 bulk RNAseq

description: Library name: WT3 mTEC


title: Tumour, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep2

description: Library name: CDKNZA_M3

value: KrasG12D p53-/- Cdkn2a-/-


title: Tumour, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep1

description: Library name: CDKNZA_M1


title: cortical thymic epithelial cell, Aebp2-wild type, replicate3, bulk RNAseq

description: Library name: WT3 cTEC


title: Tumour, KrasG12Dp53-/- tumour bearing mouse, rep3

description: Library name: Pac5_M10

value: KrasG12D p53-/-


title: Tumour, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep3

description: Library name: CDKNZA_NM


title: cortical thymic epithelial cell, Aebp2-wild type, replicate2, bulk RNAseq

description: Library name: WT2 cTEC


title: cortical thymic epithelial cell, Aebp2-wild type, replicate1, bulk RNAseq

description: Library name: WT1 cTEC


title: medullart thymic epithelial cell, Aebp2-wild type, replicate1, bulk RNAseq

description: Library name: WT1 mTEC


title: Tumour, KrasG12Dp53-/- tumour bearing mouse, rep1

description: Library name: Pac5_M1


title: Tumour, KrasG12Dp53-/- tumour bearing mouse, rep2

description: Library name: Pac5_M4


title: human H1, GM12878 and mouse ESC, RNA, batch2, rep2

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

department: Cell Biology

institute: Duke University

data_processing:
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. The final DNA reads were mapped to genome by bwa mem with options -SP. Alignments were parsed, and paired end tags were generated using the pairtools with options --min-mapq 10.
For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence). The final fastq files were processed by STAR with parameter "--soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --soloUMIlen 12 -soloStrand Forward". The R package Seurat were used to the downstream analysis: (1) genes which expressed in less than three cells were removed. (2) Cells with unique feature counts over 2500, under 200, molecule count over 5000, and greater than 25% mitochondrial RNA counts were filtered.
Assembly: mm10 and hg38
Supplementary files format and content: STARsolo output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz
Supplementary files format and content: .pairsam.gz: list of all contact pairs in that library

organism:
Homo sapiens
Mus musculus

source_name: human H1, GM12878, mouse ESC

growth_protocol: H1 hESCs (WiCell, WA01) were cultured in Matrigel (Corning, 354230) coated plates with mTeSR Plus medium (STEMCELL Technologies, #05825). mTeSR Plus was refreshed every other day. GM12878 cells were cultured in suspension in T-75 flasks using RPMI 1640 supplemented with 15% FBS (200,000 to 800,000 cells/ml).

extract_protocol:
Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.
sciHiCAR

value: human H1, GM12878, mouse ESC


title: human H1, GM12878 and mouse ESC, RNA, batch2, rep1


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep32

description:
cellline_schicar_H1_DNA.pairsam.gz
cellline_schicar_GM_DNA.pairsam.gz


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep31


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep29


title: Ketogenic Diet,Biopsy,KETO17

first: Ezequiel

middle: Carlos

last: Dantas

state: New York

address: 435 E 30th St

department: Medicine

institute: NYU Langone

description: Library name: KETO17_Biopsy

data_processing:
Reads from paired-end FASTQ files were aligned to the human reference genome GRCh37 (hg19) using STAR-Fusion, and quality controlled using FastQC.
Raw counts for each gene were generated using HTSeq with gencode v19 annotation.
RNA-Seq analysis was done in R Studio R Studio (2023-10-31), with R (4.3.2) and DESeq2 (v.1.42.1)
Gene set enrichment analysis (GSEA), was performed with the JAVA desktop application v4.3.2.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tsv text file includes raw counts for each sample

source_name: Endometrial Cancer

extract_protocol:
RNA was extracted from the biopsies and tumor resections using the Maxwell RSC simplyRNA Tissue Kit according to the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Tumor RNA samples were selected for library preparation based on the RNA Integrity Number (RIN).
Libraries were prepared using either TruSeq Stranded mRNA Sample Library Preparation Kit (PolyA method) or Illumina Stranded Total RNA Prep with Ribo-Zero Plus (rRNA depletion method) (Illumina, San Diego, CA, USA).

treatment_protocol: Patients with endometrial cancer were randomized in a 2:1 fashion to receive a VLCD or continue their standard diet during a four-week pre-surgical period between diagnosis and surgical staging.

value: Endometrial Cancer

value: Ketogenic Diet


title: Standard Diet,Resection,KETO19

description: Library name: KETO19_Resection

value: Standard Diet


title: Ketogenic Diet,Resection,KETO17

description: Library name: KETO17_Resection


title: Standard Diet,Biopsy,KETO19

description: Library name: KETO19_Biopsy


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep28


title: Standard Diet,Resection,KETO16

description: Library name: KETO16_Resection


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep27


title: Ketogenic Diet,Resection,KETO15

description: Library name: KETO15_Resection


title: Ketogenic Diet,Biopsy,KETO15

description: Library name: KETO15_Biopsy


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep26


title: medullart thymic epithelial cell, Aebp2-wild type, replicate2, bulk RNAseq

description: Library name: WT2 mTEC

value: thymus


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep25


title: Standard Diet,Resection,KETO8

description: Library name: KETO8_Resection


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep23


title: Ketogenic Diet,Resection,KETO5

description: Library name: KETO5_Resection


title: Standard Diet,Biopsy,KETO16

description: Library name: KETO16_Biopsy


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep24


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep22


title: Ketogenic Diet,Biopsy,KETO5

description: Library name: KETO5_Biopsy


title: Standard Diet,Biopsy,KETO8

description: Library name: KETO8_Biopsy


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep19


title: Ketogenic Diet,Resection,KETO12

description: Library name: KETO12_Resection


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep21


title: Ketogenic Diet,Resection,KETO6

description: Library name: KETO6_Resection


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep30


title: Ketogenic Diet,Biopsy,KETO12

description: Library name: KETO12_Biopsy


title: Ketogenic Diet,Biopsy,KETO6

description: Library name: KETO6_Biopsy


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep17


title: OE-VAMP8-SiHa-Rp3

first: dan

last: wu

address: shengyang road

institute: Obstetrics and Gynecology Hospital of Fudan University

description:
Library name: OE-VAMP8-SiHa-Rp3
Column name in raw_counts_All_samples.xls:SiHa8OE-3

data_processing:
The cleaned reads were aligned to the human reference genome (GRCh38) using HISAT2 (version 2.1.0), and gene-level expression counts were generated using featureCounts from the Subread package (version 1.6.0)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv file include FPKM values for each Sample

source_name: human cervical epithelial cell line

growth_protocol: All cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from Ect1/E6E7 and SiHa cells overexpressing VAMP8, as well as from their control counterparts, using TRIzol reagent (Ambion, USA) per the manufacturer’s protocol
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit (Illumina, USA) and sequenced on an Illumina HiSeq 2500 platform, generating 150 bp paired-end reads.

value: human cervical epithelial cell line

value: Siha

value: Human cervical epithelial cancer cell line

value: VAMP8 overexpression


title: OE-VAMP8-SiHa-Rp2

description:
Library name: OE-VAMP8-SiHa-Rp2
Column name in raw_counts_All_samples.xls:SiHa8OE-2


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep14


title: OE-VAMP8-SiHa-Rp1

description:
Library name: OE-VAMP8-SiHa-Rp1
Column name in raw_counts_All_samples.xls:SiHa8OE-1


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep13


title: OE-NC-SiHa-Rp3

description:
Library name: OE-NC-SiHa-Rp3
Column name in raw_counts_All_samples.xls:SiHaGFP-3

value: WT


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep12


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep11


title: OE-VAMP8-Ect1/E6E7-Rp2

description:
Library name: OE-VAMP8-Ect1/E6E7-Rp2
Column name in raw_counts_All_samples.xls:Ect8OE-2


title: OE-VAMP8-Ect1/E6E7-Rp3

description:
Library name: OE-VAMP8-Ect1/E6E7-Rp3
Column name in raw_counts_All_samples.xls:Ect8OE-3


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep20


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep9


title: OE-VAMP8-Ect1/E6E7-Rp1

description:
Library name: OE-VAMP8-Ect1/E6E7-Rp1
Column name in raw_counts_All_samples.xls:Ect8OE-1


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep8


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep7


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep10


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep6


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep18


title: OE-NC-Ect1/E6E7-Rp2

description:
Library name: OE-NC-Ect1/E6E7-Rp2
Column name in raw_counts_All_samples.xls:EctGFP2


title: OE-NC-Ect1/E6E7-Rp1

description:
Library name: OE-NC-Ect1/E6E7-Rp1
Column name in raw_counts_All_samples.xls:EctGFP1


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep5


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep15


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep16


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep4


title: OE-NC-SiHa-Rp2

description:
Library name: OE-NC-SiHa-Rp2
Column name in raw_counts_All_samples.xls:SiHaGFP-2


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep2


title: OE-NC-SiHa-Rp1

description:
Library name: OE-NC-SiHa-Rp1
Column name in raw_counts_All_samples.xls:SiHaGFP-1


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep1


title: OE-NC-Ect1/E6E7-Rp3

description:
Library name: OE-NC-Ect1/E6E7-Rp3
Column name in raw_counts_All_samples.xls:EctGFP3


title: LNCaP,OE_FOXA2_INPUT_Res,rep2

city: Bellinzona

first: Jean-Philippe

last: Theurillat

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute of Oncology Research

description: Library name: Sample67

data_processing:
Nextflow nf-core chipseq pipeline version 1.2.2 for ChIP-seq peak-calling, QC and differential analysis.
FASTQ files were first processed to BAM files using BWA software and aligned to reference to Genome assembly GRCh38
Peaks calling was performed using MACS2 software and created corresponding normalised bigWig files scaled to 1 million mapped reads using BEDTools.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Prostate

extract_protocol:
DNA extraction was performed using QIAquick PCR Purification Kit (Qiagen)
NebNext Ultra II DNA library prep with sample purification beads

value: Prostate

value: LNCaP

value: Epithelial

value: FOXA2 overexpression, ARCC4

value: Lentiviral infection, DMSO


title: LNCaP,OE_FOXA2_INPUT_Res,rep1

description: Library name: Sample66


title: LNCaP,OE_FOXA2_FOXA2_Res,rep2

description: Library name: Sample65


title: LNCaP,OE_FOXA2_FOXA2_Res,rep1

description: Library name: Sample64


title: LNCaP,OE_FOXA2_FOXA2,rep2

description: Library name: Sample63

value: FOXA2 overexpression


title: mouse frontal cortex, RNA, biology_rep1

description: Library name: mouse-brain-scHiCAR-RNA-BioRep1

data_processing:
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence).
RNA reads were aligned to the mouse genome (mm10) using STARsolo to generate filtered gene expression matrices. Genes expressed in fewer than 3 cells and cells with fewer than 200 detected genes were removed using Seurat. DNA R1 reads were aligned to the mm10 genome using BWA via Snaptools, and the resulting BAM files were converted to fragment-level BED format. Cells with a TSS enrichment score less than 1 or fewer than 10,000 unique fragments were excluded during the createArrowFiles step in ArchR. Paired-end DNA reads were aligned to the mm10 genome using BWA-MEM with the -SP mode, and mapped reads were parsed into deduplicated contact pairs using pairtools. Contact pairs were further filtered based on the knee point of the barcode rank curve. Finally, only cells with both RNA and DNA barcodes were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: The processed data include RNA expression matrix files (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz), ATAC-seq fragment files (DNA.ATAC.tsv.gz), and deduplicated chromatin contact pair files (DNA.dedup.pairs.gz).
Library strategy: scHiCAR

source_name: frontal cortex

extract_protocol:
The frontal cortex were dissected by tweezer from adult mouse, then were treated by douncer to get the cells. Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For the nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.

value: frontal cortex


title: mouse frontal cortex, DNA, biology_rep2

description: Library name: mouse-brain-scHiCAR-DNA-BioRep2


title: mouse frontal cortex, RNA, biology_rep2

description: Library name: mouse-brain-scHiCAR-RNA-BioRep2


title: mouse frontal cortex, DNA, biology_rep1

description: Library name: mouse-brain-scHiCAR-DNA-BioRep1


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep2, technology_rep2

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-DNA-2

data_processing:
library strategy: scHiCAR
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence).
RNA reads were aligned to the mouse genome (mm10) using STARsolo to generate filtered gene expression matrices. DNA R1 reads were aligned to mm10 using BWA via Snaptools, and the resulting BAM files were converted to fragment-level BED format. Paired-end DNA reads were aligned to mm10 using BWA-MEM with -SP mode, and mapped reads were parsed into deduplicated contact pairs using pairtools. For the RNA matrices, genes expressed in fewer than three cells and cells with fewer than 200 detected genes or lacking corresponding DNA barcodes were removed using Seurat. Filtered RNA barcodes were also used to retain matched cells in the ATAC and contact pair datasets.
Assembly: mm10
Supplementary files format and content: The processed data include RNA expression matrix files (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz), ATAC-seq fragment files (*.ATAC.tsv.gz), and deduplicated chromatin contact pair files (*.dedup.pairs.gz).

source_name: Tibialis Anterior

extract_protocol:
The Tibialis Anterior (TA) muscle were dissected by tweezer from adult mouse, then were treated by douncer to get the cells. Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For the nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.

value: Tibialis Anterior

value: BaCl2 acute muscle injury, day7


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep2, technology_rep1

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-DNA-1


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep2, technology_rep4

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-DNA-4


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-DNA-4


title: LNCaP,OE_FOXA2_FOXA2,rep1

description: Library name: Sample62


title: MRC5/hACE2 cells, R-1 sup-treated_4

city: Hachioji, Tokyo

first: Shuyi

last: Tang

address: 1-29-1 Nanakuni

department: R&D division

country: Japan

institute: Meiji Co., Ltd.

description:
Library name: Sample23
Column name in "Processed_Data_MRC5ACE2.csv.gz": R1_4

data_processing:
Read count data for each sample were obtained using the Illumina DRAGEN RNA version 4.0.4 and DRAGEN Differential Expression version 4.0.3 applications (Illumina).
Assembly: GRCh37
Supplementary files format and content: csv files include CPM for each sample

growth_protocol: MRC5 were maintained in EMEM with 10% FBS and antibiotics at 37 ℃ under 5% CO2-humidified atmosphere. MRC5/hACE2 were maintained in MEM with 10% FBS, antibiotics and 100 µg/mL hygromycin B at 37 ℃ under 5% CO2-humidified atmosphere.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Libraries were generated from purified RNA samples (>7 RIN) using an Illumina Stranded mRNA Prep Ligation kit (Illumina) according to the manufacturer’s protocol.

value: fetal lung, normal diploid fibroblast

value: MRC5 cells stably expressing angiotensin-converting enzyme 2

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #4) for 24 h


title: MRC5/hACE2 cells, R-1 sup-treated_3

description:
Library name: Sample22
Column name in "Processed_Data_MRC5ACE2.csv.gz": R1_3

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #3) for 24 h


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-DNA-2


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep2, technology_rep5

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-DNA-5


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-DNA-5


title: human H1, GM12878 and mouse ESC, DNA, batch1, rep3

description:
cellline_schicar_H1_DNA.pairsam.gz
cellline_schicar_GM_DNA.pairsam.gz

value: human H1, GM12878, mouse ESC


title: MRC5/hACE2 cells, R-1 sup-treated_2

description:
Library name: Sample21
Column name in "Processed_Data_MRC5ACE2.csv.gz": R1_2

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #2) for 24 h


title: Cymbopogon_flexuosus_rep_2

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

description:
Library name: cf_2
RNA-seq of lemongrass leaves

data_processing:
RNA-seq libraries were subjected to SortMeRNA to identify rRNA, followed by quality assessment using FastQC v0.11.2 and cleaning using Trimmomatic v0.32.
The de novo assembly of reference transcriptomes for each species was performed using Trinity and CAP3.
The raw reads from each species were separately mapped to their respective C. flexuosus and C. winterianus reference transcriptomes using Hisat2, Samtools, and HTSeq-count. The edgeR package was then used to convert raw counts into CPM (counts per million) values, retaining only nr-transcripts with CPM ≥ 1.
Assembly: De novo transcriptome assembly for both species.
Supplementary files format and content: fasta files and xlsx spreadsheets

organism: Cymbopogon flexuosus

source_name: Leaves

growth_protocol: Accessions of C. flexuosus (lemongrass) and C. winterianus (citronella) were cultivated in plots at the experimental field of the School of Agronomy “Eliseu Maciel” at the Federal University of Pelotas, located in Capão do Leão, Rio Grande do Sul, Brazil (31° 48′ S, 52° 24′ W, altitude 14 m)

extract_protocol:
Total RNA was extracted using the Plant RNA Reagent PureLink® (Invitrogen™)
TruSeq RNA Sample Preparation® Kit v2, 2 × 100 paired-end (Illumina™)

treatment_protocol: Normal/control conditions

value: Leaves


title: NPCWT15

first: Jin

last: Li

address: 300 Pasteur Dr.

institute: Stanford University

description:
WT NPC day15
NPCWT15

data_processing:
Raw sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore 0.6.4
Preprocessed reads were then mapped to the reference genome (hg38) using STAR v2.5.2a with default parameters for paired-end mapping.
We then extracted reads mapped to the transcriptome from the STAR genome mapping data based on transcripts defined by GENCODE Release 34 and then used RSEM v1.3.2 to quantify the expression level of each transcripts.
Genome_build: hg38
Supplementary_files_format_and_content: Expression data of transcripts is provided in tsv file format for each sample. Expression level is estimated using reads counts (4th column) and TPM (5th column).

source_name: Neural Progenitor Cell

extract_protocol:
Approximately 2-5 million HEK293T wild type or mutant cells were collected and the RNA was extracted using the Zymo RNA miniprep kit following the manufacture’s manual. Genomic DNA was removed by on-column digestion of DNase I. Human embryonic stem cells (hESCs) and the differentiated neural progenitor cells (NPCs) were collected and the RNA was extracted using the Trizol method. Briefly, the cells were resuspended in 500ul-1000ul Trizol and incubated at room temperature for 5 minutes and debris was removed after centrifugation. 0.2 volume of chloroform was added to the supernatant. Aqueous phase was collected after centrifugation at 4C and mixed with 1 volume of isopropanol at -20C for more than 30 minutes. RNA was precipitated at 13,000 rpm 4C. 1-2ug RNA was used for cDNA synthesis using the iScript Advanced kit (Bio-Rad) following the manual.
rRNA was depleted from total RNA using RNase H-based protocols adopted from (Adiconis et al., 2013; Morlan et al., 2012). In brief, approximately 100-1000 ng of RNA was annealed with pooled rRNA antisense DNA oligo (gift from J. Salzman lab at Stanford) by heating at 94°C  and slowly cooling down to 45°C. Hybridase Thermostable RNase H (Epicenter, Madison, WI: Lucigen H39500) was added to the mix and incubated at 45°C on a thermocycler for 30 minutes to remove rRNA. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads (Beckman Coulter: A63987). Excessive DNA oligo was removed by treatment of TURBO DNase (Invitrogen: AM1907). The RNA was then purified with RNAClean XP beads again and was used as RNAseq library prep input using the KAPA HyperPrep RNA-seq Kit (Kapa Biosystems: KK8540).

value: Neural Progenitor Cell

value: day 15

value: WT


title: Cymbopogon_winterianus_rep2

description:
Library name: cw_2
RNA-seq of citronella leaves

organism: Cymbopogon winterianus


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep2, technology_rep3

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-DNA-3


title: Cymbopogon_winterianus_rep1

description:
Library name: cw_1
RNA-seq of citronella leaves


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-DNA-1


title: Cymbopogon_flexuosus_rep_1

description:
Library name: cf_1
RNA-seq of lemongrass leaves


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep2, technology_rep5

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-DNA-5

value: BaCl2 acute muscle injury, day5


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep2, technology_rep4

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-DNA-4


title: D-EB-13

type: genomic

city: Burlington

first: Ashley

middle: Keller

last: Volaric

state: Vermont

address: 111 Colchester Avenue

department: Pathology and Laboratory Medicine

institute: University of Vermont Larner College of Medicine

description:
Excluded due to not passing QC. EBV+ DLBCL
207510040116_R07C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to human Infinium Illumina MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: iScan platform was used for BeadChip scanning.

data_processing: SeSAMe package in R environment (v4.4.1)

source_name: tissue

label_protocol: Standard Illumina protocol

growth_protocol: Not applicable

extract_protocol: Mag-Bind FFPE DNA Kit was used for DNA extraction following the manufacturer's protocol.

treatment_protocol: Tissue was fixed in 10% neutral-buffered formalin and embedded in paraffin tissue blocks. Tissue scrolls (2-3) at 10-15 microns for a total of approximately 30 microns were cut from each tissue block case and submitted for DNA extraction and processing.

tag: Sex

value: tissue


title: D-EB-15

description:
Excluded due to not passing QC. EBV+ DLBCL
207510040116_R08C01


title: D-EB-12

description:
Excluded due to not passing QC. EBV+ DLBCL
207510040116_R06C01


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep2, technology_rep3

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-DNA-3


title: MRC5/hACE2 cells, Control sup-treated_5

description:
Library name: Sample19
Column name in "Processed_Data_MRC5ACE2.csv.gz": Control_5

value: treated with unstimulated PBMCs supernatant (donor #5) for 24 h


title: MRC5/hACE2 cells, R-1 sup-treated_5

description:
Library name: Sample24
Column name in "Processed_Data_MRC5ACE2.csv.gz": R1_5

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #5) for 24 h


title: D-EB-9

description:
EBV+ DLBCL
207510040116_R03C01


title: mouse mucle, BaCl2  injure, day7, DNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-DNA-3


title: MRC5/hACE2 cells, Control sup-treated_3

description:
Library name: Sample17
Column name in "Processed_Data_MRC5ACE2.csv.gz": Control_3

value: treated with unstimulated PBMCs supernatant (donor #3) for 24 h


title: CTEBV-11

description:
Excluded due to not passing QC. EBV+ Polymorphic lymphoproliferative disorder
207510040116_R03C01


title: D-EB-8

description:
EBV+ DLBCL
207510040150_R02C01

source_name: Rectum

value: Rectum

value: M

value: R-CHOP, Radiation


title: D-EB-7

description:
EBV+ DLBCL
207510040116_R02C01

source_name: Stomach

value: Stomach

value: Unknown


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep2, technology_rep1

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-DNA-1

value: Tibialis Anterior


title: D-EB-5

description:
EBV+ DLBCL
207510040150_R01C01

value: R-CHOP, HP Antiobiotic, IVIG


title: MRC5/hACE2 cells, R-1 sup-treated_1

description:
Library name: Sample20
Column name in "Processed_Data_MRC5ACE2.csv.gz": R1_1

value: fetal lung, normal diploid fibroblast

value: MRC5 cells stably expressing angiotensin-converting enzyme 2

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #1) for 24 h


title: D-EB-37

description:
DLBCL
207510040165_R07C01

source_name: Pelvis

value: Pelvis

value: F

value: R-CHOP


title: MRC5/hACE2 cells, Untreated control_2

description:
Library name: Sample14
Column name in "Processed_Data_MRC5ACE2.csv.gz": Untreaed_2

value: untreated control


title: D-EB-36

description:
DLBCL
207510040165_R06C01

source_name: Lymph node, inguinal

value: Lymph node, inguinal

value: tissue

value: Rituximab/Dexamethasone


title: D-EB-38

description:
DLBCL
207510040165_R08C01

source_name: Lymph node, cervical

value: Lymph node, cervical


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-DNA-5

value: BaCl2 acute muscle injury, day5


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-DNA-4


title: MRC5/hACE2 cells, Control sup-treated_1

description:
Library name: Sample15
Column name in "Processed_Data_MRC5ACE2.csv.gz": Control_1

value: treated with unstimulated PBMCs supernatant (donor #1) for 24 h


title: D-EB-35

description:
High-grade B-cell lymphoma
207510040165_R05C01

value: M


title: MRC5/hACE2 cells, Untreated control_1

description:
Library name: Sample13
Column name in "Processed_Data_MRC5ACE2.csv.gz": Untreaed_1


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-DNA-3


title: D-EB-11

description:
Excluded due to not passing QC.EBV+ DLBCL
207510040116_R05C01


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-DNA-2


title: D-EB-33

description:
DLBCL
207510040165_R03C01

value: mini R-CHOP


title: MRC5/hACE2 cells, Control sup-treated_4

description:
Library name: Sample18
Column name in "Processed_Data_MRC5ACE2.csv.gz": Control_4

value: treated with unstimulated PBMCs supernatant (donor #4) for 24 h


title: D-EB-30

description:
DLBCL
207510040164_R08C01

source_name: Epidural

value: Epidural


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-DNA-1

value: Tibialis Anterior


title: D-EB-31

description:
DLBCL
207510040165_R01C01

value: R-CVP, Rituximab/Bendamustine


title: D-EB-6

description:
EBV+ DLBCL
207510040149_R08C01

value: Bendamustine/Polatuzamab


title: MRC5/hACE2 cells, Control sup-treated_2

description:
Library name: Sample16
Column name in "Processed_Data_MRC5ACE2.csv.gz": Control_2

value: fetal lung, normal diploid fibroblast

value: MRC5 cells stably expressing angiotensin-converting enzyme 2

value: treated with unstimulated PBMCs supernatant (donor #2) for 24 h


title: mouse mucle, BaCl2  injure, day5, DNA, biology_rep2, technology_rep2

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-DNA-2


title: MRC5 cells, R-1 sup-treated_4

description:
Library name: Sample11
Column name in "Processed_Data_MRC5.csv.gz": R1_4

value: WT

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #4) for 24 h


title: MRC5 cells, R-1 sup-treated_3

description:
Library name: Sample10
Column name in "Processed_Data_MRC5.csv.gz": R1_3

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #3) for 24 h


title: D-EB-29

description:
DLBCL
207510040164_R07C01

value: F

value: tissue

value: R-CHOP


title: mouse mucle, BaCl2  injure, day0, DNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-DNA-5

value: BaCl2 acute muscle injury, day0


title: D-EB-3

description:
EBV+ DLBCL
207510040149_R05C01

value: Lymph node, cervical

value: M


title: mouse mucle, BaCl2  injure, day0, DNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-DNA-4


title: D-EB-28

description:
DLBCL
207510040164_R06C01

source_name: Lymph node, supraclavicular

value: Lymph node, supraclavicular

value: Unknown


title: MRC5 cells, R-1 sup-treated_1

description:
Library name: Sample8
Column name in "Processed_Data_MRC5.csv.gz": R1_1

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #1) for 24 h


title: D-EB-32

description:
DLBCL
207510040165_R02C01

source_name: Lymph node, axillary

value: Lymph node, axillary


title: D-EB-26

description:
DLBCL
207510040164_R04C01


title: D-EB-25

description:
DLBCL
207510040164_R03C01

value: R-CHOP, Radiation


title: MRC5 cells, Control sup-treated_4

description:
Library name: Sample6
Column name in "Processed_Data_MRC5.csv.gz": Control_4

value: fetal lung, normal diploid fibroblast

value: treated with unstimulated PBMCs supernatant (donor #4) for 24 h


title: MRC5 cells, R-1 sup-treated_5

description:
Library name: Sample12
Column name in "Processed_Data_MRC5.csv.gz": R1_5

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #5) for 24 h


title: mouse mucle, BaCl2  injure, day0, DNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-DNA-2

value: Tibialis Anterior


title: D-EB-23

description:
DLBCL
207510040164_R01C01

source_name: Orbit

value: Orbit

value: Radiation


title: MRC5 cells, R-1 sup-treated_2

description:
Library name: Sample9
Column name in "Processed_Data_MRC5.csv.gz": R1_2

value: WT

value: treated with R-1 EPS stimulated PBMCs supernatant (donor #2) for 24 h


title: mouse mucle, BaCl2  injure, day0, DNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-DNA-3


title: D-EB-21

description:
DLBCL
207510040150_R07C01

value: F

value: tissue


title: D-EB-24

description:
DLBCL
207510040164_R02C01

value: Lymph node, cervical

value: R-CHOP, RICE, Bendamustine, Bendamustine/Polatuzumab/Rituximab, Auto SCT, CAR T-cell therapy


title: D-EB-34

description:
DLBCL
207510040165_R04C01

source_name: Colon

value: Colon

value: R-ICE, Auto SCT


title: D-EB-22

description:
DLBCL
207510040150_R08C01

source_name: Oropharynx

value: Oropharynx

value: Unknown


title: mouse mucle, BaCl2  injure, day0, DNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-DNA-1

value: BaCl2 acute muscle injury, day0


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep2, technology_rep5

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-RNA-5

value: BaCl2 acute muscle injury, day7


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep2, technology_rep4

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-RNA-4


title: D-EB-19

description:
High-grade B-cell lymphoma
207510040150_R05C01

value: M


title: MRC5 cells, Control sup-treated_5

description:
Library name: Sample7
Column name in "Processed_Data_MRC5.csv.gz": Control_5

value: fetal lung, normal diploid fibroblast

value: treated with unstimulated PBMCs supernatant (donor #5) for 24 h


title: D-EB-27

description:
DLBCL
207510040164_R05C01

source_name: Spleen

value: Spleen

value: R-CHOP


title: D-EB-20

description:
DLBCL
207510040150_R06C01

value: R-GCVP, IT MTX, R-DHAP, Cellular Therapy


title: MRC5 cells, Control sup-treated_3

description:
Library name: Sample5
Column name in "Processed_Data_MRC5.csv.gz": Control_3

value: WT

value: treated with unstimulated PBMCs supernatant (donor #3) for 24 h


title: D-EB-2

description:
EBV+ DLBCL, PTLD
207510040149_R07C01

source_name: Chest wall

value: Chest wall

value: tissue


title: MRC5 cells, Control sup-treated_2

description:
Library name: Sample4
Column name in "Processed_Data_MRC5.csv.gz": Control_2

value: treated with unstimulated PBMCs supernatant (donor #2) for 24 h


title: D-EB-18

description:
DLBCL
207510040150_R04C01

value: Lymph node, axillary

value: F

value: R-EPOCH


title: D-EB-17

description:
DLBCL
207510040150_R03C01

source_name: Lymph node, portal

value: Lymph node, portal


title: MRC5 cells, Control sup-treated_1

description:
Library name: Sample3
Column name in "Processed_Data_MRC5.csv.gz": Control_1

value: treated with unstimulated PBMCs supernatant (donor #1) for 24 h


title: D-EB-16

description:
EBV+ DLBCL
207510040149_R06C01

source_name: Systemic Involvement (spleen, kidneys, liver, lungs, colon, lymph nodes)

value: Prednisone, Acyclovir


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep2, technology_rep3

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-RNA-3

source_name: Tibialis Anterior

value: Tibialis Anterior

value: BaCl2 acute muscle injury, day7


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep2, technology_rep2

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-RNA-2


title: D-EB-10

description:
EBV+ DLBCL and Angioimmunoblastic T-cell Lymphoma
207510040116_R04C01

value: Lymph node, inguinal

value: M


title: CTEBV-9

description:
Control. EBV+ Polymorphic lymphoproliferative disorder
207510040149_R01C01

source_name: Liver

value: Liver

value: Ganciclovir/Valganciclovir


title: CTEBV-7

description:
Control. EBV+ Infectious mononucleosis
207510040110_R07C01

source_name: Tonsil

value: Tonsil


title: CTEBV-8

description:
Control. EBV+ Infectious mononucleosis
207510040110_R08C01

value: Lymph node, cervical


title: MRC5 cells, Untreated control_1

description:
Library name: Sample1
Column name in "Processed_Data_MRC5.csv.gz": Untreaed_1

value: fetal lung, normal diploid fibroblast

value: WT

value: untreated control


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep2, technology_rep1

description: Library name: mouse_muscle_day7-scHiCAR-replicate2-RNA-1


title: CTEBV-5

description:
Control. EBV+ Infectious mononucleosis
207510040110_R05C01

value: tissue


title: MRC5 cells, Untreated control_2

description:
Library name: Sample2
Column name in "Processed_Data_MRC5.csv.gz": Untreaed_2


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-RNA-5


title: CTEBV-3

description:
Control. Reactive follicular hyperplasia
207510040110_R03C01


title: CTEBV-6

description:
Control. EBV+ Infectious mononucleosis
207510040110_R06C01

value: Lymph node, axillary

value: F


title: CTEBV-4

description:
Control. Reactive follicular hyperplasia
207510040110_R04C01


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-RNA-4


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-RNA-3


title: CTEBV-12

description:
Control. EBV+ Polymorphic lymphoproliferative disorder
207510040149_R02C01

value: R-CHOP


title: HS5, CTR_FOXA1, rep1

source_name: Bone; Marrow; Stroma

value: Bone; Marrow; Stroma

value: Fibroblast

value: FOXA1 (ab23738 Abcam)

value: Parental


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-RNA-2

value: Tibialis Anterior

value: BaCl2 acute muscle injury, day7


title: HS5, CTR_INPUT, rep1


title: CTEBV-14

description:
Control. EBV+ plasmacytic hyperplasia, PTLD
207510040149_R04C01

source_name: Nasal sinus

value: Nasal sinus


title: CTEBV-1

description:
Control. Reactive follicular hyperplasia
207510040110_R01C01

source_name: Lymph node, inguinal

value: Lymph node, inguinal

value: M


title: MSKPCa1, CTR_FOXA2, rep1

source_name: Fresh tumor

value: Fresh tumor

value: Overexpressing FOXA2

value: FOXA2 (D56D6 CST)


title: CTEBV-2

description:
Control. Reactive follicular hyperplasia
207510040110_R02C01


title: CTEBV-13

description:
Control. EBV+ plasmacytic hyperplasia, PTLD
207510040149_R03C01


title: mouse mucle, BaCl2  injure, day7, RNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day7-scHiCAR-replicate1-RNA-1


title: thymic epithelial cell, Aebp2-ko, replicate 2, scRNAseq

description: Library name: KO2 TEC_scRNA

source_name: thymus

value: thymus

value: thymic epithelial cell

value: knockout


title: MSKPCa1, CTR_FOXA1, rep1


title: LuCaP-145.2, CTR_FOXA2, rep1


title: MSKPCa1, CTR_INPUT, rep1


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep2, technology_rep5

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-RNA-5

value: BaCl2 acute muscle injury, day5


title: thymic epithelial cell, Aebp2-flox, replicate 2, scRNAseq

description: Library name: WT2 TEC_scRNA

value: wild type


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep2, technology_rep4

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-RNA-4


title: thymic epithelial cell, Aebp2-flox, replicate 1, scRNAseq

description: Library name: WT TEC_scRNA


title: thymic epithelial cell, Aebp2-ko, replicate 1, scRNAseq

description: Library name: KO TEC_scRNA


title: patient2_3 fibroblast cells

city: zhengzhou

first: xiaoli

last: zhang

address: 河南省郑州市二七区连云路15号院11号楼29号

institute: zhengzhou university

data_processing:
Trimmomatic (version 0.36)
the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of human from GRCh38 using STRA software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: skin

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KC Stranded mRNA Library Prep Kit for Illumina® following manufacturer's protocols

value: skin

value: fibroblast

value: fibroblast cells


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep2, technology_rep2

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-RNA-2


title: PC3, T_FOXA2, rep2

source_name: Prostate

value: Prostate

value: Epithelial

value: Parental

value: Compound T


title: patient2_1 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: PC3, T_FOXA1, rep2

value: FOXA1 (ab23738 Abcam)


title: patient1_3 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: MR-J82

city: Kagoshima

first: Gang

address: 8-35-1 Sakuragaoka

department: Urology

institute: Graduate School of Medical and Dental Sciences, Kagoshima University

description:
Library name: TR_M097_009
group2_FPKM

data_processing:
Basecalls were performed using bcl2fastq2.
Adapter and low-quality sequences were removed by cutadapt (v1.2.1). After quality control, poly-A/T sequences were also removed by PRINSEQ (v0.19.2).
The trimmed reads were aligned to the reference human genome using TopHat (v2.0.13).
Mapped reads were assembled by Cufflinks (v2.2.1) , and the transcripts across all samples were merged by Cuffmerge. The “fragments per kilo base per million map reads” (FPKM) was calculated with Cuffquant, and differential expression analysis (calculating fold change and testing the statistical significance) between samples was performed with Cuffdiff (Cuffmerge, Cuffquant and Cuffdiff are programs involved in the Cufflinks package).
Assembly: GRCh37/hg19
Supplementary files format and content: xlsx files include FPKM values for each sample

growth_protocol: Cell lines were cultured in minimum essential medium (MEM) containing 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 μg/mL streptomycin in a humidified environment consisting of 95% air and 5% CO2 at 37 °C.

extract_protocol:
ISOGEN (Nippon Gene, Tokyo, Japan) was used to extract RNA of cultured cells according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: To establish MR-BCs, MMAE (CAS NO. 474645-27-7; MyBioSource) was added to the cells at increasing concentrations (4, 8, 16, 32, 64, 80, 100, and 128 nM) after cells had reached 30–50% confluence. After exposure to MMAE for 24 h, the MEM was replaced with fresh MMAE-free MEM until the surviving cells recovered favorably. When cells reached the same confluence, MMAE was added to the MEM again. Cells were exposed to each concentration 6–8 times. After approximately 10 months, cells that grew in the MEM with 128 nM MMAE were designated MR-T24 and MR-J82 cells.

value: epithelial carcinoma cells

value: MMAE-resistant