title: Brain_wholeBoneMarrow_transplantation_rep2


title: RIL50_G02_L01_4

status: Public on Jul 18 2026

type: SRA

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

description: Library name: Sample90

library_source: genomic

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute (Taudt et al. 2018)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: The MAMP was grown in climate-controlled chambers for nine selfing generations (Long day conditions, 16-h-day lengths, 18 C).

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end 150bp format.

tag: tissue

value: leaf tissue

tag: genotype

value: Ler X Cvi RIL

tag: ril line

tag: generation

tag: lineage

tag: sublineage


title: Barnyard_96well_rep53

city: Carlsbad

first: Tom

last: Chen

state: CA

address: 6155 Corte Del Cedro

department: R&D

country: USA

institute: Universal Sequencing Technology Corp.

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep53

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed with AmpliDrop software v1.0. Cell calling and data processing was generated with Cell Ranger v5.1
Within AmpliDrop software analysis, after bcl files been converted to fastq files, the pipeline generated three types of fastq files: cDNA reads, been called as "R1"; sample index reads, with 8 nucleotides, been called as "I1"; and barcode reads, with 20 nucleotides, been called as "I2", in which six nucleotides at positions of 4, 5, 10, 11, 16, and 17 were used as code. The pipeline was then demultiplexing the samples based on the sample index combined with the code used. However, the sample index and code sequences were not saved after demultiplexing. To evaluate the fastq quality, the pipeline ran the fastqc tool on each set of fastq files for the demultiplexed sample. After the barcodes were error collected and the cDNA reads were trimmed with the potential adapter sequences and poly-A nucleotides, the pipeline ran a merging algorithm to merge the barcodes that were located in the same droplet. At the end of the pipeline, the fastq files were converted into 10X Genomic cellranger compatible format.
Assembly: hg38 and mm10
Supplementary files format and content: _barcodes.tsv.gz contains all cellular barcodes, tab separated text file, gzipped; _features.tsv.gz contains feature annotations, tab separated text file, gzipped, column1: feature id, column2: feature name, and column3: type of feature, i.e., "Gene Expression"; _matrix.mtx.gz contains UMI counts in each gene and in each cellular barcode, with mtx format, gzipped.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: embryonic kidney and fibroblast cell lines

growth_protocol: All cell lines were grown in an incubator at 37C and 5% CO2 with media conditions as suggested by ATCC (293T, NIH-3T3, MCF7, HCT-116, and Jurkat) or Sigma (A2780 and A2780cis) supplemented with pen/strep antibiotics. Cells were generally grown close to confluency at the moment of collecting the cells. The WT83 clone6 of human induced-pluripotent stem cells (hiPSCs), derived from a typically developing Caucasian male 29,72, were grown on growth factor-reduced Matrigel, coated 6-cm dishes in mTeSR Plus without antibiotics. For propagation, cells were dissociated with Versene, EDTA, or Relers. To generate forebrain organoids, we followed a semi-guided protocol with a few modifications. Human iPSCs were grown in mTeSR Plus to a confluency of approximately 70% in a 6-cm plate and dissociated with a 1:1 mix of accutase/DPBS. Approximately, three million hiPSCs with a viability >95% were transferred into ultra-low attachment 6-well plates with mTeSR plus media supplemented with the SMAD inhibitors SB-431542 and Dorsomorphin, and the Rho-associated proteinase kinase (ROCK) inhibitor (RI) Y-27632. Plates were placed on orbital shaker. Alternatively, 2 million hiPSCs were transferred to a well of AggreWell-800 plate, pre-coated with Anti-Adherent Solution in mTeSR plus supplemented with RI. The AggreWell plate was centrifugated and transferred to incubator overnight. The following day, embryoid bodies (EB) were transferred to a well of 6-well plate changing the media to fresh mTsERplus supplemented with SB and Dorsomorphin as described above. Regular media and factors changes to complete generation of forebrain organoids were performed in M2 medium composed of Neurobasal supplemented with 1% Glutamax, 1% MEM non-essential amino acids solution, NEAA, and 1x B27 performing half/medium changes every two days for the first month or twice a week after.

extract_protocol:
Peripheral venous blood was drawn from voluntary donor using EDTA-treated tubes and LymphoprepTM and stored at 4°C. Cells were resuspended in 1x phosphate-buffered saline buffer solution (1xPBS) supplemented with 2% bovine serum albumin, BSA, and layered over 1.5 mL Lymphoprep Density Gradient Medium in a 15 mL conical tube, according to the manufacturer’s protocol.  The solution was centrifuged at 800xg for 20 min at room temperature without brake.  The mononuclear cell layer at the gradient interface was collected in a new tube and washed in PBS/2% FBS (10 mL total volume) and centrifuged at 120xg for 10 min at room temperature without brake.  The wash step was repeated two more times, and the cells were resuspended in PBS for sequencing library preparation.  The cells not used immediately were cryopreserved in 90% FBS/10% DMSO.
3' scRNA-seq (AmpliDrop technology); Dissociated cells (typically, >90-95% viable) in 0.1% BSA-supplemented 1x DPBS buffer were processed with AmpliDrop 3’ scRNA-seq kits following the manufacturer’s recommendations. Briefly, more than 200,000 cells were typically fixed at room temperature for 45 minutes and permeabilized for 10 minutes. For the RT and tagmentation reactions, we used 60,000 fixed and permeabilized cells. RT was conducted at 50°C for 10 minutes, and 10 cycles at 60°C for 30 sec and 50°C for 3 min, and tagmentation was conducted at 37°C for 15 minutes. Cell encapsulation was based on the following mixing protocol: 50 mixes of 170 µL at Speed 2 followed by 10 mixes of 170 µL at Speed 3. The emulsions were then moved to a thermocycler to run the following PCR/barcoding program: 72°C for 5 min, 98°C for 1 min, 26 cycles with 98°C for 15 sec, 61°C for 40 sec, and 72°C for 30 sec, and 5 cycles with 98°C for 15 sec, 50°C for 2 min, and 72°C for 40 sec, ending with 72°C for 2 min. After PCR/barcoding, the emulsions were dissolved, and the DNA was recovered from the solution  with the same volume of SPRI beads from MagBio genomics. The libraries were cleaned up with 80% ethanol for three times and finally eluted in 38 µL of 0.1x TE buffer, and half of this volume was used for indexing using Illumina adapters. Typically, we amplified the library with 9 to 12 cycles depending on the expected number of cell output (12 cycles for 1,000-2,000 cells and 9 cycles for 7,000-10,000 cells). The PCR indexing program is the following: 98°C for 30 sec, and 9-12 cycles with 98°C for 20 sec, 61°C for 30 sec, and 72°C for 30 sec, ending with 72°C for 2 min. After PCR, the library (40 µL) was diluted to 100 µL with TE buffer and cleaned up with 90 µL of SPRI beads. After washing with 80% ethanol twice, the library was eluted in 30 µL of 0.1x TE buffer. Libraries were then subject to quality control, sizing, and quantification using Agilent 4150 TapeStation system with High Sensitivity D1000 ScreenTape and Reagents.

treatment_protocol: No treatments were performed on cell lines. For seven-month-old organoids (Exp 1), mildly-perturbed conditions refer to a regimen of pipette aspiration with a wide-origfice 1mL tip and transfer of the organoids to a metal platform to mimic a mild physical manipulation of these multicellular structures. Severely-perturbed conditions refer to smashing the organoids to generate deformative compression to mimic a highly damaging physicial manipulation. Both treatments required maintaining the organoids for approximately 90 minutes outside the incubator. In the incubator, both sets of organoids were maintained withouth motion for 3 days. Non-perturbed organoids were maintained under orbital shaking all the time. For six-month-old organoids (Exp 2), everything was as in Exp1 but the non-perturbed group of organoids was also maintained 90 minutes outside the incubator. For two-month-old organoids (Exp3), one set was grown under orbital shaking always, while the other set was kept withouth motion for three days before library preparation.

tag: cell line

value: 293T and NIH3T3

tag: cell type

value: Human embryonic kidney and mouse embryonic fibroblasts

value: WT

tag: treatment


title: tamoxifen_rep3

city: Stanford

first: Marius

middle: Marc-Daniel

last: Mader

address: 265 Campus Drive

institute: Stanford University

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the mouse reference transcriptome (mm39 [GRCm39], primary assembly) using STAR (version 2.7.10a; Samtools version 1.16.1) with default parameters.
Aligned reads mapping to genes were counted with the htseq-count command (intersection-strict mode, stranded=no; HTSeq package version 0.11.2).
Assembly: mm39
Supplementary files format and content: HTSeq count data (first column = gene name; second column = counts)

molecule: total RNA

organism: Mus musculus

source_name: hematopoietic cell (early myeloid differentiation)

extract_protocol:
Cells were dissociated with Trypsin followed by staining for magnetic-activated and fluorescence activated cell sorting. CD45+ cells were isolated directly into TRIzol LS Reagent. RNA was isolated and concentrated with the RNA Clean & Concentrator-5 kit (Zymo) according to the manufacturer’s instructions including DNase treatment.
NEBNext Ultra II RNA Library PrepKit (performed by Novogene)

tag: strain

tag: Sex

value: female


title: Brain_noIntervention_microglia_rep2

source_name: Brain

extract_protocol:
Brain myeloid cells were isolated via brain dissociation and fluorescence activated cell sorting directly into TRIzol LS Reagent (ThermoFisher Invitrogen), using a CD45+CD11b+GFP+ gate for graft-derived myeloid cells and a conventional CD45low/intermediate CD11b+ gate for naïve microglia. Total RNA was extracted and then purified using a Qiagen RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to the manufacturer’s protocols. Quality and quantity of RNA was assessed on a Bioanalyzer (Agilent), and samples with RNA integrity number (RIN) >8 were used for subsequent library preparation.
The NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, E6420S) was used to generate cDNA and libraries according to the manufacturer’s protocol. The libraries were indexed using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E6420S) and cleaned up using SPRI select reagent (Beckman Beckman Coulter, B23317).

value: Brain

value: Microglia

value: no intervention


title: RIL37_G09_L01_2

description: Library name: Sample88


title: Barnyard_96well_rep55

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep55

value: embryonic kidney and fibroblast cell lines


title: Barnyard_96well_rep84

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep84


title: Brain_noIntervention_microglia_rep3


title: RIL61_G02_L02_3

description: Library name: Sample118


title: Barnyard_96well_rep54

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep54


title: vehicle_rep4

value: vehicle

value: hematopoietic cell (early myeloid differentiation)


title: RIL37_G02_L01_4

description: Library name: Sample86


title: Brain_noIntervention_microglia_rep1


title: vehicle_rep3


title: Barnyard_96well_rep74

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep74


title: RIL36_G09_L02_1

description: Library name: Sample85


title: tamoxifen_rep2


title: Barnyard_96well_rep52

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep52


title: vehicle_rep2


title: Barnyard_96well_rep51

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep51


title: tamoxifen_rep1


title: Barnyard_96well_rep50

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep50


title: vehicle_rep1


title: RIL36_G02_L02_4

description: Library name: Sample84


title: d14.HDMC_rep4

source_name: cultured myeloid cells (14 days co-culture)

extract_protocol:
Cells were dissociated with Trypsin followed by staining for fluorescence activated cell sorting. Target cells were sorted directly into TRIzol LS Reagent. RNA was isolated and concentrated with the RNA Clean & Concentrator-5 kit (Zymo) according to the manufacturer’s instructions including DNase treatment.
NEBNext Ultra II RNA Library PrepKit (performed by Novogene)


title: RIL36_G02_L02_3

description: Library name: Sample83


title: Barnyard_96well_rep49

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep49


title: d14.HDMC_rep2

value: cultured myeloid cells (14 days co-culture)


title: d14.HDMC_rep1


title: RIL36_G02_L01_4

description: Library name: Sample82


title: Barnyard_96well_rep48

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep48


title: RIL29_G02_L02_3

description: Library name: Sample81


title: d2.HDMC_rep4

source_name: cultured myeloid cells (2 days co-culture)


title: Barnyard_96well_rep47

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep47


title: d2.HDMC_rep2

value: cultured myeloid cells (2 days co-culture)


title: d2.HDMC_rep3


title: RIL133_G09_L01_1

description: Library name: Sample202


title: d2.HDMC_rep1


title: RIL29_G09_L02_2

description: Library name: Sample80


title: Barnyard_96well_rep46

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep46


title: cMG_rep4

source_name: cultured microglia

value: cultured microglia


title: cMG_rep3


title: Barnyard_96well_rep45

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep45


title: cMG_rep2


title: RIL27_G09_L02_2

description: Library name: Sample78


title: cMG_rep1


title: RIL29_G02_L02_4

description: Library name: Sample79


title: d14.HDMC_rep3


title: cHSPC_rep4

source_name: cultured hematopoietic stem and progenitor cells


title: Barnyard_96well_rep44

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep44


title: cHSPC_rep3

value: cultured hematopoietic stem and progenitor cells


title: RIL27_G09_L01_2

description: Library name: Sample77


title: RIL27_G02_L02_3

description: Library name: Sample76


title: Barnyard_96well_rep43

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep43


title: cHSPC_rep2


title: Barnyard_96well_rep42

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep42


title: RIL27_G02_L01_4

description: Library name: Sample75


title: hair germ stem cells, P69, cKO mouse 2, 2372

city: Guangzhou

first: Kechen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: Library name: 2372

data_processing:
Bulk RNA-seq data were processed through a streamlined analysis pipeline. Raw reads underwent quality assessment with FastQC and adapter trimming with TrimGalore. Clean reads were aligned to the mouse GRCm38/mm10. For MeRIP-seq data analysis, raw paired-end sequencing reads were first processed using fastp with default parameters for quality control, including removal of adapter sequences and low-quality bases. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2 under default settings. The resulting SAM files were converted to BAM format using SAMtools, followed by coordinate sorting and index generation. Alignment statistics were generated using the samtools flagstat command. For downstream genome visualization, the sorted BAM files were converted into BigWig format using the bamCoverage function from the deepTools package, with a bin size of 10 bp and normalization performed using the BPM (Bins Per Million mapped reads) method. Subsequent IP/Input peak-calling analysis was performed using exomePeak2. reference genome using STAR. PCR duplicates were removed with sambamba, and gene-level read quantification was performed using featureCounts. Differential expression analysis was conducted with DESeq2, and functional enrichment of GO terms and KEGG For RNA-seq, raw paired-end sequencing data were first processed using fastp to remove low-quality bases and sequencing adapters. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2. Alignment outputs were directly piped to SAMtools for BAM format conversion, coordinate sorting, and index generation. Gene-level quantification was subsequently performed using the featureCounts function from the Subread package based on the GENCODE (vM32) genome annotation file, by counting reads mapped to exonic regions. The resulting expression matrix was used for downstream differential expression analysis. After preprocessing and gene annotation, the raw gene count matrix was subjected to differential expression analysis. Samples were grouped according to genotype into WT and cKO groups, and batch information was included to correct for potential batch effects. Differential expression analysis was performed using the PyDESeq2 package in Python with the statistical design formula: count ~ batch + condition, where condition was used to compare expression differences between cKO and WT samples, and batch was used to account for batch effects. PyDESeq2 performed size-factor normalization, dispersion estimation, and negative binomial generalized linear model fitting on the raw count data, followed by Wald tests to evaluate expression changes in cKO relative to WT samples. Differentially expressed genes (DEGs) were identified using the thresholds of p value < 0.05 and |log2FoldChange| > 1. Pathway enrichment analysis was conducted using gseapy based on the GO, KEGG, Reactome, and WikiPathways databases to separately analyze enriched pathways among upregulated and downregulated genes.
For MeRIP-seq data analysis, raw paired-end sequencing reads were first processed using fastp with default parameters for quality control, including removal of adapter sequences and low-quality bases. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2 under default settings. The resulting SAM files were converted to BAM format using SAMtools, followed by coordinate sorting and index generation. Alignment statistics were generated using the samtools flagstat command. For downstream genome visualization, the sorted BAM files were converted into BigWig format using the bamCoverage function from the deepTools package, with a bin size of 10 bp and normalization performed using the BPM (Bins Per Million mapped reads) method. Subsequent IP/Input peak-calling analysis was performed using exomePeak2.
Assembly: GRCm39
Supplementary files format and content: raw counts, FPKM, bw, narrowPeak

source_name: skin

extract_protocol:
Cells were isolated by flow cytometric sorting, and total RNA was extracted using TRIzol. Libraries were constructed using 100 ng of total RNA for bulge hair follicle stem cells with MeRIP-seq, and 40 ng of total RNA for hair germ  stem cells with bulk RNA-seq.
RNA-seq libraries were prepared using the SMART-seq protocol, and m⁶A-seq libraries were generated using the PicoMeRIP-seq protocol.

value: skin

value: hair follicle stem cell

value: Alkbh5 cKO


title: hair germ stem cells, P69, cKO mouse 1, 1783

description: Library name: 1783


title: cHSPC_rep1


title: Barnyard_96well_rep41

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep41

value: 293T and NIH3T3


title: RIL27_G02_L01_3

description: Library name: Sample74

value: leaf tissue

value: Ler X Cvi RIL


title: hair germ stem cells, P69,  WT mouse 2

description: Library name: 2374

value: wild-type


title: Barnyard_96well_rep40

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep40

value: Human embryonic kidney and mouse embryonic fibroblasts

value: WT


title: hair germ stem cells, P69,  WT mouse 1

description: Library name: 1778


title: bulge hair follicle stem cells, P69, cKO mouse 4-input

description: Library name: cKO Input 4

data_processing:
Bulk RNA-seq data were processed through a streamlined analysis pipeline. Raw reads underwent quality assessment with FastQC and adapter trimming with TrimGalore. Clean reads were aligned to the mouse GRCm38/mm10. For MeRIP-seq data analysis, raw paired-end sequencing reads were first processed using fastp with default parameters for quality control, including removal of adapter sequences and low-quality bases. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2 under default settings. The resulting SAM files were converted to BAM format using SAMtools, followed by coordinate sorting and index generation. Alignment statistics were generated using the samtools flagstat command. For downstream genome visualization, the sorted BAM files were converted into BigWig format using the bamCoverage function from the deepTools package, with a bin size of 10 bp and normalization performed using the BPM (Bins Per Million mapped reads) method. Subsequent IP/Input peak-calling analysis was performed using exomePeak2. reference genome using STAR. PCR duplicates were removed with sambamba, and gene-level read quantification was performed using featureCounts. Differential expression analysis was conducted with DESeq2, and functional enrichment of GO terms and KEGG For RNA-seq, raw paired-end sequencing data were first processed using fastp to remove low-quality bases and sequencing adapters. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2. Alignment outputs were directly piped to SAMtools for BAM format conversion, coordinate sorting, and index generation. Gene-level quantification was subsequently performed using the featureCounts function from the Subread package based on the GENCODE (vM32) genome annotation file, by counting reads mapped to exonic regions. The resulting expression matrix was used for downstream differential expression analysis. After preprocessing and gene annotation, the raw gene count matrix was subjected to differential expression analysis. Samples were grouped according to genotype into WT and cKO groups, and batch information was included to correct for potential batch effects. Differential expression analysis was performed using the PyDESeq2 package in Python with the statistical design formula: count ~ batch + condition, where condition was used to compare expression differences between cKO and WT samples, and batch was used to account for batch effects. PyDESeq2 performed size-factor normalization, dispersion estimation, and negative binomial generalized linear model fitting on the raw count data, followed by Wald tests to evaluate expression changes in cKO relative to WT samples. Differentially expressed genes (DEGs) were identified using the thresholds of p value < 0.05 and |log2FoldChange| > 1. Pathway enrichment analysis was conducted using gseapy based on the GO, KEGG, Reactome, and WikiPathways databases to separately analyze enriched pathways among upregulated and downregulated genes.
For MeRIP-seq data analysis, raw paired-end sequencing reads were first processed using fastp with default parameters for quality control, including removal of adapter sequences and low-quality bases. The cleaned high-quality reads were then aligned to the mouse reference genome (GRCm39) using HISAT2 under default settings. The resulting SAM files were converted to BAM format using SAMtools, followed by coordinate sorting and index generation. Alignment statistics were generated using the samtools flagstat command. For downstream genome visualization, the sorted BAM files were converted into BigWig format using the bamCoverage function from the deepTools package, with a bin size of 10 bp and normalization performed using the BPM (Bins Per Million mapped reads) method. Subsequent IP/Input peak-calling analysis was performed using exomePeak2.
Assembly: GRCm39
Supplementary files format and content: raw counts, FPKM, bw, narrowPeak
Library strategy: MeRIP-Seq


title: bulge hair follicle stem cells, P69, cKO mouse 3-input

description: Library name: cKO Input 3


title: RIL25_G09_L02_1

description: Library name: Sample73


title: bulge hair follicle stem cells, P69, WT mouse 4 - Input

description: Library name: WT Input 4


title: Barnyard_96well_rep39

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep39


title: RIL25_G02_L01_4

description: Library name: Sample72


title: bulge hair follicle stem cells, P69, cKO mouse 4 - IP

description: Library name: cKO IP 4


title: RIL25_G02_L01_3

description: Library name: Sample71


title: bulge hair follicle stem cells, P69, WT mouse 3 - Input

description: Library name: WT Input 3


title: Barnyard_96well_rep38

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep38


title: Barnyard_96well_rep37

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep37


title: RIL23_G02_L02_4

description: Library name: Sample70


title: TGFB

city: Boston

first: Ian

last: Dryg

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: TGFB

data_processing:
transcripts were quantified with cell ranger 9.0.1 and Seurat’s v5 standard analysis workflow was used. Cells with less than 500 features or greater than 5 percent mitochondrial were removed. Groups were merged into one Seurat object, normalized, scaled, and then PCA, clustering, and UMAP dimensionality reduction was performed.
Assembly: GRCh38-2024-A

organism: Homo sapiens

source_name: Adipose Derived Commercial

extract_protocol:
After treatment, cells were detached with trypsin-EDTA (0.05%, Cat n. 25300054), counted and assessed for viability as per manufacturer requirement: ≥ 1M cells per sample; ≥ 80% cell viability. Cells were frozen in Bambanker solution (Bulldog Bio Inc, Cat n. NC2960954) and shipped to Novogene Corporation for single cell sequencing.
human 10x Single Cell Transcriptome Sequencing (WBI), PE150, Q30≥85%.

value: Adipose Derived Commercial

value: Mesenchymal Stem Cell

value: TGFB


title: Barnyard_96well_rep36

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep36

value: embryonic kidney and fibroblast cell lines


title: bulge hair follicle stem cells, P69, cKO mouse 3 - IP

description: Library name: cKO IP 3


title: bulge hair follicle stem cells, P69, WT mouse 3 - IP

description: Library name: WT IP 3


title: bulge hair follicle stem cells, P69, WT mouse 4 - IP

description: Library name: WT IP 4


title: RIL23_G09_L01_2

description: Library name: Sample69


title: UNTR

description: Library name: UNTR

value: Control


title: Barnyard_96well_rep35

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep35


title: RIL23_G09_L01_1

description: Library name: Sample68


title: SARS2_30dpi_4

city: Iowa City

first: Stanley

last: Perlman

state: Iowa

address: 51 Newton Road

department: Dept of Microbiology and Immunology

institute: University of Iowa

description:
Library name: sample_12
Column name in XZ4XKT-expression-matrix.csv: 30dpi_12_cpm and 30dpi_12_count

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1. Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment to the appropriate reference genome using STAR aligner v2.7.* with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAM files using samtools v1.21. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RustQC v0.2.1. Generation of comprehensive QC report using MultiQC v1.33.
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Differential expression using edgePython v0.2.5. Functional enrichment performed for human and mouse samples using gene set enrichment analysis with GSEApy v0.12 using the MSigDB Hallmark gene set.
Assembly: GRCm39_114
Supplementary files format and content: A csv file includes count and cpm values for each sample.

source_name: olfactory bulb

extract_protocol:
Mouse olfactory bulb samples were homogenized in TRIzol, and total RNA was isolated according to the manufacturer's protocol, followed by DNase treatment.
Library preparation contains the following steps: 1. Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). 2. Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. 3. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: Middle-aged B6 mice were infected with SARS2-N501YMA30 (1000 PFU/mouse)

value: olfactory bulb

tag: sample group


title: TMSC | P4M | T

description: Library name: P4MT

data_processing:
Raw paired-end FASTQ files were quantified using Salmon (v1.10.2), reads were quasi-mapped against the human GENCODE v45 reference annotation.
Assembly: GENCODE v45 (GRCh38.p13)
Supplementary files format and content: TPM plus 1, log2 transformed

source_name: Patient Derived

extract_protocol:
RNA was extracted using the commercially available RNeasy Mini Kit (Qiagen; 74104). RNA concentration was evaluated via NanoDrop spectrophotometer. Samples were diluted to the final concentration of 20ng/ul prior shipment to Novogene Corporation Inc. 2921 Stockton Blvd. Suite 1810 Sacramento CA 95817.
Human mRNA Sequencing (WOBI): 80 total RNA samples were subjected to Eukaryotic mRNA-seq on the NovaSeq 6000 (PE150) with poly-A capture and non-directional library.

value: Patient Derived

value: Tumor Mesenchymal Stem Cell

value: TGFB Treated


title: Barnyard_96well_rep34

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep34


title: SARS2_30dpi_3

description:
Library name: sample_11
Column name in XZ4XKT-expression-matrix.csv: 30dpi_11_cpm and 30dpi_11_count


title: TMSC | P4M | C

description: Library name: P4M


title: RIL23_G02_L02_3

description: Library name: Sample67


title: Barnyard_96well_rep33

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep33


title: SARS2_30dpi_2

description:
Library name: sample_10
Column name in XZ4XKT-expression-matrix.csv: 30dpi_10_cpm and 30dpi_10count


title: Barnyard_96well_rep32

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep32


title: Barnyard_96well_rep31

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep31


title: TMSC | C9 | C

description: Library name: C9


title: RIL22_G09_L02_2

description: Library name: Sample65


title: SARS2_6dpi_4

description:
Library name: sample_8
Column name in XZ4XKT-expression-matrix.csv: 6dpi_8_cpm and 6dpi_8_count


title: RIL22_G09_L01_2

description: Library name: Sample64


title: SARS2_6dpi_3

description:
Library name: sample_7
Column name in XZ4XKT-expression-matrix.csv: 6dpi_7_cpm and 6dpi_7_count


title: Barnyard_96well_rep29

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep29


title: RIL22_G02_L02_4

description: Library name: Sample63


title: SARS2_6dpi_2

description:
Library name: sample_6
Column name in XZ4XKT-expression-matrix.csv: 6dpi_6_cpm and 6dpi_6_count


title: RIL22_G02_L01_3

description: Library name: Sample62


title: Barnyard_96well_rep28

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep28


title: SARS2_6dpi_1

description:
Library name: sample_5
Column name in XZ4XKT-expression-matrix.csv: 6dpi_5_cpm and 6dpi_5_count


title: RIL21_G09_L02_2

description: Library name: Sample61


title: TEC | P4E | C

description: Library name: P4E

value: Tumor Endothelial Cell


title: Barnyard_96well_rep27

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep27


title: mock_4

description:
Library name: sample_4
Column name in XZ4XKT-expression-matrix.csv: Mock_4_cpm and Mock_4_count

value: mock


title: RIL21_G09_L02_1

description: Library name: Sample60


title: MSC | N | T

description: Library name: NT

source_name: Normal Commercial

value: Normal Commercial


title: Barnyard_96well_rep26

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep26

value: 293T and NIH3T3


title: mock_3

description:
Library name: sample_3
Column name in XZ4XKT-expression-matrix.csv: Mock_3_cpm and Mock_3_count


title: RIL21_G02_L02_4

description: Library name: Sample59

value: leaf tissue

value: Ler X Cvi RIL


title: MSC | N | C

description: Library name: N


title: Barnyard_96well_rep25

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep25

value: Human embryonic kidney and mouse embryonic fibroblasts


title: mock_2

description:
Library name: sample_2
Column name in XZ4XKT-expression-matrix.csv: Mock_2_cpm and Mock_2_count


title: RIL21_G02_L01_4

description: Library name: Sample58


title: Barnyard_96well_rep24

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep24

value: WT


title: mock_1

description:
Library name: sample_1
Column name in XZ4XKT-expression-matrix.csv: Mock_1_cpm and Mock_1_count


title: Barnyard_96well_rep23

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep23


title: MSC | BM | C

description: Library name: BM

source_name: Bone Marrow Commercial

value: Bone Marrow Commercial


title: RIL21_G02_L01_3

description: Library name: Sample57


title: RIL19_G09_L02_2

description: Library name: Sample56


title: MSC | AD | T

description: Library name: ADT

value: Adipose Derived Commercial

value: Mesenchymal Stem Cell


title: Barnyard_96well_rep22

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep22

value: embryonic kidney and fibroblast cell lines


title: RIL19_G02_L02_3

description: Library name: Sample55


title: MSC | AD | C

description: Library name: AD

value: Control


title: OX_Col_VIM24_Col_7-1

description:
Library name: Sample6
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-1

data_processing:
Reads trimmed with Trimmomatic (v0.38) with options "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true", "LEADING:3", "TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:36"
Reads aligned with STAR (v2.7.6a) with options "--alignIntronMin 60", "--alignIntronMax 6000"
Counts gathered for features using HTSeq-count (v0.13.5) with options "--mode=union". The strandedness parameter was set to --stranded=reverse for Ler_Cvi_RIL samples, and to --stranded=no for overexpression (OX), mutant, and control samples.
Assembly: TAIR10 genome and Araport11 annotation
Supplementary files format and content: HTSeq count files (.txt) with the following columns: <locus> <read count>

growth_protocol: Transgenic overexpression lines and mutant plants were grown under long-day conditions (16h light/8h dark) at 22C on soil. T1 plants were selected in the presence of 50 ug/ml kanamycin. RIL plants were grown on half-strength MS plates under long-day conditions (16h light/8h dark) at 25C for 7-9 days.

extract_protocol:
For VIM overexpression and mutant lines, total RNA was extracted from leaves of 4 to 12-week-old T1 plants with the Monarch Total RNA Miniprep Kit (N2010, NEB) and tested with Qubit RNA BR Assay (Q33223, Thermo Fisher). For Ler x Cvi RILs, total RNA was extracted from bulk seedlings following the TRIzol extraction method.
For VIM overexpression and mutant lines, library preparation and 150 bp paired-end sequencing were performed by Novogene on an Illumina NovaSeq X Plus platform. For Ler x Cvi RILs, libraries were constructed using the TruSeq Stranded mRNA Library Kit (No.20020594, Illumina) with a custom dual index workflow. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq 6000 platform.

tag: transgene

tag: allele

value: Col


title: RIL19_G02_L01_4

description: Library name: Sample54


title: CAF | P4C | T

description: Library name: P4CT

value: Patient Derived

value: Cancer Associated Fibroblast


title: OX_Col_VIM4_Col_7-7

description:
Library name: Sample5
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-7


title: Barnyard_96well_rep19

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep19


title: OX_Col_VIM4_Col_7-6

description:
Library name: Sample4
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-6


title: RIL18_G09_L01_2

description: Library name: Sample52


title: OX_Col_VIM4_Col_7-4

description:
Library name: Sample3
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-4


title: Barnyard_96well_rep18

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep18


title: RIL18_G02_L02_4

description: Library name: Sample51


title: P4 Derived MSC Low Serum VEGF

description: Library name: P4MSLSV

data_processing:
Raw paired-end FASTQ files were quantified using Salmon (v1.2.1), reads were quasi-mapped against the human GENCODE v34 reference annotation.
tximeta was used to read in the data and export counts matrix.
Assembly: GENCODE v34 (GRCh38.p13)
Supplementary files format and content: pseudocounts

tag: serum

value: Low Serum

value: VEGF


title: Barnyard_96well_rep17

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep17


title: OX_Col_VIM4_Col_7-2

description:
Library name: Sample2
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-2


title: P4 Derived MSC Low Serum Control

description: Library name: P4MSLSC


title: C405, scRNA-seq

status: Public on Jul 20 2026

city: Bunkyo-ku

first: Akiyasu

last: Iwase

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description:
Fluidigm C1
C405

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: mm10
Supplementary files format and content: Fluidigm_raw_counts.txt. Tab-separated matrix files include raw counts for each single-cell
Supplementary files format and content: Fluidigm_SCT_counts.txt. Tab-separated matrix files include normalized counts by SCTransform from Seurat for each single-cell

source_name: heart

extract_protocol:
Cardiac NCCs labeled by Wnt1-Cre; R26-EYFP mice at E11.5, 12.5, 14.5 and 17.5 around sub-region of aorticopulmonary septum were dissociated by using 0.25 w/v% trypsin / 1 mmol/L EDTA・4Na solution (Wako) at 37 °C, 15 minutes. Enzymes were neutralized with equal volume of DMEM (Wako) with 10% fetal bovine serum (FBS) (SIGMA). Cell suspensions were filtered through a 35 μm nylon mesh cell strainer（FALCON 352235.  Cells were kept on ice until cell sorting. Cell sorting was performed in a fluorescence-activated cell sorting (FACS) AriaⅡcell sorter (BD Biosciences).
EYFP-positive single cells were captured on the Fluidigm C1 Medium-cell (10-17 μm cell diameter) integrated fluidic circuit (IFC) for single cell cDNA libraries for mRNA sequencing. EYFP-positive cells were loaded on the IFC chips at concentration of 300 cells per μL. All captured cells were photographed to check whether cells were truly EYFP-positive and were dissociated for single cells by using KEYENCE BZ-X710. Single cell cDNAs were prepared on Fluidigm C1 system by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System (Clontech). Only single cell cDNAs confirmed by imaging data were performed quality check (QC) by using Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina HiSeq 2500.

value: heart

value: Wnt1-Cre; R26-EYFP


title: OX_Col_VIM4_Col_5-2

description:
Library name: Sample1
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 5-2


title: RIL18_G02_L01_3

description: Library name: Sample49


title: P4 Derived MSC Full Serum VEGF Bevacizumab

description: Library name: P4MSFSVB

value: Full Serum

value: VEGF + Bevacizumab


title: Barnyard_96well_rep15

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep15

value: 293T and NIH3T3


title: OX_Col_VIM24_Col_7-5

description:
Library name: Sample8
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-5

growth_protocol: Transgenic overexpression lines and mutant plants were grown under long-day conditions (16h light/8h dark) at 22C on soil. T1 plants were selected in the presence of 50 ug/ml kanamycin.

extract_protocol:
Genomic DNA was extracted from leaf tissue of T1 plants. 200 ng of genomic DNA was sheared with a Covaris R230 ultrasonicator into 350 bp fragments.
Libraries were generated following the protocol of NEBNext Ultra II DNA Library Prep kit (E765S, NEB) in combination with NEBNext EM-seq Adaptor (E7165AVIAL, NEB) and NEBNext Multiplex Oligos for Enzymatic Methyl-seq (E7140L, NEB). Bisulfite conversion was performed with the EZ-96 Methylation-Gold MagPrep kit (D5042, Zymo Research) prior to the PCR enrichment step, where the NEB Q5 polymerase was substituted by KAPA HiFi HotStart Uracil+ReadyMix (KK2801, Roche) to enable the amplification of uracil-containing DNA. Size selection and cleanup were performed with magnetic beads (AMPure XPbeads, A63881, Beckman Colter), and the quality of the final libraries was assessed with the Qubit dsDNA HS Assay Kit (Q32851, Invitrogen). Sequencing was performed by Novogene using an Illumina NovaSeq X Plus (PE150) platform.

value: leaf tissue


title: RIL22_G09_L01_1

description: Library name: Sample66

value: Ler X Cvi RIL


title: RIL18_G02_L01_4

description: Library name: Sample48


title: P4 Derived MSC Full Serum VEGF

description: Library name: P4MSFSV


title: Barnyard_96well_rep14

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep14

value: Human embryonic kidney and mouse embryonic fibroblasts

value: WT


title: OX_Col_VIM24_Col_7-4

description:
Library name: Sample7
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-4


title: RIL18_G02_L02_3

description: Library name: Sample50


title: RIL15_G09_L02_2

description: Library name: Sample47


title: Barnyard_96well_rep16

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep16


title: P4 Derived MSC Full Serum Control

description: Library name: P4MSFSC

value: Mesenchymal Stem Cell


title: Barnyard_96well_rep13

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep13

value: embryonic kidney and fibroblast cell lines


title: OX_Col_VIM24_Col_7-1


title: RIL15_G02_L02_4

description: Library name: Sample46


title: Barnyard_96well_rep12

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep12


title: Adipose Derived MSC Low Serum VEGF Bevacizumab

description: Library name: ADMSLSVB


title: OX_Col_VIM4_Col_7-7


title: RIL15_G02_L02_3

description: Library name: Sample45


title: Adipose Derived MSC Low Serum VEGF

description: Library name: ADMSLSV


title: TMSC | C9 | T

description: Library name: C9T

value: Tumor Mesenchymal Stem Cell

value: TGFB Treated


title: SARS2_30dpi_1

description:
Library name: sample_9
Column name in XZ4XKT-expression-matrix.csv: 30dpi_9_cpm and 30dpi_9_count

value: olfactory bulb


title: Barnyard_96well_rep11

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep11


title: TMSC | C8 | C

description: Library name: C8

value: Patient Derived

value: Control


title: Barnyard_96well_rep30

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep30


title: OX_Col_VIM4_Col_7-6

value: Col


title: TMSC | C8 | T

description: Library name: C8T


title: RIL15_G02_L01_4

description: Library name: Sample44


title: Adipose Derived MSC Low Serum Control

description: Library name: ADMSLSC

value: Low Serum


title: TEC | P4E | T

description: Library name: P4ET

value: Tumor Endothelial Cell


title: Barnyard_96well_rep10

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep10


title: OX_Col_VIM4_Col_7-4


title: RIL15_G02_L01_3

description: Library name: Sample43


title: Adipose Derived MSC Full Serum VEGF Bevacizumab

description: Library name: ADMSFSVB

value: Full Serum


title: Barnyard_96well_rep9

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep9


title: Adipose Derived MSC Full Serum VEGF

description: Library name: ADMSFSV

value: VEGF


title: RIL13_G02_L02_4

description: Library name: Sample42


title: OX_Col_VIM4_Col_7-2


title: Barnyard_96well_rep8

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep8

value: 293T and NIH3T3


title: OX_Col_VIM4_Col_5-2

value: leaf tissue


title: Adipose Derived MSC Full Serum Control

description: Library name: ADMSFSC


title: Barnyard_96well_rep7

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep7


title: MSC | BM | T

description: Library name: BMT

value: Bone Marrow Commercial


title: OX_Col_VIM24_Col_7-3

description:
Library name: Sample26
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-3


title: RIL13_G09_L02_1

description: Library name: Sample40

value: Ler X Cvi RIL


title: Barnyard_96well_rep6

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep6

value: Human embryonic kidney and mouse embryonic fibroblasts

value: WT


title: OX_Col_VIM24_Col_7-2

description:
Library name: Sample25
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-2


title: RIL13_G09_L01_1

description: Library name: Sample39


title: OX_Col_VIM24_Col_7-5


title: MSC_hTERT, SRF-RELA_3

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Library name: SRF-RELA_3

data_processing:
Read quality control was performed using FastQC software v0.11.8 (Andrews S, Babraham Bioinformatics)
Low quality reads were trimmed and adapters were removed using Trimmomatic software v0.39
Reads were aligned using the HISAT2 software v2.12.1 [9] on grch38 genome
Gene counts were generated using featureCounts software from subread-2.0.3 and Ensembl Homo_sapiens.GRCh38.105.gtf annotation file
Assembly: Ensembl Homo_sapiens.GRCh38.105.gtf
Supplementary files format and content: raw_counts.tsv en raw counts

source_name: MSC-hTERT

growth_protocol: Immortalized human mesenchymal stem cells (MSC-hTERT) were cultured in Minimum Essential medium α (MEM α) (Gibco, Watham, MA, USA) supplemented with 10% HyClone serum, 1% L-glutamine, 1 ng/ml FGF-2, 0.2 mM ascorbic acid, 2 U/ml heparin and antibiotics (50 U/ml penicillin and 50 μg/ml streptomycin)

extract_protocol:
Total RNA was extracted with TriPure Isolation Reagent (Sigma-Aldrich) and cleaned from residual genomic DNA with DNase on column (NucleoSpin RNA, Macherey-Nagel, Düren, Germany)
Libraries were prepared using the TruSeq Stranded mRNA kit and sequenced on a NovaSeq 6000 Sequencing System (Illumina, San Diego, CA, USA)

value: MSC-hTERT

value: mesenchymal stem cells, hTERT

value: SRF-RELA


title: OX_Col_VIM24_Col_5-2

description:
Library name: Sample24
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 5-2


title: Barnyard_96well_rep5

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep5

value: embryonic kidney and fibroblast cell lines


title: MSC_hTERT, SRF-RELA_2

description: Library name: SRF-RELA_2


title: RIL13_G02_L01_4

description: Library name: Sample38


title: OX_Col_VIM24_Col_7-4


title: MSC_hTERT, SRF-RELA_1

description: Library name: SRF-RELA_1


title: Barnyard_96well_rep4

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep4


title: OX_Col_VIM24_Col_5-1

description:
Library name: Sample23
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 5-1


title: RIL13_G02_L01_3

description: Library name: Sample37


title: MSC_hTERT, SRF-PDGFRB_3

description: Library name: SRF-PDGFRb_3

value: SRF-PDGFRB


title: Barnyard_96well_rep21

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep21


title: Barnyard_96well_rep3

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep3


title: MSC_hTERT, SRF-PDGFRB_2

description: Library name: SRF-PDGFRb_2


title: RIL13_G02_L02_3

description: Library name: Sample36


title: Barnyard_96well_rep2

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep2


title: OX_Col_VIM24_Col_4-1

description:
Library name: Sample21
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 4-1


title: OX_Col_VIM24_Col_4-2

description:
Library name: Sample22
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 4-2


title: RIL168_G02_L01_3

description: Library name: Sample311


title: RIL11_G09_L02_2

description: Library name: Sample35


title: RIL170_G02_L01_3

description: Library name: Sample312


title: Barnyard_96well_rep1

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep1


title: MSC_hTERT, SRF-PDGFRB_1

description: Library name: SRF-PDGFRb_1


title: RIL170_G02_L02_4

description: Library name: Sample314


title: Barnyard_96well_rep20

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep20


title: RIL172_G02_L01_3

description: Library name: Sample316


title: Barnyard_1mL_6dot5k

description:
AmpliDrop
220923_02_293T_NIH3T3_1mL_6dot5k


title: RIL11_G09_L01_2

description: Library name: Sample33


title: OX_Col_VIM4_Cvi_1-1

description:
Library name: Sample19
VIM4 (Cvi-0 allele) overexpression in Col-0 background, independent line 1-1

value: Cvi


title: Barnyard_0dot2mL_11k

description:
AmpliDrop
221104_06_293T_NIH3T3_0dot2mL_11k


title: OX_Col_VIM4_Col_7-5

description:
Library name: Sample18
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-5

value: Col


title: RIL11_G09_L01_1

description: Library name: Sample32


title: MSC_hTERT, SRF-ICA1L_1

description: Library name: SRF-ICA1L_1


title: OX_Col_VIM4_Col_7-3

description:
Library name: Sample17
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-3


title: Barnyard_0dot2mL_9k

description:
AmpliDrop
221005_04_293T_NIH3T3_0dot2mL_9k


title: MSC_hTERT, SRF-FOXO1_3

description: Library name: SRF-FOXO1_3


title: Barnyard_0dot2mL_5k

description:
AmpliDrop
221005_03_293T_NIH3T3_0dot2mL_5k


title: OX_Col_VIM4_Col_5-1

description:
Library name: Sample16
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 5-1


title: MSC_hTERT, SRF-FOXO1_2

description: Library name: SRF-FOXO1_2


title: RIL11_G02_L02_3

description: Library name: Sample30


title: OX_Col_VIM2_Cvi_3-3

description:
Library name: Sample15
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-3


title: RIL11_G02_L01_4

description: Library name: Sample29


title: MSC_hTERT, SRF-FOXO1_1

description: Library name: SRF-FOXO1_1


title: Barnyard_0dot2mL_2dot5k

description:
AmpliDrop
221005_02_293T_NIH3T3_0dot2mL_2dot5k


title: Barnyard_0dot2mL_1k

description:
AmpliDrop
221005_01_293T_NIH3T3_0dot2mL_1k


title: OX_Col_VIM2_Cvi_3-2

description:
Library name: Sample14
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-2


title: RIL11_G02_L01_3

description: Library name: Sample28


title: MSC_hTERT, SRF_3

description: Library name: SRF_3

value: SRF


title: PBMC_operator1_draw2_cryo_rep2

description:
AmpliDrop
221111_26_GM1111s3_PBMC_operator1_draw2_cryo_rep2

source_name: blood

value: blood

value: PBMC

value: Human peripheral blood mononuclear cell


title: OX_Col_VIM2_Cvi_3-1

description:
Library name: Sample13
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-1

source_name: leaf tissue


title: RIL7_G09_L02_2

description: Library name: Sample27


title: MSC_hTERT, SRF_2

description: Library name: SRF_2


title: PBMC_operator1_draw2_cryo_rep1

description:
AmpliDrop
221111_25_GM1111s2_PBMC_operator1_draw2_cryo_rep1


title: OX_Col_VIM2_Col_7-2

description:
Library name: Sample12
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 7-2


title: RIL7_G09_L01_2

description: Library name: Sample26


title: RIL13_G09_L02_2

description: Library name: Sample41


title: OX_Col_VIM2_Col_7-1

description:
Library name: Sample11
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 7-1


title: PBMC_operator1_draw2_fresh_rep2

description:
AmpliDrop
221111_22_GM1109s6_PBMC_operator1_draw2_fresh_rep2


title: RIL7_G02_L02_3

description: Library name: Sample24


title: MSC_hTERT, pMSCV_2

description: Library name: pMSCV_2

value: pMSCV


title: PBMC_operator1_draw2_fresh_rep1

description:
AmpliDrop
221111_20_GM1109s4_PBMC_operator1_draw2_fresh_rep1


title: PBMC_operator2_draw1_cryo

description:
AmpliDrop
221118_07_IM1117s2_PBMC_operator2_draw1_cryo


title: VIM4_mutant_3

description:
Library name: Sample9
vim4 T-DNA insertion mutant (NASC ID: N675753), biological replicate 3

value: leaf tissue

value: Col-0; vim4 (NASC ID:N675753)


title: MSC_hTERT, pMSCV_1

description: Library name: pMSCV_1


title: RIL7_G02_L01_4

description: Library name: Sample23

value: Ler X Cvi RIL


title: OX_Col_VIM2_Col_1-1

description:
Library name: Sample10
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 1-1


title: RIL7_G02_L01_3

description: Library name: Sample22


title: VIM4_mutant_1

description:
Library name: Sample7
vim4 T-DNA insertion mutant (NASC ID: N675753), biological replicate 1


title: PBMC_operator1_draw1_cryo

description:
AmpliDrop
221118_03_GM1117s2_PBMC_operator1_draw1_cryo


title: Mia-PaCa-2 cell line, vehicle, 48h, bioreplicate 2

city: San Antonio

first: Hanzhou

last: Wang

state: TX

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health at San Antonio

description: Library name: Sample_ct-2

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg38) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg38
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

extract_protocol:
After treatment, the cells were lysed with Qiazol (QIAGEN) for RNA isolation, and total RNA was isolated using an RNeasy mini kit (QIAGEN).
RNA-Seq

treatment_protocol: vehicle (DMSO) vs 6uM CIDD-8633 for 48h

value: vehicle Rep 2


title: RIL6_G09_L01_2

description: Library name: Sample21


title: Mia-PaCa-2 cell line, vehicle, 48h, bioreplicate 1

description: Library name: Sample_ct-1

value: vehicle Rep 1


title: VIM2_mutant_3

description:
Library name: Sample6
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 3

value: Col-0; vim2 (NASC ID:N664186)


title: RIL6_G02_L02_4

description: Library name: Sample20


title: Mia-PaCa-2 cell line, 6uM CIDD-8633, 48h, bioreplicate 2

description: Library name: Sample_8633-2

value: 6uM CIDD-8633 48h Rep 2


title: PBMC_operator1_draw1_fresh

description:
AmpliDrop
221118_01_GM1116s1_PBMC_operator1_draw1_fresh

value: WT


title: Mia-PaCa-2 cell line, 6uM CIDD-8633, 48h, bioreplicate 1

description: Library name: Sample_8633-1

value: 6uM CIDD-8633 48h Rep 1


title: VIM2_mutant_1

description:
Library name: Sample4
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 1


title: RIL6_G02_L01_3

description: Library name: Sample19


title: Mock2_A2780cisonly

description:
AmpliDrop
210526_02_A2780Cis

source_name: ovarian cancer lines

value: ovarian cancer lines

value: Human ovarian adenocarcinoma


title: Control_Col_WT_3

description:
Library name: Sample3
Wild-type Col-0 control, biological replicate 3


title: RIL4_G09_L02_2

description: Library name: Sample17


title: Mock2_A2780only

description:
AmpliDrop
210526_01_A2780


title: SEPT6 shmiR+ WT SEPT6_2

first: Safa

middle: F

last: Mohamad

address: 125 Park Drive, Apt 15

institute: Boston Children's Hospital/ Harvard Medical School

description:
Library name: Pool163-1_16
10X Genomics

data_processing:
Data preprocessing and quality control: Raw scRNA-seq data were aligned to the human reference genome (GRCh38) using the Cell Ranger pipeline (v8.0.0, 10x Genomics). Quality control, integration, clustering, annotation, and differential expression analyses were performed with the Seurat R package (v5.0.2).Cells were retained if they contained >500 detected genes, >500 transcripts, and <20% of reads mapped to mitochondrial genes. Potential doublets were identified and removed using the scDblFinder package. Genes expressed in fewer than 10 cells were excluded.  Analysis of scRNA-seq data: The count matrix was normalized using sctransform function in Seurat, filtering out mitochondrial variation. Principal component analysis (PCA) was applied to variable features. The top 30 PCs were used for batch correction and sample integration through Anchor-based reciprocal PCA integration process, nearest-neighbor graph construction and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction. Clustering was tested across multiple resolutions, and a resolution of 0.5 was selected.  Cell type annotation was performed by combining the top 20 cluster-specific markers identified with FindAllMarkers function in Seurat with predictions from the Azimuth annotation package. Non-parametric Wilcoxon rank sum test was applied to perform differential expression tests and volcano plots were generated using Enhanced Volcano package.  Pathway analysis: In the differential expression tests, genes with an absolute log2 fold change > 0.25 and p value < 0.01 were defined as differentially expressed genes (DEGs). Up- or Down-regulated DEGs were separately submitted to STRING [https://string-db.org/] for the protein-protein interaction and Gene Ontology Biological Process (GOBP) enrichment analyses. To consider the weights of all the genes, genes were ordered in a ranked list based on the fold change. Gene Set Enrichment Analysis (GSEA)(4.3.3) was used to screen the enrichment of a priori defined sets of genes in the pre-ranked gene list. The gene set database was c5.go.bp.v2025.1.Hs.symbols from the Molecular Signatures Database (MSigDB) and the number of permutations was 1,000. Top 10 up- or down-regulated gene sets were visualized as bubble plots.
Assembly: Human Reference Genome:GRCh38
Supplementary files format and content: Tab separated value files and matrix files

source_name: CD34+ cells

extract_protocol:
Human cells were resuspended in PBS with 0.4% Bovine Serum Albumin (BSA) buffer at the concentration of 1000 cells/µL. About 20,000 cells were loaded onto a ChromiumTM X instrument (10x Genomics) according to manufacturer’s instructions.
The scRNAseq libraries were processed using Chromium GEM-X Single Cell 5' Kit v3 (10x Genomics).

value: CD34+ cells


title: RIL4_G09_L02_1

description: Library name: Sample16


title: Control_Col_WT_1

description:
Library name: Sample1
Wild-type Col-0 control, biological replicate 1


title: Mock4_MCF7_A2780_293T_HCT116_8k

description:
AmpliDrop
221028_08_GM1025s8_mock4_8k

source_name: breast cancer, ovarian cancer, emryonic kidney, and colorectal cancer lines

value: Human breast adenocarcinoma, human ovarian adenocarcinoma, human embryonic kidney, and human colorectal carcinoma


title: EV Control_2

description:
Library name: Pool163-1_15
10X Genomics


title: RIL4_G09_L01_2

description: Library name: Sample15


title: Mock4_MCF7_A2780_293T_HCT116_5k

description:
AmpliDrop
221028_07_GM1025s7_mock4_5k

value: breast cancer, ovarian cancer, emryonic kidney, and colorectal cancer lines


title: SEPT6 shmiR+GM1_2

description:
Library name: Pool163-1_14
10X Genomics


title: OX_Col_VIM24_Col_7-3

description:
Library name: Sample26
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-3

value: Col


title: RIL4_G09_L01_1

description: Library name: Sample14


title: Mock4_MCF7_A2780_293T_HCT116_2dot5k

description:
AmpliDrop
221028_06_GM1025s6_mock4_2dot5k


title: RIL4_G02_L01_4

description: Library name: Sample13


title: SEPT6 shmiR+ WT SEPT6

description:
Library name: Pool163-1_4
10X Genomics


title: Mock2_A2780_A2780cis

description:
AmpliDrop
210526_03_A2780_A2780cis

value: A2780 and A2780cis


title: SEPT6 shmiR+GM1+SM_2

description:
Library name: Pool163-1_17
10X Genomics


title: OX_Col_VIM24_Col_5-2

description:
Library name: Sample24
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 5-2


title: RIL4_G02_L01_3

description: Library name: Sample12


title: EV Control

description:
Library name: Pool163-1_3
10X Genomics


title: Cell line SKMEL28, CXXC1 siRNA, biological rep 3

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: Virginia

address: Box 800759, Health System

department: Biomedical Engineering

institute: University of Virginia

description: Library name: SKMEL28_siCXXC1_Rep3

data_processing:
Raw FASTQ files were subjected to initial quality control using FastQC. Adapter sequences and low-quality bases were removed from paired-end reads using Trim Galore, with post-trimming quality assessment performed using FastQC. Trimmed reads were aligned to the human reference genome (GRCh38) using STAR (PMID: 23104886), with genome indices generated from the GENCODE v41 primary assembly FASTA and annotation files. STAR was run in paired-end mode to generate coordinate-sorted BAM files as well as transcriptome-aligned BAMs for downstream quantification. Alignment quality and read distribution metrics were assessed using Qualimap RNA-seq. Transcript- and gene-level expression quantification was performed using RSEM (PMID: 21816040) with a reference prepared from the same GENCODE v41 annotation, yielding expected counts and TPM values. Gene-level expected counts were compiled across all samples into a single expression matrix for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Gene-level read counts compiled across all samples into a single matrix (rows: genes, columns: experimental conditions)

source_name: Skin

growth_protocol: SKMEL28 cells were grown in DMEM/F12 supplemented with 1% sodium pyruvate and 5% FBS. MALME3M, LOXIMVI, and UACC62 cells were grown in RPMI 1640 supplemented with 1% sodium pyruvate and 5% FBS. 100 U/mL Penicillin-Streptomycin (10,000 U/mL) and 0.5 mg/mL Plasmocin Prophylactic were present in all cell cultures. Cells were grown at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
At harvest, cells were washed once with PBS and lysed directly in the well using Buffer RLT (Qiagen). Lysates were homogenized using QIAshredder columns (Qiagen, catalog no. 79654), and total RNA was extracted using the RNeasy Mini Kit (Qiagen, catalog no. 74104) following the manufacturer’s protocol, including on-column DNase digestion (Qiagen RNase-Free DNase Set, catalog no. 79254). RNA integrity was assessed using the Agilent TapeStation (RNA ScreenTape), and all samples used for sequencing had RINe values > 9.
Bulk RNA sequencing libraries were prepared with assistance from the University of Virginia Genome Analysis and Technology Core (RRID: SCR_018883). Poly(A)+ RNA was isolated using the NEB mRNA Isolation Module, followed by library preparation using the NEBNext UltraExpress mRNA Library Prep Kit, according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NextSeq 2000 platform using a P3-100 sequencing kit.

treatment_protocol: LOXIMVI, MALME3M, UACC62, and SKMEL28 cells were seeded in 6-well plates in biological triplicate and allowed to attach for 24 h prior to siRNA transfection. Cells were then treated with ON-TARGETplus siRNA SMARTpool targeting human CXXC1 (Horizon Discovery Biosciences; catalog no. L-014923-01-0005) or ON-TARGETplus Non-targeting siRNA #1 control (catalog no. D-001810-01-05) and cultured for 96 h post-transfection. siRNA transfections were performed using DharmaFECT transfection reagents (Horizon Discovery), including DharmaFECT 1 (catalog no. T-2001-02), DharmaFECT 2 (catalog no. T-2002-01), and DharmaFECT 3 (catalog no. T-2003-01), according to the manufacturer’s instructions.

value: Skin

value: Cutaneous melanoma

value: CXXC1 knockdown

value: CXXC1 siRNA (96 h)

tag: batch


title: OX_Col_VIM24_Col_5-1

description:
Library name: Sample23
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 5-1

value: leaf tissue


title: Cvi_G09_L01_2

description: Library name: Sample11

value: Cvi


title: Cell line SKMEL28, CXXC1 siRNA, biological rep 2

description: Library name: SKMEL28_siCXXC1_Rep2


title: OX_Col_VIM24_Col_4-2

description:
Library name: Sample22
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 4-2


title: OX_Col_VIM24_Col_7-2

description:
Library name: Sample25
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 7-2


title: Cvi_G02_L02_4

description: Library name: Sample10


title: SEPT6 shmiR+GM1+SM

description:
Library name: Pool163-1_5
10X Genomics


title: Exp3_organoid_orbital_rep3

description:
AmpliDrop
240519_10_GM510s6_Exp3_org_orbital_rep3

source_name: brain cells

value: brain cells

value: hiPSC-derived forebrain organoids

value: Human forebrain orgaboids derived from hiPSCs

value: 2-month-old culture


title: OX_Col_VIM4_Cvi_1-2

description:
Library name: Sample20
VIM4 (Cvi-0 allele) overexpression in Col-0 background, independent line 1-2


title: OX_Col_VIM24_Col_4-1

description:
Library name: Sample21
VIM2 and VIM4 (Col-0 alleles) co-overexpression in Col-0 background, independent line 4-1


title: RIL11_G09_L02_1

description: Library name: Sample34

value: Ler X Cvi RIL


title: Cvi_G02_L02_3

description: Library name: Sample9


title: Exp3_organoid_orbital_rep2

description:
AmpliDrop
240519_09_GM510s5_Exp3_org_orbital_rep2

value: WT


title: Cell line SKMEL28, CXXC1 siRNA, biological rep 1

description: Library name: SKMEL28_siCXXC1_Rep1


title: Mock4_MCF7_A2780_293T_HCT116_1k

description:
AmpliDrop
221028_05_GM1025s5_mock4_1k


title: MSC_hTERT, SRF-ICA1L_3

description: Library name: SRF-ICA1L_3

value: MSC-hTERT

value: mesenchymal stem cells, hTERT


title: MSC_hTERT, SRF-ICA1L_2

description: Library name: SRF-ICA1L_2


title: RIL11_G02_L02_4

description: Library name: Sample31


title: Cell line SKMEL28, nontargeting control siRNA, biological rep 3

description: Library name: SKMEL28_siNTC_Rep3

value: non-targeting control siRNA (96 h)


title: OX_Col_VIM4_Cvi_1-2


title: Exp3_organoid_orbital_rep1

description:
AmpliDrop
240519_08_GM510s4_Exp3_org_orbital_rep1


title: Cell line SKMEL28, nontargeting control siRNA, biological rep 2

description: Library name: SKMEL28_siNTC_Rep2


title: OX_Col_VIM4_Cvi_1-1

description:
Library name: Sample19
VIM4 (Cvi-0 allele) overexpression in Col-0 background, independent line 1-1


title: Cvi_G02_L01_4

description: Library name: Sample8


title: Ler_G09_L02_2

description: Library name: Sample7

value: Ler


title: Exp3_organoid_static_rep3

description:
AmpliDrop
240519_07_GM510s3_Exp3_org_static_rep3


title: Cell line SKMEL28, nontargeting control siRNA, biological rep 1

description: Library name: SKMEL28_siNTC_Rep1


title: OX_Col_VIM4_Col_7-5

description:
Library name: Sample18
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-5

value: Col


title: Ler_G09_L02_1

description: Library name: Sample6


title: Exp3_organoid_static_rep2

description:
AmpliDrop
240519_06_GM510s2_Exp3_org_static_rep2


title: Cell line LOXIMVI, CXXC1 siRNA, biological rep 3

description: Library name: LOXIMVI_siCXXC1_Rep3

value: Skin

value: LOXIMVI


title: RIL142_G02_L02_4

description: Library name: Sample220


title: RIL136_G02_L02_3

description: Library name: Sample212


title: Exp3_organoid_static_rep1

description:
AmpliDrop
240519_05_GM510s1_Exp3_org_static_rep1


title: Ler_G09_L01_2

description: Library name: Sample5


title: OX_Col_VIM4_Col_7-3

description:
Library name: Sample17
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 7-3


title: RIL143_G02_L02_4

description: Library name: Sample225


title: Cell line LOXIMVI, CXXC1 siRNA, biological rep 2

description: Library name: LOXIMVI_siCXXC1_Rep2

value: Cutaneous melanoma

value: CXXC1 knockdown


title: OX_Col_VIM4_Col_5-1

description:
Library name: Sample16
VIM4 (Col-0 allele) overexpression in Col-0 background, independent line 5-1

value: leaf tissue


title: MSC_hTERT, SRF_1

description: Library name: SRF_1

value: SRF


title: RIL7_G02_L02_4

description: Library name: Sample25


title: Ler_G09_L01_1

description: Library name: Sample4


title: MSC_hTERT, pMSCV_3

description: Library name: pMSCV_3

value: pMSCV


title: Cell line LOXIMVI, CXXC1 siRNA, biological rep 1

description: Library name: LOXIMVI_siCXXC1_Rep1

value: CXXC1 siRNA (96 h)


title: Exp2_organoid_severelyperturbed_rep2

description:
AmpliDrop
231201_06_GM1121s6_Exp2_org_severely_perturbed_rep2

value: brain cells

value: hiPSC-derived forebrain organoids

value: Human forebrain orgaboids derived from hiPSCs

value: 6-month-old culture


title: Ler_G02_L02_4

description: Library name: Sample3


title: OX_Col_VIM2_Cvi_3-3

description:
Library name: Sample15
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-3

value: Cvi


title: Cell line LOXIMVI, nontargeting control siRNA, biological rep 3

description: Library name: LOXIMVI_siNTC_Rep3

value: WT


title: Ler_G02_L01_4

description: Library name: Sample2


title: Exp2_organoid_nonperturbed_rep2

description:
AmpliDrop
231201_04_GM1121s4_Exp2_org_outside_inc_rep2


title: Ler_G02_L01_3

description: Library name: Sample1


title: SEPT6 shmiR+GM1

description:
Library name: Pool163-1_2
10X Genomics

value: CD34+ cells


title: OX_Col_VIM2_Cvi_3-2

description:
Library name: Sample14
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-2


title: Cell line LOXIMVI, nontargeting control siRNA, biological rep 1

description: Library name: LOXIMVI_siNTC_Rep1

value: non-targeting control siRNA (96 h)


title: Exp2_organoid_severelyperturbed_rep1

description:
AmpliDrop
231201_03_GM1121s3_Exp2_org_severely_perturbed_rep1


title: Exp2_organoid_mildyperturbed_rep2

description:
AmpliDrop
231201_05_GM1121s5_Exp2_org_mildly_perturbed_rep2


title: OX_Col_VIM2_Cvi_3-1

description:
Library name: Sample13
VIM2 (Cvi-0 allele) overexpression in Col-0 background, independent line 3-1


title: VIM4_mutant_2

description:
Library name: Sample8
vim4 T-DNA insertion mutant (NASC ID: N675753), biological replicate 2

value: Col-0; vim4 (NASC ID:N675753)


title: OX_Col_VIM2_Col_7-2

description:
Library name: Sample12
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 7-2

value: Col


title: Cell line LOXIMVI, nontargeting control siRNA, biological rep 2

description: Library name: LOXIMVI_siNTC_Rep2

value: Skin

value: LOXIMVI


title: HGC-27_BA_3

city: Shanghai

first: Zewen

last: Chu

address: 1200 Cai Lun Road

institute: Shanghai University of Traditional Chinese Medicine

description: Library name: Sample 12

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:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) 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.
Assembly: GRCH38
Supplementary files format and content: tab-delimited xlsx files include FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI-1640 medium (HyClone, Cat. No. SH30809.01, USA) supplemented with 10% fetal bovine serum (TransGen, Cat. No. FS301, China) and 1% penicillin–streptomycin solution (Beyotime, Cat. No. C0222, China). The cells were maintained in a humidified incubator at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
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. 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 NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: The two gastric cancer cell lines were treated with betulonic acid at their respective 24-h IC50 concentrations and incubated for 24 h.

value: Human gastric cancer cell HGC-27

value: Betulonic acid-treated


title: Cell line MALME3M, CXXC1 siRNA, biological rep 3

description: Library name: MALME3M_siCXXC1_Rep3

value: Cutaneous melanoma

value: CXXC1 knockdown


title: Exp2_organoid_mildyperturbed_rep1

description:
AmpliDrop
231201_02_GM1121s2_Exp2_org_mildly_perturbed_rep1


title: HGC-27_BA_2

description: Library name: Sample 11


title: OX_Col_VIM2_Col_7-1

description:
Library name: Sample11
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 7-1

value: leaf tissue


title: Cell line MALME3M, CXXC1 siRNA, biological rep 2

description: Library name: MALME3M_siCXXC1_Rep2

value: CXXC1 siRNA (96 h)


title: HGC-27_BA_1

description: Library name: Sample 10


title: Exp2_organoid_nonperturbed_rep1

description:
AmpliDrop
231201_01_GM1121s1_Exp2_org_outside_inc_rep1

value: brain cells

value: hiPSC-derived forebrain organoids


title: OX_Col_VIM2_Col_1-1

description:
Library name: Sample10
VIM2 (Col-0 allele) overexpression in Col-0 background, independent line 1-1


title: HGC-27_3

description: Library name: Sample 9

value: untreated


title: VIM4_mutant_3

description:
Library name: Sample9
vim4 T-DNA insertion mutant (NASC ID: N675753), biological replicate 3


title: Exp1_organoid_mildyperturbed_rep2

description:
AmpliDrop
230602_05_GM516S5_Exp1_org_mildly_perturbed_rep2

value: Human forebrain orgaboids derived from hiPSCs

value: 7-month-old culture


title: VIM4_mutant_2


title: HGC-27_2

description: Library name: Sample 8


title: Exp1_organoid_nonperturbed_rep2

description:
AmpliDrop
230602_04_GM516S4_Exp1_org_non_perturbed_rep2

value: WT


title: Cell line MALME3M, nontargeting control siRNA, biological rep 3

description: Library name: MALME3M_siNTC_Rep3

value: non-targeting control siRNA (96 h)


title: RIL127_G09_L01_1

description: Library name: Sample192

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end 150bp format.

value: Ler X Cvi RIL


title: RIL127_G09_L01_2

description: Library name: Sample193


title: Cell line MALME3M, nontargeting control siRNA, biological rep 2

description: Library name: MALME3M_siNTC_Rep2


title: VIM4_mutant_1

description:
Library name: Sample7
vim4 T-DNA insertion mutant (NASC ID: N675753), biological replicate 1

value: Col-0; vim4 (NASC ID:N675753)


title: Cell line MALME3M, nontargeting control siRNA, biological rep 1

description: Library name: MALME3M_siNTC_Rep1

value: Skin


title: Exp1_organoid_severelyperturbed_rep1

description:
AmpliDrop
230602_03_GM516S3_Exp1_org_severely_perturbed_rep1

extract_protocol:
Peripheral venous blood was drawn from voluntary donor using EDTA-treated tubes and LymphoprepTM and stored at 4°C. Cells were resuspended in 1x phosphate-buffered saline buffer solution (1xPBS) supplemented with 2% bovine serum albumin, BSA, and layered over 1.5 mL Lymphoprep Density Gradient Medium in a 15 mL conical tube, according to the manufacturer’s protocol.  The solution was centrifuged at 800xg for 20 min at room temperature without brake.  The mononuclear cell layer at the gradient interface was collected in a new tube and washed in PBS/2% FBS (10 mL total volume) and centrifuged at 120xg for 10 min at room temperature without brake.  The wash step was repeated two more times, and the cells were resuspended in PBS for sequencing library preparation.  The cells not used immediately were cryopreserved in 90% FBS/10% DMSO.
3' scRNA-seq (AmpliDrop technology); Dissociated cells (typically, >90-95% viable) in 0.1% BSA-supplemented 1x DPBS buffer were processed with AmpliDrop 3’ scRNA-seq kits following the manufacturer’s recommendations. Briefly, more than 200,000 cells were typically fixed at room temperature for 45 minutes and permeabilized for 10 minutes. For the RT and tagmentation reactions, we used 60,000 fixed and permeabilized cells. RT was conducted at 50°C for 10 minutes, and 10 cycles at 60°C for 30 sec and 50°C for 3 min, and tagmentation was conducted at 37°C for 15 minutes. Cell encapsulation was based on the following mixing protocol: 50 mixes of 170 µL at Speed 2 followed by 10 mixes of 170 µL at Speed 3. The emulsions were then moved to a thermocycler to run the following PCR/barcoding program: 72°C for 5 min, 98°C for 1 min, 26 cycles with 98°C for 15 sec, 61°C for 40 sec, and 72°C for 30 sec, and 5 cycles with 98°C for 15 sec, 50°C for 2 min, and 72°C for 40 sec, ending with 72°C for 2 min. After PCR/barcoding, the emulsions were dissolved, and the DNA was recovered from the solution  with the same volume of SPRI beads from MagBio genomics. The libraries were cleaned up with 80% ethanol for three times and finally eluted in 38 µL of 0.1x TE buffer, and half of this volume was used for indexing using Illumina adapters. Typically, we amplified the library with 9 to 12 cycles depending on the expected number of cell output (12 cycles for 1,000-2,000 cells and 9 cycles for 7,000-10,000 cells). The PCR indexing program is the following: 98°C for 30 sec, and 9-12 cycles with 98°C for 20 sec, 61°C for 30 sec, and 72°C for 30 sec, ending with 72°C for 2 min. After PCR, the library (40 µL) was diluted to 100 µL with TE buffer and cleaned up with 90 µL of SPRI beads. After washing with 80% ethanol twice, the library was eluted in 30 µL of 0.1x TE buffer. Libraries were then subject to quality control, sizing, and quantification using Agilent 4150 TapeStation system with High Sensitivity D1000 ScreenTape and Reagents.


title: VIM2_mutant_3

description:
Library name: Sample6
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 3

value: Col-0; vim2 (NASC ID:N664186)


title: Exp1_organoid_mildyperturbed_rep1

description:
AmpliDrop
230602_02_GM516S2_Exp1_org_mildly_perturbed_rep1


title: Cell line UACC62, CXXC1 siRNA, biological rep 3

description: Library name: UACC62_siCXXC1_Rep3


title: AGS_BA_2

description: Library name: Sample 5

source_name: AGS

value: AGS

value: Human gastric cancer cell AGS


title: Cell line UACC62, CXXC1 siRNA, biological rep 2

description: Library name: UACC62_siCXXC1_Rep2

value: Cutaneous melanoma


title: AGS_BA_1

description: Library name: Sample 4

value: Betulonic acid-treated


title: Cell line UACC62, CXXC1 siRNA, biological rep 1

description: Library name: UACC62_siCXXC1_Rep1

value: CXXC1 knockdown


title: AmpliDrop_organoids_becnhmark_rep2

description:
AmpliDrop
Ampli_2_benchmark_rep2


title: Control_Col_WT_3

description:
Library name: Sample3
Wild-type Col-0 control, biological replicate 3

value: leaf tissue


title: Cell line UACC62, nontargeting control siRNA, biological rep 3

description: Library name: UACC62_siNTC_Rep3


title: AGS_2

description: Library name: Sample 2


title: 10X_organoids_benchmark_rep2

description:
AmpliDrop
10X_bechmark_rep2

value: brain cells


title: AGS_1

description: Library name: Sample 1


title: 10X_organoids_benchmark_rep1

description:
AmpliDrop
10X_bechmark_rep1

value: hiPSC-derived forebrain organoids


title: Wild_Type

status: Public on Jul 17 2026

city: Fuzhou

first: Qingxiang

last: Gao

state: FuJian

address: Qiuyang Road No1.

institute: Fujian University of Traditional Chinese Medicine

description: Library name: Wild_Type

data_processing:
Reads were aligned using Cell Ranger v7.1.0 to a customized mouse reference genome/transcriptome.
Data were analyzed in R/Seurat: cells filtered (nFeature_RNA 200–6000, percent.mt <15%), normalized, variable genes identified (n=2000), and samples integrated. PCA (30 PCs), UMAP, and clustering (resolution=0.4) were performed. Markers were identified (Wilcoxon, logFC>0.25, min.pct=0.1, FDR<0.05) and clusters annotated as Basal (Krt5/p63), Proliferative-basal (Mki67⁺), Suprabasal (Krt4/Ivl/Claudin-4), and Superficial (Sprr/Loricrin).
Assembly: GRCm38/mm10
Supplementary files format and content: mtx.gz
Supplementary files format and content: tsv.gz

source_name: mouse esophagus

extract_protocol:
Mouse esophageal epithelial cells were prepared as single-cell suspensions and enriched for EpCAM⁺ epithelial cells while excluding dead cells and immune cells by FACS.
Libraries were generated with 10x Genomics Chromium (Single Cell 3′ V3/V3.1) targeting 8-12k cells per sample, sequenced on Illumina NovaSeq 6000 (2×150 bp, ≥50k reads/cell).

value: mouse esophagus

value: Mouse esophageal epithelial cells

value: Wild Type


title: JJ107_Mettl3_KO

description: Library name: JJ107_Mettl3_KO

data_processing:
Raw reads were quality-checked using FastQC and MultiQC, trimmed with Cutadapt, and aligned to the mouse reference genome GRCm39/mm39 using STAR.
Differential gene expression was analyzed in R v4.3 using DESeq2, with genotype as the main variable and relevant covariates such as sex or batch incorporated into the design formula when applicable. Log₂ fold-change shrinkage was performed using apeglm. Genes with an adjusted P value < 0.05 and |log₂FC| ≥ 1 were considered differentially expressed. Variance-stabilized counts were used for principal component analysis, hierarchical clustering, and heatmap visualization.
Assembly: GRCm39/mm39
Supplementary files format and content: .txt

extract_protocol:
Mouse esophageal epithelial cells were prepared as single-cell suspensions and enriched for EpCAM⁺ epithelial cells while excluding dead cells and immune cells by FACS. Four biological replicates per group were included for bulk RNA-seq analysis. Total RNA was extracted using the RNeasy Plus Micro Kit, quantified with Qubit and NanoDrop, and quality-checked using a Bioanalyzer.
Samples with RIN ≥ 8 were used for library preparation. Poly(A)⁺ mRNA was enriched, and strand-specific libraries were prepared using the NEBNext Ultra II kit with an insert size of 200–300 bp. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150-bp reads, generating ≥40 million read pairs per sample, with Q30 ≥ 85%.


title: JJ102_Mettl3_KO

description: Library name: JJ102_Mettl3_KO


title: JJ106_Wild Type

description: Library name: JJ106_Wild Type


title: JJ105_Wild Type

description: Library name: JJ105_Wild Type


title: VIM2_mutant_2

description:
Library name: Sample5
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 2

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute (Taudt et al. 2018)


title: VIM2_mutant_1

description:
Library name: Sample4
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 1


title: AGS_3

description: Library name: Sample 3

value: untreated


title: AmpliDrop_organoids_becnhmark_rep1

description:
AmpliDrop
Ampli_1_benchmark_rep1

data_processing:
Sequencing reads were processed with AmpliDrop software v1.0. Cell calling and data processing was generated with Cell Ranger v5.1
Within AmpliDrop software analysis, after bcl files been converted to fastq files, the pipeline generated three types of fastq files: cDNA reads, been called as "R1"; sample index reads, with 8 nucleotides, been called as "I1"; and barcode reads, with 20 nucleotides, been called as "I2", in which six nucleotides at positions of 4, 5, 10, 11, 16, and 17 were used as code. The pipeline was then demultiplexing the samples based on the sample index combined with the code used. However, the sample index and code sequences were not saved after demultiplexing. To evaluate the fastq quality, the pipeline ran the fastqc tool on each set of fastq files for the demultiplexed sample. After the barcodes were error collected and the cDNA reads were trimmed with the potential adapter sequences and poly-A nucleotides, the pipeline ran a merging algorithm to merge the barcodes that were located in the same droplet. At the end of the pipeline, the fastq files were converted into 10X Genomic cellranger compatible format.
Assembly: hg38 and mm10
Supplementary files format and content: _barcodes.tsv.gz contains all cellular barcodes, tab separated text file, gzipped; _features.tsv.gz contains feature annotations, tab separated text file, gzipped, column1: feature id, column2: feature name, and column3: type of feature, i.e., "Gene Expression"; _matrix.mtx.gz contains UMI counts in each gene and in each cellular barcode, with mtx format, gzipped.

value: Human forebrain orgaboids derived from hiPSCs

value: WT

value: 7-month-old culture


title: Cell line UACC62, nontargeting control siRNA, biological rep 2

description: Library name: UACC62_siNTC_Rep2

value: Skin

value: non-targeting control siRNA (96 h)


title: Control_Col_WT_2

description:
Library name: Sample2
Wild-type Col-0 control, biological replicate 2


title: inguinal white adipose tissue, Diet-induced obesity, biological replicate 3, mouse SMA_3752

city: Odense M

first: Blagoy

last: Blagoev

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
Library name: B397
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3752; Diet-induced obesity; biological replicate 3.
iWAT_raw_counts.tsv

data_processing:
The count matrix was imported into R (v4.2.2; RStudio v2023.06.1) and normalized for library size and sequencing depth, followed by log2 transformation using DESeq2 (v1.38.3). Transcripts with an average normalized log2 count <1 or containing NA values in any sample were removed prior to analysis. Differential gene expression analysis was performed using DESeq2 (v1.38.3).
Assembly: Illumina). Raw reads were aligned to the mouse genome (mm10) using STAR (v2.4.1c). Exonic peak detection was performed using iRNA (v1.1).
Supplementary files format and content: Processed data consist of tab-delimited gene expression count matrices (raw counts) generated from RNA-seq data for eWAT and iWAT samples. Differential expression results are also procided as comma-separated value (CSV) files generated using DESeq2.

source_name: inguinal white adipose tissue

extract_protocol:
Unless otherwise stated, all steps were performed on ice. Tissues were homogenized at room temperature in 500 µL TRI Reagent® (Sigma-Aldrich, T9424) and six 1.4 mm ceramic beads (OMNI International, 19-645) per 80 mg tissue using the mouse liver program on a FastPrep-24TM 5G (MP Biomedicals). Homogenates were centrifuged at 10,000 x g for 10 min at 4 °C, and the infranatant was transferred to a new DNA LoBind tube (Eppendorf), avoiding the lipid layer and debris pellet. 0.2 volumes of chloroform (Acros Organics, 383770025) were added, samples were mixed by inversion, incubated at room temperature for 5 min, and centrifuged at 10,000 x g for 10 min at 4 °C. The aqueous phase was transferred to a new DNA LoBind tube. 0.6 volumes of isopropanol (VWR Chemicals, 20880.320) were added, samples were mized by inversion, incubated at -20 °C for 1 hr, and centrifuged at 12,000 x g for 15 min at 4 °C. The supernatant was removed, and the pellet was washed with 1mL 70% ethanol (VWR Chemicals, 20824.365) prepared in DEPC-treated water (Sigma-Aldrich, D5758), followed by centrifugation at 12,000 x g for 10 min at 4 °C.
Illumina libraries were prepared using poly(A) enrichment according to the manufacturer’s instructions and sequenced with paired-end reads on a NovaSeq 6000 (Illumina).

value: inguinal white adipose tissue

value: Diet-induced obesity


title: Control_Col_WT_1

description:
Library name: Sample1
Wild-type Col-0 control, biological replicate 1


title: METTL3_KO

description: Library name: METTL3_KO


title: inguinal white adipose tissue, Diet-induced obesity, biological replicate 2, mouse SMA_3751

description:
Library name: B396
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3751; Diet-induced obesity; biological replicate 2.
iWAT_raw_counts.tsv


title: Cell line UACC62, nontargeting control siRNA, biological rep 1

description: Library name: UACC62_siNTC_Rep1

value: Cutaneous melanoma


title: inguinal white adipose tissue, Diet-induced obesity, biological replicate 1, mouse SMA_3750

description:
Library name: B395
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3750; Diet-induced obesity; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 6, mouse SMA_3728

description:
Library name: B435
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3728; Lean control at obesity time point; biological replicate 6.
iWAT_raw_counts.tsv

value: Lean control at obesity time point


title: JJ104_Mettl3_KO

description: Library name: JJ104_Mettl3_KO


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 4, mouse SMA_3726

description:
Library name: B433
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3726; Lean control at obesity time point; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 5, mouse SMA_3727

description:
Library name: B434
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3727; Lean control at obesity time point; biological replicate 5.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 3, mouse SMA_3785

description:
Library name: B412
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3785; Lean control at obesity time point; biological replicate 3.
iWAT_raw_counts.tsv


title: JJ103_Mettl3_KO

description: Library name: JJ103_Mettl3_KO


title: JJ108_Wild Type

description: Library name: JJ108_Wild Type


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 2, mouse SMA_3784

description:
Library name: B411
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3784; Lean control at obesity time point; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 6, mouse SMA_3713

description:
Library name: B426
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3713; Short-term obesity regression; biological replicate 6.
iWAT_raw_counts.tsv

value: Short-term obesity regression


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 5, mouse SMA_3712

description:
Library name: B425
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3712; Short-term obesity regression; biological replicate 5.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Lean control at obesity time point, biological replicate 1, mouse SMA_3783

description:
Library name: B410
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3783; Lean control at obesity time point; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 3, mouse SMA_3746

description:
Library name: B391
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3746; Short-term obesity regression; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 4, mouse SMA_3711

description:
Library name: B424
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3711; Short-term obesity regression; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 2, mouse SMA_3745

description:
Library name: B390
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3745; Short-term obesity regression; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term obesity regression, biological replicate 1, mouse SMA_3744

description:
Library name: B389
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3744; Short-term obesity regression; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term lean control, biological replicate 6, mouse SMA_3719

description:
Library name: B429
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3719; Short-term lean control; biological replicate 6.
iWAT_raw_counts.tsv

value: Short-term lean control


title: inguinal white adipose tissue, Short-term lean control, biological replicate 5, mouse SMA_3718

description:
Library name: B428
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3718; Short-term lean control; biological replicate 5.
iWAT_raw_counts.tsv


title: JJ101_Wild Type

description: Library name: JJ101_Wild Type


title: inguinal white adipose tissue, Short-term lean control, biological replicate 4, mouse SMA_3717

description:
Library name: B427
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3717; Short-term lean control; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term lean control, biological replicate 3, mouse SMA_3764

description:
Library name: B406
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3764; Short-term lean control; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Short-term lean control, biological replicate 1, mouse SMA_3762

description:
Library name: B404
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3762; Short-term lean control; biological replicate 1.
iWAT_raw_counts.tsv