title: Huh7 cell lines-ATAC-Sorafenib-rep3

city: Shenzhen

first: Hao

address: No. 1098, Xueyuan Road

institute: Shenzhen University

data_processing:
Illumina Casava1.7 software used for basecalling
For RNA-seq data, sequenced reads were trimmed for adaptor sequence by cutadapt, and then mapped to hg38 whole genome using hisat2 v1.1.0 with default parameters
For RNA-seq data, unique mapped reads were extracted; featureCounts v1.6.1 with parameters -T 16 -p -t exon -g gene_id was used to obtain read counts of all genes; the version of GTF files is gencode.v35
For RNA-seq data, DESeq2 was used to perform normalized to read count matrices and obtain differential genes with pvalue 0.01 and Foldchange 2 as the threashold
For ATAC seq data, sequenced reads were trimmed for adaptor sequence by cutadapt, and then mapped to hg38 whole genome using bowtie2 v2.4.1 with parameters, -X 1000
For ATAC seq data, PCR duplicates were removed with Picard. Mitochondria data and low quality reads were removed with samtools. Peaks were called by MACS2 with parameters --shift -75 --extsize 150 --nomodel -B --SPMR -g hs --keep-dup all.
Genome_build: hg38
Supplementary_files_format_and_content: For mRNA-seq: CSV files including Matrix table with normalized gene counts output by DESeq2 for all genes and all samples
Supplementary_files_format_and_content: For mRNA-seq: CSV files including baseMean, log2FoldChange value, pvalue, adjusted pvalue, etc.
Supplementary_files_format_and_content: For ATAC-seq: bigwig files were generated using bedGraphToBigWig(v4);
Supplementary_files_format_and_content: For ATAC-seq: peak text files for all samples, generated by MACS2 (v2.2.7.1)

source_name: Liver cancer cells

extract_protocol:
Cell culture mediem was removed and cells were washed by PBS, and total RNA was harvested using Trizol reagent.The RNA qulity was tested by NanoPhotometer spectrophotometer and Agilent 2100 bioanalyzer.
RNA libraries and ATAC libraries were prepared for sequencing using standard Illumina protocols

value: Huh7 cells

value: Liver

value: Sorafenib


title: Huh7 cell lines-ATAC-Sorafenib-rep4

status: Public on Apr 30 2022

type: SRA

last: Wang

state: Guangdong

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: treatment


title: Huh7 cell lines-ATAC-DMSO-rep2

value: DMSO


title: 60N

type: RNA

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

country: Taiwan

institute: NCKU

description: gene expression of surgical liver resection of HCC patients

hyb_protocol: cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray 4x44K.

scan_protocol: Arrays were scanned using the Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

source_name: Normal - 60

label_protocol: Cyanine-3 (Cya3) labeled cRNA was prepared from 2000 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

extract_protocol: Total RNA was extracted from the tumorous and adjacent nontumorous HCC tissues using TRIzol reagent (Sigma-Aldrich) and then reverse transcribed into cDNA.

treatment_protocol: The patients were regularly followed up at clinic visits every 1-3 months after hepatic resection. HCC recurrence was detected by medical imaging and biopsy confirmation. All the patients provided signed informed consent to use their surgical specimens for this research.

value: liver

tag: gender

value: Male

tag: age


title: 60T

source_name: Tumor - 60


title: 13N

source_name: Normal - 13


title: 62T

source_name: Tumor - 62


title: 9N

source_name: Normal - 9


title: 13T

source_name: Tumor - 13


title: Huh7 cell lines-Vec-rep2

library_source: transcriptomic

molecule: polyA RNA

value: empty vector


title: Huh7 cell lines-ATAC-DMSO-rep1


title: T293

city: Guangzhou

first: Lipeng

last: Mao

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

data_processing:
Illumina Casava1.7 software used for basecalling.
The original data of ATAC-seq were considered pre-analysis. The experimental process of ATAC-seq analysis includes pre-alignment quality control (QC), read alignment to a reference genome, and post-alignment QC and processing. The sequence was posted back to the reference genome by Bowtie2 software and the repetitive sequences were removed by SAM tools. In order to facilitate reading and visualization, deep tools were used for visualization, MACS2 for peak calling, data was converted into BAM file format, and then peak annotation, GO enrichment and motif analysis were carried out, respectively
Assembly: Homo sapiens Ensembl 94
Supplementary files format and content: peak files, bw files

source_name: Cell line

growth_protocol: The underlined region corresponds to the double-stranded portion of the adapter-ME sequence identified by the transposase.

extract_protocol:
The number of 293T cells and J76 cells in the logarithmic growth phase was counted by hemacytometer. 50000 cells were added to PCR tubes and centrifuged at 4 ºC at 600 x g for 5 min, discarded the supernatant. The pre-cooled 0.1% NP-40 lysis buffer solution was added to the cell precipitate and pipetted until homogeneous. The cells were lysed on ice for 3 minutes. After centrifugation at 4 ºCa t 550 x g for 5 min, discard the supernatant.
The two kinds of DNA samples were cut by adding the self-made Tn5 transposase mixed system into the precipitation, and the library was constructed before ATAC-seq sequencing. The reaction system was10 µl 5 x TAPS-MgCl2-PEG 8000, 32 µl H2O, 8 µl 0.96 µg/µl Tn5 enzyme. The reaction conditions were the same as 1.2.3 enzyme activity detection.  The DNA of Tn5 reaction system samples was purified by an Omega PCR purification kit. The purified DNA samples were collected and amplified by PCR. The DNA samples were sent to Guangzhou Nuo He Zhi Yuan Company for sequencing. A portion of the DNA was used for Q-PCR to measure the concentration of DNA.

tag: cell type

value: human embryonic kidney cells


title: Huh7 cell lines-Vec-rep1


title: 3T

source_name: Tumor - 3


title: Huh7 cell lines-Vec-rep3


title: Huh7 cell lines-MT1G-OE-rep3

value: MT1G overexpression


title: KO Rep 3

city: Duarte

first: ZUOMING

last: SUN

state: CA

address: 1500 E Duarte Rd, Duarte, CA 91010

country: USA

institute: City of Hope Medical Center

data_processing: The sequence reads were aligned to the mouse whole genome (GRCm38) with validation of quality through pre-alignment and post-alignment QA/QC. Aligned reads were further subjected to quantification using the Parteck E/M algorithm and normalization to counts per million (CPM) with 0.001 added to each

organism: Mus musculus

source_name: CD4 t cells

extract_protocol:
RNA WAS extracted with an RNA extraction kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: SRC2fl/fl/Foxp3YFP-Cre mice

tag: time point

value: 36 hours post Treg polarization


title: 9T

source_name: Tumor - 9


title: WT Rep 3

value: Foxp3YFP-Cre mice


title: KO Rep 1


title: Huh7 cell lines-MT1G-OE-rep1


title: 3N

source_name: Normal - 3


title: Huh7 cell lines-MT1G-OE-rep2


title: 68N

source_name: Normal - 68


title: WT Rep 2


title: 68T

source_name: Tumor - 68


title: Huh7 cell lines-Sorafenib-rep1


title: Huh7 cell lines-Sorafenib-rep3


title: KO Rep 2


title: 58T

source_name: Tumor - 58


title: Huh7 cell lines-DMSO-rep3


title: WT Rep 1


title: Huh7 cell lines-Sorafenib-rep2


title: Huh7 cell lines-DMSO-rep1


title: 61H.234

city: Columbus

first: Brandon

middle: M

last: Murphy

state: Ohio

address: 460 W. 12th Ave, BRT 940E

institute: The Ohio State University

data_processing:
Sequenced were aligned to mm10 using Star
Duplicates were removed using Picard (version 2.17.11)
Gene Count matrix was generated using FeatureCounts
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Murine melanoma

growth_protocol: Spontaneous melanomas were allowed to grow until reaching predetermined exclusion criteria at which point the mouse was euthanized and the tumor collected

extract_protocol:
Tumor tissue was flash frozen with liquid nitrogen followed by manual homogenization with a mortor and pestal. Homogenized tissue was then processed using the ZR-Duet DNA/RNA MiniPrep Plus Kit
Ribosomal RNA was depleted using the Illumina Ribo-Zero chemistry and then the libraries were generated using the Illumina TruSeq Total RNA Stranded Library Prep Kit

treatment_protocol: Melanomas were induced in TN GEM models through topical application of 20mM 4-hydroxytamoxifen on post-natal days 1 and 2

tag: background strain

tag: genotype

value: NRAS 61H/H

value: melanoma


title: 61H.267


title: 61H.278


title: Huh7 cell lines-DMSO-rep2


title: 48T

source_name: Tumor - 48

value: Female


title: 58N

source_name: Normal - 58


title: 48N

source_name: Normal - 48


title: 61H.165


title: medullary thymic epithelial cells, mature, donor 226 [pt226_hi_RNAseq]

city: Cold Spring Harbor

first: Hannah

middle: Verena

last: Meyer

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: ens_gene: Ensembl gene; target_id: Transcript ID; ext_gene: Gene name; pval: the Wald test pvalue (sleuth output); qval: the p-value adjusted for multiple test correction (sleuth output); b: beta value, which is the log fold changes between conditions (sleuth output); se_b: standard error of the beta value (sleuth output); mean_obs: the mean expression (log) of the transcript across all samples (sleuth output); var_obs: the biological variance of the expression (sleuth output); tech_var: the technical variance of expression (sleuth output); sigma_sq: raw estimator of the variance once the technical variance has been removed (sleuth output); smooth_sigma_sq: the smooth regression fit for the shrinkage estimation (sleuth output); final_sigma_sq: max(sigma_sq, smooth_sigma_sq) (sleuth output);length: transcript length (kallisto output); $pt_tpm: Sample transcript expression (kallisto output)

data_processing:
Quality control was conducted using FastQC (v0.11.8)
Reads were filtered with fastp (v0.11.8) for minimum phred quality (-q 25) of at most 10% unqualified bases (-u 10), a minimum length of 50bp (-l 50), at least 30% complexity (-y) and polyX tail trimming (-x)
Differential gene expression: Filtered reads were pseudo-aligned and quantified using Kallisto (v0.4.6) with 100 bootstrap samples
Differential gene expression: Sleuth (v0.30.0) was used for differential expression analysis between mTEChi and mTEClo samples, adjusting for patient effect in the reduced and full model. Transcripts with q-value ≤ 0.05 were considered differentially expressed
Raw reads were processed with bamboozle (Ziegenheim, Nature Communications, 2021) to remove genetic variation that could help de-identify samples ie any genetic variant was replaced with the corresponding reference genome variant
Assembly: GRCh38/Gencode annotation (release 33)
Supplementary files format and content: comma-separated value files including transcripts per million for each sample and differential expression statistics

source_name: thymus

extract_protocol:
mTECs were sorted as CD45-, CDR2-, EPCAM+ cells and MHCII (HLA-DR) was used to separate immature mTEClo and mature mTEChi cell populations
RNA from sorted mTEChi and mTEClo populations was extracted using the High Pure RNA Isolation Kit (Roche)
The libraries were prepared manually using the NEBNext® Ultra ™ Directional RNA Library Prep Kit according to the manufacturer’s instruction

value: thymus

value: medullary thymic epithelial cells

tag: phenotype

value: MHCII high

tag: donor age

value: 9 months

tag: donor sex

value: male


title: Dam_empty_rep2_with ETV4 and ETV5

city: Cambridge

first: Dawei

last: Sun

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Library strategy: DamID-seq
Illumina software used for conventional basecalling.
Reads were mapped to a bowtie2 indexed GRCh38 genome assembly (hg38), binned into 5’-GATC-3’ fragments.
Sox9, ETV4 and ETV5 fusion samples were normalized against a paired Dam-only control derived from the same organoid line (RPM normalization, 300 bp bins)
Macs2 (v2.1.2) was used to call broad peaks for each fusion and Dam-only pair using the bam files generated by the damidseq_pipeline.
Peaks were filtered to only those present in all replicates using bedtools (v2.26.0) and surpassing FDR<10-50 for Sox9 and ETV5; FDR<10-25 for ETV4.
Genome_build: GRCh38 genome assembly (hg38)
Supplementary_files_format_and_content: A bigWig file (.bw format) with the average of the different Dam-only normalized replicates. Bed files with the coordinates of the peaks present in all replicates.

source_name: human foetal lung progenitor organoids

growth_protocol: Organoids were maintained with self-renewing medium, conatining EGF, FGF10, FGF7, Noggin, TGFb inhibitor, R-spondin1 and GSK3b inhibitor (detailed protocol in Nikolic et al., 2017).

extract_protocol:
Genomic DNA was extracted and processed as previously described (Marshall et al., 2016).
See method and Marshall et al., 2016

treatment_protocol: Organoids were infected with lentirvus carry the relavant Dam construct and harvested 48-72 hrs after infection.

value: Human feotal lung derived tip progenitor organoids

tag: Stage

value: 8 pcw

tag: damid type

value: Empty


title: medullary thymic epithelial cells, immature, donor 226 [pt226_lo_RNAseq]

value: MHCII low


title: 61H.267E


title: Dam_empty_rep4_with ETV4 and ETV5


title: medullary thymic epithelial cells, immature, donor 221 [pt221_lo_RNAseq]

value: 4 months


title: 61H.97


title: Dam_empty_rep1_with ETV4 and ETV5


title: ETV5-Dam_rep4


title: Dam_empty_rep3_with ETV4 and ETV5


title: ETV5-Dam_rep3


title: medullary thymic epithelial cells, mature, donor 221 [pt221_hi_RNAseq]


title: ETV5-Dam_rep2


title: 61L.247

value: NRAS 61L/L


title: medullary thymic epithelial cells, immature, donor 214 [pt214_lo_RNAseq]

value: 6 days

value: female


title: ETV4-Dam_rep3


title: ETV5-Dam_rep1


title: ETV4-Dam_rep4


title: ETV4-Dam_rep2


title: 61L.115


title: 61L.159


title: medullary thymic epithelial cells, mature, donor 214 [pt214_hi_RNAseq]


title: 61L.132


title: Hypoxia SLC-0111 rep4

city: Helsinki

first: Katja

last: Eloranta

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

data_processing:
Quality check with MultiQC (v. 1.10.1) [Ewels P, Magnusson M, Lundin S and Käller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016]
Alignment / HISAT2 for paired end reads (Homo_sapiens.GRCh38.95) [Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015]
Aligned reads per genes were counted with HTSeq
Differential expression analyses using edgeR (v. 3.4.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hepatoblastoma cell line

growth_protocol: Cells were routinely maintaned in DMEM supplemented with 10% FBS, penicillin/streptomycin and glutaMAX.

extract_protocol:
Total RNA was extracted utilizing Nucleospin RNA/protein Mini kit (Macherey-Nagel)
cDNA

treatment_protocol: Cells were treated with DMSO or 100 µM of SLC-0111 (#S2866, SelleckChem). Treatments were carried out either under normoxic or hypoxic (partial pressure of O₂ = 1%) conditions for 48 h.

tag: oxygen condition

value: hypoxia


title: medullary thymic epithelial cells, immature, donor 226 [pt226_lo_5'Cap]

description: Chr: Trancription start region (TSR) Chromosome; Start: TSR start location; Stop: TSR stop location; Samples: Samples with TSR; Sample_indices: Sample level TSRs with internal indices that are present in consensus TSR cluster; Strand: Stand; Listing: Number of sample indices in TSR; Listing_subject: Number of subjects in TSR; Hi: Number of mTEChi samples with TSR; Lo: Number of mTEClo samples with TSR; $pt_$sampletype_Reads: Number of reads in TSR for each sample; $pt_$sampletype_TPM: Power-law normalized TSR expression in tags per million for each sample; Annotation: HOMER gene type annotation; Distance_to_TSS: HOMER distance to known transcription start site; Nearest_Ensembl: HOMER closest Ensembl gene to each TSR; Gene_Name: Gene name for nearest ensemble gene; Gene_Description: Gene description for nearest Ensembl; Annotations_short: Shortened version of gene Annotation; CpG%: TSR CpG%; GC%: TSR GC%; Housekeeping: In list of known housekeeping genes (True/False); TRA: In list of known tissue restricted antigens (True/False); Aire_dep: In list of known (derived from mouse orthologues) AIRE dependent genes (True/False); Fezf2_dep: In list of known (derived from mouse orthologues) FEZF2 dependent genes (True/False);  Aire_dep_TRA: TRA AND Aire_dep (True/False); Fezf2_dep_TRA: TRA AND Fezf2_dep (True/False); Other_TRA: TRA AND not Aire_dep AND not Fezf2_dep (True/False)

data_processing:
Reads were demultiplexed, UMIs trimmed via umi_tools extract (umi_tools v1.1) and screened for contamination with fastq_screen (v0.14.0)
Reads were aligned to GRCh38/Gencode annotation (release 33) using STAR (v2.7.2b) and deduplicated based on UMIs using umi_tools dedup.
Deduplicated, aligned reads were filtered for uniquely mapped reads via samtools view -b -q 255 (samtools v1.11).
Quality control of sequencing and alignment was conducted using FastQC (v0.11.8) and picard CollectRnaSeqMetrics (v2.18.20) and summarized with multiqc (v1.9)
Raw reads were processed with bamboozle (Ziegenheim, Nature Communications, 2021) to remove genetic variation that could help de-identify samples ie any genetic variant was replaced with the corresponding reference genome variant
TSS calling: only the forward (i.e. 5' end) of each read pair was retained via samtools view -h -f 0x40. TSS were then defined as the 5' position of the uniquely mapped, forward reads. The expression levels of the TSSs for each mTEC sample were normalized to tags per million using the power law normalization implemented in CAGEr (v1.32 ). After normalization, removeBatchEffect in limma (v3.46) was used to remove sequencing batch effects.
Normalized TSSs in each sample were combined into TSRs using paraclu (v9) with a minimum tag cluster expression of 2 tags per million and a maximum cluster length of 20bp. TSRs across samples were combined with bedops (v2.4.38) and consensus, strand-specific TSRs in human mTEC samples called by merging TSRs derived from different samples within 20bp proximity using bedtools merge (v2.29.2).
TSRs were annotated using HOMER (v4.11.1), including mapping to closest gene, calculation of TSR CpG/GC content (-CpG) and TATA motif search
Assembly: GRCh38/Gencode annotation (release 33)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
mTECs were sorted as CD45-, CDR2-, EPCAM+ cells and MHCII (HLA-DR) was used to separate immature mTEClo and mature mTEChi cell populations
RNA from sorted mTEChi and mTEClo populations was extracted using the High Pure RNA Isolation Kit (Roche)
The libraries were prepared manually as described in Pelechano (2014) Nature Protocols ; yielding libraries only containing molecules derived from 5'Cap RNA.


title: ETV4-Dam_rep1


title: Hypoxia CTRL rep4

value: DMSO


title: Hypoxia SLC-0111 rep2


title: 61L.100

value: melanoma


title: 61K.229

value: NRAS 61K/K


title: medullary thymic epithelial cells, immature, donor 221 [pt221_lo_5'Cap]

value: thymus


title: medullary thymic epithelial cells, mature, donor 226 [pt226_hi_5'Cap]

value: medullary thymic epithelial cells


title: Hypoxia SLC-0111 rep3


title: Hypoxia SLC-0111 rep1


title: medullary thymic epithelial cells, mature, donor 221 [pt221_hi_5'Cap]

value: MHCII high


title: Hypoxia CTRL rep2


title: Hypoxia CTRL rep3


title: Hypoxia CTRL rep1


title: IP_1

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

department: School of Biotechnology

country: India

institute: Jawaharlal Nehru University

description: Transcriptome

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning thea reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Phytozome v3.3.2
Supplementary_files_format_and_content: FPKM values in excel format

organism: Sorghum bicolor

source_name: Stem Internode

growth_protocol: Sweet Sorghum SSV84  plants were raised in an open field

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

value: Middle internode

tag: developmental stage

value: Physiological Maturity


title: medullary thymic epithelial cells, immature, donor 214 [pt214_lo_5'Cap]


title: 61K.199


title: IM_2

description: Transcriptome

value: Milky stage


title: 61L.106


title: Normoxia SLC-0111 rep4

tag: cell line

value: normoxia


title: 61K.139

tag: tissue


title: medullary thymic epithelial cells, immature, donor 212 [pt212_lo_5'Cap]

value: 2 weeks

value: male


title: medullary thymic epithelial cells, mature, donor 214 [pt214_hi_5'Cap]


title: Normoxia SLC-0111 rep3

tag: treatment


title: Normoxia SLC-0111 rep2


title: medullary thymic epithelial cells, mature, donor 212 [pt212_hi_5'Cap]


title: IB_2

description: Transcriptome

value: Booting


title: Normoxia SLC-0111 rep1


title: 61K.64


title: 61K.106


title: 61K.54


title: medullary thymic epithelial cells, immature, donor 87 [pt87_lo_5'Cap]

value: MHCII low

value: 4 months


title: 61L.120

value: NRAS 61R/R


title: medullary thymic epithelial cells, mature, donor 87 [pt87_hi_5'Cap]

value: female


title: Normoxia CTRL rep3

value: DMSO


title: P2884.1

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM gene counts for every gene and every sample

source_name: Pretherapeutic rectal cancer patient biopsy

growth_protocol: All rectal metastases samples were obtained with informed consent as approved by the local ethics committee (24/10/05).

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

treatment_protocol: Samples were collected from patients previously diagnosed with primary rectal cancer during neurosurgical removal.

value: metastatic

tag: patient


title: 61P.229

value: melanoma


title: iTreg cells, NRP1, 2-3

city: Ithaca

first: Weishan

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

description: NRP-1- iTreg cells, biol rep 3

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

source_name: iTreg cells

growth_protocol: CD44low CD62Lhigh naïve CD4+ T cells were flow-sorted from Foxp3-RFP reporter mice and cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1mM none essential amino acid, 1 mM L-glutamin, and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5 ug of mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Induced Treg (iTreg) cells were differentiated in 96-well plates (10^6 cells/ml, 0.2 ml per well) with anti-CD3/CD28 microbeads (1 bead per 5 cells, Invitrogen), IL-2 (50 U/ml, R&D) and TGF-β (2ng/ml; R&D) for 3 days.
The iTreg cell culture were sorted based on viable CD4+ Foxp3-RFP+ cells, and then divided into NRP-1+ and NRP-1- subsets.

value: iTreg cells

tag: cell subset

value: WT

value: iTreg differentiation

tag: time

value: Day 5


title: Normoxia CTRL rep2


title: Normoxia CTRL rep4


title: P2890.1


title: Normoxia CTRL rep1


title: iTreg cells, NRP1, 2-2

description: NRP-1- iTreg cells, biol rep 2

tag: cell type


title: 61L.114


title: 61P.111


title: iTreg cells, NRP1, 2-1

description: NRP-1- iTreg cells, biol rep 1


title: P2882.1


title: TEGs non-exposed to organoids (control condition) 10x

city: Utrecht

first: Maria

last: Alieva

state: Netherlands

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description:
Non_exposed_TEGs_counts
Non_exposed_TEGs_metadata

data_processing:
10X Genomics processing
Genome_build: Hg38p10
Supplementary_files_format_and_content: The data are in csv format. The table contains  counts and metadata.

source_name: TEG (non-exposed)

growth_protocol: TEGs were grown under normal conditions and subjected to 10X sequencing

extract_protocol:
TEG(>0,8x106 per condition) were grown under normal conditions and subjected to 10X sequencing
Fresh, not co-cultured, TEGs were viability-enriched via FACS by DAPI staining (1:1000; Thermo Fischer) and loaded according to the standard protocol of the Chromium Single Cell 3′ Kit (v3).

value: alphaBeta T cells engineered to express a Vgamma9/Vdelta2 T cell receptor

value: Untreated

tag: response to teg (% organoids killed in 24h)


title: IB_1

description: Transcriptome

value: Middle internode


title: P2875.1


title: iTreg cells, NRP1, 1-4

description: NRP-1+ iTreg cells, biol rep 4


title: P2781.1


title: iTreg cells, NRP1, 2-4

description: NRP-1- iTreg cells, biol rep 4


title: 61K.79

tag: background strain


title: PT_7 LNM VDJ

city: Beijing

first: Zhihua

last: Liu

state: Beijing

address: State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China

data_processing:
Raw sequencing data for each sample were converted to matrices of expression using cellranger (version 3.1.0, 10x Genomics), for GEX-seq data using cellranger count parameter and for VDJ-seq data using cellragner vdj parameter
doublet removal with Scrublet (version 0.2.3)
removal of ambient mRNA with SoupX (version 1.3.6)
normalization, logtransform, variable genes calling with Scanpy (version 1.4.1)
Integrate samples with bbknn
cells cluster with leiden
different gene analysis with Seurat (version 3.1.1)
Genome_build: GRCh38 human reference genome (official Cell Ranger reference, version 3.0.0)
Supplementary_files_format_and_content: Raw counts of filtered cell barcodes and features were provided in cell_counts_matrix.mtx. Cells annotation meta infomation were provided in meta_all.csv as comma separated text files. Cell of vdj annotaion were provided in meta_tcr.csv as comma separated text file

source_name: human breast cancer

extract_protocol:
Cells suspension from primary tumor and paired lymph node metastasis samples were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics), Samples with gene expression and T cell receptor sequencing, the Chromium Single Cell V(D)J protocol was used.  10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing)
RNA libraries were prepared for sequencing using 10x chromium single cell 5' Library or V(D)J protocals and standard Illumina protocols

value: VDJ-seq

tag: donor

tag: site

value: Lymph node metastasis

tag: pathological type

value: Invasive ductal carcinoma


title: PT_8 LNM VDJ

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College


title: iTreg cells, NRP1, 1-2

description: NRP-1+ iTreg cells, biol rep 2

tag: genotype


title: iTreg cells, NRP1, 1-3

description: NRP-1+ iTreg cells, biol rep 3


title: 61K.57


title: PT_6 LNM VDJ


title: MEFs, 61Q.6

data_processing:
Sequences were aligned to mm10 using STAR
Duplicates were removed using Picard (version 2.17.11)
Generate a count matrix for genes using featureCounts: Generated the NRAS_mutant_MEFs_RNA_raw_counts.xlsx files
Differential gene expression analysis was performed using DESeq2 (p-adjusted < 0.05). Generated the NRAS_mutant_MEFs_DESeq_normalized_counts.xlsx file
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with raw gene counts for every gene and every sample
Excel file with DESeq normalized gene counts for every gene and every sample

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were grown in DMEM containing 10% FBS, 1% penicillian-streptomycin, and 1% L-glutamine

extract_protocol:
RNA was isolated from MEFs using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research)
RNA was prepared for sequencing through ribosomal depletion using Illumina Ribo-Zero chemistry followed by library preparation using Illumina TruSeq Total RNA Stranded Library Prep kit.
rRNA depleted RNA Sequencing

treatment_protocol: MEFs were treated with Adenoviral-CMV-Cre-eGFP in low serum DMEM to induced Nras expression. MEFs were then cultured for 6 days post-induction of Nras expression as stated in the growth protocol

tag: strain

value: Mouse embryonic fibroblasts (MEFs)

value: Nras 61Q/Q


title: P2479.1


title: P2655.1


title: iTreg cells, NRP1, 1-1

description: NRP-1+ iTreg cells, biol rep 1


title: P2470.1


title: MEFs, 61Q.5


title: MEFs, 61Q.2


title: PT_5 LNM VDJ


title: MEFs, 61P.27

value: Nras 61P/P


title: PT_2 LNM VDJ


title: MEFs, 61P.21


title: P2395.1


title: PT_4 LNM VDJ


title: P2437


title: PT_3 LNM VDJ


title: MEFs, 61H.14

value: Nras 61H/H


title: MEFs, 61P.26


title: PT_1 LNM VDJ


title: Murine vaginal neutrophils, NK1.1 depleted biol rep 3, Day 5

city: St. Louis

first: Haina

last: Shin

state: MO

address: 660 South Euclid Ave

department: Internal Medicine

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned and quantitated with Illumina DRAGEN version 3.9.3-8 Bio-IT platform
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and TPM in tab-delimitted text format

source_name: vagina

extract_protocol:
RNA was harvested using RNeasy micro kit (Qiagen). Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0.
Clontech SMARTer Ultra Low RNA

treatment_protocol:
Adult female C57BL6/J mice were pre-treated with 2mg progesterone subcutaneously to synchronize estrous cycles. Mice were then treated with 200ug isotype control antibody or anti-NK1.1 intraperitoneally 3 and 1 day prior to intravaginal infection with 10^4 PFU HSV-1 McKrae.
Vaginas were harvested from euthanized and DPBS-perfused mice 5 days post-infection and processed in pairs (two biological replicates were included per sample to increase cell recovery) into single cell suspensions as follows: tissue was cut into small pieces and digested for 15 minutes at 37°C in 0.5 mg/ mL of Dispase II in DPBS. Tissues were then digested for 25 minutes at 37°C with 0.5 mg/mL Collagenase D and 15 μg/mL DNase I in RPMI media with 10% FBS. 50 μL of sterile EDTA was added to each sample and incubated at 37°C for another 5 minutes. Tissues were then mechanically disrupted through a 70-μm cell strainer into single cell suspension using a 3 mL syringe plunger. Tissues were washed with RPMI media containing 1% FBS, 1% pen/strep, and 1% 2-mercaptoethanol and centrifuged to collect the cell pellet. Fluorescent activated cell sorting (FACS) was used to isolate live Cd45+ Ly6g+ Cd11b+ neutrophils for RNA extraction.

value: vagina

value: neutrophils


title: P2301

value: metastatic


title: MEFs, 61H.16


title: PT_8 tumor VDJ

value: Primary tumor


title: P2297


title: Murine vaginal neutrophils, NK1.1 depleted biol rep 1, Day 5


title: MEFs, 61R.3

value: Nras 61R/R


title: PT_7 tumor VDJ


title: PT_5 tumor VDJ


title: Murine vaginal neutrophils, isotype control biol rep 4, Day 5

value: isotype control


title: P2112.1


title: PT_3 tumor VDJ


title: MEFs, 61R.1


title: PT_6 tumor VDJ


title: P2297.1


title: MEFs, 61H.9


title: Murine vaginal neutrophils, NK1.1 depleted biol rep 2, Day 5

value: Day 5


title: PT_2 tumor VDJ


title: P2164.1


title: PT_1 tumor VDJ


title: P2338.1


title: Murine vaginal neutrophils, isotype control biol rep 1, Day 5


title: MEFs, 61R.2


title: 47_GR1

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20).
reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis.
Reads were mapped onto the hg19 assembly of Homo sapiens genome using STAR version 2.5.3a. Gene expression quantiﬁcation was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 75 and “union” mode.
Only non-ambiguously assigned reads have been retained for further analyses. Read counts have been normalized across samples with the median-of-ratios method
Diﬀerential gene expression analysis was performed using the methodology implemented in the Bioconductor package DESeq2 version 1.16.1
P-values were adjusted for multiple testing by the method proposed by Benjamini and Hochberg
Deregulated genes were defined as genes with log2(foldchange) and adjusted p-value <0.05.
Assembly: hg19
Supplementary files format and content: xlsx file with matrix table with raw gene counts, RPKM values, log fold change expression values between non treated and treated cells for every gene and every sample

source_name: Skin

extract_protocol:
total RNA was extracted using NucleoSpin RNAplus kit from Macherey-Nagel following manufacture instructions.
Total RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Skin

tag: phenotype

value: wild-type


title: Murine vaginal neutrophils, isotype control biol rep 3, Day 5


title: PT_4 tumor VDJ


title: P1910


title: P1887


title: P1772


title: PT_8 LNM GEX

value: GEX-seq


title: HR3

first: Anna

last: Yeaton

address: 550 1st ave

institute: NYU Langone

data_processing:
Adaptors and low quality bases were trimmed with Trimmomatic
Reads were aligned with STAR
https://igordot.github.io/sns/routes/rna-star
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Bone Marrow

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

value: Bone Marrow

value: mononcytes

value: Tet2 mutant


title: P1679.1


title: 47_GR2


title: Murine vaginal neutrophils, isotype control biol rep 2, Day 5


title: 47_NEG1

value: GapmeR NEG_1


title: PT_6 LNM GEX

value: Lymph node metastasis

value: Invasive ductal carcinoma


title: P1775.1


title: HR2


title: PT_7 LNM GEX


title: WT3

value: wildtype


title: P1340


title: 501_GR2


title: PT_4 LNM GEX


title: 501_GR1


title: 501_NEG2

value: GapmeR NEG_2


title: P1360.1


title: WT1


title: 47_NEG2


title: PT_1 LNM GEX


title: PT_3 LNM GEX


title: RNA-seq, primary RPE, biol rep1

city: San Francisco

first: Kirsty

last: Jamieson

address: 400 Parnassus Ave

institute: University of California

data_processing:
For libraries having undergone paired-end sequencing, only the first read was used.
Reads were mapped using STAR and GENCODE V19 transcripts were quantified with RSEM using the standard ENCODE parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including gene expression estimates from RSEM
Supplementary files format and content: Signal tracks in bigwig format (separated for plus and minus strands)

source_name: RPE

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN #74104) according to its protocol.
The TruSeq Stranded mRNA protocol from Illumina was followed for library construction (catalog #RS-122-2101).

value: RPE

value: healthy


title: 501_NEG1


title: 3 dpi spinal cord

city: hangzhou

first: linlin

last: wang

state: zhejiang

address: Yuhangtang Road No.866

institute: zhejiang university

library_source: transcriptomic single cell

data_processing:
Mapping to GRCh38 human genome, quality control and read counting of Ensemble genes was performed by CellRanger software with default parameter (v2.1.0). Cells with more than or equal 200 genes and less than or equal 10% percentage of mitochondrial genes detected were retained for subsequent analyses.
Normalization, dimensionality reduction and clustering of single cells were also performed by CellRanger. Using top ten principal components, the dimensionality was reduced by uniform manifold approximation and projection (UMAP). Cell clustering were performed using the graph-based clustering algorithm which consists of building a sparse nearest-neighbor graph (where cells are linked if they among the k nearest Euclidean neighbors of one another), followed by Louvain Modularity Optimization.
Seurat-Bimod statistical test was used to find differentially expressed genes between each group of cells and other groups of cells (FDR <= 0.05 and |log2 Fold Change| >= 1.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized median scaling values for each cell

source_name: spinal cord

extract_protocol:
An 8 mm segment of the spinal cord centered at the injury site was dissected and digested to obtain a single cell suspension. Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed according to the manufacturer’s protocol.
Qubit was used for library quantification before pooling. The final library pool was sequenced on the Illumina Nova6000 instrument using 150-base-pair paired-end reads.

value: spinal cord

tag: age

value: 8 weeks

tag: Sex

value: pooled male and female


title: P1466.1

value: metastatic


title: PT_5 LNM GEX


title: P1325


title: P1670


title: RNA-seq, primary RPE, biol rep3


title: PT_2 LNM GEX


title: WT2


title: apoptotic osteoblasts (apoOBs)  from young  mice

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

data_processing:
After sequencing, raw reads were filtered using fastp software to remove low quality reads and residual Illumina adapters.
Filtered reads were aligned to mm10 reference genome by STAR.
The quantitative analysis of RNA-seq data were used by HTSeq software and differential gene expression was determined by edgeR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary cell

growth_protocol: For mouse apoptotic osteoblasts (apoOBs) culture, the bone tissue was cut into about 0.5mm pieces, and then cultured with complete medium (DMEM, 100 U/mL penicillin and 100 μg/mL streptomycin, 10% FBS) for 3 days, at which point nonadherent cells were removed by replenishing culture medium. Adherent cells were passaged once reaching 80%–90% confluence and after three passages, the purified bone marrow mesenchymal stem cells (BMSCs) were obtained and then cultured in osteogenic medium for 3 days to induce into osteoblasts. We obtained apoOBs by introducing osteoblasts under ultraviolet light for 0.5h (>90% Trypan Blue+).

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA libraries for RNA-seq were prepared using U-mRNASeq Library Prep Kit following manufacturer's protocols.

value: primary cell

value: apoptotic osteoblasts

value: young

value: Day 0


title: PT_8 tumor GEX

value: GEX-seq

value: Primary tumor


title: P1286.1


title: RNA-seq, iPSC-induced RPE, biol rep1

source_name: WTB

tag: cell line

value: WTB

value: iPSC-induced RPE

value: wild-type


title: PT_7 tumor GEX

value: Invasive ductal carcinoma


title: P1280.1

tag: tissue


title: RNA-seq, iPSCs, biol rep1

source_name: G3 iNGN2

value: G3 iNGN2

value: iPSCs


title: RNA-seq, iPSCs, biol rep2


title: P1267.1


title: sham spinal cord


title: BRG1 KO, H3K27ac

city: Kyoto

first: Osamu

last: Araki

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

data_processing:
Reads were aligned to the mouse reference genome (mm10) by Bowtie2 (version 2.4.2) with uniquely mapped reads extracted using Samtools (version 1.11).
Bigwig files for browser tracks visualization were generated by deepTools (version. 3.5.0)
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: pancreatic cancer cells

growth_protocol: Mouse pancreatic cancer cell lines was established from pancreatic cancer developed in the mice of Pdx1-Flp; Kras FSF-G12D; Trp53 frt/+; Rosa26 FSF-CreERT2; Brg1 lox/lox genotype and cultured with DMEM at 37C.

extract_protocol:
DNA was digested with micrococcal nuclease, and lysates were clarified from sonicated nuclei. Protein-DNA complexes were isolated with antibody.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: In the BRG1 knockout (KO) group, cancer cells were treated with 4-hydroxytamoxifen for four days. In the control group, cancer cells were treated with the solvent (methanol) for four days.

tag: disease state

value: pancreatic ductal adenocarcinoma (PDAC)

value: pancreas

value: 2D-cultured mouse pancreatic cancer cells

tag: treatment

value: Brg1 lox/lox; Pdx1-Flp; Kras FSF-G12D; Trp53 frt/frt; Rosa26 FSF-CreERT2 (treated with 4-hydroxytamoxifen)

value: BRG1 KO

tag: chip antibody


title: BRG1 KO, H3K27me3


title: PT_6 tumor GEX


title: apoptotic osteoblasts (apoOBs)  from old  mice

value: primary cell

value: old

value: Day 5


title: BRG1 wt, H3K27me3

value: Brg1 lox/lox; Pdx1-Flp; Kras FSF-G12D; Trp53 frt/frt; Rosa26 FSF-CreERT2 (treated with methanol)

value: BRG1 wt


title: P1322

value: metastatic

tag: patient


title: PT_5 tumor GEX

value: GEX-seq

value: Primary tumor


title: H1_hESC_WT_derived_hPGCLCs_p68

city: Haining

first: Wanlu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: RNA-seq of WT H1 induced hPGCLCs rep2

data_processing:
Raw reads in qseq format obtained from the sequencer were first converted to fastq files with a customized perl script. Read quality was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Illumina adaptor sequence were trimmed with Cutadapt (v2.3).
High-quality reads were aligned to the hg19 human reference genome using Tophat (v 2.0.13) by using “-no-coverage-search” option, allowing up to two mismatches, and only keeping unique reads.
The number of unique mappable reads was quantified by featureCounts (v 2.0.0) under default parameters.
Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads) in R using customized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: raw reads count of all samples

source_name: H1 WT hPGCLC

extract_protocol:
Total RNA was extracted from H1_hESC_WT_derived_hPGCLCs and H1_hESC_KLF4KO_derived_hPGCLCs at passage days 65 and 68, using RNeasy micro kit (Qiagen 74004).
Total RNA was reverse transcribed and cDNA was amplified using Nugen RNA-Seq System V2 (Nugen, 7102-32). DNA was extracted using MinElute PCR purification kit (Qiagen) and quantified using the Qubit dsDNA High-Sensitivity Kit (Life Technologies).  Amplified cDNA was fragmented using Covaris S220 Focused-ultrasonicator. RNA-sequencing libraries were generated using Nugen Rapid Library Systems (Nugen 0320-32). Libraries were subjected to single-end 125 bp sequening on HiSeq4000 with 6 indexed libraries per lane.

tag: cell type

value: H1 hESCs derived hPGCLC

value: WT

tag: passage number


title: H1_hESC_KLF4KO_derived_hPGCLCs_p68

description: RNA-seq of KLF4KO H1 induced hPGCLCs rep2

source_name: H1 KLF4KO hPGCLC

value: KLF4 KO


title: P1264.1


title: BRG1 wt, IgG

value: IgG


title: PT_3 tumor GEX

value: Invasive ductal carcinoma


title: H1_hESC_KLF4KO_derived_hPGCLCs_p65

description: RNA-seq of KLF4KO H1 induced hPGCLCs rep1


title: BRG1 wt, H3K27ac

value: pancreatic ductal adenocarcinoma (PDAC)

value: pancreas


title: PT_4 tumor GEX


title: P1266.1


title: P1283.1


title: BRG1 wt, BRG1

value: 2D-cultured mouse pancreatic cancer cells


title: PT_2 tumor GEX


title: rmPRL 5 [T5]

city: Riverside

first: Ameae

last: Walker

address: 900 University Ave.

department: Biomedical Sciences

institute: University of California Riverside

data_processing:
Whole transcriptome sequencing was performed using the Illumina NovaSeq 6000 system. Samples were enriched for mRNA (stranded) and sequenced by 100 base pair (bp) paired end (PE) reads (PE100, 80 million reads per sample).
Reads were quality assessed using FastQC quality assessment software and trimmed using a quality threshold of 15 and Truseq adapter sequences (reads shorter than 20bp were discarded, Trimmomatic)
Reads were aligned to the mouse mm10 reference genome with a splice aware short read aligner (Hisat2, Samtools)
FeatureCounts was used to quantify raw counts and two group comparison, using DESeq2 to identify differentially expressed genes between control and PRL-treated animals
Assembly: mm10
Supplementary files format and content: scaled raw counts

source_name: Infundibulum

extract_protocol:
Infundibula were removed, immediately frozen in liquid nitrogen, and RNA was extracted using Trizol reagent with on-column purification using the Qiagen RNeasy kit. Illumina TruSeq Stranded mRNA Library prep kit was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8-10 weeks

tag: estrous stage

value: proestrus

value: recombinant murine PRL

value: Infundibulum


title: PT_1 tumor GEX

tag: donor


title: rmPRL 4 [T4]


title: P1129.1

source_name: Pretherapeutic rectal cancer patient biopsy


title: rmPRL 3 [T3]


title: P1129.2


title: rmPRL 2 [T2]

value: diestrus


title: P0984.1


title: rmPRL 1 [T1]


title: P0365.1


title: P1195.1


title: P0348


title: WT saline control 5 [C5]

value: saline as a control


title: WT saline control 4 [C4]


title: H1_hESC_WT_derived_hPGCLCs_p65

description: RNA-seq of WT H1 induced hPGCLCs rep1


title: P1159.1

value: metastatic


title: DNA from 26°C embryos at stage S4_1

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
Genome mapping against Medicago reference genome MtrunA17r5.0-20161119-ANR.fasta using Bismark software.
Deduplication and identification of methylated cytosines were performed using Bismark to generate methylation calling files.
Bigwig files visualizing the whole-genome methylation contexts were generated using the jbmethylation plugin "bismark_to_bigwig_pe.py" available at https://github.com/bhofmei/jbplugin-methylation
Assembly: MtrunA17r5.0-20161119-ANR.fasta

organism: Medicago truncatula

source_name: Medicago truncatual embryos

growth_protocol: Plants were grown in a culture room in trays containing a sterile soil at 20°C/18°C (control) and 26°C/24°C (heat stress), with a 16 h light photoperiod.

extract_protocol:
DNA extraction was performed using Macherey Nagel NucleoSpin® Plant II kit following the protocol.
Samples were sent to BGI, Hong Kong, for sequencing: 1. Fragment genome DNA to 100-300bp by Sonication. 2. DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors. 3. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit. 4. Desalting, size selection, PCR amplification and size selection again. 5. Qualified library for sequencing
Sequencing PE150 using Illimina HiSeq2500 (>30M reads)

treatment_protocol: Heat treatment were applied from flowering time to mature seeds at 26°C

tag: developmental stage

value: embryo stage 4

value: produced at 26 degrees

tag: srain


title: DNA from 26°C embryos at stage S3_3

value: embryo stage 3


title: DNA from 26°C embryos at stage S3_2


title: P0331.1


title: InVitro, 24hr, OSC-19, OTS

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in OSC-19 cells treated with OTS514 for 24h

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K Microarrays (Agilent) for 17 hours at 65C°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: OSC-19, 24hr, OTS514 20 nmol/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The OSCC cell lines were incubated in a RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum. The cells were then treated with the indicated concentration of apigenin for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: oral squamous cell carcinoma (OSCC) cells

tag: gender

value: Male


title: InVitro, 24hr, SAS, OTS

description: Gene expression in SAS cells treated with OTS514 for 24h

source_name: SAS, 24hr, OTS514 20 nmol/L

value: SAS

value: Female


title: P0315.1


title: DNA from 26°C embryos at stage S4_3


title: DNA from 26°C embryos at stage S4_2


title: DNA from 26°C embryos at stage S2_3

value: embryo stage 2


title: DNA from 26°C embryos at stage S2_2


title: InVitro, 24hr, OSC-19, None

description: Gene expression in OSC-19 cells at 24 h of mock treatment

source_name: OSC-19, 24hr, no treatment

value: no treatment


title: P0391.1


title: InVitro, 24hr, HSC-3, OTS

description: Gene expression in HSC-3 cells treated with OTS514 for 24h

source_name: HSC-3, 24hr, OTS514 20 nmol/L


title: InVitro, 24hr, SAS, None

description: Gene expression in SAS cells at 24 h of mock treatment

source_name: SAS, 24hr, no treatment


title: II-M2f

value: II


title: InVitro, 24hr, HSC-2, OTS

description: Gene expression in HSC-2 cells at 24 h after OTS514 treatment

source_name: HSC-2, 24hr, OTS514 20 nmol/L


title: InVitro, 24hr, HSC-2, None

description: Gene expression in HSC-2 cells at 24 h after mock treatment

source_name: HSC-2, 24hr, no treatment


title: II-M2c


title: WT saline control 1 [C1]

tag: strain

value: 8-10 weeks


title: UUO rep2

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

description: AKI_merge_as matrix_RNA_data.zip

data_processing:
Sequencing data were parsed using Illumina bcl2fastq software (Version 2.20) and converted to FASTQ format files. The cleaned FASTQ files were processed using cellranger (Version 5.0.1).
The Seurat package was used to process the output files of cellranger. The following parameters were used to remove low-quality cells: (1) exclude cells expressing ≤500 or ≥4000 genes/cell; (2) exclude cells expressing ≤500 or ≥15000 unique molecular identifier per cell (UMIs/cell); (3) exclude cells with high cell complexity (log10GenesPerUMI) ≤0.8; (4) exclude cells with >30% mitochondrial ratio; (5) exclude doublets using the DoubletFinder (Version 2.0.3) package; (6) retain genes expressed in at least 10 cells.
The LogNormalize method of the "Normalization" function was used for expression homogenization.
We extracted the expression matrix of AKI and Ctrl from Seurat's Metadata.
Genome_build: GRCm38
Supplementary_files_format_and_content: expression matrix

source_name: Kidney

growth_protocol: C57BL/6 mice (8 – 10 weeks, 22 – 26 g, male) were obtained from the pathogen-free (SPF) facility of Fujian Medical University. All animal experiments were approved by the Laboratory Animal Management and Ethics Committee of Fujian Medical University and were performed in accordance with the "China Guide for the Protection and Use of Laboratory Animals". All mice were housed in a specific pathogen-free facility with a 12-hour light/dark cycle.

extract_protocol:
Harvested cells at the required densities were combined with gel beads containing the barcoded information along with a mixture of cells and enzymes. Oil surfactant droplets in a microfluidic "double-cross" system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled.
10X Genomics Chromium protocol

treatment_protocol: Kidneys were placed on ice-cold Dulbecco’s phosphate buffered saline (DPBS), debrided, cut longitudinally, and coronally sectioned. The renal pelvis portion of the kidney was then excised with a sterile razor, and the remaining tissue was washed in a 6 cm Petri dish with 1×DPBS to remove residues such as blood stains. Subsequently, the tissue was sheared to a size of 5×5 mm3. The cleaned samples were then transferred to 5 mL centrifuge tubes with 1×DPBS and placed on ice to rapidly shear the tissues to 1 – 3 mm3. Next, 10 times the volume of 1×DPBS was added to the sheared tissues which were cleaned by gentle blowing with a Pap sieve five times, and collected by filtering through a 70 μm cell sieve. The collected tissues were transferred into the prepared digestive enzyme solution (collagen II 2 mg/mL, collagen IV 2 mg/mL) and incubated for 30 min at 37 ℃, 100 rpm; the dissociated solution mixed with tissues and cells was transferred into 2 – 3 times the volume of 1×DPBS, washed by blowing with a Bass pipette and passed through a 40 μm cell sieve before the filtrate was collected. The filtered cell suspension was centrifuged at 300 g for 5 min at 12 °C. The supernatant was discarded and the remaining cells were collected. Any erythrocytes remaining in the cell fractions were removed by lysis in erythrocyte lysate for 3 – 10min. Subsequently, the precipitate was resuspended in 1×DPBS using 10 times the volume of cell suspension used in the previous step, washed 1 – 2 times, centrifuged again as previously described (300 g at 12 °C for 5 min). Cell densities were adjusted to 700 – 1200 cells/μL with 1640 (+5% (v/v) fetal bovine serum (FBS)) before analysis.

tag: sample group

value: unilateral ureteral obstruction (UUO)

value: Kidney


title: DNA from 26°C embryos at stage S3_1


title: InVitro, 24hr, HSC-3, None

description: Gene expression in HSC-3 cells at 24 h after mock treatment

source_name: HSC-3, 24hr, no treatment

tag: age


title: DNA from 26°C embryos at stage S1_2

value: embryo stage 1


title: DNA from 26°C embryos at stage S1_3


title: WT saline control 3 [C3]

value: proestrus

value: Infundibulum


title: UUO rep1

description: AKI_merge_as matrix_RNA_data.zip


title: SO rep2

description: AKI_merge_as matrix_RNA_data.zip

value: sodium oxalate (SO)


title: DNA from 26°C embryos at stage S1_1


title: II-L2a

description: PolyA-RNA-Seq

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM gene counts for every gene and every sample

source_name: Healthy liver tissue

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

value: Healthy liver tissue

tag: diagnosis

value: rectal cancer

tag: prognosis

value: Good - patient alive


title: SO rep1

description: AKI_merge_as matrix_RNA_data.zip

tag: tissue


title: aTCR rep1

city: 上海市

first: yansha

last: sun

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

institute: Shanghai Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,  then mapped to known_rRNA using bowtie2-2.2.6  with parameters  -p 16,then remove  rRNA reads
then mapped reads without rRNA to CRCh38  whole genome using hisat2-2.0.4 with parameters -t --dta  --known-splicesite-infile -k 1 --rna-strandness RF -p 16
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.  The whole quantitative step is completed by stringtie-1.3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt
Supplementary_files_format_and_content: FPKM.txt

source_name: aTCR

extract_protocol:
Different T cells were cocultured with GPC3 peptide for four hours. Total RNA was extracted from T cells using TRIzolTM Reagent (Invitrogen) and the RNA quality was checked using an Agilent Bioanalyzer 4200 (Agilent technologies). Then, the total RNA was purified with the RNA Clean XP Kit (A63987, Beckman Coulter) and DNase set (79254, QIAGEN).
Sequencing libraries were generated using VAHTS® mRNA-seq V2 Library Prep Kit for Illumina (NR603, Vazyme) according to the manufacturer’s instructions.

value: primary T cells

tag: genetic engineering

value: aTCR

value: cocultured with GPC3 peptide


title: aTCR rep2

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

tag: treatment


title: WT saline control 2 [C2]

value: saline as a control


title: IRI rep2

description: AKI_merge_as matrix_RNA_data.zip

value: ischemia reperfusion injury (IRI)


title: II-M2d

first: Darius

institute: Institute of Bioinformatics

description: PolyA-RNA-Seq

source_name: Liver metastasis

value: Liver metastasis


title: I-L3b

description: PolyA-RNA-Seq

value: I

value: Bad - patient died


title: BBζ CAR rep2

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

source_name: BBζ CAR

value: BBζ CAR


title: Pancreatitis-associated PSC2

city: Fukuoka

first: Weiyu

last: Guan

state: Fukuoka

address: maidashi, 3-1-1-, Higashi-ku

department: Department of Surgery and Oncology

institute: Kyushu university, Graduate school of medical science

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: pancreas, chronic pancreatitis

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from cultured cells using a High Pure RNA Isolation kit (#11828665001; Roche Diagnostics GmbH, Mannheim, Germany), according to the manufacturer’s instructions.

value: Chronic pancreatitis

value: pancreatic stroma tissue


title: DNA from 20°C embryos at stage S4_3

value: embryo stage 4

value: produced at 20 degrees


title: DNA from 20°C embryos at stage S4_2


title: I-L3a

city: Göttingen

address: Goldschmidtstr. 1

description: PolyA-RNA-Seq


title: Cancer-associated PSC5

source_name: pancreas, cancer

value: Pancreatic cancer


title: Cancer-associated PSC3


title: DNA from 26°C embryos at stage S2_1

value: embryo stage 2

value: produced at 26 degrees


title: BBζ CAR rep1

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403


title: DNA from 20°C embryos at stage S4_1


title: IRI rep1

description: AKI_merge_as matrix_RNA_data.zip

value: Kidney

value: 8-10 weeks


title: Pancreatitis-associated PSC3


title: 28ζ CAR rep2

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

source_name: 28ζ CAR

value: primary T cells

value: 28ζ CAR


title: I-M3e

description: PolyA-RNA-Seq

value: rectal cancer


title: FA rep2

description: AKI_merge_as matrix_RNA_data.zip

value: folic acid (FA)


title: DNA from 20°C embryos at stage S3_3

source_name: Medicago truncatual embryos

value: embryo stage 3


title: II-M2e

description: PolyA-RNA-Seq

value: Liver metastasis

value: II

value: Good - patient alive


title: 28ζ CAR rep1

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

value: cocultured with GPC3 peptide


title: FA rep1

description: AKI_merge_as matrix_RNA_data.zip


title: I-M3d

description: PolyA-RNA-Seq

value: I

value: Bad - patient died


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX9 g7-RNA-Seq

city: Cambridge

first: Dawei

last: Sun

address: Tennis Court Road

institute: University of Cambridge

data_processing:
Illumina software used for conventional basecalling
Reads were aligned to GRCh38 genome assembly (hg38) using STAR version 2.7.1a
Reads were summarized using featureCounts
Differentially gene expression analysis was performed using DESeq2 with cutoff (fold change >= 1; p_adjusted <= 0.05)
Genome_build: GRCh38 genome assembly (hg38)
Supplementary_files_format_and_content: DESeq2 output file with log2 (normalized read count+1), log2(fold change between selected groups) and adjusted p-value

source_name: human fetal lung organoid cells

growth_protocol: Organoids were maintained with self-renewing medium, containing EGF, FGF10, FGF7, Noggin, TGFb inhibitor, R-spondin1 and GSK3b inhibitor (detailed protocol in Nikolic et al., 2017).

extract_protocol:
mRNA was extracted using Qiagen RNeasy Mini Kit (74104)
Library was constructed using Eukaryotic RNA-seq (lib prep) service from Novogene (UK)

treatment_protocol: Organoids infected with inducible CRISPRi and the relevant gRNAs were treated with Dox and TMP for 5 days before being harvested for RNA-Seq (detailed infection and treatment protocol in Sun et al., 2021)

tag: organoid line

value: human fetal lung tissue derived organoid cells

value: 8 pcw human fetal lung

tag: grnas

value: SOX9 g7

value: Dox and TMP


title: CP rep1

description: AKI_merge_as matrix_RNA_data.zip

value: cisplatin (CP)

value: Kidney


title: I-M3b

last: Wlochowitz

description: PolyA-RNA-Seq

tag: patient


title: CP rep2

description: AKI_merge_as matrix_RNA_data.zip

value: 8-10 weeks


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX2 g8-RNA-Seq

tag: cell type

value: SOX2 g8


title: I-M3c

description: PolyA-RNA-Seq

value: rectal cancer


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX9 g1-RNA-Seq

value: SOX9 g1


title: P36

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description: pre-treatment breast cancer tumor from patient 36

data_processing:
Samples were aligned to hg19 using the STAR aligner using a GTF from GENCODE
We estimated the read counts using HTSeq-Count.
We checked data quality using CollectRnaSeqMetrics and CollectAlignmentSummaryMetrics from picard, as well as with custom code.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file contains read counts

growth_protocol: Pre-treatment tumor biopsies were collected from breast cancer patients.

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from tumors, treated with Dnase I, and depleted of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero Gold.
TruSeq Stranded Total RNA after depletion of cytoplasmic and mitochondrial ribosomal RNA.  Libraries were sequenced on an Illumina HiSeq 2000 instrument.

tag: mutation

tag: response

value: RCB-I


title: Contro rep2

description: Ctrl_merge_as matrix_RNA_data.zip

value: Control


title: DNA from 20°C embryos at stage S2_3

tag: developmental stage

value: embryo stage 2

value: produced at 20 degrees


title: DNA from 20°C embryos at stage S3_1

value: embryo stage 3

tag: srain


title: DNA from 20°C embryos at stage S2_2


title: P35

description: pre-treatment breast cancer tumor from patient 35

value: pCR


title: DNA from 20°C embryos at stage S2_1


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_NT2-RNA-Seq


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX2 g2-RNA-Seq

value: SOX2 g2


title: P34

description: pre-treatment breast cancer tumor from patient 34

value: RCB-II


title: P32

description: pre-treatment breast cancer tumor from patient 32


title: Control rep1

description: Ctrl_merge_as matrix_RNA_data.zip


title: HDBRN13393_human fetal lung organoid cells_CRISPRi_NT1-RNA-Seq

value: human fetal lung tissue derived organoid cells

value: 8 pcw human fetal lung


title: DNA from 20°C embryos at stage S1_3

value: embryo stage 1


title: DNA from 20°C embryos at stage S1_2


title: P31

description: pre-treatment breast cancer tumor from patient 31


title: P2_L4_M

city: Darlinghurst

first: Amy

last: Nicks

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

data_processing:
Sequencing reads were trimmed and adaptors using Trimmomatic4
Alignment to mm10 mouse reference genome was performed using STAR version 2.7.3a
Gene expression was quantified from read counts calculated by RNA STAR
Genome_build: mm10
Matrix table with raw gene counts for every gene and every sample

source_name: purified cardiomyocytes

extract_protocol:
RNA was extracted from cardiomyocytes by homogenising samples in QIAzol Lysis Reagent and performing column-based purification of RNA using miRNeasy Mini Kit (Qiagen).
Sequencing libraries were constructed from 1 µg of total RNA using stranded TruSeq total RNA library preparation kit (Illumina)
Libraries were sequenced on an Illumina NovaSeq 6000 aiming for a depth of 20 million 1x100bp single end reads per sample to generate RNA-Seq datasets.

value: postnatal day 2

tag: litter origin

value: litter 4

tag: Sex

value: male


title: P2_L3_F

tag: strain

value: litter 3

value: female


title: DNA from 20°C embryos at stage S3_2


title: BRC1915_human fetal lung organoid cells_CRISPRi_SOX9 g7-RNA-Seq

value: SOX9 g7

value: Dox and TMP


title: DNA from 20°C embryos at stage S1_1


title: P30

description: pre-treatment breast cancer tumor from patient 30


title: P2_L3_M

tag: age


title: P2_L2_F

value: litter 2


title: BRC1915_human fetal lung organoid cells_CRISPRi_SOX9 g1-RNA-Seq

value: SOX9 g1


title: P29

description: pre-treatment breast cancer tumor from patient 29


title: BRC1915_human fetal lung organoid cells_CRISPRi_SOX2 g2-RNA-Seq


title: Dom3_Brain

city: rehovot

first: Berta

last: Levavi-Sivan

state: Israel

address: Hertzel

department: Animal sciences

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Libraries were subjected to next generation sequencing using Illumina Genome Analyzer (HighSeq 2500, Illumina), which performed 100 bp single-end read sequencing
Raw reads (FASTQ files) were inspected for quality issues with FastQC v0.11.4 and trimmed for quality and adaptor removal using Trim Galore default settings
Single-end reads were mapped to O.niloticus using STAR v2.201
Uniquely mapped reads per gene were counted using HTSeq-count
Differential expression analysis was performed using the DESeq2 R package
Genome_build: GCA_001858045.3
Supplementary_files_format_and_content: Tab-delimited text file matrix includes normalized read counts for each gene in each sample
Supplementary_files_format_and_content: Tab-delimited text file matrix includes fold change and p value according to DESeq analysis, for each gene dominant and subordinate fish

organism: Oreochromis niloticus

source_name: mature male brain

growth_protocol: Nile tilapia (Oreochromis niloticus, Lake Manzala strain) were kept and bred in a recirculating water system at 26–28 °C and fed twice daily with commercial pellets (47% protein, 6% fat, Raanan Shivuk, Israel)

extract_protocol:
Total RNA isolation from pituitaries and brains was performed using miRNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. RNA quality and quantity were verified using 2100 Bioanalyzer instrument (Agilent Technologies)
RNA libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA)

treatment_protocol: Individual tanks were populated with two males and four to six females. Each male was marked using PRO MX reactive dye (PRO Chemicals & Dye) on the head or tail for identification. The tanks were monitored for social behavior twice a day for 14 days, pituitaries and brains from socialy stable dominant and subordinate males were harvested after 14 days.

tag: hierarchical status

value: Dominant

value: Brain

tag: gender


title: BRC1915_human fetal lung organoid cells_CRISPRi_SOX2 g8-RNA-Seq

value: SOX2 g8


title: Sub3_Brain

value: Subordinate

tag: tissue


title: P2_L4_F


title: Sub2_Brain


title: P25

description: pre-treatment breast cancer tumor from patient 25

value: RCB-II


title: P27

description: pre-treatment breast cancer tumor from patient 27


title: P2_L1_F

value: litter 1


title: Sub1_Brain


title: P2_L2_M


title: BRC1915_human fetal lung organoid cells_CRISPRi_NT1-RNA-Seq

value: human fetal lung tissue derived organoid cells

value: 8 pcw human fetal lung


title: Dom2_Brain


title: P24

description: pre-treatment breast cancer tumor from patient 24

value: pCR


title: P2_L1_M

value: postnatal day 2


title: LaubLab_Pacbio_DNApackaging_gafYZ_xyl

first: Kevin

last: Gozzi

state: MA

address: 31 Ames St

institute: Massachusetts Institute of Techonology

description: double-stranded DNA

data_processing:
For sample 1, raw reads from SMRTbell sequencing were consolidated to consensus reads via standard protocols by the BioMicroCenter at MIT. Consensus reads were mapped to the Caulobacter genome using the following function: bowtie2 -p 6 -x NA1000 -U Laublab_PacBio_Pxyl-gafYZ_Cc_GTApackaging_fastq -S {}.sam. The sam file was converted to a bam using: samtools view -Sbo {}.bam {}.sam. The bam file was sorted with: samtools sort {}.bam {}_sorted. Genome coverage of reads was calculated using the bedtools function: genomeCoverageBed -ibam {}_sorted -g NA1000 -bg > output.txt. Final conversion of the bedgraph file to a wig file (finaloutput.txt) was performed manually with a simple R script.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: File ending with .txt: tab-delimited text file of nucleotide-resolution coverage from PacBio data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: For sample 1, additional 0.3% xylose was added to induce expression of gafYZ from the xylose promoter prior to DNA extraction.

extract_protocol:
For sample 1, total DNA was extracted from cells using Qiagen Cell Lysis and Protein Precipitation. Protocols are listed in the Supplementary Materials.
other (PacBio SMRTbell sequencing)
SMRTbell sequencing

treatment_protocol: Sample 1 was treated with exogenous 0.3% xylose (final concentration) to induce expression from the plasmid.

tag: sample type

value: mixed population, stationary phase

tag: genotype

value: CB15N with pBXMCS-2::Pxyl-gafYZ

value: 0.3% xylose


title: Dom1_Brain

value: male


title: CBL-B2

city: Innsbruck

first: Dominik

last: Wolf

address: Anichstrasse 35

department: Dpt. Hematology and Oncology

country: Austria

institute: Medical University Innsbruck

data_processing:
Filtering, mapping and gene expression quantification using Cell Ranger v3.0.2
Filtering and normalization using Seurat v3.0.0 with sctransfrom normalization approach
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables (csv) with filtered and normalized (sctransformed) single-cell gene expression values

source_name: in vitro differentiated Th9 cells

extract_protocol:
Th9 cells were generated in vitro from naïve CD4+ T cells that were isolated from the murine spleen using the naive CD4+ T cells isolation kit from Miltenyi Biotec. Cells from 6 samples in total (3*WT, 3*Cblb-/-) were polarized into Th9 cells (3ng/ml hTGFβ, 20ng/ml IL-4 and 20µg/ml anti-IFNγ) for 48h and purified using CD4 (L3T4) MicroBeads from Miltenyi Biotec.
Library preparation was performed using the 10x Genomics Single Cell 3’ reagent Kits v3 according to manufacturer’s specifications.
single-cell RNA-seq

value: Cblb-/-


title: Sub3_Pit

source_name: mature male Pituitary

value: Pituitary


title: P23

description: pre-treatment breast cancer tumor from patient 23


title: PBMCs, mRNA-derived cDNA

city: San Francisco

first: Jessica

last: Neely

state: California

address: 550 16th Street

department: Pediatrics

institute: UCSF

description: RNA counts matrix

data_processing:
CellRanger (v3.1.0) was run to align reads to the GRCh38 genome build and generate counts matrices and binary alignment files (BAMs).
Each BAM was inputted into freemuxlet for donor-of-origin annotation and doublet removal. To assign cells to donors of origin in our multiplexed design, we used the genetic demultiplexing tool freemuxlet and a sample matching script, each being part of the popscle suite of population genetics tools (https://github.com/statgen/popscle) to assign cells to donors
Heterotypic doublets detected by demuxlet were removed, and additional homotypic doublets (i.e. two cells from the same individual co-encapsulated) were removed using doubletdetector.
Gene and protein expression matrices (4 each) were subsequently processed using Scanpy (v1.5.1).  A full description of data processing can be found here: https://www.medrxiv.org/content/10.1101/2021.09.18.21263581v1
Genome_build: hg38
Supplementary_files_format_and_content: counts_for_GEO.csv (RNA counts matrix)
Supplementary_files_format_and_content: adts_for_GEO.csv (ADT counts matrix)
Supplementary_files_format_and_content: metadata_for_GEO.csv (sample metadata)
Supplementary_files_format_and_content: long1_umap_coords.csv (UMAP coordinates to reconstruct UMAP)

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated and cryopreserved until the day of the experiment.
Our experimental protocol followed the manufacturer’s user guide (10X 3’V3 Document CG000185 Rev B, 10X Genomics) with certain modifications to isolate and amplify antibody-derived DNA tags (ADTs). Full details can be found here: https://www.medrxiv.org/content/10.1101/2021.09.18.21263581v1

tag: individual

value: 4 treatment-naïve JDM (TN-JDM) subjects and 4 subjects with inactive disease

tag: time

value: 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months

value: peripheral blood mononuclear cells (PBMCs)

tag: data type

value: RNA


title: MARC145-highpx-3

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

data_processing:
Raw sequences were checked the quality of the data  with FastQCv0.11.7 program before proceeding.
The adapter sequences were removed using BBDuk adaptor and quality trimming version 38.84 (Bushnell, B.,2014).
The trimmed reads of the low-passaged and high-passaged virus were mapped to the sequence of shaan virus (GenBank accession number. MG230624.1) using the Geneious Prime Bowtie 2 plugin version 2.3.0.
Transcript expression level in cells infected with shaan virus were calculated based on annotation on a reference shaan virus (MG230624.1). The transcript abundance was counted and normalized to the TPM (Transcript per Million mapped reads) value considering the read count, transcript length, and depth of coverage.
Assembly: Genbank accession no. MG230624.1

organism: Chlorocebus aethiops

growth_protocol: MARC-145 cell lines derived from African green monkey kidney, were cultured in DMEM (Gibco, NY, USA, Cat.11995) supplemented with antibiotic-antimycotic (100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 µg/mL amphotericin B, Gibco, NY, USA, Cat.15240) and 10% foetal bovine serum (Hyclone, NY, USA, Cat.SV30207). HEK-293, A549, and HRT18 cell lines of human kidney, lung, and colon origin, were cultured in MEM(Gibco, NY, USA, Cat.10370) and RPMI1640(Gibco, NY, USA, Cat.A10491) media with 10% foetal bovine serum (FBS) and antibiotic-antimycotic, respectively. All cells were maintained in an incubator at 37℃ with 5% CO2. Shaan virus isolate (B16-40, Genbank accession no. MG230624.1) was cultured in MARC-145 cells. To amplify the isolated shaan virus B16-40, 1 × 105/mL of MARC-145 cells were seeded into tissue culture flasks in DMEM (5% FBS) and incubated overnight. A monolayer of MARC-145 cells was infected with shaan virus (B16-40) at a multiplicity of infection (MOI) of 0.1 and the cytopathic effect (CPE) was confirmed in infected cells at 5 days post-inoculation (DPI). The virus harvested by freeze-thawing the infected cells was further used to infect a new monolayer of MARC-145 cells for the next passages.

extract_protocol:
The infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing.
The RNA libraries were prepared with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing accroding to the manufacturer's instruction.

treatment_protocol: The prepared low- (p4) and high passaged shaan virus (p44) in MARC-145 cells were inoculated in triplicate to different host cells, HEK-293, A549, and HRT18 cell lines at M.O.I of 0.5 for 2 hours. The infected cells were incubated with the maintenance medium for each cell line for 24hrs.

value: kidney

tag: cell type

value: Epithelial cells

tag: cell line

tag: treatment

value: infected with Shaan virus p43


title: P21

description: pre-treatment breast cancer tumor from patient 21

tag: mutation

tag: response

tag: patient


title: Dom3_Pit

value: Dominant


title: CBL-B1


title: BRC1915_human fetal lung organoid cells_CRISPRi_NT2-RNA-Seq

tag: organoid line

value: human fetal lung tissue derived organoid cells

tag: developmental stage

value: 8 pcw human fetal lung

tag: grnas

value: Dox and TMP


title: WT4

value: wild-type control


title: MARC145-highpx-2


title: P17

description: pre-treatment breast cancer tumor from patient 17

value: pCR


title: P18

description: pre-treatment breast cancer tumor from patient 18

value: RCB-III


title: MARC145-highpx-1


title: Sub2_Pit

tag: hierarchical status

value: Subordinate

value: male


title: P26

description: pre-treatment breast cancer tumor from patient 26


title: Sub1_Pit

value: Pituitary

tag: gender


title: MARC145-lowpx-3

tag: tissue

value: infected with Shaan virus p3


title: P19

description: pre-treatment breast cancer tumor from patient 19


title: WT1


title: MARC145-lowpx-2


title: MCF7, input

city: Los Angeles

first: MICHAEL

last: KRONENBERG

state: CA

address: 615 Charles E Young Drive S

department: Biological Chemistry

institute: UCLA

data_processing:
Fastq reads were QC'd with fastqc.
Fastq reads were trimmed from the 5' end to remove non-specific basecalling.
Fastq reads were aligned to the UCSC hg19 genome using bowtie2. Reads with a MAPQ score less than 30 were removed. Duplicate reads were removed. Uniquley mapped reads with greater than 2 mismatches were removed.
Peak summits were called using MACS2 with the significance cut off value of q = 0.01.
Bigwig files were generated using Python Deeptools package. Scores represent the log2 enrichment in counts per million between IP and input in 50bp bins.
Assembly: hg19
Supplementary files format and content: bigWig, bed

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1% antibiotic/antimycotic. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 10% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode BioRuptor.
ChIP-seq libraries were prepared using the KAPA HyperPrep kit complemented with KAPA UDI adaptors. 10ng of DNA was used as starting material for input and ip samples. Samples were subject to double-sided size selection at a range of 150-350bp. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Epithelial metastatic breast adenocarcinoma

tag: chip antibody


title: WT3

tag: genotype


title: P16

description: pre-treatment breast cancer tumor from patient 16

value: RCB-I


title: P15

description: pre-treatment breast cancer tumor from patient 15


title: MCF7, ACTR5 ChIP

value: Proteintech, Cat# 21505-1-AP, RRID:1234


title: CBL-B3

value: Cblb-/-


title: Dom2_Pit


title: MARC145-lowpx-1

value: kidney

value: Epithelial cells


title: Dom1_Pit

value: Dominant


title: T-dVMV-RIG-3 [T-dVMV-RIG-3_GCCAAT]

status: Public on Apr 29 2022

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
To compute coverage on viruses, Bowtie version 1.2.2 14 , with default parameters, was used for alignment on the reference genomes. Only first base of each read are used as input of genomeCoverageBed from Bedtools 15 . Minus and plus strand coverage are separated by a simple awk command.
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: DESeq2 output

organism:
Homo sapiens
Measles morbillivirus

source_name: INPUT RNA extracted on RIG-I protein

extract_protocol: Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 or 6 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

tag: cell line background

tag: genotype/variation

value: RIG-I protein tagged 1-STrEP tag

tag: infection

value: measles virus (deltaV)


title: T-dVMV-RIG-2 [T-dVMV-RIG-2_CTTGTA]


title: T-dVMV-Ch-3 [T-dVMV-Ch-3_GATCAG]

source_name: INPUT RNA extracted on Cherry protein

value: Cherry protein tagged 1-STrEP tag


title: T-dVMV-RIG-1 [T-dVMV-RIG-1_ACAGTG]


title: B-dVMV-RIG-2 [B-dVMV-RIG-2_CTTGTA]

source_name: OUTPUT RNA extracted on RIG-I protein


title: T-dVMV-Ch-1 [T-dVMV-Ch-1_ACTTGA]


title: B-dVMV-RIG-3 [B-dVMV-RIG-3_GCCAAT]


title: T-dVMV-Ch-2 [T-dVMV-Ch-2_TTAGGC]


title: B-dVMV-Ch-3 [B-dVMV-Ch-3_GATCAG]

source_name: OUTPUT RNA extracted on Cherry protein


title: B-dVMV-RIG-1 [B-dVMV-RIG-1_ACAGTG]


title: B-dVMV-Ch-1 [B-dVMV-Ch-1_ACTTGA]


title: T-RIG-HIV1-1

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
To compute coverage on viruses, Bowtie version 1.2.2 14 , with default parameters, was used for alignment on the reference genomes. Only first base of each read are used as input of genomeCoverageBed from Bedtools 15 . Minus and plus strand coverage are separated by a simple awk command.
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: Matrix count for each sample (after genomeCoverageBed)

organism:
Homo sapiens
Human immunodeficiency virus 1

growth_protocol: Cells were maintained in DMEM-Glutamax (GIBCO, Thermo Fisher Scientific, Waltham, Massachusetts) supplemented with 10% heat-inactivated FCS (Invitrogen, Thermo Fisher Scientific, Waltham, Massachusetts),100 U/ml/100 mg/ml of Penicillin-Streptomycin (GIBCO), and G418 at 500 mg/ml (#G8168, SIGMA, St. Louis, Missouri).

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 or 6 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

treatment_protocol: ST-RLR4X4 (tagged) cells were co-cultivated with HIV-1-infected cells MT4C5 cells .5*107 MT4C5 (donor cells) were exposed 150ng (equivalent p24) of HIV-1 NL4.3 for 2hr at 37°C. After washing the virus, the cells were grown for 48h. The infection was monitored by flow cytometry analysis by intracellular Gag staining. Infection was then performed via coculture of ST-RLR4X4 cells and MT4C5 cells at a donor:target cell ratio of 1:1. 24 h post infection, cells were lysed and affinity purification of ST-tagged proteins and RNA extraction was performed as described in DOI: 10.7554/eLife.11275


title: T-MDA5-HIV1-3

source_name: INPUT RNA extracted on MDA5 protein

value: MDA5 protein tagged 1-STrEP tag


title: T-MDA5-HIV1-2


title: T-RIG-HIV1-3


title: T-LGP2-HIV1-3

source_name: INPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag