title: SKBR3-EPZ-9d

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: SKBR3 cells treated with EPZ-5676 for 9 days

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: MCF7 cells cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum. SKBR3 cells cultured in McCoy5A supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: Breast cancer cell lines were treated with DMSO, 1 μM SGC0946 (Sigma-Aldrich) or 1 μM EPZ-5676 (Chemietek) for 6 to 12 days replacing the drug and medium every 3 days.

tag: drug

tag: treatment period

value: 9 days


title: Trunk neural crest-derived mesenchymal stem cells, 2

status: Public on Nov 28 2025

type: SRA

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Library name: Sample 14

library_source: transcriptomic

data_processing:
Count data were analyzed in Rstudio version 4.2. After filtering genes with low expression levels (mean ≤ 10), 13448 genes remained. The raw counts were then normalized and stabilized according to Anders and Huber (2010) [7580], who first introduced VST, which is recommended for medium-to-large datasets (e.g., more than 30 samples). Normalized counts were used for further analysis
Assembly: Human (Homo sapiens) GRCh38 / hg38
Supplementary files format and content: .csv

molecule: total RNA

organism: Homo sapiens

source_name: Neural crest

growth_protocol: iPSCs and their intermediate derivatives, along with the corresponding expanded cells, were generated and cultured as described in the Methods section.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) and treated with the DNase I kit (Qiagen) to remove any residual genomic DNA following producer's protocols. Then, 10 ng of total RNA was reverse-transcribed into single-stranded cDNA using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific)
For NGS library construction targeting the Ion AmpliSeq Transcriptome, we utilized the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (Thermo Fisher Scientific), and the Ion Chef (Thermo Fisher Scientific) instruments, following the manufacturer's protocol. Briefly, a reverse transcription master mix was prepared by combining 5X VILO Reaction Mix and 10X SuperScript III Enzyme Mix. The mix was then aliquoted into reaction plates, with 10 ng of total RNA added to each. The plates were loaded into a thermal cycler and subjected to incubation at 42°C for 30 min, followed by 85°C for 5 min, and then held at 10°C. During library preparation on the Ion Chef instruments, the following consumables and cartridges were loaded: Ion AmpliSeq Chef Solutions DL8 cartridge, Ion AmpliSeq Chef Reagents DL8 cartridge, Ion AmpliSeq Tip Cartridge L8, PCR Frame Seal, IonCode 96 Well PCR Plate, PCR Plate Frame, Empty Tip Cartridge L8, and Enrichment Cartridge. Notably, IonCode 96 Well PCR Plates used for reverse transcription reactions contained an IonCode barcode adapter. Additionally, the tube containing the Ion AmpliSeq Transcriptome Human Gene Expression Panel was inserted into an Ion AmpliSeq Chef Reagents DL8 cartridge. Multiplex PCR was performed in the thermal cycler within the Ion Chef, with 13 cycles of 16-minute annealing/extension reactions. Subsequent steps involved primer digestion with FUPA reagents, ligation of IonCode barcode adapters, library purification using magnetic beads, equalization of library concentrations, and mixing in a single tube

treatment_protocol: Both iMSCs and tMSCs were cultured on fibronectin (Millipore, Bedford, CA, USA)-coated six-well plates in PRIME-XV MSC Expansion XSFM medium (FUJIFILM Irvine Scientific, Tokyo, Japan). The cells were passaged every 3 days or when they reached 80% confluence. At each passage, iMSCs were assessed by Trypan Blue in triplicate; only cultures with ≥90% viability proceeded to downstream assays, and all lineages met this criterion.

tag: tissue

value: Neural crest

tag: cell line

tag: cell type

value: Multipotent progenitor


title: SKBR3-DMSO-12d

type: RNA

description: SKBR3 cells treated with DMSO for 12 days

value: DMSO

value: 12 days


title: Fed 3, 0hr,  ATAC-seq

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

country: USA

institute: University of Pittsburgh

description: 10x Genomics

library_source: genomic

data_processing:
The raw sequence reads were mapped to mm10 after trimming and aligned using default parameters in bowtie2(v2.4.5)
were called using MACS2 and quantified using R package Diffbind
Assembly: mm10
Supplementary files format and content: Tab-separated bed files

molecule: genomic DNA

organism: Mus musculus

source_name: CD8 T cells

growth_protocol: Mice were fasted or ad libitum for 12hr and next day sacrificed, spleen and peripheral lymph nodes harvested. CD8 purified from mix of lymph nodes and spleen single cell suspension; for ex vivo, cells were processed for ATAC-seq sample preparation using H3K27Ac antibody following kit manual (Active motif). For 24hr group, cells were given TCR stimulation for 24hr in the presence of mIL2 (50 IU/mL). Post stimulation cells were collected and processed for ATAC-seq sample preparation using H3K27Ac antibody followiing kit manual (Active motif).

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8 T cells

tag: treatment

value: Primary CD8 T cells from spleen of fed mice (ad libitum)

tag: strain

tag: age

value: 6-8 weeks old


title: SKBR3-SGC-12d

description: SKBR3 cells treated with SGC0942 for 12 days


title: Fed 2, 0hr,  ATAC-seq

description: 10x Genomics


title: WT_R1

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: 6

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter using the auto detection mode.
Then reads were mapped to the mouse Ensembl GRCh38 transcriptome index using salmon (v.1.5.0).
Gene-level normalization and differential gene expression analysis were performed with Bioconductor (Gentleman et al., 2004; Huber et al., 2015) package DESeq2 v.1.28 (Love et al., 2014) using the R environment v.4.0 (R Core Team, 2015).
The Wald test was used for significance testing and the resulting false discovery rate (FDR) p-values were adjusted for multiple comparisons using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) and genes were considered differentially expressed (DEGs) only at FDR < 0.05
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit Qiagen (Cat. 74134) from at least 4x10^6 PBMCs
RNA-Seq library for mRNA sequencing was prepared with Truseq Stranded mRNA Prep Kit. All extracted RNA samples were quality controlled for integrity with a 2100 Bioanalyzer system (Agilent Technologies) and libraries were sequenced on a NovaSeq 6000 System (Illumina)

value: peripheral blood mononuclear cells

tag: Sex

value: F

tag: genotype

value: Ctrl


title: Somite, 2

description: Library name: Sample 16

source_name: Paraxial mesoderm

value: Paraxial mesoderm

value: Mesoderm


title: SKBR3-SGC-9d

description: SKBR3 cells treated with SGC0942 for 9 days


title: Expand trunk neural crest cells, 2

description: Library name: Sample 12


title: SKBR3-EPZ-6d

description: SKBR3 cells treated with EPZ-5676 for 6 days

value: 6 days


title: SKBR3-DMSO-6d

description: SKBR3 cells treated with DMSO for 6 days


title: WT_R3

description: Library name: 9

value: M


title: Fasted 3, 0hr,  ATAC-seq

description: 10x Genomics

value: Primary CD8 T cells from spleen of fasted mice


title: mut_R4

description: Library name: 4

value: Angptl3 p.s17*/p.s17*


title: Expand trunk neural crest cells, 1

description: Library name: Sample 11


title: MCF7-EPZ-12d

description: MCF7 cells treated with EPZ-5676 for 12 days


title: Fasted 2, 0hr,  ATAC-seq

description: 10x Genomics


title: SKBR3-SGC-6d

description: SKBR3 cells treated with SGC0942 for 6 days


title: mut_R3

description: Library name: 3


title: mut_R2

description: Library name: 2


title: Trunk neural crest cells, 2

description: Library name: Sample 10


title: Trunk neural crest cells, 1

description: Library name: Sample 9


title: Fasted 1, 0hr,  ATAC-seq

description: 10x Genomics


title: Trunk neural crest-derived mesenchymal stem cells, 1

description: Library name: Sample 13


title: 24hr Fed 2

data_processing:
The raw sequence reads were mapped to mm10 and quantified using default parameters in kallisto(v 0.46.1)
Read count extraction and normalization were performed using Sleuh (v 0.30.1)
Assembly: mm10
Supplementary files format and content: comma-separated values file include counts and FPKM values for each Sample

source_name: Primary T cells expanded in vitro post TCR stimulation

growth_protocol: Mice were fasted or ad libitum for 12hr and next day sacrificed, spleen and peripheral lymph nodes harvested. CD8 purified from mix of lymph nodes and spleen single cell suspension; for ex vivo analysis,  cells were processed for RNA purification and sequencing and for activated samples, cells were given TCR stimulation in the presence of mIL2 (50 IU/mL). Cells were collected at given time points, RNA purified and subjected for sequencing.

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

value: T cells

value: WT

value: T cells from fed mice given TCR stimulation in the presence of mIL2 and collected at 24hr post stimulation

tag: time

value: 24 hrs


title: mut_R5

description: Library name: 5


title: Fed 1, 0hr,  ATAC-seq

description: 10x Genomics


title: RNAseq_BJ_R204W_exp3

city: Naples

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

department: Department of Biology

institute: University of Naples "Federico II"

data_processing:
Binary base call files were converted in FASTQ file through bcl2fastq1
Sequence reads were trimmed using BBDuk software
to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6).
Alignment was performed with STAR RNA-seq aligner on hg38 reference assembly  expression analysis was performed using edgeR5
The expression levels of genes were determined with htseq-count by using cellRanger pre-build genes annotations (Ensembl Assembly 93)
All genes having < 1 cpm in less than n_min samples and Perc MM reads > 20% simultaneously were filtered out
Assembly: hg38
Supplementary files format and content: rawCounts

molecule: polyA RNA

source_name: BJ

extract_protocol:
RNA was isolated from three independent experiments using the RNAeasy Mini Kit (Qiagen).
polyA RNA was sequenced at the 3’ end using Quant-Seq FWD 30 mRNA-Seq Kit

value: BJ

value: Human fibroblast

value: expressing R204W mutant and Klf4


title: mut_R1

description: Library name: 1


title: MCF7-SGC-12d

description: MCF7 cells treated with SGC0942 for 12 days

value: 12 days


title: Cranial neural crest-derived mesenchymal stem cells, 2

description: Library name: Sample 8

value: Neural crest

value: Multipotent progenitor


title: MCF7-EPZ-6d

description: MCF7 cells treated with EPZ-5676 for 6 days


title: Cranial neural crest-derived mesenchymal stem cells, 1

description: Library name: Sample 7


title: PDAC.|.018.|.PanCK+

first: Ugo

last: Chianese

address: via Luigi De Crecchio

department: Department of Precision Medicine

institute: Universita degli Studi della Campania Luigi Vanvitelli

description:
Library name: DSP-1006911270830-F-C07
PanCK+_marker_AOI

data_processing:
Subsequently, samples were processed and profiled on the GeoMx Digital Spatial Profiler (NanoString Technologies, Seattle, WA, USA) through the Technology Access Program, following the manufacturer’s instructions. RNA targets were analyzed via region-specific UV photocleavage and collection of the indexing oligos for downstream quantification. Cleaved indices were then quantified using NanoString nCounter Technology, generating digital quantification of RNA expression with spatial context. Quality control (QC) and data normalization were carried out following the standard workflow recommended by NanoString for GeoMx analysis. ROIs were filtered based on the following QC criteria: more than 1,000 reads per ROI, over 80% of reads successfully trimmed, stitched, and aligned, sequencing saturation greater than 50%, minimum negative control counts above 5, no-template control (NTC) counts below 3,000, more than 100 nuclei per ROI, and an ROI area larger than 1,000 μm².
Assembly: GRCh38/hg38
Supplementary files format and content: DCC files along with PKC file are provided
Library strategy: Spatial Transcriptomics

source_name: Pancreatic Ductal Adenocarcinoma

extract_protocol:
GeoMX RNA in situ hybridization (ISH) was used to localize mRNA within tissue samples
GeoMx RNA assay was performed for the multiplexed detection of mRNA targets in formalin-fixed paraffin-embedded (FFPE) tissues. Briefly, 5 μm FFPE sections were dewaxed, digested with proteinase K, post-fixed, and incubated overnight with RNA detection probes linked to indexing oligo barcodes via a photocleavable linker. After washing, fluorescently labeled antibodies were added to serve as morphology markers. Regions of interest (ROIs) were then defined: PanCK+ staining was used to segment ductal cells, PanCK− for acinar cells, and Ins+ and Gcg+ for β- and α-cells, respectively. ROIs were manually drawn around specific structures in each stained tissue core.

value: Pancreatic Ductal Adenocarcinoma


title: RNAseq_BJ_R204W_exp2


title: MCF7-DMSO-6d

description: MCF7 cells treated with DMSO for 6 days

value: DMSO


title: RNAseq_BJ_R204W_exp1


title: Expand cranial neural crest cells, 2

description: Library name: Sample 6


title: PDAC.|.017.|.PanCK-

description:
Library name: DSP-1006911270830-F-C06
PanCK-_marker_AOI


title: MCF7-DMSO-12d

description: MCF7 cells treated with DMSO for 12 days


title: MCF7-SGC-6d

description: MCF7 cells treated with SGC0942 for 6 days


title: PDAC.|.017.|.PanCK+

description:
Library name: DSP-1006911270830-F-C05
PanCK+_marker_AOI


title: Expand cranial neural crest cells, 1

description: Library name: Sample 5


title: SKBR3-EPZ-12d

description: SKBR3 cells treated with EPZ-5676 for 12 days


title: 18hr Fed 1

value: Primary T cells expanded in vitro post TCR stimulation

value: T cells from fed mice given TCR stimulation in the presence of mIL2 and collected at 18hr post stimulation

value: 18 hrs


title: RNAseq_BJ_R304W_exp2

value: expressing R304W mutant and Klf4


title: PDAC.|.016.|.PanCK-

description:
Library name: DSP-1006911270830-F-C04
PanCK-_marker_AOI


title: RNAseq_BJ_R304W_exp1


title: Cranial neural crest cells, 2

description: Library name: Sample 4


title: Cranial neural crest cells, 1

description: Library name: Sample 3


title: 24hr Fasted 1

value: T cells from fasted mice given TCR stimulation in the presence of mIL2 and collected at 24hr post stimulation


title: 24hr Fasted 2

value: T cells


title: iPS cells, 2

description: Library name: Sample 2

source_name: Connective tissue (skin)

value: Connective tissue (skin)

value: induced pluripotent stem cells


title: 24hr Fed 1

value: WT

value: T cells from fed mice given TCR stimulation in the presence of mIL2 and collected at 24hr post stimulation

value: 24 hrs


title: PDAC.|.016.|.Glucagon

description:
Library name: DSP-1006911270830-F-C03
Glucagon_marker_AOI


title: 18hr Fasted 1

value: T cells from fasted mice given TCR stimulation in the presence of mIL2 and collected at 18hr post stimulation


title: PDAC.|.015.|.PanCK+

description:
Library name: DSP-1006911270830-F-C02
PanCK+_marker_AOI


title: RNAseq_BJ_R298Q_exp3

value: BJ

value: Human fibroblast

value: expressing R298Q mutant and Klf4


title: RNAseq_BJ_R304W_exp3


title: 18hr Fed 2


title: 18hr Fasted 2


title: RNAseq_BJ_R298Q_exp1


title: iPS cells, 1

description: Library name: Sample 1


title: RNAseq_BJ_R298Q_exp2


title: PDAC.|.014.|.Insulin

description:
Library name: DSP-1006911270830-F-B12
Insulin_marker_AOI

value: Pancreatic Ductal Adenocarcinoma


title: RNAseq_BJ_R227Q_exp3

value: expressing R227Q mutant and Klf4


title: DSS treated WT mice-3

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

country: China

institute: West China Hospital of Sichuan University

description: Library name: WT-3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm39
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: csv fles include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was harvested using Trizol from colon tissues
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: colon

value: 2.5%DSS treated 7 days


title: SKBR3-DMSO-9d

description: SKBR3 cells treated with DMSO for 9 days

value: DMSO

value: 9 days


title: Fed 1, 0hr

source_name: primary T cells

value: primary T cells

value: Control group (ad libitum)

value: 0 hr


title: RNAseq_BJ_R227Q_exp2


title: DSS treated WT mice-2

description: Library name: WT-2


title: Fasted 2, 0hr

value: T cells

value: mouse fasted overnight


title: PDAC.|.013.|.PanCK-

description:
Library name: DSP-1006911270830-F-B11
PanCK-_marker_AOI


title: PDAC.|.013.|.PanCK+

description:
Library name: DSP-1006911270830-F-B10
PanCK+_marker_AOI


title: RNAseq_BJ_R227Q_exp1


title: DSS treated WT mice-1

description: Library name: WT-1

value: WT


title: RNAseq_BJ_empty_exp3

value: expressing Klf4


title: Fasted 1, 0hr


title: DSS treated ADAMTS4 knockout mice-3

description: Library name: KO-3

value: KO


title: PDAC.|.012.|.PanCK+

description:
Library name: DSP-1006911270830-F-B09
PanCK+_marker_AOI


title: PDAC.|.014.|.Glucagon

description:
Library name: DSP-1006911270830-F-C01
Glucagon_marker_AOI


title: PDAC.|.011.|.PanCK-

description:
Library name: DSP-1006911270830-F-B08
PanCK-_marker_AOI


title: Ex vivo Fed 3


title: DSS treated ADAMTS4 knockout mice-2

description: Library name: KO-2


title: DSS treated ADAMTS4 knockout mice-1

description: Library name: KO-1


title: RNAseq_BJ_empty_exp2

value: BJ


title: PDAC.|.011.|.PanCK+

description:
Library name: DSP-1006911270830-F-B07
PanCK+_marker_AOI


title: PDAC.|.010.|.Glucagon

description:
Library name: DSP-1006911270830-F-B06
Glucagon_marker_AOI


title: Ex vivo Fed 1


title: RNAseq_BJ_empty_exp1

value: Human fibroblast


title: RNAseq_BJ_WT_exp3

value: expressing DNp63alpha and Klf5


title: EpA fato rep2

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

institute: Southern Medical University

description: Library name: sample11

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Hisat2 tools soft were used to map with reference genome. Quantification of gene expression was estimated by fragments per kilobase of transcript per million fragments (FPKM).
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: splenocytes

extract_protocol:
RNAex Pro RNA Reagent was used to obtain total RNA of Th9 cells
A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using TruseqTM RNA sample prep Kit (Illumina) following manufacturer’s recommendations.

value: splenocytes

value: T cell

value: EpA+fato


title: RNAseq_BJ_WT_exp2

value: expressing DNp63alpha and Klf4


title: PDAC.|.010.|.Insulin

description:
Library name: DSP-1006911270830-F-B05
Insulin_marker_AOI

value: Pancreatic Ductal Adenocarcinoma


title: Ex vivo Fed 2


title: Ex vivo Fast 3


title: EpA fato rep3

description: Library name: sample12


title: Ex vivo Fast 2


title: PDAC.|.009.|.PanCK+

description:
Library name: DSP-1006911270830-F-B04
PanCK+_marker_AOI


title: EpA fato rep1

description: Library name: sample10


title: RNAseq_BJ_WT_exp1


title: Ex vivo Fast 1


title: DMSO fato rep3

description: Library name: sample9

value: DMSO+fato


title: PDAC.|.008.|.PanCK-

description:
Library name: DSP-1006911270830-F-B03
PanCK-_marker_AOI


title: PDAC.|.008.|.PanCK+

description:
Library name: DSP-1006911270830-F-B02
PanCK+_marker_AOI


title: DMSO fato rep2

description: Library name: sample8


title: Fed 2, 0hr

value: primary T cells


title: MC38_RIG-I_1

city: Portland

first: sudarshan

last: anand

address: 2720 S Moody Ave

department: CDCB

institute: oregon health & science university

description:
MC38_RIG-I_1
RNA201216SA_M-R2_S2_R1_001

data_processing:
Sequencing done on either a HiSeq 2500 or a NovaSeq 6000
Base calling was done using RTA 1.18.66.3 (HiSeq) or RTA 2.11.3 (NovaSeq)
Protocols executed by RaNA-seq Software (Prieto and Barrios, 2019)
Aligment was done using Salmon. Mouse genome, Mus musculus (GRCm38) was used as reference.
Samples were quantified with Salmon algorithm (Patro et al. 2017) setting following parameters: single-end,
Differential Expression analysis was performed with DESeq2 (Love, Anders, and Huber 2014).
Assembly: default paramters
Supplementary files format and content: Data files in tsv format containing the counts

growth_protocol: CT26 cell line, derived from BALB/c colorectal carcinoma cells, was grown in RPMI+10% of Fetal Bovine Serum. CT26 cells were seeded to 100,000 cells/well in 6 well plates. E0771, a murine mammary cancer cell line that was originally isolated from a spontaneous tumour in C57BL/6, was grown in RPMI + 10% of Fetal Bovine Serum. E0771 cells were seeded to 100,000 cells/well in 6 well plates. MC38, derived from C57BL6 murine colon adenocarcinoma cells and grown in DMEM+10% of Fetal Bovine Serum, were seeded to 100,000 cells/well in 6 well plates.

extract_protocol:
Total RNA extraction using GeneMATRIX Universal RNA Purification Kit from Eurx
RNA-Seq library preparation - stranded with poly(A)+ selection - Illumina

treatment_protocol: 0.5ug/ml of RIG-I or control agonist for 24h

value: Cell Line derived from C57BL6 murine colon adenocarcinoma cells

value: RIG-I agonist


title: MC38_RIG-I_2

description:
MC38_RIG-I_2
RNA201216SA_M-R4_S8_R1_001


title: PDAC.|.007.|.Glucagon

description:
Library name: DSP-1006911270830-F-B01
Glucagon_marker_AOI


title: Leaf, boron deficiency, 25d, rep3

city: kunming

first: xiuyao

last: yang

state: yunnan

address: Southwest Forestry University, 300 Bailong Road, Qingyun Street, Panlong District, Kunming, Yunnan Province, China

institute: Southwest Forestry University

description: Boron deficiency stress in Citrus sinensis

data_processing:
Sequencing data were removed using Fastp to remove sequences with junctions at the 3' end and to remove Reads with average quality scores lower than Q20; the filtered Reads were compared to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml). Data quality was checked using FastaQC to ensure that all transcriptome data had a Q value greater than 30, resulting in high-quality Clean Data.Read Count values were statistically compared to each gene using HTSeq and normalised using FPKM values.
Assembly: Using the Citrus sinensis genome as a reference genome
Supplementary files format and content: fastq

organism: Citrus sinensis

source_name: leaf blade of a plant

growth_protocol: Citrus sinensis seedling

extract_protocol:
0.5g of each sample from the treatment and control were sent to Suzhou Panomic Biomedical Technology Co. for transcriptome sequencing.
Filtered Reads were compared to the reference genome using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ) software for TopHat2.
HISAT2 uses an improved BWT algorithm for library construction. Default parameters are used for non-strand-specific libraries, while strand-specific libraries require the library type to be specified (i.e., use --rna-strandness RF for first, --rna-strandness FR for second).

treatment_protocol: Sweet orange histocultured seedlings treated at 0.01 mg/L boron for 25 days

value: leaf blade of a plant

value: nucleus

value: cDNA

value: Boron content


title: Leaf, boron deficiency, 25d, rep1


title: DMSO fato rep1

description: Library name: sample7


title: Leaf, boron deficiency, 25d, rep2


title: PDAC.|.006.|.Full.ROI

description:
Library name: DSP-1006911270830-F-A11
FullROI_marker_AOI


title: EpA rep2

description: Library name: sample5

value: EpA


title: PDAC.|.007.|.Insulin

description:
Library name: DSP-1006911270830-F-A12
Insulin_marker_AOI


title: Leaf blades, Sufficient boron, 25d,  rep3

description: Sufficient boron content in sweet oranges


title: PDAC.|.005.|.PanCK-

description:
Library name: DSP-1006911270830-F-A10
PanCK-_marker_AOI


title: MC38_Control_1

description:
MC38_Control_1
RNA201216SA_M-C2_S1_R1_001

value: Control agonist


title: E0771-RIG-2

description:
E0771-RIG-2
RNA201216SA_E-R2_S6_R1_001

value: Murine mammary carcinoma from B6 mouse


title: Leaf blades, Sufficient boron, 25d,  rep2


title: EpA rep1

description: Library name: sample4


title: MC38_Control_2

description:
MC38_Control_2
RNA201216SA_M-C4_S7_R1_001


title: E0771-RIG-1

description:
E0771-RIG-1
RNA201216SA_E-R1_S5_R1_001


title: Leaf blades, Sufficient boron, 25d,  rep1


title: PDAC.|.005.|.PanCK+

description:
Library name: DSP-1006911270830-F-A09
PanCK+_marker_AOI


title: DMSO rep3

description: Library name: sample3

value: DMSO


title: PDAC.|.004.|.PanCK-

description:
Library name: DSP-1006911270830-F-A08
PanCK-_marker_AOI


title: E0771-CONTROL-2

description:
E0771-CONTROL-2
RNA201216SA_E-C2_S4_R1_001


title: DMSO rep2

description: Library name: sample2

value: splenocytes


title: E0771-CONTROL-1

description:
E0771-CONTROL-1
RNA201216SA_E-C1_S3_R1_001


title: EpA rep3

description: Library name: sample6

value: T cell


title: CD45+ cells, ADU-S100_Doxorubicin_3

city: Goyang

first: Wonyoung

last: Choi

state: Gyeonggi

address: 323 Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

description:
Library name: Sample 9
Column name in processed data file: ADU_doxorubicin_3_Read_Count

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9.
After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b
Gene-level and Transcript-level quantification were calculated as raw read count
Assembly: mm10
Supplementary files format and content: excel file (.xlsx) includes raw counts for each sample

source_name: immune cell (CD45+)

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared with Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).

value: immune cell (CD45+)

value: ADU-S100 + Doxorubicin


title: CT26_RIG-I_3

value: Murine colorectal carcinoma cell line from BALB/c mouse

value: BALB/c


title: PDAC.|.002.|.PanCK-

description:
Library name: DSP-1006911270830-F-A05
PanCK-_marker_AOI

value: Pancreatic Ductal Adenocarcinoma


title: DMSO rep1

description: Library name: sample1


title: PDAC.|.003.|.PanCK+

description:
Library name: DSP-1006911270830-F-A06
PanCK+_marker_AOI


title: PDAC.|.002.|.PanCK+

description:
Library name: DSP-1006911270830-F-A04
PanCK+_marker_AOI


title: CT26_RIG-I_2


title: CD45+ cells, ADU-S100_Doxorubicin_2

description:
Library name: Sample 8
Column name in processed data file: ADU_doxorubicin_2_Read_Count


title: CT26_RIG-I_1


title: CT26_Control_3


title: PDAC.|.001.|.Glucagon

description:
Library name: DSP-1006911270830-F-A03
Glucagon_marker_AOI


title: CD45+ cells, Doxorubicin_2

description:
Library name: Sample 5
Column name in processed data file: doxorubicin_2_Read_Count

value: Doxorubicin


title: CD45+ cells, ADU-S100_Doxorubicin_1

description:
Library name: Sample 7
Column name in processed data file: ADU_doxorubicin_1_Read_Count


title: CT26_Control_2


title: PDAC.|.001.|.Insulin

description:
Library name: DSP-1006911270830-F-A02
Insulin_marker_AOI


title: CT26_Control_1


title: PDAC.|.004.|.PanCK+

description:
Library name: DSP-1006911270830-F-A07
PanCK+_marker_AOI


title: CD45+ cells, Doxorubicin_1

description:
Library name: Sample 4
Column name in processed data file: doxorubicin_1_Read_Count


title: TALL-1 DMSO2

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description:
TALL-1_DMSO
Gene expression data from TALL-1 cell line, treated with DMSO for 12 hours, replicate 2.

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using RMA

label: biotin

source_name: TALL-1 cell line

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Cells were cultured in RPMI 1640  medium with 20% Fetal Bovine Serum, glutamine, penicillin  and streptomycin  at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was extracted after 12 hours of treatment with the RNeasy Mini Kit (QIAGEN).

treatment_protocol: Cells were treated with 1µM dex or an equivalent DMSO volume for 12 hours.

value: DMSO 12h

tag: sample


title: P12 DMSO3

description:
P12_DMSO
Gene expression data from P12-ICHIKAWA cell line, treated with DMSO for 12 hours, replicate 3.

source_name: P12-ICHIKAWA cell line


title: P12 Dex2

description:
P12_Dex
Gene expression data from P12-ICHIKAWA cell line, treated with 1µM dex for 12 hours, replicate 2.

value: Dex 1µM 12h


title: C2, C3, C4, C5

city: Seattle

first: Weiming

last: Li

state: WA

address: 4032 8th ave ne

department: Center for developmental biology and regenerative medicine

institute: Seattle children's research institute

description:
Library name: Pool4
10x genomics

library_source: transcriptomic single cell

data_processing:
Single cell RNA sequencing data processing and analysis started with raw data from PBMCs generated via the 10x flex kit. ‘cellranger-arc’ (version: 2.0.2) and ‘cellranger’ (version: 7.1.0) software were used to perform read alignment, low-quality read filtration, barcode counting, and UMI tallying, consistently applying default parameters.
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Blood

extract_protocol:
The PBMCs were isolated using the Stemcell EasySep™ Direct Human PBMC Isolation Kit. The isolated PBMCs were frozen in ice-cold cryopreservation solution – 50% FBS/40% growth media/10% DMSO
Fixed RNA Profiling 10x flex kit, scRNA

value: Blood

value: PBMCs

value: Shear and static


title: PBMCs,  Day 2, ATAC replicate 3

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

description: Library name: R3D2

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters --f BAMPE --verbose 3 --shift 0 -g hs -q 0.01 -B Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p14
Supplementary files format and content: ATAC-seq_Consensus.csv - Matrix of raw values corresponding to each specific peak summit (rows) across all samples (columns) generated by DiffBind,

source_name: peripheral blood

extract_protocol:
ATAC-seq: nuclei were isolated from 100,000 PBMCs by incubation in 50 µl lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL CA-630; 0.01% digitonin). After 3 minutes on ice, 1 ml wash buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added. Nuclei were pelleted and subjected to transposition using a Tn5 transposase reaction mix (Illumina), supplemented with 0.01% digitonin and 0.1% Tween-20. The transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer. Transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research), followed by PCR amplification, purification, and size selection with SPRISelect beads (Beckman Coulter). Library quality was assessed using an Agilent TapeStation. Indexed libraries were quantified, pooled, and prepared for sequencing.
ATAC-seq  libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Peripheral blood samples were obtained from a single healthy male participant (age 59) enrolled in the VitDHiD trial (ClinicalTrials.gov Identifier: NCT03537027). The study was approved by the Ethics Committee of the Northern Savo Hospital District (Approval No. 515/2018).

value: peripheral blood

value: PBMC

value: monocytes, T and B cells

value: Vitamin D3 bolus (80.000 IU) at day 2


title: TALL-1 DMSO3

description:
TALL-1_DMSO
Gene expression data from TALL-1 cell line, treated with DMSO for 12 hours, replicate 3.


title: P12 DMSO1

description:
P12_DMSO
Gene expression data from P12-ICHIKAWA cell line, treated with DMSO for 12 hours, replicate 1.


title: PBMCs,  Day 1, ATAC replicate 3

description: Library name: R3D1

value: Vitamin D3 bolus (80.000 IU) at day 1


title: B3, B4, B5, C1

description:
Library name: Pool3
10x genomics


title: Template_Control

description:
Library name: DSP-1006911270830-F-A01
Template_Control


title: CD45+ cells, Control_1

description:
Library name: Sample 1
Column name in processed data file: control_1_Read_Count

value: Control


title: A4, A5, B1, B2

description:
Library name: Pool2
10x genomics


title: CD45+ cells, Doxorubicin_3

description:
Library name: Sample 6
Column name in processed data file: doxorubicin_3_Read_Count

value: immune cell (CD45+)


title: TALL-1 DMSO1

description:
TALL-1_DMSO
Gene expression data from TALL-1 cell line, treated with DMSO for 12 hours, replicate 1.


title: A1a, A1b, A2, A3

description:
Library name: Pool1
10x genomics


title: PBMCs,  Day 2, ATAC replicate 2

description: Library name: R2D2


title: P12 DMSO2

description:
P12_DMSO
Gene expression data from P12-ICHIKAWA cell line, treated with DMSO for 12 hours, replicate 2.


title: CD45+ cells, Control_3

description:
Library name: Sample 3
Column name in processed data file: control_3_Read_Count


title: PBMCs,  Day 1, ATAC replicate 2

description: Library name: R2D1


title: Daoy cell, shFABP4, rep2

city: 合肥市

first: 林贵

last: 顾

state: 安徽省

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

institute: 安徽医科大学

description: Library name: Fkd2

data_processing:
The quality of fastq data was controlled by Fastqc and analyzed using the RNA-seq pipeline described as "Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016, 11(9):1650-1667."
Assembly: GRch38
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes RPKM values for each sample

source_name: Daoy

extract_protocol:
RNA was prepared using TRIzol (Ambion, #400008) .5 μg of total RNA was used for the construction of sequencing libraries
mRNA were enriched using VAHTS® mRNA Capture Beads (Vazyme #N401), and fragmentation was made using Tn5 (Transgen, Cat# KP101-11).

treatment_protocol: DaoY cells were infected with lentivirus of shFABP4 or Ctrl.

value: Daoy

value: tumor cell

value: FABP4 knockdown

value: infected with shFABP4 virus


title: PBMCs, Day 0, ATAC replicate 3

description: Library name: R3D0

value: Vitamin D3 bolus (80.000 IU) at day 0


title: TALL-1 Dex3

description:
TALL-1_Dex
Gene expression data from TALL-1 cell line, treated with 1µM dex for 12 hours, replicate 3.


title: CD45+ cells, Control_2

description:
Library name: Sample 2
Column name in processed data file: control_2_Read_Count


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT dPA14_63940 3

city: Braunschweig

first: Nicolas

middle: Oswaldo

last: GOMEZ

state: Lower Saxony

address: Inhoffenstraße 7

country: Germany

institute: Helmholtz Center for Infection Research

description: Library name: nog20_RNASeq_PA14cntL_MCM_3

data_processing:
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
Assembly: NC_008463.1
Supplementary files format and content: bed files - reads per gene (featureCounts)

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: bacteria

growth_protocol: planctonic growth in MCM medium at 37°C, 180 RPM, PET flasks, 10h

extract_protocol:
RNeasy Plus kit (Qiagen) in combination with QIAshredder columns (Qiagen) was used according to the manufacturer’s manual. Modifications:  Cell lysis was performed with 8 mg/mL lysozyme in Tris-EDTA-buffer (pH 8.0). RLT buffer with mecaptoethanol was added. Samples were frozen at -70°C for 60 min and then processed with QIAshredder columns. The remaining steps were performed according to the manufacturer's manual. After RNA elution, samples were treated with DNase (DNA-free Kit DNase Treatment & Removal, Ambion).
RNA was fragmented (150–350 bp) by FastAP buffer (Thermo). End repair was performed with DNase (Thermo) and FastAP. Barcodes were ligated to each sample by T4 RNA ligase 1 (NEB). Samples were purified with the RNA Clean & Concentrator-25 Kit (Zymo). Depletion was performed according to Engelhardt., et al  (2020). cDNA libraries were generated using SMARTscribe reverse transcriptase (Clonetech). Enrichment was done by AccuPrime HiFi Taq (Thermo) and all purification steps using RNAClean XP beads (Agencourt). Libraries were sequenced in paired-end mode on an Illumina Novaseq 6000 device (2 x 50 bp)

value: bacteria

value: dcntL

value: total RNA

tag: batch


title: TALL-1 Dex2

description:
TALL-1_Dex
Gene expression data from TALL-1 cell line, treated with 1µM dex for 12 hours, replicate 2.

value: Dex 1µM 12h


title: TALL-1 Dex1

description:
TALL-1_Dex
Gene expression data from TALL-1 cell line, treated with 1µM dex for 12 hours, replicate 1.


title: P12 Dex3

description:
P12_Dex
Gene expression data from P12-ICHIKAWA cell line, treated with 1µM dex for 12 hours, replicate 3.


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT dPA14_63940 2

description: Library name: nog20_RNASeq_PA14cntL_MCM_2


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT dPA14_63940 1

description: Library name: nog20_RNASeq_PA14cntL_MCM_1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 3

description: Library name: nog20_RNASeq_PA14WT_MCM_3

value: WT


title: PBMCs, Day 0, ATAC replicate 2

description: Library name: R2D0

value: peripheral blood


title: Daoy cell, PLKO, rep2

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

description: Library name: Fwt2

value: infected with PLKO virus


title: RPMI-8402 sh143 Dex4

description:
shNFATC2_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 4, treated  with 10µM  Dex for 12 hours.

source_name: RPMI-8402 cell line

growth_protocol: Cells were cultured in RPMI 1640 medium with 20% Fetal Bovine Serum , glutamine, penicillin  and streptomycin, with 1µg/µL puromycin, at 37°C in a humidified atmosphere with 5% CO2.

treatment_protocol: Cells were exposed to lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette (named, Sh143) or a control ShRNA sequence (ShRNA CNTR). Transduced cells were then treated  with 10µM dex or an equivalent DMSO volume for 12 hours.

value: shNFATC2 + Dex 10µM 12h


title: PBMCs,  Day 2, ATAC replicate 1

description: Library name: R1D2

value: PBMC

value: monocytes, T and B cells

value: Vitamin D3 bolus (80.000 IU) at day 2


title: Daoy cell, PLKO, rep1

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

description: Library name: Fwt1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 2

description: Library name: nog20_RNASeq_PA14WT_MCM_2


title: PBMCs,  Day 1, ATAC replicate 1

description: Library name: R1D1

value: Vitamin D3 bolus (80.000 IU) at day 1


title: PBMCs, Day 0, ATAC replicate 1

description: Library name: R1D0


title: PBMCs, Day 2, RNA replicate 3

description: Library name: R3D2

data_processing:
RNA-seq: Single-end reads were aligned using STAR aligner. Read quantification performed with FeatureCounts (version 2.0.6) with settings for reverse-strand.
Assembly: GRCh38.p14
Supplementary files format and content: Gene_count_matrix.csv - raw gene counts matrix with counts of protein coding genes , without mitochondrially encoded genes and genes missing HGNC symbols

extract_protocol:
RNA was extracted from PBMCs using the High Pure RNA Isolation Kit (Roche), following the manufacturer's instructions. RNA quality was evaluated on an Agilent TapeStation. Ribosomal RNA was depleted using kits from New England Biolabs, and libraries were prepared according to the manufacturer’s protocols.
RNA-seq libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).


title: PBMCs, Day 1, RNA replicate 3

description: Library name: R3D1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 1

description: Library name: nog20_RNASeq_PA14WT_MCM_1


title: BM, experiment, postbiotic,2

city: Puebla

first: Elizabeth

last: Bautista-Rodriguez

state: Puebla

address: 11 poniente 2316

department: Ingenieria en Biotecnología

country: Mexico

institute: Universidad Popular Autonoma del Estado de Puebla

description:
Sample BM_3
Biological replicate 2 of 2. Control colorectal cancer cells SW480 treated with Bacillus mojavensis postbiotic, grown in MRS, harvested 10 hours after treatment.
Hcan_06_04.xlsx

hyb_protocol: nor provided by submitter

scan_protocol: ScanArray 4000 system  (Packard BioChips, Billerica, MA, USA)

data_processing:
Microarray fluorescence data were normalized using the Z-score transformation method. Pathway and enrichment analyses were carried out in R software (v4.2.2) using RStudio, with the Bioconductor package clusterProfiler v4.9. Visualization and pathway mapping were performed using Pathview and Heatmapper. Additional functional enrichment of the top up- and down-regulated genes was performed using g:Profiler
Genes with a z-ratio > ±1.5 were considered significantly differentially expressed.

label: Alexa fluor 647

source_name: Sw480 cell line, 15%, BM postbiotic treated

label_protocol: 5 μg of total RNA were reverse-transcribed into cDNA and labeled with Alexa Fluor 555 and Alexa Fluor 647 dyes

growth_protocol: SW480 were grown in DMEM F12 media supplemented with 10% of fetal bovine serum. Bacillus mojavensis was grown in MRS media

extract_protocol: cells were washed with PBS and total RNA was obtained using Trizol following manufacturer's instructions

treatment_protocol: SW480 were treated with MRS 15% (V/V) as control or with B. mojavensis postbiotic 15% during 10 hours

value: adenocarcinoma of the colon

value: 15% MRS media


title: ES2_EC_Olap_5

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Assembly: GRCh38
Supplementary files format and content: Text file for FPKM values of each gene

source_name: Ovarian cancer cells

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: OVC

value: Human ovarian cancer cell line

value: elesclomol+olaparib


title: PBMCs, Day 0, RNA replicate 3

description: Library name: R3D0

value: Vitamin D3 bolus (80.000 IU) at day 0


title: RPMI-8402 sh143 Dex2

description:
shNFATC2_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 2, treated  with 10µM  Dex for 12 hours.


title: ChIP_Mock_3

city: Boston

first: Renato

last: Santos

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: ChIP_Mock_3

data_processing:
For ChIP: Sequencing reads were aligned to the Vibrio cholerae reference genome (NC_002505.1 and NC_002506.1) using Bowtie2 v2.4.1. Fragments ≤ 400 bp were retained. Peaks were called with QuEST v2.4.24 using an untagged V5 mock strain as background, with a >2-fold enrichment threshold. For RNA-seq: Reads were demultiplexed using barcode sequences with up to one allowed mismatch that did not cause barcode reassignment. Terminal G residues from template switching and adapter sequences were removed before alignment.
Assembly: Vibrio cholerae N16961 reference genome from NCBI RefSeq: NC_002505.1 and NC_002506.1.
Supplementary files format and content: Processed files consist of BED peak-calling output (MACS/QuEST-style enriched regions) for each ChIP-seq sample. Processed data consist of a gene-level count matrix (all_counts.tsv) containing raw read counts for all annotated V. cholerae transcripts.

organism: Vibrio cholerae

source_name: Vibrio cholerae C6706

extract_protocol:
ChIP DNA libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7645S) following the manufacturer’s instructions. Libraries were amplified for 10 PCR cycles without size selection and sequenced at the Harvard Biopolymers Facility on an Illumina NovaSeq 6000. Total RNA was extracted from 5 mL exponential-phase cultures using the Direct-zol RNA MiniPrep Plus kit (Zymo Research #R2072), including on-column DNase digestion to remove genomic DNA.
ChIP DNA libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7645S) following the manufacturer’s instructions. Libraries were amplified for 10 PCR cycles without size selection and sequenced at the Harvard Biopolymers Facility on an Illumina NovaSeq 6000 (paired-end). Illumina cDNA libraries were prepared using a modified RNAtag-Seq protocol (Shishkin et al., 2015). Briefly, 500 ng–1 µg total RNA was fragmented, DNA-depleted, dephosphorylated, and ligated to barcoded 5′-AN₈-3′ adapters. Barcoded RNAs were pooled and rRNA-depleted with the RiboZero rRNA Removal Kit (Epicentre). cDNA synthesis used a template-switching primer (SMARTScribe RT, Clontech), followed by PCR amplification with Illumina P5/P7 primers. Libraries were sequenced on an Illumina NextSeq 500 (paired-end 75 bp).

value: Vibrio cholerae C6706


title: Daoy cell, shFABP4, rep1

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

description: Library name: Fkd1

value: Daoy

value: tumor cell

value: FABP4 knockdown

value: infected with shFABP4 virus


title: BM, experiment, postbiotic,1

description:
Sample BM_2
Biological replicate 1 of 2. Control colorectal cancer cells SW480 treated with Bacillus mojavensis postbiotic, grown in MRS, harvested 10 hours after treatment.
Hcan_06_02.xlsx


title: MRS, control, 2

description:
Sample MRS_3
Biological replicate 2 of 2. Control colorectal cancer cells SW480 treated with MRS, control, harvested 10 hours after treatment.
Hcan_06_04.xlsx

label: Alexa fluor 555

source_name: Sw480 cell line, 15%, MRS treated


title: PBMCs, Day 2, RNA replicate 2

description: Library name: R2D2

value: peripheral blood


title: ES2_EC_Olap_3


title: PBMCs, Day 1, RNA replicate 2

description: Library name: R2D1


title: ES2_EC_Olap_2


title: ChIP_Mock_2

description: Library name: ChIP_Mock_2


title: ES2_EC_Olap_4


title: RPMI-8402 sh143 Dex3

description:
shNFATC2_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 3, treated  with 10µM  Dex for 12 hours.

value: shNFATC2 + Dex 10µM 12h


title: RPMI-8402 shCNTR Dex4

description:
shCNTR_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 4, treated  with 10µM  Dex for 12 hours.

value: shCNTR + Dex 10µM 12h


title: MRS, control, 1

description:
Sample MRS_2
Biological replicate 1 of 2. Control colorectal cancer cells SW480 treated with MRS, control, harvested 10 hours after treatment.
Hcan_06_02.xlsx


title: PBMCs, Day 0, RNA replicate 2

description: Library name: R2D0

value: PBMC

value: monocytes, T and B cells


title: RPMI-8402 shCNTR Dex3

description:
shCNTR_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 3, treated  with 10µM  Dex for 12 hours.


title: ES2_EC_Olap_6


title: RPMI-8402 sh143 Dex1

description:
shNFATC2_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 1, treated  with 10µM  Dex for 12 hours.


title: ES2_EC_Olap_1


title: ChIP_4xR_3

description: Library name: ChIP_4xR_3


title: RPMI-8402 sh143 DMSO4

description:
shNFATC2_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 4, treated with DMSO for 12 hours.

value: shNFATC2 + DMSO 12h


title: ES2_Olap_6

value: olaparib


title: RPMI-8402 shCNTR Dex2

description:
shCNTR_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 2, treated  with 10µM  Dex for 12 hours.


title: RPMI-8402 shCNTR Dex1

description:
shCNTR_Dex
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 1, treated  with 10µM  Dex for 12 hours.


title: RPMI-8402 sh143 DMSO2

description:
shNFATC2_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 2, treated with DMSO for 12 hours.


title: RPMI-8402 sh143 DMSO1

description:
shNFATC2_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 1, treated with DMSO for 12 hours.


title: PBMCs, Day 1, RNA replicate 1

description: Library name: R1D1

value: Vitamin D3 bolus (80.000 IU) at day 1


title: ChIP_4xR_1

description: Library name: ChIP_4xR_1


title: ES2_Olap_5

value: OVC


title: PBMCs, Day 0, RNA replicate 1

description: Library name: R1D0


title: ChIP_Mock_1

description: Library name: ChIP_Mock_1


title: ChIP_4xR_2

description: Library name: ChIP_4xR_2


title: ES2_Olap_4

value: Human ovarian cancer cell line


title: ChIP_4xQ_3

description: Library name: ChIP_4xQ_3


title: P12 Dex1

description:
P12_Dex
Gene expression data from P12-ICHIKAWA cell line, treated with 1µM dex for 12 hours, replicate 1.

value: Dex 1µM 12h


title: RPMI-8402 sh143 DMSO3

description:
shNFATC2_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette, replicate 3, treated with DMSO for 12 hours.


title: ES2_Olap_3


title: RPMI-8402 shCNTR DMSO4

description:
shCNTR_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 4, treated with DMSO for 12 hours.

value: shCNTR + DMSO 12h


title: ES2_Olap_2


title: ChIPseq_BJ_R304W_exp1

description: narrow_Peaks_ChIPseq_BJ_expressing R304W.bed

data_processing:
ChIP-seq fastq files were mapped to the Homo sapiens genome (hg38 build) using Bowtie2 v2.3.4.3. MACS2 peak-calling was used to call peaks from two replicates
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: BJ

extract_protocol:
Cells were cross-linked with 1% formaldehyde in PBS, lysed in SDS lysis Buffer for 10 min in ice, and sonicated using a Bandelin Sonopuls device. The immunoprecipitated DNA was purified using MinElute PCR purification kit (#28004, Qiagen)
library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504)
The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols

value: expressing R304W mutant and Klf4

value: BJ

value: Human fibroblast

tag: chip antibody


title: ChIPseq_BJ_R304W_exp2


title: PBMCs, Day 2, RNA replicate 1

description: Library name: R1D2

value: Vitamin D3 bolus (80.000 IU) at day 2


title: ChIP_4xQ_2

description: Library name: ChIP_4xQ_2

value: Vibrio cholerae C6706


title: ChIPseq_BJ_R298Q_exp1

description: narrow_Peaks_ChIPseq_BJ_expressing R298Q.bed

value: expressing R298Q mutant and Klf4


title: ChIPseq_BJ_R298Q_exp2


title: RPMI-8402 shCNTR DMSO3

description:
shCNTR_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 3, treated with DMSO for 12 hours.


title: ChIP_4xQ_1

description: Library name: ChIP_4xQ_1


title: ES2_Olap_1


title: ChIP_CRPWT_3

description: Library name: ChIP_CRPWT_3


title: ES2_EC_6

value: elesclomol


title: RPMI-8402 shCNTR DMSO1

description:
shCNTR_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 1, treated with DMSO for 12 hours.


title: TALL-1 shCNTR Dex4

description:
shCNTR _ Dex
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 4, treated with 1µM Dex for 12 hours.

growth_protocol: Cells were cultured in  RPMI 1640 medium with 20% Fetal Bovine Serum, glutamine, penicillin  and streptomycin, with 1µg/µL puromycin, at 37°C in a humidified atmosphere with 5% CO2.

treatment_protocol: Cells were exposed to lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc1  expression cassette (named, Sh335) or a control ShRNA sequence (ShRNA CNTR). Transduced cells were then treated with 1µM dex or an equivalent DMSO volume for 12 hours.

value: shCNTR + Dex µM 12h


title: ChIP_CRPWT_2

description: Library name: ChIP_CRPWT_2


title: ChIPseq_BJ_R227Q_exp2

description: narrow_Peaks_ChIPseq_BJ_expressing R227Q.bed

value: expressing R227Q mutant and Klf4


title: ChIP_CRPWT_1

description: Library name: ChIP_CRPWT_1


title: TALL-1 shCNTR DMSO4

description:
shCNTR _ DMSO
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 4, treated with DMSO for 12 hours.


title: ChIPseq_BJ_R227Q_exp1


title: ChIPseq_BJ_input

description: Control sample used during MACS2 peak-calling

value: expressing Klf4


title: ES2_EC_4


title: VcC6706-wt-replicate3

description: Library name: wt_r3


title: ES2_EC_3


title: VcC6706-wt-replicate2

description: Library name: wt_r2


title: RPMI-8402 shCNTR DMSO2

description:
shCNTR_DMSO
Gene expression data from RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 2, treated with DMSO for 12 hours.


title: ChIPseq_BJ_empty_exp2


title: VcC6706-wt-replicate1

description: Library name: wt_r1


title: ES2_EC_2


title: ChIPseq_BJ_empty_exp1


title: TALL-1 shCNTR DMSO3

description:
shCNTR _ DMSO
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 3, treated with DMSO for 12 hours.


title: VcC6706-k52q-replicate3

description: Library name: K52Q_r3


title: TALL-1 shCNTR Dex2

description:
shCNTR _ Dex
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 2, treated with 1µM Dex for 12 hours.


title: ChIPseq_BJ_DNp63alpha_exp2

description: narrow_Peaks_ChIPseq_BJ_expressing DNp63alpha.bed

value: expressing DNp63alpha and Klf4


title: TALL-1 shCNTR Dex3

description:
shCNTR _ Dex
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 3, treated with 1µM Dex for 12 hours.


title: ES2_6

value: control


title: ES2_EC_5


title: VcC6706-k52q-replicate2

description: Library name: K52Q_r2


title: ChIPseq_BJ_DNp63alpha_exp1


title: ES2_5


title: TALL-1 shCNTR DMSO2

description:
shCNTR _ DMSO
Gene expression data from TALL-1 cell line transducedwith a second generation lentiviral plasmids containing  a control ShRNA sequence (ShRNA CNTR), replicate 2, treated with DMSO for 12 hours.


title: ATACseq_BJ_empty_exp2

data_processing:
ATAC-seq fastq files were mapped to the Homo sapiens genome (hg38 build) using Bowtie2 v2.3.4.3. MACS2 peak-calling was used to call peaks from two replicates
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
DNA purification was performed using AMPure XP for PCR Purification (Beckman Coulter Life Sciences, #A63880)
library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504)
The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols

value: TDE (Tagment DNA Enzyme)


title: VcC6706-k52q-replicate1

description: Library name: K52Q_r1


title: TALL-1 sh335 DMSO4

description:
shNFATc1_DMSO
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 4, treated with DMSO for 12 hours.

value: shNFATc1 + DMSO 12h


title: TALL-1 sh335 Dex4

description:
shNFATc1_Dex
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 4, treated with 1µM  Dex for 12 hours.

value: shNFATc1 + Dex 1µM 12h


title: ES2_4

value: OVC

value: Human ovarian cancer cell line


title: ATACseq_BJ_empty_exp1


title: VcC6706-crp-v5-replicate3

description: Library name: crp_chr_r3


title: ES2_3


title: TALL-1 sh335 DMSO3

description:
shNFATc1_DMSO
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 3, treated with DMSO for 12 hours.


title: VcC6706-crp-v5-replicate2

description: Library name: crp_chr_r2


title: ES2_2


title: TALL-1 sh335 Dex3

description:
shNFATc1_Dex
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc1 expression cassette, replicate 3, treated with 1µM Dex for 12 hours.


title: ATACseq_BJ_DNp63alpha_exp1

description: narrow_Peaks_ATACseq_BJ_expressing DNp63alpha.bed


title: VcC6706-crp-v5-replicate1

description: Library name: crp_chr_r1


title: ATACseq_BJ_DNp63alpha_exp2


title: ES2_1


title: ES2_EC_1


title: TALL-1 sh335 DMSO2

description:
shNFATc1_DMSO
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 2, treated with DMSO for 12 hours.


title: Pa14C

status: Public on Nov 27 2025

city: Cincinnati

first: Andrew

last: Waters

state: Ohio

address: Vontz Center for Molecular Studies, Rm 1234, 3125 Eden Ave

institute: University of Cincinnati

description: Library name: Sample 9

data_processing:
Completed libraries were sequenced on an Illumina NovaSeq 6000, generating  high quality 100 base long paired end reads.
Quality control check on the FASTQ files was performed using FastQC.
Reads were trimmed to remove adapters and low quality reads using default parameters in Trimmomatic Version 0.33.
Trimmed reads were mapped to a reference genome using default parameters with RF strandness option in Hisat2 Version 2.0.5.
Transcript abundance was determined using Kalliso Version 0.43.1, creating a transcriptome index using Ensemble cDNA sequences for the reference genome. This index was used to quantify transcript abundance in raw counts and TPM.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file with transcripts per million for each gene

source_name: pancreas

growth_protocol: Cells were maintained in DMEM or RPMI supplemented with 10% FBS and cultured at 37C with 5% CO2.

extract_protocol:
RNA was purified using the Rneasy mini plus kit (Qiagen) and 150-300 ng of total RNA was used for the construction of the library.
RNA was poly-A-selected and reverse-transcribed using Illumina's TruSeq standard mRNA library preparation kit according to the manufacturers instructions.

value: pancreas

value: PDAC

value: KRAS G12D


title: PANC-1

description: Library name: Sample 11

source_name: pancreas duct

value: pancreas duct


title: DSID65 Whole maternal blood after delivery

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

description: Library name: DSID65_WBafter

data_processing:
Sequenced reads were mapped to the SILVA 132 database using QIIME2-2017.2. An operational taxonomic units (OTU) table was generated which contained the OTUs identified in each sample along with the number of sequence reads and the taxonomic classification of each OTU. The classification was further collapsed at either genera, family, order or phylum level for subsequent analyses using the MicrobialAnalyst web-based platform. Because blood samples were expected to have low number of reads, we thought it more important to be inclusive of low abundance taxa even if these could represent sequencing errors, therefore the default R code was modified to exclude the abundance filters. The Chao-1 index (measure of α-diversity) was used to estimate OTU richness in different types of samples. Enrichment of taxa between groups was further analyzed by LEfSe (linear discriminant analysis effect size) and EdgeR methods built within the platform. These computational algorithms designed primarily for highly multidimensional data, employ a combination of statistical tests to extract features (e.g. OTU) that show significant differences in abundance (enrichment) in different samples while accounting for the effect size of the differences.
Assembly: SILVA_132 reference database
Supplementary files format and content: OTU counts for each sample (tab delimited) and corresponding OTU table

organism: human blood metagenome

source_name: whole blood

extract_protocol:
All specimens were collected using sterile gloves, and all procedures were carried out under strict sterile conditions. For sequencing of 16S RNA genes and microbial community analysis, genomic DNA was extracted and the 16S rRNA amplified using V4 primers. 16S amplicon multiplex libraries were sequenced on Illumina platform at the Sequencing Facility of the Argonne National Laboratory.
Genomic DNA was amplified using primers targeting the V4 region of the 16S rRNA gene with Illumina overhang adapters. Amplicon PCR was performed with KAPA HiFi HotStart ReadyMix under the following conditions: 95 °C for 3 min; 25 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 30 s; final extension at 72 °C for 5 min. PCR products were purified using AMPure XP beads (0.8× ratio). Dual indices and Illumina sequencing adapters were added in a second PCR (8 cycles) using Nextera XT index primers, followed by another AMPure XP bead cleanup. Libraries were quantified with Qubit and validated for size using Bioanalyzer. Equimolar pooling was performed prior to sequencing on an Illumina MiSeq platform (paired-end).

value: whole blood


title: Pa02C

description: Library name: Sample 7

source_name: liver met

value: liver met

value: KRAS Q61H


title: CML CD34+CD38- vehicle

city: Dalian

first: Ting

last: Song

address: No.2 LingGong Road, GanJingZi District, Dalian, Liaoning, China

institute: Faculty of Medicine, Dalian University of Technology

description: Library name: Sample 1

data_processing:
1. Adapters and low-quality reads were filtered using fastp.
2. Clean reads were mapped to the Homo sapiens genome (hg38) using HISAT2.
3. Read counts for each gene were calculated using featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing raw read counts.

source_name: primary cells

growth_protocol: Primary CD34+ cells were cultured in Iscove’s Modified Dulbecco’s Medium with BIT, supplemented with IL-3, IL-6, KL, Flt-3 ligand, and GM-CSF.

extract_protocol:
Total RNA was extracted using Trizol reagent.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used for library construction.

treatment_protocol: Cells were treated with 1 μM S1g-10 or vehicle (DMSO) for 24 hours.

value: bone marrow

value: CML stem cells

value: Vehicle (1%DMSO)


title: DSID65 Whole maternal blood before delivery

description: Library name: DSID65_WBbefore


title: TALL-1 sh335 Dex1

description:
shNFATc1_Dex
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 1, treated with 1µM  Dex for 12 hours.

source_name: TALL-1 cell line


title: Pa16C

description: Library name: Sample 10


title: CML CD34+CD38- S1g

description: Library name: Sample 2

value: 1 μM S1g


title: Pa01C

description: Library name: Sample 6


title: DSID63 Whole maternal blood after delivery

description: Library name: DSID63_WBafter


title: TALL-1 sh335 Dex2

description:
shNFATc1_Dex
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 2, treated with 1µM  Dex for 12 hours.


title: DSID62 Whole maternal blood after delivery

description: Library name: DSID62_WBafter


title: DSID63 Whole maternal blood before delivery

description: Library name: DSID63_WBbefore


title: Hs766T

description: Library name: Sample 3


title: Pa04C

description: Library name: Sample 8

source_name: lung met

value: lung met

value: KRAS G12V


title: DSID57 Whole maternal blood after delivery

description: Library name: DSID57_WBafter


title: AsPC-1

description: Library name: Sample 1

source_name: ascites

value: ascites


title: DSID62 Whole maternal blood before delivery

description: Library name: DSID62_WBbefore


title: DSID58 Whole maternal blood after delivery

description: Library name: DSID58_WBafter


title: T3M4

description: Library name: Sample 12

source_name: lymph node met

value: lymph node met


title: Multiplexed sample: Cyst_3 (BC_001), Cyst_4 (BC_002), MRONJ_4 (BC_003), and MRONJ_5 (BC_004)

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description:
Library name: Cyst3_Cyst4_MRONJ4_MRONJ5
10X genomics

data_processing:
The prepared libraries were pooled and sequenced on an Illumina NovaSeq X Plus using 150 bp paired-end reads, generating approximately 2 billion reads (approximately 300 Gb total). Demultiplexing was performed using Cell Ranger mkfastq (v7.2.0) and bcl2fastq2 (v2.20), 12 producing FASTQ files that underwent quality assessment. Raw sequencing data were processed into expression matrices using default parameters in Cell Ranger single-cell software (v7.2.0; 10x Genomics) with the GRCh38 human reference genome. Prior to downstream analysis, the resulting count matrices were processed with CellBender remove-background (v0.3.0) to identify non-empty droplets and remove ambient RNA using customized parameters. Data analysis was carried out using Seurat (v4.1.1) within the R 4.2.1 environment. Mitochondrial genes were removed during initial filtering, and only cells expressing between 300 and 6000 genes, with mitochondrial gene content below 6%, and expressing each gene in at least three cells were retained to exclude doublets and low-quality cells.
Assembly: GRCh38
Supplementary files format and content: 10X Cellranger format

source_name: Oral cavity

extract_protocol:
Single-cell gene expression profiling was performed using the Chromium Fixed RNA Profiling workflow (CG000527; 10x Genomics). Library preparation involved the Chromium Fixed RNA Kit (Human Transcriptome) and the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit
Following hybridization of detection probes to RNA within fixed cells, adjacent probes were joined through a ligation reaction. Samples were then pooled to normalize cell counts across groups and processed on the Chromium X instrument, where cells were encapsulated with barcoded primer beads.

value: Oral cavity


title: DSID57 Whole maternal blood before delivery

description: Library name: DSID57_WBbefore


title: HEK293T, TRUB1KO, small RNA, PRAISE treated, rep 2

first: Wenqing

last: Liu

address: No. 5, Yiheyuan Road, Haidian District, Beijing

institute: Peking University

description:
Library name: TRUB1KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in TRUB1-KO cells
ST7.HEK293T_TRUB1KO_tRNA_pseudouridineList_2replicates.xls

library_source: other

data_processing:
The PRAISE library construction enables reads 2 to retain the original RNA direction, so only reads2 was used for analysis in this study. First, Cutdatapt (version 4.8) was used to remove the adapter and make quality control of the sequencing reads. The key parameters are: cutadapt -j 28 --times 1 -e 0.1 -O 3 --quality-cutoff 25 -m 55.
After that, based on the 8 bp unique molecular identifier (UMI) at the 5′ end of reads 2, the duplacated sequences were removed by Seqkit (version 0.13.2). The key parameters are: seqkit rmdup -s.
Finally, the 8bp UMI was extracted by umi_tools (version 1.0.0). The key parameters are: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNNNNNN.
In addition, the library construction added 6bp bases at the 3' end of insertion, which was also removed by umi_tools (version 1.0.0). The key parameters are: umi_tools extract --extract-method=string --3prime --bc-pattern=NNNNNN.
A two-step strategy was implemented to ensure the alignment accuracy: (1) BWA MEM was used to align the cleaned reads to the reference transcriptome of total small RNAs. The key parameter is: bwa mem -Y. (2) A custom Python program was used to realign the mapped reads from the previous step. This program was based on biopython and adopted an optimized scoring matrix to precisely resolve deletion signals. The key parameters were: python realignment.py –fast -ms 4.8.
After that, the custom Python program remove_end_signal.py was used to remove 3'-end deletion signals to reduce false-positive sites. Samtools (v1.14).  was used to convert the BAM file into an mpileup format file. The key parameters are: samtools mpileup -d 1500000 -BQ0 --ff UNMAP, QCFAIL -aa.
Finally, the information in the mpileup file was counted and converted into a BMAT format file for subsequent signal identification.
Assembly: GRCh38
Supplementary files format and content: The processed data file format is xls. The content is the Ψ sites detected in 2 biological replicates.

molecule: other

source_name: Epithelial

growth_protocol: HEK293T cells were maintained in DMEM medium (Corning) supplemented with 10% FBS (Gibco), 1% GlutaMAX (Gibco), and 0.5% penicillin-streptomycin (Gibco) at 37 °C with 5% CO2. Cells within passage 6 were used for experiments.

extract_protocol:
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen). The resulting total RNA was treated with DNase I (NEB) to avoid DNA contamination. Size selection was performed using MEGAclear Transcription Clean-Up Kit (Ambion) to deplete large RNA. The small RNA fraction was subsequently purified by ethanol precipitation. 300 ng of small RNA from each technical replicate was denatured and demethylated by incubating with 2× molar ratio of wild-type AlkB, and subsequently recovered through phenol-chloroform extraction and ethanol precipitation. 100 ng demethylated small RNA was transferred into a new nuclease-free tube and used as “untreated” and stored at - 80°C. Other demethylated small RNA was treated using PRAISE.
“Treated” and “Untreated” small RNA samples were subjected to library construction according to the eCLIP protocol with several modifications

value: Epithelial

value: human embryonic kidney 293 cells

value: TRUB1 KO


title: Multiplexed sample: Cyst_1 (BC_001), Cyst_2 (BC_002), MRONJ_1 (BC_003), and MRONJ_3 (BC_004)

description:
Library name: Cyst1_Cyst2_MRONJ1_MRONJ3
10X genomics


title: DSID50 Whole maternal blood before delivery

description: Library name: DSID50_WBbefore


title: TALL-1 sh335 DMSO1

description:
shNFATc1_DMSO
Gene expression data from TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA)  NFATc1  expression cassette, replicate 1, treated with DMSO for 12 hours.

value: shNFATc1 + DMSO 12h


title: DSID50 Whole maternal blood after delivery

description: Library name: DSID50_WBafter


title: HEK293T, TRUB1KO, small RNA, PRAISE untreated, rep 1

description:
Library name: TRUB1KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in TRUB1-KO cells
ST7.HEK293T_TRUB1KO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, PUS7KO, small RNA, PRAISE treated, rep 1

description:
Library name: PUS7KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS7-KO cells
ST6.HEK293T_PUS7KO_tRNA_pseudouridineList_2replicates.xls

value: PUS7 KO


title: DSID47 Whole maternal blood after delivery

description: Library name: DSID47_WBafter

value: whole blood


title: DSID45 Whole maternal blood after delivery

description: Library name: DSID45_WBafter


title: HuPT3

description: Library name: Sample 4

value: pancreas

value: PDAC

value: KRAS G12R


title: DSID47 Whole maternal blood before delivery

description: Library name: DSID47_WBbefore


title: HEK293T, PUS7KO, small RNA, PRAISE treated, rep 2

description:
Library name: PUS7KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS7-KO cells
ST6.HEK293T_PUS7KO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, PUS7KO, small RNA, PRAISE untreated, rep 1

description:
Library name: PUS7KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS7-KO cells
ST6.HEK293T_PUS7KO_tRNA_pseudouridineList_2replicates.xls


title: DSID42 Whole maternal blood after delivery

description: Library name: DSID42_WBafter


title: DSID58 Whole maternal blood before delivery

description: Library name: DSID58_WBbefore


title: HPAC

description: Library name: Sample 2

value: HPAC

value: KRAS G12D


title: DSID45 Whole maternal blood before delivery

description: Library name: DSID45_WBbefore


title: HEK293T, RPUSD3KO, small RNA, PRAISE treated, rep 2

description:
Library name: RPUSD3KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD3-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls

value: RPUSD3 KO


title: HEK293T, RPUSD3KO, small RNA, PRAISE treated, rep 1

description:
Library name: RPUSD3KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD3-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: DSID41 Whole maternal blood after delivery

description: Library name: DSID41_WBafter


title: DSID38 Whole maternal blood after delivery

description: Library name: DSID38_WBafter


title: DSID41 Whole maternal blood before delivery

description: Library name: DSID41_WBbefore


title: DSID42 Whole maternal blood before delivery

description: Library name: DSID42_WBbefore


title: HEK293T, RPUSD2KO, small RNA, PRAISE treated, rep 2

description:
Library name: RPUSD2KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD2-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls

value: RPUSD2 KO


title: HEK293T, RPUSD3KO, small RNA, PRAISE untreated, rep 1

description:
Library name: RPUSD3KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD3-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, RPUSD2KO, small RNA, PRAISE untreated, rep 1

description:
Library name: RPUSD2KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD2-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: DSID38 Whole maternal blood before delivery

description: Library name: DSID38_WBbefore


title: HEK293T, RPUSD2KO, small RNA, PRAISE treated, rep 1

description:
Library name: RPUSD2KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD2-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, TRUB1KO, small RNA, PRAISE treated, rep 1

description:
Library name: TRUB1KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in TRUB1-KO cells
ST7.HEK293T_TRUB1KO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, RPUSD1KO, small RNA, PRAISE treated, rep 2

description:
Library name: RPUSD1KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD1-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls

value: RPUSD1 KO


title: MIA PaCa-2

description: Library name: Sample 5

value: MIA PaCa-2

value: KRAS G12C


title: DSID36 Whole maternal blood after delivery

description: Library name: DSID36_WBafter


title: HEK293T, RPUSD1KO, small RNA, PRAISE untreated, rep 1

description:
Library name: RPUSD1KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD1-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: DSID36 Whole maternal blood before delivery

description: Library name: DSID36_WBbefore


title: HEK293T, RPUSD1KO, small RNA, PRAISE treated, rep 1

description:
Library name: RPUSD1KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in RPUSD1-KO cells
ST5.HEK293T_RluAKO_tRNA_pseudouridineList_2replicates.xls


title: HEK293T, PUS1KO, small RNA, PRAISE treated, rep 2

description:
Library name: PUS1KO-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS1-KO cells
ST4.HEK293T_PUS1KO_tRNA_pseudouridineList_2replicates.xls

value: PUS1 KO


title: HEK293T, PUS1KO, small RNA, PRAISE untreated, rep 1

description:
Library name: PUS1KO-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS1-KO cells
ST4.HEK293T_PUS1KO_tRNA_pseudouridineList_2replicates.xls

value: Epithelial


title: DSID26 Whole maternal blood after delivery

description: Library name: DSID26_WBafter


title: HEK293T, PUS1KO, small RNA, PRAISE treated, rep 1

description:
Library name: PUS1KO-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in PUS1-KO cells
ST4.HEK293T_PUS1KO_tRNA_pseudouridineList_2replicates.xls

value: human embryonic kidney 293 cells


title: HEK293T, DKC1KD, small RNA, PRAISE treated, rep 2

description:
Library name: DKC1KD-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-KD cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls

value: DKC1 KD


title: DSID26 Whole maternal blood before delivery

description: Library name: DSID26_WBbefore


title: DSID25 Whole maternal blood after delivery

description: Library name: DSID25_WBafter


title: DSID25 Whole maternal blood before delivery

description: Library name: DSID25_WBbefore


title: HEK293T, DKC1KD, small RNA, PRAISE treated, rep 1

description:
Library name: DKC1KD-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-KD cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls


title: DSID22 Whole maternal blood before delivery

description: Library name: DSID22_WBbefore


title: HEK293T, DKC1NC, small RNA, PRAISE treated, rep 1

description:
Library name: DKC1NC-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-NC cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls

value: DKC1 NC


title: DSID22 Whole maternal blood after delivery

description: Library name: DSID22_WBafter


title: HEK293T, DKC1NC, small RNA, PRAISE treated, rep 2

description:
Library name: DKC1NC-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-NC cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls


title: DSID21 Whole maternal blood before delivery

description: Library name: DSID21_WBbefore


title: DSID19 Whole maternal blood after delivery

description: Library name: DSID19_WBafter


title: IMR32 cells, combination rep 2

city: London

first: Yurui

last: Ma

state: london

address: du cane road

country: United Kingdom

institute: imperial college london

description: Library name: IMR32_IndAle2

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9). Adapter trimming and low-quality base removal were performed using Trimmomatic (v0.39).
Clean reads were aligned to the Homo sapiens reference genome GRCh38 using HISAT2 (v2.2.1) with default parameters
Gene-level expression quantification was performed using featureCounts (v2.0.1) with GENCODE v39 annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited .xlsx files include gene-level read counts for each sample.

growth_protocol: IMR32 human neuroblastoma cells were cultured in MEM (Minimum Essential Medium) supplemented with 10% fetal bovine serum (FBS),1% penicillin/streptomycin (P/S), 1 mM sodium pyruvate, and 2 mM L-glutamine , and 1% penicillin-streptomycin at 37°C in 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with poly(A) selection. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Cells were treated with either  DMSO (vehicle), 4 μM Alectinib, 1.25 μM Indisulam, or the combination of Alectinib (4 μM) and Indisulam (1.25 μM) for 24 hours prior to RNA extraction.

value: Neuroblastoma

value: WT

value: Alectinib 4uM+Indisulam 1.25uM


title: IMR32 cells, combination rep 3

description: Library name: IMR32_IndAle3


title: IMR32 cells, combination rep 4

description: Library name: IMR32_IndAle4


title: DSID18 Whole maternal blood after delivery

description: Library name: DSID18_WBafter

value: whole blood


title: DSID31 Whole maternal blood after delivery

description: Library name: DSID31_WBafter


title: DSID19 Whole maternal blood before delivery

description: Library name: DSID19_WBbefore


title: DSID31 Whole maternal blood before delivery

description: Library name: DSID31_WBbefore


title: DSID18 Whole maternal blood before delivery

description: Library name: DSID18_WBbefore


title: DSID16 Whole maternal blood before delivery

description: Library name: DSID16_WBbefore


title: IMR32 cells, Alectinib rep 4

description: Library name: IMR32_Ale4

value: Alectinib 4uM


title: IMR32 cells, Alectinib rep 2

description: Library name: IMR32_Ale2


title: DSID16 Whole maternal blood after delivery

description: Library name: DSID16_WBafter


title: DSID12 Whole maternal blood after delivery

description: Library name: DSID12_WBafter


title: DSID12 Whole maternal blood before delivery

description: Library name: DSID12_WBbefore


title: IMR32 cells, Alectinib rep 1

description: Library name: IMR32_Ale1


title: HEK293T, DKC1KD, small RNA, PRAISE untreated, rep 1

description:
Library name: DKC1KD-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-KD cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls


title: IMR32 cells, Alectinib rep 3

description: Library name: IMR32_Ale3


title: DSID21 Whole maternal blood after delivery

description: Library name: DSID21_WBafter


title: HEK293T, DKC1NC, small RNA, PRAISE untreated, rep 1

description:
Library name: DKC1NC-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in DKC1-NC cells
ST3.HEK293T_DKC1KD_snRNA_snoRNA_pseudouridineList_2replicates.xls


title: IMR32 cells, Indisulam rep 4

description: Library name: IMR32_Ind4

value: Indisulam 1.25uM


title: DSID08 Whole maternal blood after delivery

description: Library name: DSID08_WBafter


title: IMR32 cells, Indisulam rep 3

description: Library name: IMR32_Ind3


title: IMR32 cells, Indisulam rep 2

description: Library name: IMR32_Ind2


title: DSID08 Whole maternal blood before delivery

description: Library name: DSID08_WBbefore


title: DSID10 Whole maternal blood before delivery

description: Library name: DSID10_WBbefore


title: IMR32 cells, Indisulam rep 1

description: Library name: IMR32_Ind1


title: IMR32 cells, combination rep 1

description: Library name: IMR32_IndAle1


title: DSID05 Whole maternal blood after delivery

description: Library name: DSID05_WBafter


title: IMR32 cells, DMSO rep 4

description: Library name: IMR32_VC4

value: DMSO


title: IMR32 cells, DMSO rep 3

description: Library name: IMR32_VC3


title: DSID05 Whole maternal blood before delivery

description: Library name: DSID05_WBbefore


title: DSID02 Whole maternal blood before delivery

description: Library name: DSID02_WBbefore


title: DSID02 Whole maternal blood after delivery

description: Library name: DSID02_WBafter


title: IMR32 cells, DMSO rep 1

description: Library name: IMR32_VC1


title: IMR32 cells, DMSO rep 2

description: Library name: IMR32_VC2


title: HEK293T, small RNA, PRAISE treated, rep 2

description:
Library name: 293T-T2
NGS data for profiling the Ψ quantitative landscape of small RNAs in HEK293T cells
ST2.HEK293T_WT_mt-tRNA_pseudouridineList_2replicates.xls


title: TB3

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

description: Library name: TB3

data_processing:
The adaptors and low quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39 using the following options: TRAILING:20, MINLEN:235 and CROP:235. Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.0.1. FeatureCounts 1.6.2 was subsequently employed to convert aligned short reads into read counts for each sample. Genes with less than ten counts in two or more samples were removed. The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with fold-change > 2 and Benjamini–Hochberg (BH)-adjusted P < 0.1 as compared to NC group77. Cluster analysis and visualization was performed using the pheatmap Bioconductor package (v1.0.12).
Assembly: GRCh38.p2
Supplementary files format and content: txt
Supplementary files format and content: The expression of lncRNAs from Exosome, including count, RPKM and TPM format.

source_name: Exosomes from TB plasma replicate 3

extract_protocol:
Plasma was harvested and centrifuged at 2,000×g at 4℃ for 30 min to remove cells and cell debris. The supernatant was transferred to a new tube followed by diluting to 20 mL by PBS, and filtered through a filter with a pore size of 0.22 μm to exclude particles larger than 200 nm. Then density gradient centrifugation was used to isolate exosomes with 4 ml Tris/sucrose/D2O solution loaded to the bottom of a 70Ti tube, and 20 ml supernatant added to the top of this sucrose cushion, subsequently centrifuging for 75 min at 100,000×g at 4 °C in a 70Ti rotor. Next, 3.5 mL of the Tris/sucrose/ D2O cushion was removed from the centrifuged tube and transferred to two new centrifuge tubes with 1.75 ml per tube. This mixture was then be diluted with 25 mL PBS, and centrifuged for 70 min at 100,000×g at 4 °C. Discard the supernatant, the resulting pellet contains the isolated EVs was resuspended in 100 μL PBS.
RNA libraries were then constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2200 TapeStation and Qubit® 2.0 (Life Technologies). Sequencing was performed by RiboBio Co., Ltd. on an Illumina NovaSeq 6000 machine with paired-end 150-bp reads.

value: Total RNA from exosome

value: Exosomes from TB plasma


title: DSID01 Whole maternal blood before delivery

description: Library name: DSID01_WBbefore


title: HEK293T, small RNA, PRAISE untreated, rep 1

description:
Library name: 293T-uT
NGS data for profiling the Ψ quantitative landscape of small RNAs in HEK293T cells
ST2.HEK293T_WT_mt-tRNA_pseudouridineList_2replicates.xls


title: TB2

description: Library name: TB2

source_name: Exosomes from TB plasma replicate 2


title: DSID10 Whole maternal blood after delivery

description: Library name: DSID10_WBafter


title: HEK293T, small RNA, PRAISE treated, rep 1

description:
Library name: 293T-T1
NGS data for profiling the Ψ quantitative landscape of small RNAs in HEK293T cells
ST2.HEK293T_WT_mt-tRNA_pseudouridineList_2replicates.xls


title: dna_h1batch_Col0_rep1

city: Los Angeles

first: Shuya

last: Wang

state: California

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Library name: dna_h1batch_Col0_rep1

data_processing:
WGBS were filtered and Illumina adaptors were removed using Trim Galore (v 0.6.7, Babraham Institute). Reads with three or more consecutively methylated CHH sites were treated as non-converted reads and filtered out. Bismark (v 0.19.1, Babraham Institute) was used to map the reads to the Arabidopsis reference genome (TAIR10) and Col-Cen-v1.2 genome assembly. ViewBS (v 0.1.11) was used to generate the plots.
Assembly: TAIR10/Col-Cen-v1.2
Supplementary files format and content: bed: methylation level

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under 16h light: 8h dark condition (on soil), or under constant light (on plates).

extract_protocol:
14-day old seedlings were harvested from Col-0, cdca7a, cdca7b, cdca7a cdca7b+/-, cdca7a cdca7b, h1.1 h1.2, h1.1 h1.2 cdca7a cdca7b, and ddm1-2. Samples were immediately frozen in liquid nitrogen. DNA were extracted using the DNeasy Plant Mini kit (Qiagen). RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research).
A total of 100ng DNA from was sheared to ~200bp using the Covaris S2 (Covaris). Then the libraries were constructed using the Ovation Ultralow Methyl-seq kit (NuGEN), and bisulfite conversion was achieved using the Epitect Bisulfite Conversion kit (QIAGEN). Finally, the libraries were sequenced on Illumina Novaseq X plus instruments.

value: seedling


title: dna_h1batch_cdca7acdca7b_rep2

description: Library name: dna_h1batch_cdca7acdca7b_rep2


title: TB1

description: Library name: TB1

source_name: Exosomes from TB plasma replicate 1


title: R3

description: Library name: R3

source_name: Exosomes from TB resister plasma replicate 3

value: Exosomes from TB resister plasma


title: dna_h1batch_cdca7acdca7b_rep1

description: Library name: dna_h1batch_cdca7acdca7b_rep1


title: dna_h1.1h1.2cdca7acdca7b_rep2

description: Library name: dna_h1.1h1.2cdca7acdca7b_rep2


title: R2

description: Library name: R2

source_name: Exosomes from TB resister plasma replicate 2


title: dna_h1.1h1.2cdca7acdca7b_rep1

description: Library name: dna_h1.1h1.2cdca7acdca7b_rep1


title: R1

description: Library name: R1

source_name: Exosomes from TB resister plasma replicate 1


title: L2

description: Library name: L2

source_name: Exosomes from latent tuberculosis infection plasma replicate 2


title: L3

description: Library name: L3

source_name: Exosomes from latent tuberculosis infection plasma replicate 3


title: dna_h1.1h1.2_rep1

description: Library name: dna_h1.1h1.2_rep1


title: L1

description: Library name: L1

source_name: Exosomes from latent tuberculosis infection plasma replicate 1


title: HC3

description: Library name: HC3

source_name: Exosomes from healthy control plasma replicate 3

value: Exosomes from healthy control plasma


title: HC2

description: Library name: HC2

source_name: Exosomes from healthy control plasma replicate 2


title: dna_cdca7b_rep2

description: Library name: dna_cdca7b_rep2


title: dna_cdca7b_rep1

description: Library name: dna_cdca7b_rep1


title: dna_Col0_rep2

description: Library name: dna_Col0_rep2


title: HC1

description: Library name: HC1

source_name: Exosomes from healthy control plasma replicate 1


title: dna_Col0_rep1

description: Library name: dna_Col0_rep1


title: dna_h1.1h1.2_rep2

description: Library name: dna_h1.1h1.2_rep2


title: dna_h1batch_Col0_rep2

description: Library name: dna_h1batch_Col0_rep2