title: HeLa MOES-EVs

type: RNA

city: Roma

first: antonella

last: minutolo

state: RM

address: Via montpellier 1

department: Experimental medicine

institute: university of rome tor vergata

description: human cell line treated with plant extracellular vesicles

hyb_protocol: cDNA was obtained from total RNA by cDNA Reverse Transcription Kit (Thermo Fisher Scientific, MA; USA). The expression analyses was perform using a miScriptTM miRNA PCR Array Human Cancer Pathway array (cat # MIHS-102Z, Qiagen, Hilden, Germany). The assays were performed in a Bio-rad instrument (CFX96 Real-Time System, Biorad, Hercules, California, USA) using SYBR Green chemistry (Fast QPCR Master Mix, SmoBio, Taiwan), following the manufacturer’s instructions.

data_processing: The miRNA profiling data were analyzed by web-based miRNA PCR Array Data Analysis software (http://pcrdata-analysis.sabiosciences.com/mirna/arrayanalysis.php) to identify differentially expressed miRNAs between the groups. This software automatically performs fold-change calculations from the user’s uploaded Ct values obtained in miRNA PCR. The basal miRs expression detected in untreated HeLa cells was categorized in three groups with respect to Ct values: group n.1 from 15 to 20 Ct; group n.2 from 21 to 30 Ct; group n.3 >30 Ct.

source_name: human cervical carcinoma cells line

label_protocol: SYBR Green chemistry (Fast QPCR Master Mix, SmoBio, Taiwan).

growth_protocol: Mycoplasma-free human cervical carcinoma HeLa cells (ATCC, Gaithersburg, USA) were cultured as adherent monolayers at a concentration of 0.15 × 10⁶ cells/mL in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 10% fetal bovine serum (Invitrogen), 2 mM glutamine (HyClone) and 50 U/mL penicillin/streptomycin (HyClone).

extract_protocol: Total RNA was isolated from the pellets of MOES-EVs treated and untreated HeLa cells by TRIzol extraction method, according to the manufacturer’s instructions (Invitrogen, CA, USA). RNA was quantified using a NanoDropTM light spectrophotometer (Thermo Fisher Scientific, MA; USA) and stored at -20 °C until use

treatment_protocol: HeLa cells (0.5 × 10⁵ cells/mL) were treated for 72 h with EVs purified from 20 mg fresh weight equivalent of MOES

value: human cervical carcinoma cells line


title: RB_Patient tumor-SJRB030403_D2-FFPE

status: Public on Oct 02 2025

type: genomic

city: Memphis

first: Gang

last: Wu

address: 262 Danny Thomas Place

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina EPIC v1 (850K) array following Illumina standard protocol

scan_protocol: Standard Illumina protocol

data_processing:
Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using 'minfi' Bioconductor package.
processed value definition: Average beta value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Eye

label_protocol: Standard Illumina protocol

extract_protocol: Genomics DNA was extracted from froze tumor tissues using  Qiagen kit (catalog #65904) or FFPE tumors using Promega Maxwell DNA FFPE Kit according to standard instructions recommended by the kit

tag: Sex

value: M

value: RB

tag: tissue

value: Eye

tag: treatment

value: N

tag: sample type

value: Patient tumor

tag: tumor group

tag: age at collection (yr)


title: CRC06_T_tissue

type: SRA

city: Beijing

first: Xinnan

last: Ling

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: BIOPIC

country: China

institute: Peking University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data generated were aligned and quantified against the GRCh38 human reference genome, and filtered using the Cell Ranger pipeline (version 3.1). The resulting feature-barcode matrices were used for downstream filtering and analysis. The matched TCR data based on 10x protocol was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied human VDJ reference genome. Bulk RNA-seq data were filtered using Skewer (version 0.2.2). Adapter sequences and low-quality reads (＜30) from the 3’ ends were removed. The bulk RNA expression was quantified by kallisito (version 0.44)60. Gene expression were calculated by aggregating transcript expression (TPM) belonging to the same gene using tximport (version 1.22.0), and the TPM of gene were then logarithmically transformed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: colorectum

extract_protocol:
PBMCs were isolated from peripheral blood by Ficoll density gradient centrifugation. In brief, Ficoll was added into a 15ml centrifuge tube according to the amount of the whole blood, and then the whole blood was slowly added. Centrifuge the tube with acceleration speed 1, and deceleration speed 0 at 800 g for 30 min. After centrifugation, the middle white film layer was taken and washed by PBS containing 2% FBS to remove Ficoll. Red blood cells were removed by Red blood cell lysis solution (Miltenyi Biotec,130-095-929). The number of PBMCs was calculated by Countstar cell counter. Patient tumor tissues were weighed, and dissociated with Tumor Dissociation Kit, human (Miltenyi Biotec,130-095-929). In brief, tumor tissues were cut into small pieces in a C tube (Miltenyi Biotec,130-093-237) and three dissociating enzymes from the kit were added according to the tumor tissue weight. Place the C tube to the gentleMACS™ Octo Dissociator with Heaters and use 37C_h_TDK_1 program for tissue dissociation for 1 h. After dissociation, cells were filtered through a 70 μm filter membrane, and then washed with 10 ml of PBS containing 2% FBS. The suspension was centrifuged at 300g for 10 min. We next collected the cell pellet and counted using Trypan blue staining.
Cell pellets obtained from PBMC and tumor tissue were re-suspended in sorting buffer (PBS with 1% FBS), followed by staining with DAPI, anti-CD45, and anti-CD235a antibodies for FACS with a BD FACSAria™ III instrument (BD Biosciences). Live cells were identified as DAPI-negative. Subsequently, CD235a-negative and CD45-positive single cells from PBMC and CD235a-negative single cells from tumor tissue cell suspension were sorted. 10,000~20,000 cells were loaded for library construction using the 10x Chromium Single cell 5` Library (10X Genomics, PN-1000263), according to the manufacturer’s instructions. Purified libraries were attained through Library Construction Kit (10X Genomics, PN-1000190) according to the manufacturer’s instructions, and then sequenced by BGI MGISEQ-2000 sequencer. TCR sequences were amplified with the Chromium Single Cell Human TCR Amplification Kit (10X Genomics, PN-1000252). V(D)J Libraries were generated with Library Construction Kit (10X Genomics, PN-1000190), and sequenced by Illumina Novaseq6000 sequencer.

value: colorectum


title: HeLa Control

country: Italy

description: human cell line


title: D14_KO_CD8T_2

city: Guangzhou

first: Jing

last: Liao

state: Guangdong

address: No.1 Xinzao Road, Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

description: Library name: Sample 18

library_source: transcriptomic

data_processing:
This data processing pipeline adheres to a standard RNA sequencing analysis workflow: first, Quality Control was performed using fastqc for initial assessment, followed by read cleaning via trimmomatic to remove adapters, trim low-quality bases, and filter by minimum length. Next, the high-quality reads were Aligned to the reference genome, after index construction, using the STAR aligner. Finally, Gene Expression Quantification was completed by employing featureCounts to tally the number of reads mapped to each gene locus, generating the necessary raw count data for downstream differential expression analysis.
This data processing pipeline adheres to a standard TCR repertoire analysis workflow: first, Unique Molecular Barcodes (UMBs) were applied to correct PCR and sequencing errors and to eliminate PCR duplicates, thereby maximizing sequencing accuracy and quantification. This was followed by mapping the sequences against the IMGT® database to define V, D, J, and C segments. Next, the CDR3 regions were extracted and clonotypes were assembled, undergoing a critical quality control step that eliminated sequences with out-of-frame or stop codons. Finally, the abundance of each TRB clonotype was accurately determined by summing the number of individual clones sharing the identical CDR3 nucleotide sequence.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: The tab-delimited text file comprehensively contains all sequencing information for both the TCR alpha (α) chain and the TCR beta (β) chain of the corresponding sample. Specifically, the file details VDJC segment usage, precise CDR3 sequences, and the abundance counts for each unique clonotype after error correction and deduplication.

organism: Mus musculus

source_name: Splenic CD8+ T

growth_protocol: MC38 murine colon cancer cell line were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% L-glutamine under a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Library construction began with the enrichment of mRNA using Oligo(dT) beads (by binding to the poly-A tail). The enriched mRNA was fragmented and reverse transcribed into cDNA. The resulting cDNA fragments were then processed using the NEBNext Ultra RNA Library Prep Kit for Illumina, which involved end repair, A-tailing, and ligation of Illumina sequencing adapters to finalize the cDNA library.
Library construction utilized the ImmuHub® TCR profiling system, employing a 5' RACE unbiased amplification protocol. Unique molecular barcodes (UMBs) were introduced during first-strand cDNA synthesis, along with a common adaptor and a reverse primer corresponding to the constant (C) regions of the TRB. This method facilitates the high-throughput sequencing of TRB (TCR β) sequences by using UMBs to control bottlenecks and eliminate PCR and sequencing errors.

treatment_protocol:
Six- to eight-week-old immunocompetent wild-type C57BL/6 mice received a single intraperitoneal injection of azoxymethane at 8 mg/kg on day 0. Mice were subsequently given 2.5% dextran sodium sulfate in their drinking water during weeks 1, 4, 7, and 10, with regular water provided at other times. Colorectal tumors were harvested on day 70 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously injected with 1 × 10⁶ Ctrl or Galnt7-/- MC38 cells. Tumors were harvested on day 8 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously inoculated with 2 × 10⁶ Ctrl or Galnt7-/- MC38 cells. On day 14, CD8⁺ T cells were isolated from the spleens of tumor-bearing mice using magnetic beads for RNA sequencing and T cell receptor sequencing.

tag: cell type

value: Splenic CD8+ T

value: CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl or MC38-Galnt7⁻/⁻ cells


title: RB_Patient tumor-SJRB012408_D1-frozen

source_name: Orbit

value: F

value: Orbit

value: Y


title: D14_KO_CD8T_1

description: Library name: Sample 17


title: CRC04_tissue

description: 10X Genomics


title: CRC03_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB046162_X1-frozen

value: Xenograft


title: RB_Patient tumor-SJRB063841_D1-FFPE


title: D14_WT_CD8T_1

description: Library name: Sample 14

value: CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl cells


title: D14_WT_CD8T_2

description: Library name: Sample 15


title: RB_Patient tumor-SJRB063840_D1-FFPE


title: S_biol_rep_2

city: Hospitalet de Llobregat

first: Loris

last: Mularoni

state: Barcelona

address: Gran Via de l'Hospitalet, 199

department: P-CMR[C]

country: Spain

institute: IDIBELL

description: Library name: S_2

data_processing:
Sequencing data analysis was performed using standard bioinformatics tools and pipelines. Raw sequencing reads were processed to remove adapters and low-quality bases using Trimmomatic (Bolger et al., 2014). Processed reads were aligned to the reference genome [reference genome version] using STAR (Dobin et al., 2013). Gene expression levels were quantified using featureCounts (Liao et al., 2014), and downstream analyses, including clustering, dimensionality reduction, and differential expression analysis, were performed using the Seurat package in R (Stuart et al., 2019)
Assembly: hg38
Supplementary files format and content: Matrix of gene-level raw counts across all samples
Supplementary files format and content: Matrix of gene-level TPM values across all samples

molecule: polyA RNA

source_name: hiPSCs

extract_protocol:
200 hematopoietic progenitor cells (CD34+, CD43+, CD33+ and DAPI -) derived from parental and mutant hiPSC were sorted at day 15 of EB differentiation directly in 8µl lysis buffer to 0.2% Triton X-100, and 2 U/μL RNase inhibitor (e.g., SUPERase•In, Thermo Fisher Scientific)
Reverse Transcription (RT) and cDNA Amplification: The released RNA was reverse transcribed into complementary DNA (cDNA) using the Smart-seq2 protocol. Briefly, a template-switching oligo (TSO) (5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3') was annealed to the RNA molecules, and reverse transcription was performed using SuperScript II reverse transcriptase (Invitrogen) at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes. The cDNA was then purified using AMPure XP beads (Beckman Coulter) and amplified using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) with 18 cycles of PCR amplification

value: hiPSCs

tag: cell line

value: CD34+CD43+CD33+ iPSC-derived cells


title: Tcf7del17+22 3

city: SAINT LOUIS

first: Takeshi

last: Egawa

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: Sample 6

data_processing:
Data were demultiplexed with  Illumina’s bcl2fastq software.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: mm10
Supplementary files format and content: excel file of log2 normalized counts per million of genes for each sample

source_name: spleen

extract_protocol:
Trizol-lysed cells were prepared using the Zymo research Direct-zol RNA microprep kit.
RNA quality was assessed using an Agilent 2100 Bioanalyzer. Libraries were prepared using the Takara-Clontech SMARTer kit. DNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Libraries sequenced for 300 cycles on a NovaSeq X Plus, targeting 30 million reads per library (Illumina).

treatment_protocol: WT P14 TCR transgenic cells electroporated with Cd19 control Cas9 RNPs or Tcf7∆+22kb P14 TCR transgenic cells electroporated with Tcf+17kb Cas9 RNPs were adoptively transferred into congenic recipient mice, which were infected with LCMV-Arm one day post-transfer. Control and Tcf7∆+22/+17 KLRG1+ cells were sorted on 8 dpi and resuspended in Trizol.

value: spleen

value: CD8+ T cells

tag: genotype

value: Tcf7 + 17 RNP


title: RB_Patient tumor-SJRB063839_D1-FFPE

value: M

value: RB


title: Tcf7del17+22 2

description: Library name: Sample 5


title: S_biol_rep_1

description: Library name: S_1


title: RB_Patient tumor-SJRB063838_D1-FFPE

value: Eye

value: N


title: Tcf7del17+22 1

description: Library name: Sample 4


title: D14_WT_CD8T_3

description: Library name: Sample 16


title: WT 3

description: Library name: Sample 3

value: WT

value: Cd19 RNP


title: RB_Patient tumor-SJRB063836_D1-frozen

value: Patient tumor


title: RB_Patient tumor-SJRB063842_D1-frozen

value: F


title: A_biol_rep_2

description: Library name: A_2


title: A_biol_rep_1

description: Library name: A_1


title: siLCRMP-1

city: Taipei

first: Yuan-Ling

last: Hsu

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University, College of Medicine

hyb_protocol: Samples were hybridized using Phalanx OneArray Plus Protocol. 5ug Cy5-labeled aRNA was used.

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: GPR files were loaded into Rosetta Resolver System (Rosetta Biosoftware) to process data analysis. The error due to random factors and systematic biases were estimated by an error model. Data from repeated probes were averaged and median-scaling (normalization) was performed on dataset without flagged and control data.

source_name: CL1-5 cell line_siLCRMP-1

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization.

growth_protocol: The stable cells were cultured at 37℃, 5%C02, in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 0.1mg/ml streptomycine and 100U/ml pencillin.

extract_protocol: Cells were washed once with 1X PBS, and collected by trypsin, and pelleted. After washing with 1XPBS, total RNA was prepared from cell pellet using TRIZOL (Invitrogen), and eluted with DEPC water, based on the manufacturer's protocol.

treatment_protocol: Cells were transfected with mock plasmid, mock siRNA, LCRMP-1 plasmid, LCRMP-1 siRNA by Lipofectamine 2000 (Invitrogen). The stable cell lines were be selected by 600ug/ml G418.

value: High invasive lung adenocarcinoma cell line

value: Cells transfected LCRMP-1 siRNA


title: RB_Patient tumor-SJRB063837_D1-FFPE


title: GS_biol_rep_4

description: Library name: GS_4

value: GATA2+/- SETBP1mut D868N


title: Vector

source_name: CL1-0 cell line_Vector

value: Low invasive lung adenocarcinoma cell line

value: Cells transfected Control Plasmid


title: LCRMP-1_clone2

source_name: CL1-0 cell line_LCRMP1_clone2

value: Cells transfected LCRMP-1 Plasmid (Stable cell clone 2)


title: WT 2

description: Library name: Sample 2

value: spleen


title: MAP2K3_WT_1t_4_(Clariom_S_Human)

city: Heidelberg

first: Torsten

last: Schmenger

address: Im Neuenheimer Feld 267

country: Germany

institute: BioQuant Heidelberg

description: Gene expression data from Trex HEK293 cells transfected with pDest30_MAP2K3_WT with 24h Tetracycline induction.

hyb_protocol: Hybridization was done according to manufacturer’s protocol on Thermo Fisher Scientific (Affymetrix) human Clariom S Arrays by the Microarray Unit of the Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ).

scan_protocol: Chip scanning Gene Expression Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the respective Manual for Cartridge Arrays and performed by the Microarray Unit of the Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ).

data_processing:
Upon receiving the raw data files an analysis pipeline was set up according to the “maendtoend” package. To summarize, the raw data was loaded and data quality assessed through principal component analysis (PCA), using the R package “arrayQualityMetrics”. After cleaning the data and removing any flagged chips the data was then background corrected and calibrated. To remove low-intensity signals the data was filtered by setting a threshold based on median intensities. The detected transcripts were annotated and translated into more human-readable gene names before contrasts were defined, in order to group repetitions of a given sample condition together for comparison against wildtype or control conditions. These contrast groups were subjected to empirical bayes statistics for differential expression (eBayes) and results were extracted. For this, R/limma’s lmFit, eBayes and topTable functions were used. The topTable function employs Benjamini Hochberg correction for multiple testing on all p-values. Genes were called significant if their adjusted p-value was smaller than 0.05 and genes were only considered if the absolulte foldchange was >= 1.5.
Values in the final data table are RMA normalized expression values received after calling the R command oligo::rma.

label: biotin

source_name: Trex HEK293 cells

label_protocol: For microarray chip analysis total RNA was extracted from cells and hybridized on an Affymetrix Clariom S human array performed by the Microarray Unit of the Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ).

growth_protocol: T- REx-293 cells were maintained in T-REx Standard Culture Medium in presence of 5 μg/mL blasticidin at 37 °C and 5% CO2.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen, Rneasy).

treatment_protocol: Vectors with the pDest30 backbone were used to transiently overexpress wildtype or mutant proteins in T-REx-293 cells, stably expressing the Tet repressor (on pcDNA6/TR, Thermo Fisher) in the presence of 5 μg/mL blasticidin.  Transfection was performed in T-REx Standard Culture Medium. Medium was then exchanged after 24 hours and 350 μg/mL Geneticin was added. Cells were split after 48 h – 72 h, depending on their confluence. Surviving cells typically reached 50 % confluency 144 h after transfection at which they would be induced with 1 μg/mL tetracycline for 24 h.

value: Mammalian immortilized cell line

value: Trex HEK293


title: LCRMP-1_clone1

source_name: CL1-0 cell line_LCRMP1_clone1

value: Cells transfected LCRMP-1 Plasmid (Stable cell clone 1)


title: MAP2K3_WT_1t_3_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_WT with 24h Tetracycline induction.


title: MAP2K3_WT_0t_2_(Clariom_S_Human)

description: Gene expression data from Trex HEK293 cells transfected with pDest30_MAP2K3_WT without Tetracycline.


title: MAP2K3_WT_1t_1_(Clariom_S_Human)


title: GS_biol_rep_3

description: Library name: GS_3

value: hiPSCs

value: CD34+CD43+CD33+ iPSC-derived cells


title: MAP2K3_WT_0t_3_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_WT without Tetracycline.


title: WT 1

description: Library name: Sample 1

value: CD8+ T cells

value: WT

value: Cd19 RNP


title: Scramble

source_name: CL1-5 cell line_Scramble

value: High invasive lung adenocarcinoma cell line

value: Cells transfected Cotrol siRNA


title: MAP2K3_WT_1t_2_(Clariom_S_Human)


title: OS_Patient tumor-SJOS001112_M2-frozen

source_name: Lung

value: M

value: OS

value: Lung

value: N

value: Patient tumor


title: d21 TPEX, DKO RNA-seq 4

description: Library name: DKO 4

data_processing:
Data were demultiplexed with  Illumina’s bcl2fastq software.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: mm10
Supplementary files format and content: tab delimited text file of log2 normalized counts per million of genes for each sample

treatment_protocol: TPEX were sorted from spleens of LCMV-c13 infected mice on 21 dpi. Cells were treated in DNase for 30 minutes, followed by two washes in PBS.

value: spleen

value: DKO


title: MAP2K3_WT_0t_4_(Clariom_S_Human)

value: Mammalian immortilized cell line

value: Trex HEK293


title: GA_biol_rep_4

description: Library name: GA_4

value: hiPSCs

value: GATA2+/- ASXL1mut


title: OS_Patient tumor-SJOS001116_R1-FFPE

source_name: Chest

value: F

value: Chest


title: GA_biol_rep_3

description: Library name: GA_3

value: CD34+CD43+CD33+ iPSC-derived cells


title: d21 TPEX, DKO RNA-seq 3

description: Library name: DKO 3

value: CD8+ T cells


title: GA_biol_rep_2

description: Library name: GA_2


title: d21 TPEX, DKO RNA-seq 2

description: Library name: DKO 2


title: MAP2K3_WT_0t_1_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_WT without Tetracycline.


title: OS_Patient tumor-SJOS001108_M1-frozen


title: RB_Patient tumor-SJRB063835_D1-frozen

value: RB

value: Eye


title: MAP2K3_A84T_1t_4_(Clariom_S_Human)

description: Gene expression data from Trex HEK293 cells transfected with pDest30_MAP2K3_A84T with 24h Tetracycline induction.


title: OS_Patient tumor-SJOS001107_M2-frozen

value: M

value: OS

value: Y


title: d21 TPEX, DKO RNA-seq 1

description: Library name: DKO 1


title: OS_Patient tumor-SJOS013769_D1-frozen

source_name: Tibia

value: Tibia

value: Patient tumor


title: GA_biol_rep_1

description: Library name: GA_1


title: MAP2K3_A84T_1t_3_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_A84T with 24h Tetracycline induction.


title: CTRL_biol_rep_4

description: Library name: CTRL_4

value: WT


title: d21 TPEX, WT RNA-seq 4

description: Library name: WT 4

value: spleen


title: OS_Xenograft-SJOS001107_X3-frozen

value: Lung

value: N

value: Xenograft


title: MAP2K3_A84T_1t_2_(Clariom_S_Human)

value: Mammalian immortilized cell line

value: Trex HEK293


title: CTRL_biol_rep_3

description: Library name: CTRL_3

value: hiPSCs

value: CD34+CD43+CD33+ iPSC-derived cells


title: OS_Patient tumor-SJOS030876_R2-frozen_rep2

source_name: Femur

value: F

value: Femur


title: Ampulla, early luteal, rep3

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

data_processing:
The FastQC (v.0.11.4) was used for quality check (QC) of FASTQ files and adaptor and low-quality sequences were removed by Trim Galore. Clean reads were mapped using STAR to Sus scrofa (pig) reference genome assembly (Sscrofa11.1, INSDC Assembly GCA_000003025.6). The quantification of feature specific expression counts was done using R package Rsubread.
The low count features with average CPM below one, were removed with NOISeq R package, which yielded a total of 16791 filtered features out of 35670 raw features (47.07 % pass).
The expression counts was normalized by Trimmed Mean of the M-values (TMM) method and the R package NOISeq was used to obtain significant differentially expressed (DE) features with probability of differential expression (1-FDR) value ≥ 0.95 and log2 fold change (log2FC) ≥ 1. The DE features annotated to protein coding gene-type were filtered to obtain significant up- and down-regulated DE genes (DEGs).
Assembly: Sscrofa11.1, INSDC Assembly GCA_000003025.6
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: Tab delimited text file includes TMM values for each sample

organism: Sus scrofa

source_name: Oviduct

extract_protocol:
Total RNA was harvested from post ovulatory stage ampulla (POA; n =3) and early luteal stage ampulla (ELA; n =3) tissues using RNeasy mini kit (Qiagen)
The total RNA was quantified using NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Qubit 4 Fluorometer (Thermo Fisher Scientific -IN). The quality of RNA was evaluated using the Tapestation 4200TM (Agilent Technologies, Santa Clara, US). The stranded mRNA-Seq libraries were prepared with the KAPA mRNA HyperPrep Kit with QC passed RNA (500 ng) according to the manufacturers protocol. The RNA-Seq Illumina libraries were then sequenced using Illumina NextSeq2000 to generate 40M, 2 x 150 bp reads/sample data.

value: Oviduct

value: Oviductal cells

tag: cell subtype

value: Oviduct ampullary cells

value: Female

tag: developmental stage

value: early luteal


title: OS_Patient tumor-SJOS071782_D1-frozen

source_name: Humerus

value: OS

value: Humerus

value: Y

value: Patient tumor


title: d21 TPEX, WT RNA-seq 1

description: Library name: WT 1

value: spleen

value: CD8+ T cells

value: WT


title: G_biol_rep_2.2

extract_protocol:
200 hematopoietic progenitor cells (CD34+, CD43+, CD33+ and DAPI -) derived from parental and mutant hiPSC were sorted at day 15 of EB differentiation directly in 8µl lysis buffer to 0.2% Triton X-100, and 2 U/μL RNase inhibitor (e.g., SUPERase•In, Thermo Fisher Scientific)
Reverse Transcription (RT) and cDNA Amplification: The released RNA was reverse transcribed into complementary DNA (cDNA) using the Smart-seq2 protocol. Briefly, a template-switching oligo (TSO) (5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3') was annealed to the RNA molecules, and reverse transcription was performed using SuperScript II reverse transcriptase (Invitrogen) at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes. The cDNA was then purified using AMPure XP beads (Beckman Coulter) and amplified using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) with 18 cycles of PCR amplification
Prepared cDNA libraries were generated using Nextera Low Input library preparation kit for whole transcriptome sequencing on the HiSeq2000

value: GATA2+/- R396Q mutation


title: tdTomato+, KLRG1-, d6 Arm 2

description: Library name: TDT+KLRG1-2

data_processing:
Data were demultiplexed with  Illumina’s bcl2fastq software.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: mm10
Supplementary files format and content: Microsoft excel file of log2 normalized counts per million of genes for each sample

source_name: Spleen

treatment_protocol: Prdm1-creER R26-lsl-tdTomato P14 TCR transgenic T cells were transferred into congenic recipient mice, which were infected with LCMV-Arm one day post transfer. Tamoxifen was administered by oral gavage on 3 and 4 days post infection. On day 6 post-infection, KLRG1+ and KLRG1- cells were sorted, with tdTomato + and tdTomato- cells being separated into distinct tubes for each population. Biological duplicates were sorted for each sample.

value: Spleen

value: CD8+ T cell

tag: cell population

value: tdTomato+, KLRG1-


title: rhFAPB4_0ng

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: 0ng

data_processing:
Each pair-end sample had an average throughput of 18Gb. BCL files produced by the sequencing run were converted into FASTQ files by the NextSeq 2000 onboard software DRAGEN™ Bio-IT Platform using BCL conversion application (version 3.10.12). Galaxy analysis platform  were used to proceed alignment, expression estimation and tests for differential expression.
Assembly: hg38
Supplementary files format and content: .xlsx
Supplementary files format and content: log2FC

source_name: HCC cell line

extract_protocol:
Total RNA was harvested from treated HCC cell line by using the RNease Plus Mini Kit (QIAGEN).
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for library construction. One microgram of total RNA was used. Ribosomal RNA was depleted and cDNA was sysnthesized. Pre-index anchors were ligated to cDNA fragments. Libraries were amplified, followed by cleanup process.

value: HCC cell line


title: d21 TPEX, WT RNA-seq 2

description: Library name: WT 2


title: MAP2K3_A84T_0t__(Clariom_S_Human)

description: Gene expression data from Trex HEK293 cells transfected with pDest30_MAP2K3_A84T without Tetracycline.

value: Mammalian immortilized cell line

value: Trex HEK293


title: MAP2K3_A84T_0t_2_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_A84T without Tetracycline.


title: OS_Patient tumor-SJOS030876_R1-FFPE

value: F

value: Lung


title: G_biol_rep_2.1

value: hiPSCs

value: CD34+CD43+CD33+ iPSC-derived cells


title: MAP2K3_A84T_0t_3_(Clariom_S_Human)


title: tdTomato+, KLRG1-, d6 Arm 1

description: Library name: TDT+KLRG1-1


title: MAP2K3_A84T_1t_1_(Clariom_S_Human)

value: transfected with pDest30_MAP2K3_A84T with 24h Tetracycline induction.


title: Ampulla, early luteal, rep1

value: Oviduct

value: Oviductal cells

value: Oviduct ampullary cells

value: Female

value: early luteal


title: OS_Patient tumor-SJOS030645_R1-FFPE

value: M

value: OS

value: N

value: Patient tumor


title: MAP2K3_A84T_0t_1_(Clariom_S_Human)

value: Mammalian immortilized cell line


title: d21 TPEX, WT RNA-seq 3

description: Library name: WT 3

value: spleen

value: CD8+ T cells

value: WT


title: G_biol_rep_1.2

value: GATA2+/- R396Q mutation


title: OS_Patient tumor-SJOS063822_A1-frozen

value: Lung

value: Y


title: Ampulla, post-ovulatory, rep3

value: post-ovulatory


title: rhFABP4_100ng

description: Library name: 100ng

value: HCC cell line


title: tdTomato+, KLRG1+, d6 Arm 1

description: Library name: TDT+KLRG1+1

value: Spleen

value: CD8+ T cell

value: tdTomato+, KLRG1+


title: Ampulla, post-ovulatory, rep2

value: Oviduct

value: Oviductal cells

value: Oviduct ampullary cells

value: Female


title: OS_Xenograft-SJOS001108_X1-frozen

value: F

value: OS

value: N

value: Xenograft


title: Ampulla, early luteal, rep2

value: early luteal


title: OS_Xenograft-SJOS012409_X1-frozen

value: Femur


title: GSA_biol_rep_2.2

value: hiPSCs

value: GATA2+/- SETBP1mut ASXL1mut G646X

value: CD34+CD43+CD33+ iPSC-derived cells


title: tdTomato-, KLRG1-, d6 Arm 1

description: Library name: TDT-KLRG1-1

value: tdTomato-, KLRG1-


title: OS_Patient tumor-SJOS030648_D2-frozen

value: M

value: Tibia

value: Y

value: Patient tumor


title: Ampulla, post-ovulatory, rep1

value: Oviduct

value: Oviductal cells

value: post-ovulatory


title: tdTomato-, KLRG1+, d6 Arm 2

description: Library name: TDT-KLRG1+ 2

value: Spleen

value: CD8+ T cell

value: tdTomato-, KLRG1+


title: tdTomato-, KLRG1-, d6 Arm 2

description: Library name: TDT-KLRG1-2


title: tdTomato-, KLRG1+, d6 Arm 1

description: Library name: TDT-KLRG1+ 1


title: OS_Xenograft-SJOS001127_X1-frozen

value: OS

value: Lung

value: N

value: Xenograft


title: GS_biol_rep_1.2

value: hiPSCs

value: GATA2+/- SETBP1mut D868N


title: GSA_biol_rep_1.2

value: GATA2+/- SETBP1mut ASXL1mut G646X

value: CD34+CD43+CD33+ iPSC-derived cells


title: eSKIN biol rep 2

city: Cambridge

first: Maria

middle: Pilar

last: Alcolea

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: SINAE9
10X genomics

library_source: genomic single cell

data_processing:
The dataset was aligned to the refernce genome using cellranger-atac 2.2.0
Assembly: Mouse mm10
Supplementary files format and content: Cellranger-atac output files

source_name: Epithelia

extract_protocol:
Epithelia (esophageal control, eEE; and esophageal-derived skin, eSKIN) were harvested 10 days post-culture, at which point the epithelia were carefully peeled from their underlying stroma following a 50mM EDTA incubation for 15min at 37°C. The peeled epithelia was rinsed with PBS, and incubated with 0.5mg/ml Dispase (Sigma) for 5min. EDTA was then added to the samples at a final concentration of 5mM, and the suspension diluted 1/5 by adding PBS + 0.04% BSA buffer. A cell suspension was obtained by filtering through a 30um cell strainer, centrifuging at 300g for 5min at 4 degrees and resuspending in PBA + 0.04% BSA. After assessing viability and cell number, nuclei were isolated following 10X CG000169 protocol.
Libraries were prepared following manufacturer's instructions for Chromium Next GEM Single Cell ATAC Kit v2

value: Epithelia


title: GS_biol_rep_1.1

source_name: hiPSCs


title: d21 TPEX, DKO 3

description: Library name: DKO 3

library_source: genomic

data_processing:
Reads were analyzed using the ENCODE ATACseq pipeline (v2.2.0) and mapped to the mm10 genome.
Assembly: mm10
Supplementary files format and content: Narrowpeaks files of accessible chromatin regions are provided for each sample.

source_name: spleen

extract_protocol:
Nuclei were isolated for tagmentation according to the OmniATAC pipeline using the using the Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit (Illumina, Cat # 20034197). Tagmented nuclear DNA was purified using the Qiagen MinElute Reaction Cleanup Kit.
The libraries were indexed with the IDT for Illumina DNA UD Index Set D (Illumina, Cat # 20027213). Amplified libraries were cleaned up using double-sided bead purification with AMPure XP beads (Beckman Coulter, Cat # A63880). Library concentrations were determined by Qubit prior to pooling, and the pooled library was sequenced for a target of 500 million read pairs on an Illumina NovaSeq X Plus (300 cycles).

value: spleen

value: CD8+ T cells

value: DKO


title: GSA_biol_rep_2.1


title: sSKIN biol rep 1 and 2

description:
Library name: SINAF9
10X genomics


title: GSA_biol_rep_1.1


title: G_biol_rep_1.1

value: GATA2+/- R396Q mutation


title: eSKIN biol rep 1

description:
Library name: SINAD9
10X genomics


title: d21 TPEX, Tcf7 KO 1

description: Library name: Tcf7 KO 1

value: Tcf7 KO


title: OS_Xenograft-SJOS001132_X1-frozen

value: F


title: OS_Xenograft-SJOS001107_X1-frozen

value: M

value: Humerus


title: tdTomato+, KLRG1+, d6 Arm 2

description: Library name: TDT+KLRG1+2

value: Spleen

value: CD8+ T cell

value: tdTomato+, KLRG1+


title: CTRL_biol_rep_2.2

value: WT


title: eEE biol_rep 3

description:
Library name: SINAB9
10X genomics


title: OS_Xenograft-SJOS030605_X1-frozen

value: OS

value: Chest

value: Y

value: Xenograft


title: OS_Xenograft-SJOS001105_X1-frozen

value: Femur

value: N


title: sSKIN biol rep 3

description:
Library name: SINAG9
10X genomics

value: Epithelia


title: OS_Xenograft-SJOS030645_X2-frozen

value: Lung


title: eEE biol_rep 1 and 2

description:
Library name: SINAA9
10X genomics


title: MLN, naïve, vaccination, rep2

city: Ithaca

first: Tawny

middle: L

last: Chandler

address: 235 Hungerford Hill Rd

institute: Cornell University

description:
Library name: Sample 4
10x Genomics

data_processing:
Fastq files were processed by the cloud-based cellranger count (version 8.0.0) available through 10x Genomics using default parameters and a murine reference (Mouse (GRCm39) 2024-A).
Assembly: GRCm39
Supplementary files format and content: matrix.h5 raw and filtered features from cellranger count

source_name: mesenteric lymph node

extract_protocol:
Single cells were isolated from the lymph node by mechanical disruption through a 70 um cell strainer. Cells were washed once with RPMI+10%FBS and resuspended in PBS+0.04%BSA before filtering through a 35 um cell strainer. Cells were washed once with PBS+0.04%BSA before cell counting.
Single cell suspensions were run on a Chromium X instrument and libraries were prepared following the Chromium Next GEM Single Cell 3’ RNA-Seq - Dual Index Assay version 3.1 (10x Genomics, user guide CG000315, RevE) by the Cornell BRC Genomics Facility (RRID:SCR_021727). We targeted 10,000 cells and used 13 cycles of cDNA amplification. Sample quality was confirmed using a Qubit (DNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to confirm fragment size integrity. Libraries were sequenced on a NovaSeqX, 10B flowcell with 2 x 150bp read length.

treatment_protocol: At 7 d of age, pups born to dams without (naïve, n = 2) or with (MatAb, n = 2) rotavirus antibodies were infected with 10^-3 uL of EMcN rotavirus. At 10 days post infection, pups were euthanized and the mesenteric lymph node chains were harvested into cold RPMI+10%FBS.

value: mesenteric lymph node

value: lymphocytes

tag: age

value: 17 days old

tag: time

value: 10 days post infection

value: naïve

tag: vaccination

value: rotavirus EMcN


title: CTRL_biol_rep_2.1

value: hiPSCs

value: CD34+CD43+CD33+ iPSC-derived cells


title: d21 TPEX, Prdm1 KO 1

description: Library name: Prdm1 KO 1

value: spleen

value: CD8+ T cells

value: Prdm1 KO


title: OS_Xenograft-SJOS030597_X1-frozen

value: F

value: OS

value: Y


title: d21 TPEX, DKO 1

description: Library name: DKO 1

value: DKO


title: OS_Xenograft-SJOS010929_X1-frozen

value: M

value: Femur

value: N

value: Xenograft


title: MLN, naïve, vaccination, rep1

description:
Library name: Sample 3
10x Genomics

value: mesenteric lymph node

value: lymphocytes

value: WT

value: 17 days old


title: CTRL_biol_rep_1.2

value: hiPSCs


title: RNA-Seq_fasting

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

description: Library name: Sample_8

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom human or mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCh39.p13;GRCm39
Supplementary files format and content: comma-delimited text files including sense and antisense peak positions for trans-RNA-seq samples.
Supplementary files format and content: comma-delimited text files including normalized read density around start and stop codons for Ribo-seq samples.
Supplementary files format and content: comma-delimited text files including RPKM and TPM of RNA-seq samples.

source_name: liver

extract_protocol:
For Ribo-seq, RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. To enrich capped small RNAs, 50 μg of total cellular RNA was fractionated using the RNA Clean & Concentrator kit (Zymo research). Briefly, adjusted RNA Binding Buffer was prepared by mixing an equal volume of buffer and 100% ethanol. Total RNA sample were mixed with 2 volumes of the adjusted buffer and transferred to the column. The mix was then centrifuged at 16,000 g for 30 s, and the flow-through was collected. 1 volume of ethanol were mixed with flow-through and transferred to a new column. The mix were centrifuged at 16,000 g for 30 s, and the flow-through was discarded. The column was washed by RNA Prep Buffer and Wash buffer, and the bound RNA was eluted with 50 μl DNase/RNase-Free water.  The eluted RNAs were dephosphorylated with 50 U of CIP (NEB) in a 100 μl reaction containing 1 × rCutSmart Buffer and 0.5 U/μl SUPERase·In at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. Three-fourths of resulting RNAs were decapped with 0.75 μl of 5 U/μl Cap-Clip Acid Pyrophosphatase (Cellscript) in 1 × Cap-Clip Acid Pyrophosphatase Buffer at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The remaining one-fourth RNAs were phosphorylated with 20 U of T4 PNK in a 20 μl reaction containing 0.5 U/μl SUPERase·In, 2 mM ATP and 1 × T4 PNK Buffer at 37 °C for 1 h, followed by ethanol precipitation.
For Ribo-seq, trans-RNA-seq, and RNA-seq, 14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).

value: liver

value: fasting


title: MLN, MatAb, vaccination, rep1

description:
Library name: Sample 1
10x Genomics

value: 10 days post infection

value: maternal antibodies

value: rotavirus EMcN


title: MLN, MatAb, vaccination, rep2

description:
Library name: Sample 2
10x Genomics


title: d21 TPEX, WT2

description: Library name: WT 2

value: spleen

value: CD8+ T cells


title: OS_Xenograft-SJOS030279_X1-frozen

value: F

value: OS

value: Y


title: d21 TPEX, WT1

description: Library name: WT 1


title: RNA-Seq_fed

description: Library name: Sample_7


title: d21 TPEX, Prdm1 KO 2

description: Library name: Prdm1 KO 2

value: Prdm1 KO


title: RNA-Seq_fasting_trans1

description: Library name: Sample_9

value: fasting, transfection with trans-RNA against ATF4


title: OS_Xenograft-SJOS030101_X1-frozen

value: M

value: Femur

value: Xenograft


title: d21 TPEX, WT3

description: Library name: WT 3

value: WT


title: LCS-379B

status: Public on Oct 01 2025

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Illumina Hybridization Protocol Other: Hybridization was performed following the manufacturer's protocol for Illumina's Infinium Human Methylation27 BeadChip microarrays.

scan_protocol: Illumina Scanning Protocol Other: Illumina's Infinium Human Methylation27 BeadChip microarrays were scanned using a HiScan (Illumina). Images were analyzed using BeadStudio software (Illumina).

data_processing:
Data Processing Protocol
Calculation Method: Raw data from the Infinium Human Methylation27 BeadChip microarrays were extracted using BeadStudio software (Illumina). Thereafter, the SSN method in the R lumi package was used to normalize the data. Further analysis was carried out using the lumi package in R. IlluminaHumanMethylation27k.db_1.4.7 package (http://www.bioconductor.org) was used for annotation. Only probes which did not have any NAs were included which resulted in 23,972 probes.

label: Cy5 and Cy3

label_protocol:
Zymo EZ DNA Methylation
Other: Used 1 ug of high quality DNA and completed the bisulfite conversion according to the manufacturer's protocol (Zymo Research Corporation, Irvine, CA).

extract_protocol:
Phenol/Chloroform Extraction Protocol
Other: DNA was extracted using Phenol/Chloroform/Isoamyl Alcohol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol.

tag: gender

value: male

value: Liver Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: H

tag: alt

value: low

tag: main tumor size

value: small

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-393B

description: No additional information.

tag: age

tag: tissue

value: N

value: large

value: I


title: LCS-393A

description: No additional information.

tag: gender

value: Liver Tumor Tissue


title: LCS-398A

description: No additional information.

tag: disease state

value: Yes

value: IIIA

value: C

value: high

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: LCS-391B

description: No additional information.

value: female

value: Liver Tissue

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

tag: multinodular

tag: cirrhosis

value: B


title: LCS-378B

description: No additional information.

value: male

value: Hepatocellular carcinoma (HCC)

value: low

tag: tnm staging

tag: bclc staging

tag: clip staging

tag: afp

value: Alive

value: False


title: LCS-378A

description: No additional information.

tag: age

value: N

value: large

value: No

value: I

value: A


title: LCS-395B

description: No additional information.

tag: tissue

value: Yes


title: LCS-382B

description: No additional information.

tag: gender

value: small


title: LCS-372B

description: No additional information.

tag: disease state

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-396B

description: No additional information.

tag: hbv viral status


title: LCS-370B

description: No additional information.

tag: alt

value: high

value: IIIC

tag: survival status

tag: survival months

tag: recurr status

tag: recurr months


title: LCS-385B

description: No additional information.

value: Liver Tissue

tag: main tumor size

tag: multinodular

tag: cirrhosis

tag: tnm staging

tag: bclc staging


title: LCS-373A

description: No additional information.

tag: gender

tag: age

tag: tissue

value: Liver Tumor Tissue

value: AVR-CC

value: IIIA

value: C

tag: clip staging

tag: afp

value: Dead

value: True


title: LCS-387B

description: No additional information.

value: male

tag: disease state

value: Hepatocellular carcinoma (HCC)

value: CC

value: low

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-391A

description: No additional information.

value: female

tag: hbv viral status

tag: alt

value: large

value: B

tag: survival status

tag: survival months

tag: recurr status


title: LCS-365A

description: No additional information.

tag: main tumor size

tag: multinodular

value: Yes

tag: cirrhosis

tag: tnm staging

tag: recurr months


title: LCS-376B

description: No additional information.

tag: gender

tag: age

tag: tissue

value: No

value: I

tag: bclc staging

value: A

tag: clip staging

value: high


title: LCS-370A

description: No additional information.

value: Liver Tumor Tissue

tag: disease state

value: N

value: IIIC

tag: afp

value: Alive

value: False


title: LCS-397A

description: No additional information.

value: male

tag: hbv viral status

value: H

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-365B

description: No additional information.

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: CC

tag: alt

tag: main tumor size

value: IIIA

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True


title: LCS-369A

description: No additional information.

tag: gender

value: AVR-CC

value: small

tag: multinodular

value: No

tag: cirrhosis

value: Yes

tag: tnm staging

value: low

tag: recurr months


title: LCS-362B

description: No additional information.

tag: age

tag: tissue

tag: disease state

tag: bclc staging

value: A

tag: clip staging


title: LCS-363B

description: No additional information.

value: female

tag: hbv viral status

value: large

value: C

tag: afp

value: high


title: LCS-369B

description: No additional information.

value: male

tag: alt

value: I

value: Alive

value: False


title: LCS-360B

description: No additional information.

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: CC

tag: main tumor size

value: IIIB


title: LCS-358B

description: No additional information.

value: N

value: small

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-352B

description: No additional information.

tag: gender

value: H

tag: multinodular

value: Yes

value: No

value: B


title: LCS-363A

description: No additional information.

value: female

value: Liver Tumor Tissue

value: AVR-CC

value: low

value: large

tag: cirrhosis

tag: tnm staging

value: IIIA

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True


title: LCS-356B

description: No additional information.

value: male

tag: age

tag: tissue

value: Liver Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: bclc staging

tag: recurr months


title: LCS-358A

description: No additional information.

tag: hbv viral status

value: N

tag: alt

tag: main tumor size

value: C

tag: clip staging

tag: afp


title: LCS-357B

description: No additional information.

tag: gender

value: CC

value: small

value: I

value: high


title: LCS-349B

description: No additional information.

tag: multinodular

value: No

value: Yes

value: A

value: Alive

value: False


title: LCS-356A

description: No additional information.

value: Liver Tumor Tissue

value: low

value: large

tag: cirrhosis

value: IIIA

value: B


title: LCS-362A

description: No additional information.

value: male

value: Hepatocellular carcinoma (HCC)

value: H

tag: tnm staging

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-352A

description: No additional information.

value: female

tag: age

tag: tissue


title: LCS-345B

description: No additional information.

value: Liver Tissue

tag: disease state

value: AVR-CC

tag: bclc staging

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True


title: LCS-344B

description: No additional information.

tag: hbv viral status

value: N

tag: alt

tag: main tumor size

value: No

value: Yes

value: I

tag: clip staging

value: high

tag: recurr months


title: LCS-339B

description: No additional information.

tag: gender

tag: hbv viral status:

value: low

value: small

tag: multinodular

tag: cirrhosis

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

tag: afp

value: Alive

value: False


title: LCS-346B

description: No additional information.

value: male

tag: age

tag: tissue

tag: disease state


title: LCS-344A

description: No additional information.

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

value: large

tag: tnm staging

tag: bclc staging

value: A

tag: survival status

tag: survival months

tag: recurr status


title: LCS-349A

description: No additional information.

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

tag: clip staging

tag: recurr months


title: LCS-333B

description: No additional information.

tag: gender

value: Liver Tissue

tag: multinodular

tag: cirrhosis

value: IIIB

value: C

value: Dead


title: LCS-341B

description: No additional information.

value: No

value: Yes

tag: afp


title: LCS-343B

description: No additional information.

tag: age

tag: hbv viral status:

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

value: high

value: True


title: LCS-334A

description: No additional information.

tag: tissue

tag: disease state

value: H

tag: tnm staging

value: I

tag: bclc staging

value: low

tag: survival status


title: LCS-342B

description: No additional information.

value: male

tag: hbv viral status

tag: alt

tag: main tumor size

tag: survival months

tag: recurr status


title: LCS-347B

description: No additional information.

tag: gender

tag: multinodular

tag: cirrhosis

tag: recurr months


title: LCS-340B

description: No additional information.

tag: age

value: AVR-CC

value: IIIC

value: B

tag: clip staging

tag: afp

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-332B

description: No additional information.

tag: tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

value: N

value: small

tag: tnm staging

tag: bclc staging

value: A


title: LCS-341A

description: No additional information.

value: Liver Tumor Tissue

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

value: IIIB

value: C

tag: survival status

value: Alive

tag: survival months

value: False


title: LCS-331A

description: No additional information.

tag: gender

value: high

value: large

tag: multinodular

value: Yes

tag: cirrhosis

value: No

tag: recurr status

tag: recurr months


title: LCS-333A

description: No additional information.

value: male

tag: age

value: low

tag: clip staging

tag: afp

value: Dead

value: True


title: LCS-331B

description: No additional information.

tag: tissue

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)


title: LCS-327A

description: No additional information.

tag: disease state

value: AVR-CC

value: IIIA

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-328B

description: No additional information.

value: female

tag: hbv viral status

tag: alt

tag: main tumor size

tag: tnm staging

tag: bclc staging

value: B


title: LCS-330B

description: No additional information.

tag: gender

tag: multinodular

tag: cirrhosis

value: A

tag: survival status

tag: survival months


title: LCS-295B

description: No additional information.

tag: age

value: CC

value: small

value: I

tag: clip staging

tag: afp

value: Alive

tag: recurr status

tag: recurr months


title: LCS-326A

description: No additional information.

tag: tissue

value: Liver Tumor Tissue

tag: disease state

value: Yes

value: II

value: high

tag: survival status:

tag: survival months:

tag: recurr status:


title: LCS-254A

description: No additional information.

value: male

tag: hbv viral status

tag: alt

value: low

tag: main tumor size

value: No

tag: tnm staging

value: False


title: LCS-327B

description: No additional information.

tag: gender

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: AVR-CC

value: large

tag: multinodular

tag: cirrhosis

tag: bclc staging

value: C

tag: recurr months:


title: LCS-397B

description: No additional information.

tag: age

value: H

value: B

tag: clip staging

tag: afp


title: LCS-254B

description: No additional information.

tag: tissue

value: CC

value: small

value: I

value: A

tag: survival status

tag: survival months

tag: recurr status

tag: recurr months


title: LCS-196B

description: No additional information.

tag: disease state

tag: hbv viral status

value: Yes

value: II

value: Dead

value: True


title: LCS-326B

description: No additional information.

value: male

tag: alt

value: low

tag: main tumor size

value: high

tag: survival status:

tag: survival months:

tag: recurr status:


title: LCS-329B

description: No additional information.

tag: gender

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

tag: bclc staging


title: LCS-069B

description: No additional information.

tag: age

tag: tissue

value: large

value: IIIB

value: C

tag: clip staging

tag: afp


title: LCS-072A

description: No additional information.

value: Liver Tumor Tissue

value: CC

tag: survival status

value: Alive

tag: survival months

tag: recurr status

tag: recurr months


title: LCS-373B

description: No additional information.

tag: disease state

tag: hbv viral status

value: AVR-CC

tag: alt

tag: main tumor size

value: IIIA


title: LCS-292B

description: No additional information.

tag: gender

value: female

value: H

value: Yes

value: B

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-294B

description: No additional information.

value: male

tag: age

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: II

tag: bclc staging

value: low

value: True


title: LCS-062B

description: No additional information.

tag: tissue

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: high

tag: clip staging

tag: afp

tag: survival status

value: Dead

tag: survival months


title: LCS-334B

description: No additional information.

tag: disease state

tag: hbv viral status

tag: alt

value: large

value: No

value: I

value: A

tag: recurr status

tag: recurr months


title: LCS-057B

description: No additional information.

tag: gender

value: AVR-CC

tag: main tumor size

value: Alive

value: False


title: LCS-054A

description: No additional information.

tag: age

value: Liver Tumor Tissue

value: small

value: Yes


title: LCS-054B

description: No additional information.

value: male

tag: multinodular


title: LCS-046A

description: No additional information.

value: CC

value: low

tag: cirrhosis

value: IIIA

value: C


title: LCS-072B

description: No additional information.

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

tag: tnm staging

value: II

value: True


title: LCS-049B

description: No additional information.

value: high

value: large

tag: bclc staging


title: LCS-292A

description: No additional information.

value: female

tag: tissue

value: H

value: No

value: B

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-046B

description: No additional information.

tag: disease state

tag: clip staging

tag: afp

tag: survival status

value: Dead

tag: survival months


title: LCS-045B

description: No additional information.

tag: gender

tag: hbv viral status

tag: alt

value: small

value: Yes

value: A

value: Alive

tag: recurr status

value: False

tag: recurr months


title: LCS-064B

description: No additional information.

value: male

tag: age

value: CC

tag: main tumor size

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: I


title: LCS-067B

description: No additional information.

tag: tissue

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: AVR-CC

value: II

tag: bclc staging


title: LCS-064A

description: No additional information.

value: Liver Tumor Tissue

tag: disease state

value: high

value: large


title: LCS-062A

description: No additional information.

value: IIIB

value: C

tag: clip staging

value: True


title: LCS-063B

description: No additional information.

value: small

value: Yes

value: B

tag: afp

value: low

value: Dead


title: LCS-038B

description: No additional information.

value: male

value: CC

value: IIIA

tag: survival status

value: Alive

value: False


title: LCS-056B

description: No additional information.

value: female

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: AVR-CC

value: No

value: I

value: A

tag: survival months


title: LCS-043B

description: No additional information.

tag: gender

value: high

value: small

value: True


title: LCS-057A

description: No additional information.

value: Liver Tumor Tissue

tag: hbv viral status

value: large

value: Yes

value: II

value: low


title: LCS-027B

description: No additional information.

value: male

value: CC

tag: alt

value: Alive


title: LCS-027A

description: No additional information.

tag: recurr status

value: False


title: LCS_007B

description: No additional information.

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

tag: recurr months


title: LCS-036B

description: No additional information.

tag: age

value: No


title: LCS-042B

description: No additional information.

tag: main tumor size


title: LCS-033B

description: No additional information.

tag: multinodular

value: III

value: B

value: Dead


title: LCS-009B

description: No additional information.

value: AVR-CC

value: high

value: small

tag: cirrhosis

value: A


title: LCS-427A

description: No additional information.

value: Liver Tumor Tissue

value: large

tag: tnm staging

value: I

value: True


title: LCS-426A

description: No additional information.

value: female

tag: tissue

value: CC

value: low

value: Yes


title: USDA110 nodules at 0.1 mM Pi, biological rep 1

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

description:
Nodules_N4
Gene expression data from nodules treated with low inorganic phosphate level

hyb_protocol: Fragmented cDNA was hybridized with the Affymetrix GeneChip Soybean Genome Array (66K) with protocols adapted from the supplier (Affymetrix, Inc.).

scan_protocol: Hybridized array slides were scanned with the Agilent G2505B DNA Microarray Scanner System (Agilent Technologies)

data_processing:
Processed data analysis was accomplished by the appropriate programs (Affymetrix Expression Console and GeneSpring) following the software standard procedures from Affymetrix and Agilent Technologies, respectively
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = SoyGene-1_0-st-v1
program-name = Expression Console
program-version = 1.3.0.187

organism: Glycine max

source_name: USDA110 nodules at low Pi

label_protocol: cDNA clones were labeled following the experimental manual of the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: Plants were grown in a growth chamber with continuous 30°C temperature, photoperiod of 12 h/12 h, 80 μmol m−2 s−1 photon flux density, and 60% relative humidity

extract_protocol: Total RNA was isolated from the resulting frozen nodules using Trizol reagent (Invitrogen) following the manufacturer’s experimental manual.

treatment_protocol: Nodule samples were collected at 35 day after sowing, flash-frozen in liquid N2 and kept at −80°C until RNA isolation.

value: Root nodules

tag: treatment

value: at 0.1 mM Pi


title: LCS-423A

description: No additional information.

tag: disease state

value: Hepatocellular carcinoma (HCC)

value: IIIA

tag: bclc staging


title: LCS-422B

description: No additional information.

value: Liver Tissue

value: No

tag: clip staging

tag: afp

value: Alive

value: False


title: CB1809 nodules at 0.1 mM Pi, biological rep 1

description:
Nodules_N33
Gene expression data from nodules treated with low inorganic phosphate level

source_name: CB1809 nodules at low Pi


title: USDA110 nodules at 2.0 mM Pi, biological rep 1

description:
Nodules_N10
Gene expression data from nodules treated with sufficient inorganic phosphate level

source_name: USDA110 nodules at sufficient Pi

value: at 2.0 mM Pi


title: CB1809 nodules at 2.0 mM Pi, biological rep 3

description:
Nodules_N46
Gene expression data from nodules treated with sufficient inorganic phosphate level

source_name: CB1809 nodules at sufficient Pi


title: LCS-425B

description: No additional information.

value: AVR-CC

value: A

tag: survival status

tag: survival months


title: LCS-415A

description: No additional information.

tag: gender

value: male

value: Liver Tumor Tissue

tag: hbv viral status

value: small

value: I

value: Dead


title: LCS-426B

description: No additional information.

value: female

value: CC

tag: alt

value: low

value: Yes

tag: recurr status


title: CB1809 nodules at 2.0 mM Pi, biological rep 1

description:
Nodules_N44
Gene expression data from nodules treated with sufficient inorganic phosphate level

value: Root nodules


title: LCS-423B

description: No additional information.

tag: age

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: large

value: IIIA

value: B

value: high

value: True

tag: recurr months


title: USDA110 nodules at 0.1 mM Pi, biological rep 3

description:
Nodules_N6
Gene expression data from nodules treated with low inorganic phosphate level

value: at 0.1 mM Pi


title: USDA110 nodules at 0.1 mM Pi, biological rep 2

description:
Nodules_N5
Gene expression data from nodules treated with low inorganic phosphate level


title: LCS-413B

description: No additional information.

value: male

value: N

tag: main tumor size

tag: multinodular

value: No

value: A

value: Alive


title: CB1809 nodules at 0.1 mM Pi, biological rep 2

description:
Nodules_N37
Gene expression data from nodules treated with low inorganic phosphate level


title: CB1809 nodules at 0.1 mM Pi, biological rep 3

description:
Nodules_N38
Gene expression data from nodules treated with low inorganic phosphate level


title: LCS-424B

description: No additional information.

tag: hbv viral status:

tag: cirrhosis

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

value: False


title: LCS-412B

description: No additional information.

tag: tissue

tag: disease state

value: CC

tag: tnm staging

value: IIIB

tag: bclc staging

value: C

tag: clip staging

value: low

value: Dead


title: CB1809 nodules at 2.0 mM Pi, biological rep 2

description:
Nodules_N45
Gene expression data from nodules treated with sufficient inorganic phosphate level

value: Root nodules

tag: treatment

value: at 2.0 mM Pi


title: LCS-415B

description: No additional information.

tag: gender

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

tag: alt

value: small

value: Yes

value: I

tag: afp

tag: survival status

tag: survival months


title: USDA110 nodules at 2.0 mM Pi, biological rep 2

description:
Nodules_N11
Gene expression data from nodules treated with sufficient inorganic phosphate level


title: LCS-420B

description: No additional information.

value: male

tag: age

tag: main tumor size

value: large

tag: multinodular

value: IIIA

value: B

value: high

tag: recurr status

tag: recurr months


title: LCS-412A

description: No additional information.

tag: tissue

value: Liver Tumor Tissue

value: CC

value: No

tag: cirrhosis

value: True


title: LCS-427B

description: No additional information.

tag: disease state

tag: tnm staging

value: A

value: Dead


title: LCS-406B

description: No additional information.

tag: hbv viral status:

tag: tnm staging:

tag: bclc staging:

tag: clip staging:


title: LCS-403A

description: No additional information.

tag: gender

tag: hbv viral status

tag: alt

tag: bclc staging

tag: clip staging

value: Alive


title: LCS-400B

description: No additional information.

tag: age

value: Liver Tissue

tag: main tumor size

tag: afp

tag: survival status

tag: survival months


title: LCS-422A

description: No additional information.

value: female

tag: tissue

value: Hepatocellular carcinoma (HCC)

value: low

tag: multinodular

tag: cirrhosis

tag: recurr status

value: False

tag: recurr months


title: LCS-399A

description: No additional information.

value: male

tag: disease state

value: Yes

tag: tnm staging

value: I


title: Treated, Batch 4, Sample 7

city: Stanford

first: Aleena

last: Patel

state: CA

address: 279 Campus Dr

institute: Stanford University

description: 10X Genomics

data_processing:
The demultiplexing, barcoding, gene counting and aggregation were made using the CellRanger software v4.0.0 for Treated_B2_S4, v6.0.1 for Untreated_B1_S1, and v7.1.0 for all other samples.
Assembly: GRCz11
Supplementary files format and content: Tab separated value files and matrix files

organism: Danio rerio

source_name: 50% epiboly embryo

extract_protocol:
50% epiboly zebrafish embryos were dechorionated manually after chorions were softened with pronase and deyolked manually in embryo water. Deyolked embryos were transferred to a 1.5 ml eppendorf tube, resuspended in 200 µl embryo water, and cells were dissociated by flicking the tube 20 times and pipetting gently up and down 3 times. PBS with .1% BSA was added to the dissociated cells, and cells were spun down into a pellet at 300xg for 30 seconds. The supernatant was removed, being careful not to disturb the pellet, and the pellet was resuspended in 15-20µl PBS with .1% BSA
Library was constructed according to manufacturer's instructions (10X Genomics)

value: 50% epiboly embryo


title: LCS-399B

description: No additional information.

tag: gender

value: large


title: Treated, Batch 2, Sample 4

description: 10X Genomics


title: Untreated, Batch 4, Sample 3

description: 10X Genomics


title: LCS-421B

description: No additional information.

tag: hbv viral status

value: N

value: high


title: Untreated, Batch 1, Sample 1

description: 10X Genomics


title: LCS-404A

description: No additional information.

value: Liver Tumor Tissue

value: CC

tag: alt

value: IIIA

value: C


title: Treated, Batch 3 (replicate 2), Sample 6

description: 10X Genomics


title: LCS-411B

description: No additional information.

value: small

value: No

value: II

tag: bclc staging

value: A

value: Dead

value: True


title: LCS-405B

description: No additional information.

value: male

value: Liver Tissue

value: Hepatocellular carcinoma (HCC)

value: AVR-CC

value: low

tag: clip staging

value: Alive


title: LCS-410B

description: No additional information.

tag: age

value: high

value: Yes

value: B

value: False


title: HCT116_si11_rep1_atac

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

data_processing:
The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”. The resulting filtered reads were aligned to their respective reference genome using STAR aligner (v2.7.10b) with default parameters. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Exon mapped reads were counted using featureCounts from the subread package (v2.0.6). ATAC-seq datasets were processed to remove the Nextera adapter (CTGTCTCTTATACACATCT) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”115. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2122). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1). Reads were further processed using alignmentSieve from deepTools (v3.5.5) to account for transposon dimerization before insertion. Positive and negative strand alignments were shifted by +4 bp and −5 bp, respectively. Additionally, fragments of 100 bp, corresponding to nucleosome-free regions (NFRs), were retained with the parameters “--minMappingQuality 25 --maxFragmentLength 100 --ATACshift --BED”. Peaks were called on the resulting BEDPE files using MACS3 (v3.0.1) MACS3 with the parameters “--call-summits --bdg --nomodel --nolambda --gsize hs --keep-dup all --format BEDPE --qvalue 0.05”. The predicted peaks were filtered for ENCODE project blacklisted regions using BEDTools (v2.31.0) intersect.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: HCT116_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: HCT116_si11_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_si11_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_si11_rna_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: mESC_diff_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_nfr_atac_raw_counts.tsv  is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: mESC_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
To prepare samples for RNA-seq, 3 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
The ATAC-seq library was prepared as described in Corces, M.R. et al.Nat Methods, 2017. After quality control using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), the libraries were sequenced (150 bp paired-end reads) on an Illumina HiSeq Sequencer (Illumina Inc., San Diego, CA). For RNA-seq, the quality of the isolated RNA was determined using a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further used for library preparation. The Illumina Ribo Zero Plus (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (25-1000 ng) were depleted of ribosomal RNA and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before ligation of an anchor. Fragments containing the anchor on both ends were selectively enriched with PCR at the same time adding the index with unique dual indexes (UDI). The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The libraries were normalized to 10 nM in Tris-HCl 10 mM, pH8.5 with 0.1% Tween20.

tag: cell line

tag: cell type

value: Human colon cancer cell line

tag: genotype


title: LCS-403B

description: No additional information.

value: CC

tag: main tumor size

value: large

value: I

tag: afp

tag: survival status

tag: survival months


title: Untreated, Batch 3, Sample 2

description: 10X Genomics

tag: tissue

value: 50% epiboly embryo


title: LCS-404B

description: No additional information.

tag: multinodular

tag: cirrhosis

value: IIIA

value: C

value: Dead

tag: recurr status

tag: recurr months


title: HCT116_si11_rep3_atac


title: LCS-398B

description: No additional information.

tag: gender

value: male

value: Liver Tissue

tag: disease state

tag: hbv viral status

value: H

value: No

tag: tnm staging

value: True


title: HCT116_ctrl_rep4_atac


title: HCT116_ctrl_rep3_atac


title: HCT116_ctrl_rep1_atac


title: HCT116_WT_rep3_atac


title: LCS-401B

description: No additional information.

tag: age

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status:

tag: alt

value: low

value: small

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

value: Alive


title: HCT116_WT_rep2_atac

tag: cell line

tag: cell type

value: Human colon cancer cell line

tag: genotype


title: HCT116_WT_rep1_atac


title: HCT116_si11_rep4_atac


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep3_atac


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep2_atac


title: HCT116_LBR_TMPO_KO_HLTd3_rep1_atac


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep1_atac


title: HCT116_LBR_TMPO_KO_HLTd3_rep2_atac


title: ALI_229_MPHAG_D3_D

city: Richland

first: Lindsey

middle: N

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to the human genome version GRCh38.p14 using STAR (https://github.com/alexdobin/STAR).
Aligned reads were mapped to genes using featureCounts from the subread package (https://subread.sourceforge.net/).
Assembly: human genome GRCh38.p14
Supplementary files format and content: tab-delimited columns in .txt files are as follows: Gene ID, chromosome name, gene start site, gene end site, strand orientation, gene length, counts. Counts are in fractions since counting was conducted in fraction mode, where fractions of reads are added to totals when reads map to multiple loci.

source_name: lung epithelium

growth_protocol: Macrophages were isolated from primary human PBMC obtained from Lonza. Macrophages were isolated in RPMI media with 10% FBS, non-essential amino acids, and 25 ng/mL GM-CSF. Adherent macrophages were collected after seven days of culturing (changing media every other day).  Primary human lung cells were isolated from distal lung tissue and processed as described previously (Fulcher et al (2013) Methods Mol Biol 945:109–121 and Bove PF, et al. (2010) J Biol Chem 285(45):34939–34949.)

extract_protocol:
Following treatment 500uL Trizol added to the surface of each culture. Trizol was collected allowed to sit for 5 minutes and frozen prior to shipment. RNA isolation was performed by Genewiz (Azenta Life Sciences, Chelmsford, MA, USA).
Enrichment using poly-A tailed RNA was performed by Genewiz (Azenta Life Sciences, Chelmsford, MA, USA).

treatment_protocol: Cells were mock-infected (phosphate buffered saline) or infected with human coronavirus 229E (MOI 3) for 24 hours prior to harvest in Trizol.

tag: tissue

value: lung epithelium

tag: presence or_absence_of_macrophages

value: macrophages

value: primary lung epithelial cells

tag: time

value: 24 hours post infection

tag: treatment

value: human CoV 229E


title: ALI_229_MPHAG_D3_C


title: ALI_229_MPHAG_D3_B


title: ALI_229_MPHAG_D3_A


title: ALI_229_D3_C


title: ALI_229_D3_B


title: ALI_MOCK_MPHAG_D3_D

value: mock infection


title: ALI_229_D3_A


title: ALI_229_D3_D


title: ALI_MOCK_MPHAG_D3_C


title: Treated, Batch 3 (replicate 1), Sample 5

description: 10X Genomics

value: 50% epiboly embryo


title: ALI_MOCK_MPHAG_D3_A


title: ALI_MOCK_D3_C


title: HCT116_LBR_TMPO_KO_HLTd3_rep3_atac


title: ALI_MOCK_D3_B


title: ALI_MOCK_D3_A


title: ALI_229_D1_D

growth_protocol: Primary human lung cells were isolated from distal lung tissue and processed as described previously (PMID:23097104 and PMID:20801871).

tag: infection


title: ALI_229_D1_C


title: ALI_229_D1_B


title: ALI_229_D1_A


title: ALI_MOCK_D1_D


title: ALI_MOCK_D1_C


title: LentiMPRA RNA fraction library (rep1)

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
For mapping inserted fragments to MPRA barcodes, the paired-end reads were first merged using pear=0.9.6, and aligned to the fragment library using bowtie2=2.3.5. Then barcodes uniquely assigned to fragments were selected and a dataset mapping barcodes to inserted fragments was created.
For counting unique reads for each fragment in the assay, first the UMI read (R2) was appended to the read names (R1 and R3). Sequences were then merged using pear=0.9.6, and counted for both the RNA and DNA fractions.
A logistic regression model was then used to test the ratio of ratio differences between referernce, mutated, and scrambled sequences.
Assembly: hg38
Supplementary files format and content: TSV file containing the MPRA enrichment scores
Library strategy: lentiMPRA

growth_protocol: C4-2B cells were continually cultured in RPMI-1640 + 10% FBS + 1X Amphotericin B + 1X Pen-Strep in 5% C02 at 37C.

extract_protocol:
Cells were transduced with lentiMPRA library and 48 hours post-transduction, gDNA and RNA extracted via AllPrep DNA/RNA Mini Kit (Qiagen Cat. #80204).
LentiMPRA library was constructed according to previous publication (rf Gordon et. al 2020).

value: Prostate cancer epithelial


title: LentiMPRA RNA fraction library (rep2)


title: ALI_MOCK_D1_A


title: LentiMPRA gDNA fraction library (rep3)


title: ALI_MOCK_D1_B


title: LentiMPRA gDNA fraction library (rep2)


title: LentiMPRA gDNA fraction library (rep1)


title: CLIP-seq C4-2B, anti-SF3A1 (rep1)

data_processing:
UMIs, which are in R2, were first appended to read names in R1
cutadapt=3.5 was used to trim the reads and aligned using bwa 0.7.17
reads were then processed using samtools=1.6 and deduplicated using umi_tools=1.0
The resulting files were then analyzed using the CLIP toolkit (CTK)
Assembly: hg38
Supplementary files format and content: BED interval format with the location of binding sites

extract_protocol:
C4-2B cell pellets were harvested 48h after seeding. Cells were crosslinked with 254nm UV crosslinker set to 400mJ/cm2, then pellets were frozen at -80C prior to lysis.
CLIP-seq was conducted as per methods section in this study. For the IP, 2μg anti-SF3A1 (Proteintech Cat. #15858-1-AP) was used.

tag: antibody


title: CRISPRi in vitro sgRNA library screen (~10 doublings)

data_processing:
Reads were first collpapsed, and then umi_tools=1.0.0 was used to extract the barcode from the 5' end of the reads (NNNNNNXXXXXXX).
cutadapt=3.5 was then used to extract the guides with the following flags: -m 19 -M 21 -q 15 -a "^CTTGTTG...GTTTAAGAGCTAAGCTG"
bowtie2=2.3.5 was used to align the reads to the guide library reference (--sensitive --end-to-end -N 1 ) and correctly aligned and uniquely aligned reads were recovered (using samtools=1.6).
umi_tools was then used to remove PCR duplicates, and the guides were then counted.
Logistic regression was then used to compare the in vivo to in vitro sample (10 doublings).
Assembly: hg38
Supplementary files format and content: TSV contatning the guide enrichment scores
Library strategy: custom PCR

source_name: prostate

extract_protocol:
Mouse tumor gDNA was extracted at screen endpoint via Quick-DNA midiprep plus kit (Zymo Research Cat. #D4075).
in vivo CRISPRi library was constructed according to Weissman lab protocol, rf Horlbeck et al. 2024.

value: prostate

value: C4-2B CRISPRi-ready

value: guide library


title: ALI_MOCK_MPHAG_D3_B


title: CRISPRi in vivo sgRNA library screen endpt (RH1R)


title: CRISPRi in vivo sgRNA library screen endpt (RH3R)


title: CLIP-seq C4-2B, anti-SF3A1 (rep2)


title: CRISPRi in vivo sgRNA library screen endpt (RH2R)


title: ALI_MOCK_D3_D


title: CRISPRi in vivo sgRNA library screen endpt (RH3L)


title: CRISPRi in vivo sgRNA library screen endpt (RH2L)


title: BMP450_96hr_R2

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

description: H1 hESCs cultured in BMP4 50 ng/mL for 96 hours Rep2

data_processing:
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.5
Reads were aligned to the human genome GRCh38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.3.0 against human annotation release 86 from Ensembl
Assembly: Ensembl GRCh38 release-86
Supplementary files format and content: raw count matrix of sequencing reads

growth_protocol: The hESC line H1 was grown on growth factor-reduced Matrigel (Corning) and maintained in mTeSR1 (STEMCELL Technologies)

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit as per manufacturer's instructions
Libraries were prepared from 400 ng of RNA according to manufacturer’s instructions using the KAPA RNA HyperPrep Kit (Roche, Kit Code: KK8580)

treatment_protocol: For differentiation experiments cells were cultured in TeSR E5 (STEMCELL Technologies) with Insulin 3.2µM (Sigma I1882),   human FGF2 20 ng/mL (Invitrogen PHG0026) and LY29004 1µM (Cambridge Biosciences CAY70920) with BMP4 (Invitrogen PHC9534) and/or Activin A (Cambridge Biosciences GFH6-10) at specified concentrations.

value: Embryonic stem cells

tag: treatment duration

tag: repeat


title: BMP450_96hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 96 hours Rep1


title: BMP450_96hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 96 hours Rep3


title: BMP450_72hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 72 hours Rep2


title: BMP450_72hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 72 hours Rep1


title: BMP450_48hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 48 hours Rep3


title: BMP450_48hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 48 hours Rep1


title: LentiMPRA RNA fraction library (rep3)


title: BMP450_36hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 36 hours Rep3


title: BMP450_36hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 36 hours Rep1


title: BMP450_36hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 36 hours Rep2


title: BMP450_24hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 24 hours Rep3


title: BMP450_24hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 24 hours Rep2


title: BMP450_24hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 24 hours Rep1


title: BMP450_12hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 12 hours Rep2


title: BMP450_12hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 12 hours Rep3


title: CRISPRi in vivo sgRNA library screen endpt (RH1L)


title: BMP450_12hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 12 hours Rep1


title: BMP450_6hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 6 hours Rep2


title: BMP450_6hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 6 hours Rep1


title: BMP450_6hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 6 hours Rep3


title: BMP450_1hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 1 hour Rep2


title: BMP450_1hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 1 hour Rep3


title: Activin100BMP410_96hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 96 hours Rep3


title: USDA110 nodules at 2.0 mM Pi, biological rep 3

description:
Nodules_N13
Gene expression data from nodules treated with sufficient inorganic phosphate level

value: Root nodules

value: at 2.0 mM Pi


title: BMP450_72hr_R3

description: H1 hESCs cultured in BMP4 50 ng/mL for 72 hours Rep3


title: Activin100BMP410_96hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 96 hours Rep2


title: Activin100BMP410_96hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 96 hours Rep1


title: BMP450_1hr_R1

description: H1 hESCs cultured in BMP4 50 ng/mL for 1 hour Rep1


title: Activin100BMP410_72hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 72 hours Rep3


title: Activin100BMP410_72hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 72 hours Rep2


title: BMP450_48hr_R2

description: H1 hESCs cultured in BMP4 50 ng/mL for 48 hours Rep2


title: Activin100BMP410_72hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 72 hours Rep1


title: Activin100BMP410_48hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 48 hours Rep2


title: Activin100BMP410_48hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 48 hours Rep1


title: Activin100BMP410_48hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 48 hours Rep3


title: Activin100BMP410_36hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 36 hours Rep2


title: Activin100BMP410_36hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 36 hours Rep3


title: Activin100BMP410_36hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 36 hours Rep1


title: Activin100BMP410_24hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 24 hours Rep3


title: Activin100BMP410_24hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 24 hours Rep2


title: Activin100BMP410_24hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 24 hours Rep1


title: Activin100BMP410_12hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 12 hours Rep2


title: Activin100BMP410_12hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 12 hours Rep3


title: Activin100BMP410_6hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 6 hours Rep3


title: Activin100BMP410_6hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 6 hours Rep2


title: Activin100BMP410_1hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 1 hour Rep1


title: Untreated_0hr_R2

description: H1 hESCs cultured in mTeSR Rep2

value: mTeSR


title: Untreated_0hr_R3

description: H1 hESCs cultured in mTeSR Rep3


title: Activin100BMP410_1hr_R3

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 1 hour Rep3