title: HeLa,ACSS2,CHIP,rep2

city: Tianjin

first: wang

middle: si

last: yu

address: No. 22, Meteorological Tai Road, Heping District

institute: Tianjin Medical University

data_processing:
Sequencing quality was evaluated by FastQC version (v0.11.9). All reads were aligned to the human genome build hg38 using the Bowtie2 (v2.4.5) with the default parameters.
Duplicate reads were removed using Picard tools (version 2.27.4). Then Samtools version (1.15.1) was used to convert and sort files to bam format.
Uniquely mapped reads were normalized using deepTools (version 3.5.1) with the parameters --normalizeUsing RPKM --binSize 50 to visualize CUT&Tag signals at specific genomic loci by IGV (version 2.15.1)
Peaks were identified for each sample and biological replicate using MACS2 (version 2.2.7.1) with command line options “macs2 callpeak -q 0.05 -g hs -f BAM --nomodel”.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: cervix

growth_protocol: Cells were cultured with DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were cultured at 37 °C at 5% CO2.

extract_protocol:
HeLa cells were collected and counted for incubation with pre-treated ConA beads. Subsequently, cells are resuspended in an Antibody Buffer and incubated overnight at 4 °C with the corresponding primary antibody of HBO1 or H3K9la. The secondary antibodies were diluted in appropriate proportions and incubate them with the cells at room temperature. Subsequently, pA/G-Tnp transposons were rotated and incubated with the samples for 1h to activate the translocase fragment DNA and extract DNA.
DNA library was constructed with TruePreP Index Kit V2 for Illumina. The library was purified by VAHTS DNA Clean Beads and sequenced by Illumina novaseq 150PE.

treatment_protocol: Cells were treated with 10 mM BHB for 24 h.

value: cervix

value: HeLa

value: Human cervical cancer cell

value: treatment of BHB


title: WT_F_Flu1

status: Public on Jul 02 2025

type: SRA

city: NEW HAVEN

first: Yifan

last: Yuan

state: CT

address: 10 Amistad st, 314

country: USA

institute: yale university school of medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
RNA-Seq Data Filtration, Normalization, Scaling, Integration, and Clustering: Aligned data was processed using Seurat v3.1.2 under R environment. Default parameters were used for each function unless otherwise specified. After creating Seurat objects for each sample, we filtered on the percent mitochondrial genes to exclude damaged and dying cells and on the number of genes and transcripts to remove debris and doublets. All samples after filtration were integrated by the IntegrateData function in Seurat. The gene counts in the integrated object were then normalized to the total counts and multiplied by a 10,000 scaling factor. We used Variance Stabilizing Transformation (VST) to select highly variable genes. The top 200 genes within the selected genes were retained for downstream analysis. Variable genes were scaled using Seurat’s ScaleData function and subsequently were used for principal component analysis (PCA) to generate clusters. The numbers of clusters produced using PCA analysis are controlled by a resolution parameter with higher values giving more clusters and by the number of PCs. All cells across different samples were assigned into two-dimensional Uniform Manifold Approximation and Projection (UMAPs).
Assembly: GRCm38.p6(GCA_000001635.8)
Supplementary files format and content: barcodes.tsv.gz; matrix.mtx.gz; features.tsv.gz; CellRanger processed data

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Lung samples from WT and TLR9-/- animals were obtained on day 4 post-infection to determine cell-specific differences in early infection and antiviral responses.

extract_protocol:
Lung samples across different conditions were digested with collagenase type 4 (2mg/ml) and DNase (20U/ml) in DMEM with 10% FBS to prepare single-cell suspension for an expected cell recovery population of 10,000 cells per lane.
scRNAseq libraries were generated with the Chromium Single Cell 3’ assay (10x Genomics) and were sequenced on the NovaSeq platform per library in Yale Center for Genomics Analysis. Downstream processing was conducted with Cellranger 3.0.2 with the default parameters.

treatment_protocol: No treatment was provided other than the infection or mock infection (with PBS) under ketamine/xylazine anesthesia.

tag: tissue

value: Lung

tag: genotype

value: Wildtype

tag: treatment

value: Flu


title: WT_PBS1 (M+F)

description: 10x Genomics

value: PBS


title: BMDM, 0h, RRP1,RIP,replicate2

city: Suzhou

first: Zhou

last: Yumei

address: No.100,Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences

library_source: other

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Seqtk v1.0-r82-dirty, discarding reads left with < 20 bp
RIP-seq reads were aligned to the ensembl mm10 genome using Tophat2 version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to FPKM)
Peaks were called using RIPSeeker with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include peak values for each Sample

molecule: other

source_name: bone marrow

growth_protocol: Bone marrow was harvested from C57BL/6 mice and cultured in DMEM medium supplemented with 25 ng ml−1 murine M-CSF, 10% FBS, and 1 Penicillin-Streptomycin.The cells were cultured for 7 days with fresh media changed every other day

extract_protocol:
Cells were harvested using RIP lysis buffer. A primary antibody that recognized RRP1 or control IgG was added to the supernatants overnight at 4°C. Protein A/G Magnetic Beads were then added and gently mixed for 1 h at 4°C. The beads were washed with NT2 buffer 5 times before digestion with Proteinase K in buffer for 30 min at 55°C to remove proteins. The RNA was isolated using TRIzol LS and further assessed by high-throughput sequencing.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using randomhexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. Endreparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCRamplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: Cells were treated with 50 ng/mL IL-1β for the indicated hous.

value: bone marrow

tag: cell line

value: bone marrow derived macrophages

tag: cell type

value: macrophages

value: wilde tye

value: no IL-1B stimulated


title: HeLa,ACSS2,CHIP,rep1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: HRCRC3310_RNA-seq

city: Daejeon

first: Jeewoo

last: Seo

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

library_source: transcriptomic

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.7.3a).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

molecule: total RNA

source_name: non-mucinous colorectal cancer tissue

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were assessed using the RNA Integrity Number (RIN).
TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA)

tag: disease state

value: Non-mucinous adenocarcinoma

tag: Sex

value: male

tag: age

tag: tumor stage

value: IV

value: non-mucinous colorectal cancer tissue


title: TLR9_KO_M_Flu2

description: 10x Genomics


title: CLIP-seq_BCAS_SpB_IgG_rep2

city: Beijing

first: changchang

last: cao

state: China

address: Datun, 15

institute: IBP

data_processing:
*library strategy: CLIP-seq
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
For CLIP-seq, UMIs were first trimmed and added to the name of read names. After removing adaptor sequences, CLIP-seq reads longer than 18nt were mapped to the reference mouse genome (mm10) with Bowtie. Duplicated reads were collapsed based on both UMIs and mapping positions.
For RNA-seq, paired-end clean reads were aligned to this reference genome using HISAT2 software (version 2.0.5). FeatureCounts (version 1.5.0) was then employed to enumerate reads mapped to each gene. Following this, an FPKM value of each gene was calculated, factoring in both the gene's length and the read count mapped to it. Differential gene expression between Bcas2-cKO and control mice (comprising a biological replicate per condition) were conducted using the DESeq2 R package (version 1.20.0). Genes demonstrating a padj value ≤0.05, as identified by DESeq2, were delineated as differentially expressed.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software

source_name: Spleen

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the 100000000 isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of BCAS2 (Abmart, Catalog # PA2466S) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3’RNA linker ligation and 5’end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed BCAS2 smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5’ RNA linker and reverse transcribed by superscript reverse transcriptase III (life technologies, catalog# 18080-051). The PCR products were sequenced with illumina Hiseq 2500 platform. RNA-seq was performed as follows. mRNA from B cells was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, a transcriptome sequencing library was established. Utilizing a TruSeq PE Cluster kit v3-cBot-HS (Illumina) on a cBot Cluster Generation System, index-coded samples were clustered in strict accordance with the manufacturer’s guidelines. Upon completion of the clustering process, the library preparations were subjected to sequencing on the Illumina NovaSeq platform, generating 150 bp paired-end reads. Rigorous quality control measures were implemented post-sequencing to ensure that downstream analyses were performed exclusively on pristine, high-quality data.

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days.

value: Spleen

tag: strain

value: B cells

value: Wild type

value: No treatment

tag: antibody

value: anti-IgG


title: Li-Ma-KD (CD45+ immune cells, Liver with Tim3-KD metastasis, Macrometastasis timepoint)

city: Barcelona

first: Toni

last: Celià-Terrassa

address: C/ del Dr. Aiguader, 88, Ciutat Vella,

country: Spain

institute: Hospital del Mar Research Institute

description:
Li-Ma.barcodes.tsv.gz
Li-Ma.barcodes.tsv.gz
Li-Ma.matrix.mtx.gz

data_processing:
Reads 2 with a white-listed cell barcode extracted from Reads 1 were selected.
Reads were trimmed using TrimGalore (v.0.4.3) with default parameters.
Then they were mapped using STAR (v.2.7.7a) using default parameters.
Only reads mapping to exons or introns were used for downstream analyses.
Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Only cells with more than 1000 umi-corrected reads, less than 0.5M umi-corrected reads, more than 1000 genes, and less than 20% mitochondrial read fraction were kept for downstream analysis.
Doublet identification was performed using the python package scrublet, setting the doublet score at 0.15.
Highly variable genes were identified as those with mean expression between 0.025 and 3; and minimum dispersion equal to 0.5.
Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Assembly: GRCm38, Ensembl 102
Supplementary files format and content: barcodes.tsv: These files contain the unique molecular identifiers (UMIs) associated with individual cells. There is one for each fenotype (Li-Ma, Li-Mi, Li-NT).
Supplementary files format and content: features.tsv: These files contain the genes whose expression is quantified in the experiment. It contains a list of genes and their corresponding identifiers. There is one for each fenotype (Li-Ma, Li-Mi, Li-NT).
Supplementary files format and content: matrix.mtx: These files contain the gene expression data for each fenotype (Li-Ma, Li-Mi, Li-NT). It is a tabular representation of each row (features) and each column (barcodes).

source_name: Liver

extract_protocol:
5x5mm sections of liver metastasis was isolated to obtain immune cell suspension to perform CD45+ cell sorting. Then, single cells were submitted to squencing.
cDNA sequencing libraries were prepared using the Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000268)
Briefly, after GEM-RT clean up, cDNA was amplified during 12 cycles and cDNA quality control and quantification were performed on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). cDNA libraries were indexed by PCR using the PN-1000215 Dual Index Kit TT Set A. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). Finally, sequencing of cDNA libraries was carried out on an Illumina NovaSeq 6000 using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10bp (i5 index) + 90 bp (Read 2), to obtain approximately 20-30.000 reads per cell.

value: Liver

value: CD45+ Immune cells

tag: time

value: Day 12


title: RNA-seq_cKO_rep1

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
For CLIP-seq, UMIs were first trimmed and added to the name of read names. After removing adaptor sequences, CLIP-seq reads longer than 18nt were mapped to the reference mouse genome (mm10) with Bowtie. Duplicated reads were collapsed based on both UMIs and mapping positions.
For RNA-seq, paired-end clean reads were aligned to this reference genome using HISAT2 software (version 2.0.5). FeatureCounts (version 1.5.0) was then employed to enumerate reads mapped to each gene. Following this, an FPKM value of each gene was calculated, factoring in both the gene's length and the read count mapped to it. Differential gene expression between Bcas2-cKO and control mice (comprising a biological replicate per condition) were conducted using the DESeq2 R package (version 1.20.0). Genes demonstrating a padj value ≤0.05, as identified by DESeq2, were delineated as differentially expressed.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software

value: Bcas2 KO

value: LPS+IL4 treatment

value: No antibody


title: Li-Ma-C (CD45+ immune cells, Liver with Control metastasis, Macrometastasis timepoint)

value: Control


title: Lenti DNA seq rep 2

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

data_processing:
Barcodes were mapped to the barcode map processed file to construct a barcode count matrix
Assembly: hg19
Supplementary files format and content: AD_MPRA_countTable.txt; barcode counts across all samples and their respective variant to be used for downstream processing, AD_MPRA_Barcode_Map.txt; barcode to variant mapping
Library strategy: MPRA

source_name: lentiviral construct

growth_protocol: THP-1 monocytes were cultured in RPMI 1640 media with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from resting and treated macrophages and reverse transcribed into cDNA. cDNA was amplified with GFP primers to select for barcodes.
Modified MPRA library preparation

treatment_protocol: THP-1 monocytes were transduced with lenti-MPRA and grown for 5 days before being differentiated into macrophages by treatingw ith 25 µM PMA for 24h. After 72h rest, macrophages were treated with 10 ng/mL of LPS and  20 ng/mL INFγ for 24h to induce a proinflammatory state.

value: lentiviral construct


title: WT_M_Flu3

description: 10x Genomics

value: Lung

value: Wildtype

value: Flu


title: HRCRC3304_RNA-seq

value: Non-mucinous adenocarcinoma

value: female

value: IIIC

value: non-mucinous colorectal cancer tissue


title: HeLa-HBO1-KO,H3K9bhb,CHIP,rep1

value: cervix

value: HeLa

value: Human cervical cancer cell


title: CLIP-seq_BCAS_SpB_IgG_rep1

value: Spleen

value: B cells

value: Wild type

value: No treatment

value: anti-IgG


title: HRCRC3258_RNA-seq

value: IIIB


title: HeLa,H3K9bhb,CHIP,rep2

value: treatment of BHB


title: TLR9_KO_PBS1 (M+F)

description: 10x Genomics

value: Lung

value: PBS


title: Li-Mi-KD (CD45+ immune cells, Liver with Tim3-KD metastasis, Micrometastasis timepoint)

description:
Li-Mi.barcodes.tsv.gz
Li-Mi.features.tsv.gz
Li-Mi.matrix.mtx.gz

value: Liver

value: CD45+ Immune cells

value: Day 3


title: HRCRC3245_RNA-seq

value: Non-mucinous adenocarcinoma

value: male

value: IIA


title: CLIP-seq_BCAS_SpB_LPS_rep2

value: LPS treatement


title: Li-Mi-C (CD45+ immune cells, Liver with Control metastasis, Micrometastasis timepoint)

value: Control


title: HeLa,H3K9bhb,CHIP,rep1

value: cervix

value: HeLa

value: Human cervical cancer cell


title: HRCRC3232_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: MTCRT551_RNA-seq


title: CLIP-seq_BCAS_SpB_rep2

value: Spleen

value: B cells

value: Wild type

value: No treatment


title: Li-NT-C (CD45+ immune cells, Liver with Control metastasis, No tumor sample)

description:
Li-NT.barcodes.tsv.gz
Li-NT.features.tsv.gz
Li-NT.matrix.mtx.gz

value: Liver


title: HeLa,HBO1,CHIP,rep2

value: treatment of BHB


title: Li-NT-KD (CD45+ immune cells, Liver with Tim3-KD metastasis, No tumor sample)

value: CD45+ Immune cells

value: Day 3


title: CLIP-seq_BCAS_SpB_rep1


title: HeLa-HBO1-KO,H3K9bhb,CHIP,rep2


title: HeLa,HBO1,CHIP,rep1


title: MTCRT549_RNA-seq

value: Non-mucinous adenocarcinoma

value: I


title: MTCRT546_RNA-seq

value: male

value: IIIB


title: shYBX1_MNNG/HOS_3

city: Wuhan

first: Li

last: Cao

state: Hubei

address: Hangkong Road 13, Wuhan, China

department: Wuhan Union Hospital

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (YBX1-AS) and regulated alternative splicing events (YBX1-RAS) between shYBX1 and shNC samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MNNG/HOS cells

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: MNNG/HOS cells

value: YBX1 knock down in MNNG/HOS cell


title: L13a knockout replicate 9 (treated by IL4)

city: Cleveland

first: Peng

last: Jiang

address: 2399 Euclid Avenue, FH468

institute: Cleveland State University

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
Genome_build: mm10
Supplementary_files_format_and_content: text and gene expression values

source_name: Bone marrow derived macrophages

extract_protocol:
RNA was abstracted from macrophage
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer  primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
RNA-seq: The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on  Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: M1 and M2 cytokines

tag: macrophages

value: L13a KO


title: EpRas cells, Brain, Balb/c, replicate 2

data_processing:
Quality checking of raw data (fastq files) was performed with FastQC software (v.0.11.9).
Estimation of ribosomal RNA in the raw data was obtained with riboPicker74.
Raw reads were trimmed using TrimGalore (v.0.6.6) with a quality cutoff of 30.
The trimmed data was then aligned with the STAR (v.2.7.8a) mapper75 to the Mus musculus genome
The raw count of reads per gene and per sample were obtained with STAR (quantMode TranscriptomeSAM GeneCounts option)
The R/Bioconductor package DESeq2 (v.1.30.1) was used to assess differential expression between experimental groups (Wald statistical test plus false discovery rate (FDR) correction). Genes for which the sum of raw counts across all samples was <1 were discarded. Genes are considered differentially expressed if their absolute log2 fold change was >1 and their adjusted p-value < 0.05.
Assembly: Gencode release M24 of the GRCm38/mm10 assembly
Supplementary files format and content: htseq_.txt: Tab-delimited text file containing the feature Ids and their corresponding read counts.

source_name: Brain

growth_protocol: EpRas cells were mantained in DMEM media supplemented with 10% of Fetal Bovine Serum (FBS), 2mM L-Glutamine (Glu) and 1% Penicilin/Streptomycin (P/S).

extract_protocol:
Metastatic organs (liver, lung, brain) were mechanically and enzymatically digested into single cells. Sorting of GFP+ tumor cells was performed and then RNA was harvested using RNAeasy Mini Kit (QIAGEN).
Poly-A sequencing was selected for library preparation

treatment_protocol: Intracardiac injection of tumor cells were performed in Balb/c mice (20.000 cells) and in NSG mice (10.000 cells).

value: Brain

value: EpRas

value: EpH4 cells transformed by oncogenic Ha-Ras

value: WT

value: Day 25


title: EpRas cells, Brain, NSG, replicate 2

value: Day 24


title: shYBX1_MNNG/HOS_2


title: L13a knockout replicate 7 (treated by IL4)


title: MTCRT544_RNA-seq

value: non-mucinous colorectal cancer tissue


title: EpRas cells, Liver, Balb/c, replicate 2

value: Liver

value: Day 23


title: shYBX1_MNNG/HOS_1


title: L13a knockout replicate 6 (treated by IFN)

value: IFN


title: MTCRT543_RNA-seq

value: Non-mucinous adenocarcinoma

value: female

value: IIA


title: EpRas cells, Liver, NSG, replicate 2

value: Day 22


title: shNC_MNNG/HOS_3

value: MNNG/HOS cells

value: MNNG/HOS cells (control lentivirus)


title: CLIP-seq_BCAS_SpB_LPS_rep1

value: Spleen

value: B cells

value: Wild type

value: LPS treatement


title: L13a knockout replicate 5 (treated by IFN)

value: L13a KO


title: EpRas cells, Lung, Balb/c, replicate 2

value: Lung

value: EpRas

value: EpH4 cells transformed by oncogenic Ha-Ras

value: WT

value: Day 21


title: MTCRT547_RNA-seq

value: male

value: IV

value: non-mucinous colorectal cancer tissue


title: MTCRT540_RNA-seq

value: Non-mucinous adenocarcinoma

value: female

value: IIA


title: EpRas cells, Lung, NSG, replicate 2

value: Day 20


title: L13a knockout replicate 4 (treated by IFN)

value: IFN


title: shNC_MNNG/HOS_2

value: MNNG/HOS cells

value: MNNG/HOS cells (control lentivirus)


title: L13a knockout replicate 3 (no treatment)


title: EpRas cells, Parental, replicate 2

source_name: no

value: no

value: Day 0


title: shYBX1_U2_3

source_name: U2 OS cells

value: U2 OS cells

value: YBX1 knock down in U2 OS cell


title: MTCRT533_RNA-seq

value: IIIB


title: L13a knockout replicate 2 (no treatment)

value: L13a KO


title: shYBX1_U2_2


title: 4TO7-Tim3-KD cells, Lung,Balb/c

growth_protocol: 4TO7 cells were mantained in DMEM media supplemented with 10% of Fetal Bovine Serum (FBS), 2mM L-Glutamine (Glu) and 1% Penicilin/Streptomycin (P/S).

extract_protocol:
Metastatic organs (liver and lung) were mechanically and enzymatically digested into single cells. Sorting of GFP+ tumor cells was performed and then RNA was harvested using RNAeasy Mini Kit (QIAGEN).
Poly-A sequencing was selected for library preparation

treatment_protocol: Intracardiac injection of tumor cells were performed in Balb/c mice (20.000 cells).

value: Lung

value: breast cancer cell


title: L13a knockout replicate 8 (treated by IL4)


title: MTCRT536_RNA-seq


title: MTCRT539_RNA-seq

value: IV


title: shNC_MNNG/HOS_1


title: L13a knockout replicate 1 (no treatment)


title: 4TO7-Tim3-KD cells, Liver,Balb/c

value: Liver


title: shYBX1_U2_1


title: Control replicate 9 (treated by IL4)

value: WT


title: MTCRT534_RNA-seq

value: Non-mucinous adenocarcinoma

value: male

value: IIIA

value: non-mucinous colorectal cancer tissue


title: 4TO7-Control cells, Lung,Balb/c

value: Day 20


title: shNC_U2_2

value: U2 OS cells (control lentivirus)


title: shNC_U2_3


title: Control replicate 8 (treated by IL4)


title: MTCRT532_RNA-seq

value: IIA


title: 4TO7-Control cells, Liver,Balb/c


title: MTCRT535_RNA-seq

value: I


title: Control replicate 7 (treated by IL4)


title: 6-week-old Th-MYCN+/-

city: Nagoya

first: Shoma

last: Tsubota

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Molecular Biology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: 10x Genomics

data_processing:
The sequenced reads were aligned to the mouse genome reference mm10 enriched with the human MYCN transgene sequence using the Cell Ranger analysis pipeline (10x Genomics).
Droplets devoid of cells were filtered out using EmptyDrops, with a (FDR < 0.01). The resulting count matrices were further analyzed using the Seurat R package. Cell cycle scores for the S and G2M phases were calculated using published cell cycle gene sets. Cells with fewer than 200 detected genes, over 60% ribosomal gene content, or more than 10% mitochondrial gene content were excluded.
Of the initial set, 11,982 cells were retained. These cells were normalized using the SCTransform function of Seurat, regressing out 2,000 variable genes with factors such as the number of genes, number of counts, mitochondrial and ribosomal gene percentages, and cell cycle scores for the S and G2M phases. Principal component analysis was performed, and component variances guided the determination of cutoffs for subsequent clustering and dimensionality reduction. In addition, the clustree R package was used to identify a stable clustering resolution parameter.
Assembly: mm10 (custum with human MYCN transgene sequence)
Supplementary files format and content: rds files containing processed/normalized data to visualize figures

source_name: the superior mesenteric ganglion

extract_protocol:
Upon euthanization, the SMG of mice was meticulously dissected under the microscope. The SMG is anchored to the mesenteric artery and is proximal to the renal vein. Care was taken to detach the SMG using forceps without perturbing the adjacent blood vessels. Any attached fat was excised. The appearance of the dissected SMG was slightly white and transparen. This tissue was subsequently incubated in an equal ratio mix of collagenase IV (2.5 mg/mL, C5138, Sigma-Aldrich) and TrypLE Express Enzyme (12604013, Thermo Fisher Scientific) at 37°C for 40 min. Afterward, 10 volumes of D-PBS (045-29795, FUJIFILM Wako Chemicals) containing 1% BSA (15260037, Thermo Fisher Scientific), DNase I (0.1 mg/mL, DN25, Sigma-Aldrich), and 10 mM MgCl2 were added, and the tissue was dissociated using a fire-polished Pasteur pipette until no substantial particles remained visible. The resultant cell suspension was centrifuged to obtain a cell pellet, which was then reconstituted in 1% BSA/D-PBS for subsequent analyses.
For scRNA-seq, libraries were prepared using Chromium Single Cell 3' Reagent Kits v1 (10x Genomics) according to the user guide. Due to the limited number of cells in an SMG, the target cell recovery was set at 1,200 cells per sample.

value: the superior mesenteric ganglion

value: hemizygote


title: shNC_U2_1

value: U2 OS cells


title: MTCRT529_RNA-seq


title: Control replicate 6 (treated by IFN)

value: IFN


title: Control replicate 5 (treated by IFN)


title: 3-week-old Th-MYCN+/-_biol rep 7

description: 10x Genomics


title: ChIP-seq Serum+/KD PHGDH ChIP, replicate1

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
ChIP-seq: Adaptors for raw reads were trimmed using fastp with default parameters and aligned to the human reference genome hg38 with parameters “--end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 100 -X 800” using bowtie2. Samtools were used to remove duplicates from mapped reads using `samtools rmdup` and then sort and index .bam files. ChIP-seq signals (.bigwig and .bedGraph) were derived from the bam files using bamCoverage from the deepTools suite. MACS2 was used to identify peaks of each ChIP-seq sample using IgG as background with parameters `--nomodel -q 0.1`.
scRNA-seq: Raw sequencing data were processed using the Cell Ranger pipeline (version 6.0.1) which takes the raw FASTQ files and aligned them to the hg38 genome to generate gene expression count matrix based on the reference refdata-gex-GRCh38-2020-A. Single cell gene expression count matrix is imported and processed by Seurat package.
Assembly: hg38
Supplementary files format and content: The processed data of ChIP-seq experiment include bigwig. The processed data for 10x scRNA-seq is the output from CellRanger pipeline.

source_name: Human Brain Organoid

growth_protocol: Human brain organoids were generated from H1 human embryonic stem cells using a cerebral organoid establishment Kit (STEMCELL Technologies, 08570). At the 130th day, the organoids were subjected to either normal medium or normal medium with added 10% human serum. Organoids were harvested on the 142th day for characterization.

extract_protocol:
For ChIP-seq, brain organoids were fixed with 1% formaldehyde at room tempture for 10 minutes. Cells lysis and chromatin fragmentation were performed using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9005). For scRNA-seq, single nuclear were prepared following the standard protocol of Chromium Nuclei Isolation Kit with RNase Inhibitor (10X Genomics, PN-1000494).
For ChIP-seq, libraries were prepared using NEBNext UltraTM II DNA Library Prep Kit for Illumina (NEB, E7645S). For scRNA-seq, library preparation was preformed following the manufacter's protocol of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000268).

treatment_protocol: At the 130th day, the organoids were subjected to either normal medium or normal medium with added 10% human serum. On the 133th day, organoids were infected by GFAP-promoter dirven AAV expressing scramble shRNA or shRNA against PHGDH. Organoids were harvested on the 142th day for characterization.

value: Human Brain Organoid

value: treated with Serum, PHGDH shRNA1

tag: chip antibody

value: anti-PHGDH (Proteintech, 14719-1-AP)


title: 3-week-old Th-MYCN+/-_biol rep 10

description: 10x Genomics


title: MTCRT531_RNA-seq

value: female


title: ChIP-seq Serum+/KD PHGDH ChIP, replicate2


title: Control replicate 4 (treated by IFN)

value: WT


title: MTCRT527_RNA-seq

value: Non-mucinous adenocarcinoma


title: ChIP-seq Serum+/KD IgG, replicate2

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: ChIP-seq Serum+/Scr IgG, replicate2

value: treated with Serum


title: 3-week-old Th-MYCN+/-_biol rep 8

description: 10x Genomics


title: 3-week-old Th-MYCN+/-_biol rep 6

description: 10x Genomics


title: Control replicate 3 (no treatment)


title: MTCRT521_RNA-seq

value: male

value: IIIC

value: non-mucinous colorectal cancer tissue


title: Control replicate 2 (no treatment)


title: ChIP-seq Serum+/KD IgG, replicate1


title: MTCRT530_RNA-seq


title: 3-week-old Th-MYCN+/-_biol rep 9

description: 10x Genomics


title: MTCRT520_RNA-seq

value: IIIB


title: Control replicate 1 (no treatment)


title: 3-week-old Th-MYCN+/-_biol rep 5

description: 10x Genomics


title: ChIP-seq Serum+/Scr PHGDH ChIP, replicate2


title: ChIP-seq Serum+/Scr IgG, replicate1


title: N1_PAIsoseq

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
The sequenced reads were processed as described in previous article. Simply, the subreads were converted into circular consensus sequencing (CCS) reads by using ccs software (v 6.4.0), and the ccs reads were further converted into .fastq files by using bedtools (v 2.30.0). Then the .fastq files were splitted into samples by barcodes and trimmed into clean reads, and the clean reads were aligned to the mm10 genome using minimap2 (v 2.24). The poly(A) information were further extracted by using scripts applied in previous article.
Assembly: mm10
Supplementary files format and content: pA_length.xlsx

source_name: oocytes

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, #15596026) and chloroform (Sinopharm, #10006818), and precipitated with isopropanol (Sinopharm, #80109218) and dissolved with nuclease-free water.
Purified total RNA were used for templated end extension by dU-containing end-extension oligo and Klenow fragment 3’-5’ exo- (NEB, #M0212L). Then the templated RNA were cleaned by USER enzyme (NEB, #M5505S) and RNA Clean & Concentrator-5 kit (Zymo Research, #R1016). Purified templated RNA were retro-transcripted into cDNA by using SuperScript Ⅱ reverse transcriptase (Invitrogen, #18064-014) and TSO primer[1]. The full-length cDNA were further pre-amplified by using 2×KAPA HiFi HotStart ReadyMix (KAPA Biosystems, #KK2601) and cleaned by SPRIselect beads (Beckman Coulter, #B23318). For each sample, 20 ng purified cDNA were used for final amplification and cleaning as pre-amplification. Finally, cDNAs from different samples were mixed together according to the concentration and fragments length, and 500ng mixed cDNA were used for SMRTbell template library and sequencing by using Pacbio sequell Ⅱ.

value: oocytes


title: 3-week-old Th-MYCN+/-_biol rep 4

description: 10x Genomics

value: the superior mesenteric ganglion


title: MTCRT538_RNA-seq

value: I


title: 3-week-old Th-MYCN+/-_biol rep 3

description: 10x Genomics

value: hemizygote


title: H2170 cells, ACK1 (IDRmut)-2

first: Wei

last: Wang

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

description: Library name: Sample 6

data_processing:
The raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters.
The resulting Clean RNA-seq reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.2.1), sorted and indexed using Samtools (v1.14).
The number of reads (raw_counts) per gene was determined using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Human Lung Squamous Cell Carcinoma  Cell line

growth_protocol: H2170 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

value: ACK1 (IDRmut) overexpression


title: MTCRT524_RNA-seq


title: ChIP-seq Serum+/Scr PHGDH ChIP, replicate1

value: Human Brain Organoid


title: ChIP-seq Serum-/Scr IgG, replicate1

value: no treatment


title: 3-week-old Th-MYCN+/-_biol rep 2

description: 10x Genomics


title: HRCRC3446_RNA-seq

value: IV


title: HRCRC3443_RNA-seq


title: H2170 cells, ACK1 (WT)-2

description: Library name: Sample 4

value: Human Lung Squamous Cell Carcinoma  Cell line

value: ACK1 (WT) overexpression


title: H2170 cells, ACK1 (WT)-1

description: Library name: Sample 3


title: 3-week-old Th-MYCN+/-_biol rep 1

description: 10x Genomics


title: HRCRC3442_RNA-seq

value: Non-mucinous adenocarcinoma


title: HRCRC3441_RNA-seq


title: ChIP-seq Serum-/Scr PHGDH ChIP, replicate1

value: anti-PHGDH (Proteintech, 14719-1-AP)


title: H2170 cells, Control-1

description: Library name: Sample 1

value: Control


title: H2170 cells, Control-2

description: Library name: Sample 2


title: ChIP-seq Serum-/Scr PHGDH ChIP, replicate2


title: G10731-L1_S14_L002_001 Colon AE

city: Braunschweig

first: Tim

last: Kacprowski

address: Rebenring 56

department: Division Data Science in Biomedicine

country: Germany

institute: TU Braunschweig

data_processing:
initial trimming of reads using trim_galore (version 0.6.4) to satisfy a Phred score of at least 30
RNASeq data was processed with the ‘nf-core/rnaseq‘ pipeline (version 1.4.2)  and aligned to the GRCm38 genome using the ‘STAR‘ aligner (version 2.6.1d). Quantification of transcripts was performed using Salmon (version 0.14.1). All sequence properties were inspected in MultiQC and passed the quality thresholds.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

growth_protocol: Transgenic mice were housed either in SPF or GF colonization conditions

extract_protocol:
RNA of colonic IECs was isolated according to the manufacturer’s instructions (NucleoSpin RNAII kit, Macherey-Nagel) and measured by NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
TruSeq stranded Total RNA kit (Illumina Inc) was used for the construction of strand-specific sequencing libraries from the isolated colonic IEC RNA.

treatment_protocol: Constitutive mice were sampled at five weeks of age. Inducible transgenic mice were treated for 7 days using Tamoxifen (4-OHT) and sampled 4 days after complete induction.

value: Colon

value: nATF6 Vil-CreERT2

value: IEC

value: tg/tg


title: HRCRC3447_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: 3-week-old wild-type

description: 10x Genomics

value: the superior mesenteric ganglion

value: wild type


title: HRCRC3438_RNA-seq

value: male


title: G10728-L1_S11_L002_001 Colon AE

value: fl/fl


title: Ufx_DCL_4

city: Valencia

first: Ana

last: Corachán

state: València

address: Avenida Fernando Abril Martorell, 106, torreA, Planta 7

institute: Universidad de Valencia - IVI Foundation

data_processing:
The quality of the raw fastq files were evaluated by FastQC 0.11.9. Subsequent adapter trimming was executed with Trimgalore 0.6.7 to eliminate adapter sequences.
Reads were then mapped to the human reference genome (GRCh38) using STAR 2.7.9a
Gene counts were quantified using Salmon 1.5.2 to assign reads to genes. Lowly expressed genes and non-protein-coding genes were removed for downstream analysis.
Normalization (log2cpm) was applied to account for variations in sequencing depth.
Differential expression analysis was conducted using edgeR 3.36.0 to identify genes that were significantly differentially expressed between experimental conditions.
Assembly: Differential expression analysis was conducted using edgeR 3.36.0 to identify genes that were significantly differentially expressed between experimental conditions.
Supplementary files format and content: gene_counts_salmon_VD3.csv, raw data of VD3 experiment samples
Supplementary files format and content: gene_counts_salmon_DCL.csv, raw data of DCL experiment samples
Supplementary files format and content: log2_cpm_filtered_norm_VD3.txt, normalized data of VD3 experiment samples
Supplementary files format and content: log2_cpm_filtered_norm_DCL.txt, normalized data of DCL experiment samples

source_name: Human Uterine Fibroid xenografted in mouse

growth_protocol: Human UF were xenografted into female NOD-SCID mice.

extract_protocol:
Total RNA from UFx was extracted according to the protocol described by Untergasser Lab (Untergasser, 2008) using Qiazol reagent and RNeasy Micro Kit.
cDNA synthesis and library generation were performed using Illumina TruSeq Stranded mRNA and sequenced in an Illumina NovaSeq 6000 (Illumina, CA, USA)

treatment_protocol: Mice were treated for 6 weeks with the bioactive form of Vitamin D3 (VD3), 1α,25(OH)2D3  and the synthetic Vitamin D2 analog Doxercalciferol (DCL). According to the treatment two different studies were conducted: 1) VD3 0.5 µg/kg/day (n=3) and 3) DCL 0.3 µg/kg/day (n=4). Each study had her own control group, in which animals were treated with the corresponding drug vehicle.

value: Human Uterine Fibroid

value: MED12 mutant

value: Doxercalciferol


title: Ufx_DCL_3

value: Human Uterine Fibroid xenografted in mouse


title: Ufx_DCL_2


title: A549 cells, 6 μM EM-2, 24 hours, rep2

city: Shenzhen,Guangdong

first: Jinxia

last: Cheng

address: No.66,Gongchang Road,Guangming District

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
SOAPnuke (v1.5.2), HISAT2 (v2.0.4), Bowtie2 (v2.2.5), DESeq2(v1.4.5)
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: xlsx format file includes GO and KEGG enrichment analysis data with Q value and rich ratio.
Supplementary files format and content: xlsx format file includes ER stress related gene expression.

growth_protocol: The human lung carcinoma cell line A549 was cultivated in DMEM supplemented with 10% fetal bovine serum in a 5% CO₂ humidified atmosphere at 37 °C.

extract_protocol:
Total RNA was isolated from A549 cells, using TRIzol Reagent (Invitrogen Corporation) according to the manufacturer’s protocol.
RNA libraries for RNA-Seq were prepared using MGIEasy RNA library preparation kit following manufacturer’s protocols.

treatment_protocol: A549 cells were treated separately by DMSO and 6 μM EM-2 for 24 h.

value: non-small-cell lung cancer

value: 6 uM EM-2


title: G10730-L1_S13_L002_001 Colon AE


title: A549 cells, 6 μM EM-2, 24 hours, rep1


title: HRCRC3439_RNA-seq

value: Non-mucinous adenocarcinoma

value: IV


title: HRCRC3311_RNA-seq


title: G10727-L1_S10_L002_001 Colon AE

value: Colon

value: nATF6 Vil-CreERT2


title: H2170 cells, ACK1 (IDRmut)-1

description: Library name: Sample 5

value: Human Lung Squamous Cell Carcinoma  Cell line

value: ACK1 (IDRmut) overexpression


title: A549 cells, DMSO, 24 hours, rep2

value: DMSO


title: ChIP-seq Serum-/Scr IgG, replicate2

value: Human Brain Organoid

value: no treatment

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: Ufx_DCL_1


title: G10726-L1_S9_L001_001 Colon AE

value: IEC

value: tg/tg


title: HRCRC3425 _RNA-seq

value: male

value: non-mucinous colorectal cancer tissue


title: G10725-L1_S8_L001_001 Colon AE


title: G10724-L1_S7_L001_001 Colon AE

value: fl/fl


title: Ufx_CONT_DCL_4

value: Human Uterine Fibroid xenografted in mouse

value: Human Uterine Fibroid

value: MED12 mutant


title: HRCRC3427_RNA-seq

value: Non-mucinous adenocarcinoma

value: IV


title: G10723-L1_S6_L001_001 Colon AE

value: Colon

value: nATF6 Vil-CreERT2


title: Ufx_CONT_DCL_3


title: G10721-L1_S4_L001_001 Colon AE


title: HRCRC3393_RNA-seq


title: Ufx_CONT_DCL_2


title: Ufx_CONT_DCL_1


title: HRCRC3394_RNA-seq


title: HWx_52

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

description: Library name: 105170-001-044

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: Hippocampus

growth_protocol: Male Ldlr-/-.Leiden mice were obtained from an internal breeding stock of TNO Metabolic Health Research (Leiden, the Netherlands) and housed in the Pre-clinical Imaging Center (PRIME) of Radboud university medical center (Nijmegen, the Netherlands). The animals in this study are part of a larger study which is comparable to a previous longitudinal study in C57BL/6J mice, and approved by an independent Animal Welfare Body (approval number TNO-458) and the Veterinary Authority of Radboud university medical center (approval number 2017-0063-004). All procedures performed on these animals were in accordance with European Union regulations and guidelines on animal research. All animals were group-housed (2-4 mice per cage) in Digitally Ventilated Cages (Techniplast SPA, Buguggiate, Italy) and cages from different groups were randomized over shelves in a clean-conventional animal room (relative humidity 50-60%, temperature 21°C, 12-hour light/dark cycle). The animals received unlimited food and water throughout the study. Until the start of the study all mice were fed a standardized chow diet (Sniff R/M-H diet, Sniff Spezialdiäten GmbH, Soest, Germany).

extract_protocol:
Brain tissue was collected in 1 ml cold Trizol (Invitrogen, Paisley, UK) and homogenized using a dispersing machine (ultra-Turrax; IKA Werke GmbH & Co. KG, Staufen, Germany). After chloroform extraction and isopropyl alcohol precipitation, total RNA was dissolved in 25 μl RNase-free diethylpyrocarbonate (DEPC)-treated water. The RNA concentration of the tissue was measured with a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific Inc, Wilmington, DE, USA).
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-70 million read counts per sample. Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At the start of the experiment the animals (Male Ldlr-/-.Leiden, fed on standard Chow diet ) were 10-12 weeks old (corresponding to young adults). A healthy control group was (Chow) was kept for 28 weeks on Chow diet (n=15). Another group was kept for 28 weeks on obesigenic energy-dense diet (HFD = High Fat Diet, n=34). At 8 weeks half of the HFD group underwent a surgical procedure to remove 70% of eWAT tissue (HFD+WATx group, n=17), while the other half underwent sham surgery (HFD+sham, n=17). Sham surgery is a similar operation as WATx without removing the WAT tissue and serves as a control for operation effects. At 28 weeks mice were sacrified and RNAseq was performed on isolated right hemisphere hippocampi totRNA.

value: Hippocampus

value: HWx

tag: treatmdescript

value: HFD+WATx

tag: animalnr


title: Ufx_VD3_3

value: Vitamin D


title: HWx_454

description: Library name: 105170-001-023


title: HWx_60

description: Library name: 105170-001-050


title: Ufx_VD3_2


title: HRCRC3398_RNA-seq


title: HWx_445

description: Library name: 105170-001-017


title: A549 cells, DMSO, 24 hours, rep1

value: non-small-cell lung cancer

value: DMSO


title: HRCRC3404_RNA-seq


title: G10720-L1_S3_L001_001 Colon AE

value: IEC


title: G10719-L1_S2_L001_001 Colon AE

value: tg/tg


title: HRCRC3392_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: Ufx_VD3_1

value: Human Uterine Fibroid xenografted in mouse


title: G10718-L1_S1_L001_001 Colon AE


title: HWx_62

description: Library name: 105170-001-051


title: HRCRC3390_RNA-seq

value: male


title: Ufx_CONT_VD3_3

value: Human Uterine Fibroid

value: MED12 mutant


title: HWx_50

description: Library name: 105170-001-043


title: HRCRC3316_RNA-seq

value: Non-mucinous adenocarcinoma

value: IV


title: Ufx_CONT_VD3_2


title: F14631-L1_S76_L008_001 Colon AVd

value: Colon

value: fl/fl


title: HRCRC3403_RNA-seq


title: F14630-L1_S75_L008_001 Colon AVd


title: HWx_432

description: Library name: 105170-001-006

value: Hippocampus

value: HWx


title: Ufx_CONT_VD3_1


title: HWx_35

description: Library name: 105170-001-030

value: HFD+WATx


title: hiPSC-neurospheroids, day-1, treated, replicate 4

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Transcriptome datasets were analyzed inRstudio(version 4.2.1)using Bioconductor tools.Transcript counts were normalizedusing theDESeq2package (Love, Huber and Anders, 2014) andannotated withAnnotationDbipackage (Pagès H, Carlson M, Falcon S, 2021).Differential expression analyses were performed using DESeq2bycontrastingTNF-α, IL-1α and C1Q-treatedsamples with control samples.
Assembly: GRCh38
Supplementary files format and content: Tab-separated TPM_values and raw_counts

source_name: Royan iPSC clone 1

growth_protocol: Two hiPSC lines (Royan iPSC clone 1, also known as R1-hiPSC1 or RIi001-A, and iPSC(IMR90)-clone 4 line) were used in this work. R1-hiPSC1 neural progenitor cells (NPCs) were derived from dermal fibroblasts as described previously, and kindly provided by Dr Tomo Saric (Totonchi et al., 2010) and iPSC(IMR90)-clone 4 were acquired from WiCell Research Institute. iPSC(IMR90)-clone 4 Both hiPSC lines were was expanded on Growth Factor Reduced Matrigel Matrix (BD Biosciences) in mTeSR1 medium (StemCell Technologies) under feeder-free culture conditions. Complete medium exchange was performed every day. Cells were maintained under humidified atmosphere with 5 % CO2, at 37 °C. iPSC(IMR90)-clone 4 were replated at 0.8x105 cell/cm2 in mTeSR1 and allowed to adhere for 24 hours. Afterwards, culture medium was changed to DualSMADi medium: N2B27 medium supplemented with SB431542 at 1 mM and LDN193184 at 10 mM (both from STEMCELL™Technologies). N2B27 medium is composed by ½ DMEM/F-12 and ½ Neurobasal, N2-supplement (1x), B27 supplement without vitamin A (0.5x), GlutaMAX (1x), Penicillin-Streptomycin (1%), MEM Non-Essential Amino Acids Solution (1%) and 2-mercaptoethanol (50 μM) (all from Gibco™), and Insulin (20 μg/mL) (Sigma-Aldrich). A 100% medium exchange was performed daily, for 10 days. On day 6 or day 10, single cells were plated on previously prepared poly-L-ornithine-laminin (PLOL)-coated surfaces. PLOL coating was prepared by performing a 3-hour incubation at 37°C with 0.16 mg/mL solution of poly-L-ornithine in PBS (with Ca2+ and Mg2+), followed by a washing step and a 3-hour incubation at 37°C with 1 μg/mL solution of laminin in PBS (with Ca2+ and Mg2+). Cells were then maintained in DMEM/F12 media with Glutamax (Life Technologies) supplemented with 1% N2 supplement (Life Technologies), 0.1% B27 supplement (Life Technologies), 1.6 μg/mL glucose (Sigma-Aldrich), 20 μg/mL insulin (Sigma-Aldrich), 20 ng/mL rhu-bFGF (Peprotech) (Koch et al., 2009). iPSC(IMR90)-clone 4 cell line was maintained on PLOL-coated surfaces in the NPC expansion medium, composed of DMEM/F12 media with Glutamax (Life Technologies) supplemented with 1% N2 supplement (Life Technologies), 0.1% B27 supplement (Life Technologies), 1.6 μg/mL glucose (Sigma-Aldrich), 20 μg/mL insulin (Sigma-Aldrich), 20 ng/mL rhubFGF (Peprotech) and 20 ng/ml rhu-EGF (Sigma-Aldrich). Medium was changed every other day until confluent cell culture was obtained. For further expansion and maintenance hiPSC-NPC were split typically every 4-5 days at 90-100% confluence. Cells were dislodged through incubation with 0.05% Trypsin-EDTA for 1-2 minutes, resuspended in DMEM supplemented with 10% FBS (Life Technologies), sedimented by centrifugation and the resultant pellet resuspended in NPC expansion medium. Cell concentration and viability were determined by the trypan blue exclusion method in a Fuchs-Rusenthal hemocytometer. The cell suspension was used to inoculate PLOL-coated T-flasks, at a cell density of 3 x 104 cell/cm2. A 50 % media exchange was performed at day 2 of culture. Cells were maintained under humidified atmosphere, in a multi-gas cell incubator (Sanyo), with 5 % CO2 and 3 % O2, at 37 °C. hiPSC-NPC were expanded and harvested as described in the previous section. The resulting cell suspension was passed through a 70 µm nylon strainer (Millipore) before bioreactor inoculation, to eliminate cell clumps. The obtained single cell suspension was diluted for a cell density of 4x105 cell/mL in aggregation medium (AM), which composition is EM with reduced EGF/FGF concentration (5 ng/mL) and the addition of 5 μM Y-27632. Cells were then inoculated into a software-controlled stirred-tank DASGIP® Bioblock bioreactor system (Eppendorf), as described previously (Simão et al., 2016a, 2018). Culture conditions were set to maintain cells under 3 % dissolved oxygen (15 % of air with 21 % of oxygen), pH 7.4, 37 °C, and a stirring rate of 70 rpm. To control the aggregate size and avoid aggregate fusion, the stirring rate was gradually increased up to 90 rpm with 10 rpm steps, based on visual inspection of the culture. After 72 hours of culture, perfusion operation mode was activated, with a dilution rate of 0.33 day-1 (i.e., 33 % working volume exchange per day) under gravimetric control. To prevent the loss of aggregates through the outlet perfusion line, a metallic filter of 20 μm pore size was adopted as cell retention device (Simão et al., 2016a). After a 7-day aggregation period with AM, differentiation was induced by replacing the perfusion medium with differentiation medium (DM) and maintaining the culture for further 23 days (a total of 30 days). DM was prepared by supplementing DMEM/F12 with Glutamax with 2 % B27 supplement, 1.6 μg/mL glucose, 10 μg/mL insulin, 10 μg/mL putrescin, 63 ng/mL progesterone, 50 μg/mL apotransferrin, 50 ng/mL sodium selenium (all from Sigma-Aldrich) and 200 mM ascorbic acid (Wako).

extract_protocol:
Human neurospheroid samples were harvested from the bioreactor and sedimented by centrifugation at 300 xg, for 5 min. The supernatant was discarded and resulting cell pellet was washed twice with PBS, followed by additional centrifugation. Dry cell pellets were snap-frozen in liquid nitrogen. The frozen samples were shipped on dry ice to Genewiz (Leipzig, Germany) for RNA sequencing analysis. The RNA sequencing workflow after RNA isolation included initial PolyA selection-based mRNA enrichment, mRNA fragmentation, and random priming were performed.
First- and second-strand complementary cDNA synthesis and end-repair 5′ phosphorylation and adenine nucleotide (dA)–tailing were performed.

treatment_protocol: Reactive astrogliosis was induced in vitro through the addition of Il-1α (3ng ml−1, Sigma, I3901), TNFα (30ng ml−1, Cell Signaling Technology, 8902SF), and C1q (400ng ml−1 , MyBioSource, MBS143105) to the 3D human neurospheroids culture medium. The stimuli was maintained throughout a period of 72 hours, without changing the culture medium. Afterward, cells were collected for posterior processing or analYSIS.

value: Royan iPSC clone 1

value: hiPSC-derived neural cells

value: WT

value: TNF-α, IL-1α and C1Q (Activated)


title: HRCRC3397_RNA-seq

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.7.3a).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

source_name: non-mucinous colorectal cancer tissue

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were assessed using the RNA Integrity Number (RIN).
TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA)


title: F14628-L1_S73_L008_001 Colon AVd

value: IEC


title: HRCRC3209_RNA-seq

value: female

value: IIIB

value: non-mucinous colorectal cancer tissue


title: Hs_448

description: Library name: 105170-001-020

value: Hs

value: HFD+sham


title: F14627-L1_S72_L008_001 Colon AVd


title: Hs_447

description: Library name: 105170-001-019


title: F14626-L1_S71_L008_001 Colon AVd

value: tg/tg


title: hiPSC-neurospheroids, day-3, treated, replicate 3


title: RSDR2054_RNA-seq

value: Non-mucinous adenocarcinoma

value: IV


title: F14632-L1_S66_L007_001 Colon AVd

value: Colon

value: fl/fl


title: hiPSC-neurospheroids, day-1, treated, replicate 3


title: HWx_434

description: Library name: 105170-001-008R

value: Hippocampus

value: HWx


title: HWx_444

description: Library name: 105170-001-016

value: HFD+WATx


title: HeLa, ACSS2 inhibitors, BHB, rep3

city: Tianjin

first: wang

last: yu

address: No. 22, Meteorological Tai Road, Heping District

institute: Tianjin Medical University

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cervix

extract_protocol:
Total RNA extraction according to standard protocal in trizol-extracted approach.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HBO1-WT or HBO1-KO HeLa cells with or without 30 uM ACSS2 inhibitors in presence or absence of 10 mM BHB for 24 h.

value: cervix

value: HeLa

value: Human cervical cancer cell

value: Treatment of ACSS2 inhibitors and BHB


title: Hs_446

description: Library name: 105170-001-018


title: F14625-L1_S70_L008_001 Colon AVd

value: IEC


title: hiPSC-neurospheroids, day-3, treated, replicate 2

value: Royan iPSC clone 1

value: hiPSC-derived neural cells

value: WT

value: TNF-α, IL-1α and C1Q (Activated)


title: F14629-L1_S74_L008_001 Colon AVd


title: HRCRC3371_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: hiPSC-neurospheroids, day-3, treated, replicate 4


title: Hs_443

description: Library name: 105170-001-015

value: Hs

value: HFD+sham


title: hiPSC-neurospheroids, day-1, treated, replicate 2


title: HWx_34

description: Library name: 105170-001-029


title: HeLa, ACSS2 inhibitors, BHB, rep1

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt


title: F14623-L1_S68_L008_001 Colon AVd

value: Colon

value: tg/tg


title: F14624-L1_S69_L008_001 Colon AVd


title: Hs_436

description: Library name: 105170-001-010

value: Hippocampus


title: hiPSC-neurospheroids, day-3, treated, replicate 1


title: F14622-L1_S67_L008_001 Colon AVd


title: hiPSC-neurospheroids, day-1, treated, replicate 1


title: HeLa, Control-DMSO, BHB, rep3

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt

value: Treatment of DMSO and BHB


title: Hs_433

description: Library name: 105170-001-007


title: HeLa, Control-DMSO, BHB, rep1

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt

value: cervix


title: hiPSC-neurospheroids, day-3, control, replicate 4

value: Control (Non-activated)


title: Hs_41

description: Library name: 105170-001-035


title: F12366-L1_S59_L007_001 Colon AV

value: fl/fl


title: Hs_40

description: Library name: 105170-001-034


title: HeLa, Control, rep2

value: HeLa

value: Human cervical cancer cell


title: hiPSC-neurospheroids, day-0, control, replicate 4

value: Royan iPSC clone 1


title: HeLa, Control, rep3


title: F12365-L1_S58_L007_001 Colon AV

value: IEC


title: HeLa, ACSS2 inhibitors, BHB, rep2

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt

value: Treatment of ACSS2 inhibitors and BHB


title: Hs_38

description: Library name: 105170-001-033


title: F12364-L1_S57_L007_001 Colon AV


title: HeLa, Control, rep1


title: hiPSC-neurospheroids, day-3, control, replicate 3

value: hiPSC-derived neural cells

value: WT


title: F12362-L1_S55_L006_001 Colon AV


title: F12363-L1_S56_L006_001 Colon AV


title: hiPSC-neurospheroids, day-0, control, replicate 3


title: Hs_37

description: Library name: 105170-001-032


title: hiPSC-neurospheroids, day-1, control, replicate 3


title: HeLa, Control-DMSO, BHB, rep2

description: HeLa_DMSO_ACSS2 inhibitors_BHB.txt


title: Hs_36

description: Library name: 105170-001-031


title: HeLa-HBO1-KO, BHB, rep2

value: HBO1-KO; BHB stimulation


title: Hs_435

description: Library name: 105170-001-009

value: Hs


title: F14621-L1_S46_L005_001 Colon AVd


title: F12361-L1_S54_L006_001 Colon AV


title: hiPSC-neurospheroids, day-3, control, replicate 2


title: hiPSC-neurospheroids, day-1, control, replicate 4


title: Hs_33

description: Library name: 105170-001-028

value: HFD+sham


title: HeLa, BHB, rep3

description: HeLa_HBO1-WT_HBO1-KO_BHB.txt/HeLa_BHB_Control.txt

value: BHB stimulation


title: hiPSC-neurospheroids, day-1, control, replicate 2


title: F12360-L1_S53_L006_001 Colon AV

value: Colon

value: tg/tg


title: Hs_32

description: Library name: 105170-001-027

value: Hippocampus


title: HeLa-HBO1-KO, BHB, rep1

value: cervix


title: Hs_29

description: Library name: 105170-001-026


title: hiPSC-neurospheroids, day-0, control, replicate 2

value: Control (Non-activated)


title: HeLa, BHB, rep2


title: Hs_27

description: Library name: 105170-001-025


title: F12358-L1_S51_L006_001 Colon AV


title: F12359-L1_S52_L006_001 Colon AV


title: HeLa, BHB, rep1


title: F12357-L1_S50_L006_001 Colon AV


title: hiPSC-neurospheroids, day-3, control, replicate 1


title: oC_55

description: Library name: 105170-001-046

value: oC

value: Chow


title: HeLa-HBO1-KO, BHB, rep3

value: HeLa

value: Human cervical cancer cell


title: hiPSC-neurospheroids, day-1, control, replicate 1

value: Royan iPSC clone 1


title: SCA patient vehicle treated 7

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence (using cutadapt) low-quality sequences removed (using fastp)
Trimmed sequence reads were mapped to human hg38 transcriptome using STAR2 v2.6.0b and salmon v0.14.1
Raw counts were collected using htseq v0.11.0 and TPM calculated using gencode reported gene lengths
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 converted TPM values for each Sample

source_name: blood

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer

treatment_protocol: Vehicle or GYY4137 treatement for 24h

value: blood

value: CD8+ T cell

value: SCA

value: Vehicle


title: F12356-L1_S49_L006_001 Colon AV

value: IEC


title: hiPSC-neurospheroids, day-0, control, replicate 1

value: hiPSC-derived neural cells

value: WT


title: oC_54

description: Library name: 105170-001-045


title: oC_453

description: Library name: 105170-001-022


title: F12355-L1_S48_L006_001 Colon AV

value: Colon


title: SCA patient vehicle treated 5


title: SCA patient vehicle treated 6


title: F12354-L1_S47_L006_001 Colon AV

value: tg/tg


title: oC_452

description: Library name: 105170-001-024

value: Hippocampus


title: L-02 cells PBAT treated group B

city: Guangzhou City

first: congying

last: chen

state: Guangdong Province

address: Tianhe District

department: COLLEGE OF FOOD SCIENCE

institute: South China Agricultural University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: L-02 cells

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: L-02 cells

value: Human normal hepatocytes

value: Human Source

value: treated with PBAT for 48 hours


title: SCA patient vehicle treated 4


title: L-02 cells PBAT treated group A


title: L-02 cells PBAT treated group C


title: oC_451

description: Library name: 105170-001-021

value: oC

value: Chow


title: Veh+PD1, biological replicate 5

data_processing:
Sequence reads were trimmed for adaptor sequence (using cutadapt) low-quality sequences removed (using fastp)
Trimmed sequence reads were mapped to mm10 transcriptome using STAR2 v2.6.0b and salmon v0.14.1
Raw counts were collected using htseq v0.11.0 and TPM calculated using gencode reported gene lengths
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2 converted TPM values for each Sample

source_name: kidney tumor

value: kidney tumor

value: Renal medullary carcinoma

value: Mice treated with Veh and PD1


title: oC_45

description: Library name: 105170-001-039R


title: Veh+PD1, biological replicate 4


title: L-02 cells normal control group

value: untreated


title: oC_44

description: Library name: 105170-001-038


title: XGQP851188HC

city: Guangzhou

first: Rui

address: 2rd ZhongShan Road

institute: Guangdong Provincial Hospital

data_processing:
Sequencing was carried out using an Illumina HiSeq 4000 Sequencing System for 150 cycles (KangChen Bio-tech Inc, Shanghai, China).
Edger software (v3.16.5) was used to normalize the data and perform differentially expressed circRNA analysis.
Cuffdiff software (v2.2.1, part of Cufflinks) was used to obtain the fragments per kilobase of exon per million (FPKM) for the expression profiles of mRNAs, and fold change and P value were calculated based on the FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: Left ventricular

extract_protocol:
Total RNA extraction was carried out from interventricular septum specimens. Respective total RNAs were extracted and random primers were used to generate cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ventricular septum

tag: disease stage

value: Hypertrophic Cardiomyopathy


title: Veh+PD1, biological replicate 3

tag: tissue


title: SCA patient vehicle treated 2

value: blood

value: CD8+ T cell

tag: genotype

value: SCA

value: Vehicle


title: SCA patient vehicle treated 1

tag: treatment


title: LXYP845366HC


title: oC_43

description: Library name: 105170-001-037

value: Hippocampus

tag: cell line


title: Veh+PD1, biological replicate 2

tag: cell type


title: SCA patient GYY treated 7

value: GYY4137 treat for 24h


title: Veh+PD1, biological replicate 1


title: LCQG11110HC


title: SCA patient GYY treated 6


title: CZXP830077HC


title: SCA patient GYY treated 5


title: Veh+IgG, biological replicate 5

value: Mice treated with Veh and IgG


title: SCA patient vehicle treated 3


title: CWFP854898HC


title: Veh+IgG, biological replicate 3


title: SCA patient GYY treated 4


title: oC_42

description: Library name: 105170-001-036


title: oC_421

description: Library name: 105170-001-001


title: XCL8

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

institute: UCR

description: Library name: XCL8_Liver_tsRNA-Glu-CTC Oligo-1_mRNA_3

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Liver

growth_protocol: 8 week old C57BL/6 male mice were injected control oligo and tsRNA-Glu-CTC-1 oligos for 2 weeks

extract_protocol:
Total RNAs were extracted by Trizol (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: tsRNA-Glu-CTC Oligo-1


title: YLP833970NC

value: Healthy control


title: SCA patient GYY treated 3


title: Veh+IgG, biological replicate 2


title: XCL7

description: Library name: XCL7_Liver_tsRNA-Glu-CTC Oligo-1_mRNA_2


title: Veh+IgG, biological replicate 1


title: SCA patient GYY treated 1


title: QYMP807716NC


title: XCL6

description: Library name: XCL6_Liver_tsRNA-Glu-CTC Oligo-1_mRNA_1


title: oC_423

description: Library name: 105170-001-003

value: oC

value: Chow


title: GYY4137+PD1, biological replicate 5

value: kidney tumor

value: Renal medullary carcinoma

value: Mice treated with GYY and PD1


title: healthy donor vehicle treated 7

value: wild type


title: LBP832290NC

value: Ventricular septum


title: oC_422

description: Library name: 105170-001-002


title: Veh+IgG, biological replicate 4


title: XCL5

description: Library name: XCL5_Liver_Control Oligo_mRNA_4

value: Control Oligo


title: healthy donor vehicle treated 6

value: blood

value: CD8+ T cell


title: XCL4

description: Library name: XCL4_Liver_Control Oligo_mRNA_3


title: healthy donor vehicle treated 5

value: Vehicle


title: GYY4137+PD1, biological replicate 3


title: XCL3

description: Library name: XCL3_Liver_Control Oligo_mRNA_2


title: XCL2

description: Library name: XCL2_Liver_Control Oligo_mRNA_1


title: WLMP840582NC


title: GYY4137+PD1, biological replicate 1


title: healthy donor vehicle treated 4


title: 58492_WB3_L

city: Moscow

first: Alexander

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

country: Russia

institute: EIMB

data_processing:
read trimming with Trimmomatic (0.39)
read alignment with STAR (2.7.3a)
read counting with featureCounts (2.0.0)
Assembly: dm6
Supplementary files format and content: Tab-separated file containing read counts for exonic regions of each annotated gene feature

organism: Drosophila melanogaster

source_name: Whole body

extract_protocol:
Total RNA was extracted from adult five-day-old flies or ovaries from control 58492 and knockout strains using guanidine isothiocyanate RNAzol RT (Molecular Research Center, USA) following the manufacturer’s protocol.
Libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) according to the manufacturer's guidelines

value: Whole body


title: 58492_WB2_R


title: SCA patient GYY treated 2

value: SCA

value: GYY4137 treat for 24h


title: GYY4137+PD1, biological replicate 2


title: healthy donor vehicle treated 3


title: HFD+2% DSS, colon, Sample 3

city: Beijing

first: Tian

last: Xu

state: Beijing

address: No.1 Shuaifuyuan, Dongcheng District, Beijing,China

institute: Peking Union Medical College Hospital

description: Library name: Sample 12

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: colon

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

value: colon

value: WT

value: HFD+2% DSS


title: 58492_WB2_L


title: GYY4137+IgG, biological replicate 5

value: Mice treated with GYY and IgG


title: healthy donor vehicle treated 2


title: HFD+2% DSS, colon, Sample 2

description: Library name: Sample 11


title: GYY4137+IgG, biological replicate 4


title: 58492_WB1_R


title: healthy donor vehicle treated 1


title: GYY4137+PD1, biological replicate 4


title: HQYP820164NC

value: Healthy control


title: GYY4137+IgG, biological replicate 3

value: kidney tumor


title: HFD+2% DSS, colon, Sample 1

description: Library name: Sample 10


title: 58492_WB1_L


title: 58492_WB3_R


title: GYY4137+IgG, biological replicate 2

value: Renal medullary carcinoma


title: healthy donor GYY treated 7


title: CD+2% DSS, colon, Sample 3

description: Library name: Sample 9

value: CD+2% DSS


title: CD+2% DSS, colon, Sample 2

description: Library name: Sample 8


title: GYY4137+IgG, biological replicate 1


title: healthy donor GYY treated 6

value: wild type


title: CSE_OV2

source_name: Ovary

value: Ovary

value: cse-(CSE-/-)


title: healthy donor GYY treated 5

value: blood


title: CD+2% DSS, colon, Sample 1

description: Library name: Sample 7


title: WD1151

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
Sequencing reads were aligned to to the reference sequence (GRCm38) using HISAT2 (version 2.1.0), after Illumina adapter sequences and poly-A stretches were trimmed from the row reads.
Transcript abundance level (Transcript count) was generated using HTSeq (version 0.11.2).
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0).
Differential expression was performed using edgeR R package.
Assembly: GRCm38
Supplementary files format and content: .txt files containing read counts per gene

growth_protocol: Mice were housed under standard conditions with ad libitium access to water and chow/western diet. Mice were euthanized, the liver was isolated, digested and different liver cell types were isolated using density centrifugation/FACS, collected in lysis buffer and lysates were stored at -80ºC.

extract_protocol:
RNA was extracted using Reliaprep (Promega) according to manurfacturer's protocol.
Illumina TruSeq stranded mRNA Library prep kit and resulting cDNA libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol on an Illumina HiSeq2500 sequencer.

treatment_protocol: Male mice expressing floxed alleles of Zeb2 with endothelial cell-specific Cre expression were treated with tamoxifen (1mg/day for 5 consecutive days) to delete Zeb2 in endotheilal cells; tamoxifen-treated Cre-positive mice with a tamoxifen-inducible GFP reporter cassette but without floxed alleles of Zeb2 were used as wild-type counterparts.

value: endothelial-specific Zeb2 knock-out

tag: condition

value: high fat diet challenged

tag: developmental stage

value: adult

value: liver


title: CSE_OV1


title: healthy donor GYY treated 4

value: CD8+ T cell

value: GYY4137 treat for 24h


title: CBS_OV6

value: cbs-(CBS-/-)


title: WD1137


title: HFD, colon, Sample 3

description: Library name: Sample 6

value: colon

value: WT

value: HFD


title: WD1127


title: CBS_OV5


title: HFD, colon, Sample 1

description: Library name: Sample 4


title: healthy donor GYY treated 1


title: CBS_OV4


title: WD1071


title: healthy donor GYY treated 2


title: CD, colon, Sample 2

description: Library name: Sample 2

value: CD


title: CD, colon, Sample 3

description: Library name: Sample 3


title: WD1067


title: CBS_OV3


title: CBS_OV2


title: CSE_OV3


title: WD1069


title: CBS_OV1


title: WD1166

value: wild-type


title: SK-DSRCT2_shWT1-UTR_dox_rep2

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Applied Biosystems™ GeneChip® Human Genome U133 Plus 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: Raw data were processed applying the Robust Multi-chip Average (RMA) algorithm, including background adjustment, quantile normalization and summarization. For RMA normalization custom brainarray Chip Description Files (CDF; ENTREZG, v25) were used, yielding one optimized probe set per gene.

label: biotin

source_name: Desmoplastic small round cell tumor cell linee stably transduced with inducible shRNA expressing construct targeting EWSR1::WT1 fusion oncogene

label_protocol: The Applied Biosystems™ Gene Chip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA.

growth_protocol: One million DSRCT cells harboring either shRNA against WT1-CDS or WT1-UTR were resuspended in PBS and mixed with Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix in 1:1 proportion, and slowly injected subcutaneously in the right flank of 10–12 weeks old NOD/scid/gamma (NSG) mice.

extract_protocol: Xenografts were lysed in lysis buffer from the Macherey-Nagel NucleoSpin RNA kit. Total RNA was isolated following manufacturer's protocol. RNA was stored at -80°C.

treatment_protocol: When the tumors reached an average volume of 80 mm3, mice were randomized into two groups. 96h prior to the pre-determined end of the experiment, mice were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of EWSR1::WT1 (DOX (+)), or 5% sucrose (control, DOX (−)).

tag: material

value: in vivo subcutaneous xenograft

tag: shRNA

value: doxycycline


title: HFD, colon, Sample 2

description: Library name: Sample 5

tag: strain


title: CD, colon, Sample 1

description: Library name: Sample 1


title: p21_biol_rep1

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: BIOMEDICAL SCIENCE  MC0477,STEGER HALL

department: Biomedical Science

institute: Virginia Tech

description:
Library name: p21_rep1
FFPE coronal brain section spatial transcriptome sequencing

data_processing:
The FFPE Visium sequencing reads were mapped to the mouse reference genome (mm10) using the short-read probe alignment algorithm for FFPE ‘count’ method in Space Ranger (v2.1.0) from 10x Genomics.
The FFPE Visium data was filtered by (1) removal of spots with fewer than 250 unique genes, (2) removal of spots with fewer than 500 unique molecular identifiers (UMIs).
Normalization, dimensionality reduction, clustering, UMAP embedding and Marker genes identification were conducted using the Seurat R package (v5.1.0).
The differential gene expression analysis was performed using FindMarkers function, which applies a pairwise Wilcoxon Rank Sum test the spots within the same cluster between P21 and adult(12-15weeks) and between aged(28months) and adult(12-15weeks) groups
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.ipg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors ison.ison.gz:scalefactors in ison format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv.gz: gene expression levels across spatial regions
Library strategy: Spatial transcriptomics

source_name: Brain (coronal section)

growth_protocol: Male C57BL/6J mice (12 weeks) were purchased from Jaxson laboratory; Male C57BL/6J mice (28 months) were purchased from the NIA; Male C57BL/6J mice (postnatal day 21) were obtained by breeding wild-type C57BL/6J males and females purchased from Jaxson laboratory. All mice were maintained in a 12-hour light/dark cycle under standard pathogen-free conditions.

extract_protocol:
Mice were harvested and fresh mouse brain tissues were fixed in 10% neutral buffered formalin (NBF) at room temperature (RT) overnight for preparing formalin-fixed paraffin-embedded (FFPE) tissue blocks.
Visium Spatial Gene Expression (VGSE) libraries were prepared using the Visium Spatial Gene Expression Slide Kit (10x genomics, cat# PN-1000185) following the manufacturer’s User Guide (CG000407).

treatment_protocol: No treatments were performed on the mice

value: Brain (coronal section)


title: BE_OV6

value: Ovary


title: healthy donor GYY treated 3

value: blood

value: wild type


title: WD1126

value: high fat diet challenged


title: WD1124

value: adult


title: WD1068

value: liver


title: p21_biol_rep2

description:
Library name: p21_rep2
FFPE coronal brain section spatial transcriptome sequencing


title: SK-DSRCT2_shWT1-UTR_control_rep2

value: sucrose


title: BE_OV5


title: BE_OV4


title: WD1066


title: SK-DSRCT2_shWT1-UTR_dox_rep1


title: 12-15Weeks_biol_rep1

description:
Library name: adult_rep1
FFPE coronal brain section spatial transcriptome sequencing


title: 12-15Weeks_biol_rep2

description:
Library name: adult_rep2
FFPE coronal brain section spatial transcriptome sequencing


title: SK-DSRCT2_shWT1-UTR_control_rep1


title: BE_OV3


title: WD1181

value: endothelial-specific Zeb2 knock-out

value: unchallenged


title: 28 Months_biol_rep2

description:
Library name: aged_rep2
FFPE coronal brain section spatial transcriptome sequencing


title: 28 Months_biol_rep1

description:
Library name: aged_rep1
FFPE coronal brain section spatial transcriptome sequencing


title: BE_OV2


title: SK-DSRCT2_shWT1-CDS_dox_rep2


title: BE_OV1


title: WD1179


title: Spleen_inf_72h_5

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

description:
Library name: Sample 40
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_inf_72h_5

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Normalized data was log2-transformed, and a minimal expression threshold of 2 was set
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

source_name: Spleen

extract_protocol:
0,24, and 72 hours post infection mice were sacrificed by cervical dislocation, and the desired tissues (ileum, caecum, Payer's patches and spleen) were removed for analysis.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

treatment_protocol: Female C57BL/6 mice, 7-9 weeks old, were orally infected with 1*10^9 CFU of Salmonella Typhimurium strain SL1344 (in 100μl suspension in DPBS) or treated with sterile DPBS (control).

value: Spleen

value: enriched for immune cells

value: infected

tag: time post_infection_(hours)

tag: replicate


title: WD1154


title: SK-DSRCT2_shWT1-CDS_control_rep2


title: SK-DSRCT2_shWT1-CDS_control_rep1


title: 58492_WB6

value: Whole body


title: SK-DSRCT2_shWT1-CDS_dox_rep1


title: Spleen_inf_72h_4

description:
Library name: Sample 39
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_inf_72h_4


title: WD1109


title: Spleen_inf_72h_3

description:
Library name: Sample 38
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_inf_72h_3


title: JN-DSRCT-1_shWT1-UTR_dox_rep2


title: 58492_WB4


title: Spleen_inf_72h_2

description:
Library name: Sample 37
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_inf_72h_2


title: WD1095


title: Spleen_inf_72h_1

description:
Library name: Sample 36
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_inf_72h_1


title: JN-DSRCT-1_shWT1-UTR_control_rep2


title: WD1094


title: 58492_WB3


title: WD1182

value: wild-type


title: JN-DSRCT-1_shWT1-UTR_dox_rep1

value: in vivo subcutaneous xenograft


title: Spleen_naive_5

description:
Library name: Sample 35
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_naive_5

value: naive


title: WD1180


title: 58492_WB2


title: Spleen_naive_4

description:
Library name: Sample 34
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_naive_4


title: 58492_WB1


title: JN-DSRCT-1_shWT1-UTR_control_rep1


title: WD1178


title: JN-DSRCT-1_shWT1-CDS_dox_rep2

value: doxycycline


title: 58492_WB5


title: 58492_OV3

value: Ovary


title: JN-DSRCT-1_shWT1-CDS_control_rep2


title: Spleen_naive_3

description:
Library name: Sample 33
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_naive_3


title: WD1111


title: 58492_OV2


title: JN-DSRCT-1_shWT1-CDS_dox_rep1


title: 58492_OV1


title: WD1057


title: Spleen_naive_1

description:
Library name: Sample 31
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_naive_1


title: WD1108


title: JN-DSRCT-1_shWT1-CDS_control_rep1