title: PB2_TGFb1_IgG

city: Houston

first: Anand

last: Singh

address: 1901 East Road

institute: MD Anderson Cancer Center

data_processing:
For the analysis, paired_end FASTQ files were processed using the nf-core-cutandrun pipeline (v3.1) Adapter sequences were removed with Trim Galore. Reads were aligned with Bowtie2 to GRCh37 and duplicates were removed using picard. Aligned reads were normalized offers normalization by Reads Per Kilobase per Million mapped reads (RPKM) scaling factor by using bamCoverage of deepTools. Peaks were called using MACS2 and visualized on an Integrative Genome Viewer (IGV) plot.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: Cut&RUN-seq

source_name: Blood

extract_protocol:
Briefly,~500,000 untreated and TGF-b treated NK cells were immobilized to activated Concanavalin A-coated magnetic beads (Bangs laboratories), then permeabilized with wash buffer containing 0.05% digitonin. Samples were incubated with rabbit IgG (Millipore) or BATF (Cell Signaling Technologies) overnight at 4°C. Targeted chromatin digestion was achieved by pAG-MNase (EpiCypher) binding followed by incubation with CaCl2.
CUT&RUN DNA fragments were purified using MinElute columns (Qiagen) and libraries were created using NEBNext Ultra II DNA Library prep kit (New England Biolabs) following modified protocol for BATF CUT&RUN DNA as previously described. Libraries were sequenced using Illumina NextSeq 500 system to obtain 75bp paired end reads per sample.

value: Blood

value: NK cells

value: primary cells

tag: chip antibody

value: anti-IgG (Millipore)


title: EpOME_10 (t=week9)

status: Public on Aug 31 2024

type: SRA

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

description: 16S rRNA

library_source: genomic

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.
The sequencing data was further trimmed and analyzed by QIIME software qiime2-2020.11.
Sequences were then clustered into operational taxonomic unites (OTUs) using a public dataset (SILVA release 132) with 99% similarity threshold.
QIIME2 output were imported to R to build a phyloseq project.
Differential  abundance analysis in the polysome fraction was determine using AVONA.
Supplementary files format and content: tab-delimited text files include differential  abundance analysis results

molecule: genomic DNA

organism: mouse gut metagenome

source_name: colon

growth_protocol: C57BL/6 mice were stimulated with AOM/DSS to induce colon tumorigenesis,

extract_protocol:
DNA was extracted from mouse fecal samples using DNeasy PowerSoil Kit (Qiagen) following instructions from the manufacturer with an additional bead-beating step.
The quantity of the extracted DNA was measured using a NanoDrop Spectrophotometer (Thermo Fisher Scientific). The DNA was then subjected to 16S rRNA sequencing analysis that was conducted by Novogene

treatment_protocol: then treated with 12,13-EpOME.

tag: tissue

value: colon

tag: treatment

tag: genotype

value: EpOME (t=week9)


title: EpOME_8 (t=week9)

description: 16S rRNA


title: S1393Nr51_LoVo_C3

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

library_source: transcriptomic

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.19).
Quality check of the reads has been performed by FastQC and adapters were trimmed with trimmomatic toolkit,then trimmed raw reads were aligned to the human reference genome (hg38) using HISAT2.
Read count extraction and normalization were performed using R packages
Differential Gene Expression Analysis were performed with DESeq2 also we calculate exon gene sizes with the GenomicFeatures Package in R and FeaturesCount which are required to calculate FPKM values in DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Colon Cancer

growth_protocol: Standard, ATCC-derived protocls for 2D in vitro growth for each cell line.

extract_protocol: RNA libraries were prepared for sequencing using TruSeq Stranded TotalRNA (Illumina) protocols

treatment_protocol: Cell lines indicated in the file names were 48h post knock-out of the oncogenes with CRISPR/Cas9 techniques in biological triplicates (numbers 1-3). Total RNA was exracted from cells and subjected to mRNA sequencing.

value: Colon Cancer

tag: cell line

value: LoVo

tag: cell type

value: epithelial cells

value: non-specific gRNA control


title: PB2_TGFb1_BATF_CST

country: USA

value: anti-BATF (CST)


title: S1393Nr52_LoVo_K1

value: KRAS


title: S1393Nr48_RKO_M3

value: RKO

value: hyperactive CMYC


title: PB1_TGFb1_IgG


title: PB2_Control_IgG

value: Untreated


title: EpOME_6 (t=week9)

description: 16S rRNA


title: PB2_BATF_CST


title: EpOME_9 (t=week9)

description: 16S rRNA


title: EpOME_4 (t=week9)

description: 16S rRNA


title: EpOME_5 (t=week9)

description: 16S rRNA


title: S1393Nr47_RKO_M2


title: PB1_TGFb1_BATF_CST


title: 7dIOP3_2

city: Beijing

first: Shen

last: Wu

state: - 选择州/省 -

address: No.17 hougou hutong, Dongcheng district，Beijing

country: China

institute: institute of ophthalmology

data_processing:
barcodes.tsv.gz:list of spatial barcodes
features.tsv.gz:list of gene IDs
matrix.mtx.gz:gene expression count data in matrix market exchange format
Assembly: Rattus_norvegicus.Rnor_6.0
Library strategy: spatial transcriptomics

molecule: polyA RNA

organism: Rattus norvegicus

source_name: eye

extract_protocol:
fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10x Genomics visium spatial gene expression slides and reagent kit according to manufacturer's construction

value: eye

value: hydrogel injection


title: S1393Nr46_RKO_M1


title: PB1_Control_IgG

value: Blood


title: PB1_BATF_CST_antibody

value: NK cells


title: EpOME_3 (t=week9)

description: 16S rRNA


title: S1393Nr45_RKO_C3


title: S1393Nr44_RKO_C2


title: S1393Nr49_LoVo_C1


title: EpOME_7 (t=week9)

description: 16S rRNA


title: S1393Nr43_RKO_C1


title: sgRNA from cells with lowest 1% of fluorescence

city: Dallas

first: Jennifer

last: Kohler

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Bcl files were demultiplexed using bcl2fastq (v2.20)
sgRNA sequences were trimmed using cutadapt (v1.16)
Enriched genes and normalized read counts were identified via MAGeCK (v0.5.6)
Assembly: Human Brunello genome-wide CRISPR KO pooled library
Supplementary files format and content: Tab-delimited text files that includes the gene summary

extract_protocol:
Genomic DNA (gDNA) was isolated  using the Blood and Cell Culture DNA Maxi Kit (Qiagen, catalog no. 13362) . To amplify sgRNA sequences for Next Generation Sequencing (NGS), four parallel 100 μL PCR reactions were initially run for each condition, and pooled. Each 100 uL PCR reaction contained 1 - 2 ug of gDNA, Ex Taq polymerase (Takara Bio, catalog no. RR01CM) and an appropriate PCR primer pair. Amplified DNA was then indexed and barcoded for NGS in another PCR reaction including 5 uL of DNA from the initial PCR, Ex Taq polymerase, pooled P5 and barcoded P7 primers. DNA was then pooled and purified for sequencing using AMPure XP beads (Agencourt). 300 uL of pooled PCR product was mixed with 150 uL beads and incubated for 5 minutes to remove gDNA. Beads bound to gDNA were pelleted on the DynaMag-2 Magnet (Invitrogen) and the supernatant was then mixed with 540 uL of fresh beads and incubated for 5 minutes to bind the PCR products. After discarding the supernatant, beads were washed twice with 1 mL 70 % ethanol and then dried for approximately 5 min. Bound DNA was eluted from the beads using 300 uL sterile, nuclease-free water.
Human Brunello genome-wide CRISPR KO pooled library (Addgene #73178)
CRISPR


title: Veh_13 (t=week9)

description: 16S rRNA

value: Vehicle (t=week9)


title: sgRNA from cells with highest 1% of fluorescence


title: EpOME_1 (t=week9)

description: 16S rRNA


title: S1393Nr42_DLD1_K3


title: sgRNA from cells immediately after transduction


title: sgRNA from cells 13 days post-transduction and at time of FACS


title: B10

city: Buenos Aires

first: Adriana

last: De Siervi

state: Buenos Aires

address: Vuelta de Obligado 2490

department: Instituto de Biología y Medicina Experimental

country: Argentina

institute: CONICET

description: Plasma from breast cancer patients

data_processing:
DESeq2_1.22.2
Raw sequencing files were merged for each sample to generate a single fastq file per sample. Cutadapt 2.3 with Python 3.6.8 was used to remove adapter sequences
Trimmed reads were aligned to two references, the miRBase dataset for human miRs using bowtie with the following parameters: hg19: bowtie -S -n 1 -l 19 -a -m 25 --best --strata -e 2000 --un /unalignedFolder -q~/path/to/hg19_index/hg19 /path/to/fastq /samFilesFolder/sample.sam 2> /alignStatFolder.txt; hsa_mirs and YM500v3: bowtie -S -n 1 -l 17 -a -m 25 --best --strata -e 2000 --un/unalignedFolder/sample.unal.fa -q ~/path/to/hsa_mirs/hsaMirs/path/to/fastq >/samFilesFolder/sample.sam 2> /alignStatFolder.txt
Samtools 1.7, using htslib 1.7-2, was used to convert and sort the SAM files into sorted BAM files.  A count matrix was made using a proprietary Python program.
Differential expression is calculated using the DESeq2 package in R
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Normalized counts values for each Sample

source_name: Plasma

extract_protocol:
GenoHub (Real Seq Bioscience INC, USA) performed miRNA isolation using Quick-cfRNA Serum and Plasma (Zymo Research, USA)
Libraries were amplified by 16 cycles of PCR. Libraries were sequenced in two NextSeq 550 runs with the NextSeq 500/550 High Output Kit v2.5 (75 cycles), sequencing was done with Single End 75 nt reads and dual 6 nt indexes

value: Plasma

tag: Sex

value: Female

tag: disease state

value: Breast cancer


title: S1393Nr41_DLD1_K2

value: Colon Cancer


title: S1393Nr40_DLD1_K1


title: Veh_11 (t=week9)

description: 16S rRNA

value: colon


title: Veh_10 (t=week9)

description: 16S rRNA


title: S1393Nr39_DLD1_M3

value: epithelial cells


title: Veh_9 (t=week9)

description: 16S rRNA


title: B9

description: Plasma from breast cancer patients


title: B8

description: Plasma from breast cancer patients


title: Veh_8 (t=week9)

description: 16S rRNA


title: B7

description: Plasma from breast cancer patients


title: S1393Nr37_DLD1_M1


title: S1393Nr38_DLD1_M2


title: EpOME_2 (t=week9)

description: 16S rRNA

value: EpOME (t=week9)


title: peripheral blood, bladder cancer-r1 (IO0078)

type: RNA

city: Richmond

first: Adam

last: Dempsey

state: VA

address: 8751 Park Central Drive, Suite 200

institute: StageZero Life Sciences

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 4, Affymetrix).

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.

treatment_protocol: Blood plasma was removed after centrifugation and a hypotonic buffer was added at a 3:1 volume ratio to lyse the red blood cells. The mixture was centrifuged to yield a pellet for subsequent total RNA isolation.

value: peripheral blood

tag: gender

value: F

tag: age

tag: cancer dx

value: bladder cancer


title: S1393Nr36_DLD1_P3

value: mut. TP53


title: Veh_7 (t=week9)

description: 16S rRNA


title: B6

description: Plasma from breast cancer patients


title: B5

description: Plasma from breast cancer patients


title: S1393Nr35_DLD1_P2


title: S1393Nr34_DLD1_P1


title: Veh_5 (t=week9)

description: 16S rRNA


title: A4

description: Plasma from healthy donors

value: Healthy


title: Veh_12 (t=week9)

description: 16S rRNA


title: A3

description: Plasma from healthy donors


title: A2

description: Plasma from healthy donors


title: S1393Nr33_DLD1_C3

value: non-specific gRNA control


title: Veh_3 (t=week9)

description: 16S rRNA


title: Veh_1 (t=week9)

description: 16S rRNA


title: S1393Nr32_DLD1_C2


title: Veh_6 (t=week9)

description: 16S rRNA


title: Veh_2 (t=week9)

description: 16S rRNA


title: HL60_KO-2G-DMSO-2_ATAC

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
RNA-Seq and ATAC-Seq were performed using Illumina NextSeq 500.
The level of gene expression was assessed after DESeq2 normalization. For the ATAC-Seq data analysis, the genomic regions with high levels of transposition/tagging events were determined.  using the MACS2 peak calling algorithm
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 transformed DESeq2 values for RNA-Seq and avarage peak values as well as genome regions for ATAC-Seq.

source_name: AML HL60 cell line

extract_protocol: Total RNA was extracted from the treated cells for the RNA-Seq analysis using an RNeasy Mini Plus RNA isolation kit a (Qiagen). DNA from the cell lysate was isolated for the ATAC-Seq analysis.

treatment_protocol: HL60 HK3-null and Cas9 expressing control cells were treated with either 1µM of ATRA or DMSO (0.01%) for 36h. Next, treated cells were harvested for RNA-Seq and ATAC-Seq analysis.

value: AML HL60 cell line

value: treated with DMSO


title: Veh_4 (t=week9)

description: 16S rRNA


title: S1393Nr29_VMRC_P2

source_name: Lung Cancer

value: Lung Cancer

value: VMRC


title: EpOME_11 (t=week0)

description: 16S rRNA

value: EpOME (t=week0)


title: S1393Nr30_VMRC_P3


title: EpOME_10 (t=week0)

description: 16S rRNA


title: S1393Nr28_VMRC_P1


title: HL60_KO-2G-DMSO-1_ATAC


title: EpOME_9 (t=week0)

description: 16S rRNA


title: A1

description: Plasma from healthy donors

value: Plasma

value: Female


title: HL60_KO-2G-ATRA-2_ATAC

value: treated with ATRA


title: S1393Nr27_VMRC_C3


title: HL60_KO-2G-ATRA-1_ATAC


title: EpOME_8 (t=week0)

description: 16S rRNA

value: colon


title: HL60_CAS9-DMSO-2_ATAC

value: Cas9 expressing control cells


title: EpOME_7 (t=week0)

description: 16S rRNA


title: S1393Nr31_DLD1_C1

value: Colon Cancer

value: epithelial cells


title: S1393Nr25_VMRC_C1


title: HL60_CAS9-DMSO-1_ATAC


title: EpOME_6 (t=week0)

description: 16S rRNA


title: S1393Nr26_VMRC_C2


title: EpOME_4 (t=week0)

description: 16S rRNA


title: EpOME_5 (t=week0)

description: 16S rRNA


title: HL60_CAS9-ATRA-1_ATAC


title: S1393Nr24_A549_K3

value: KRAS


title: S1393Nr21_A549_C3


title: HL60_CAS9-ATRA-2_ATAC


title: HL60_KO-2G-DMSO-3_RNASeq


title: S1393Nr22_A549_K1


title: EpOME_2 (t=week0)

description: 16S rRNA


title: S1393Nr20_A549_C2


title: EpOME_1 (t=week0)

description: 16S rRNA


title: HL60_KO-2G-DMSO-1_RNASeq


title: HL60_KO-2G-ATRA-3_RNASeq


title: HL60_KO-2G-ATRA-2_RNASeq


title: S1393Nr18_H1299_M3

value: hyperactive CMYC


title: Veh_13 (t=week0)

description: 16S rRNA

value: Vehicle (t=week0)


title: HL60_KO-2G-DMSO-2_RNASeq


title: Veh_12 (t=week0)

description: 16S rRNA


title: HL60_KO-2G-ATRA-1_RNASeq


title: Veh_11 (t=week0)

description: 16S rRNA


title: S1393Nr17_H1299_M2


title: S1393Nr23_A549_K2


title: S1393Nr15_H1299_C3


title: HL60_CAS9-DMSO-3_RNASeq


title: EpOME_3 (t=week0)

description: 16S rRNA


title: HL60_CAS9-DMSO-2_RNASeq


title: S1393Nr14_H1299_C2


title: Veh_9 (t=week0)

description: 16S rRNA


title: HL60_CAS9-DMSO-1_RNASeq


title: Veh_8 (t=week0)

description: 16S rRNA


title: S1393Nr13_H1299_C1


title: S1393Nr19_A549_C1


title: Veh_7 (t=week0)

description: 16S rRNA


title: HL60_CAS9-ATRA-2_RNASeq


title: HL60_CAS9-ATRA-3_RNASeq


title: Veh_6 (t=week0)

description: 16S rRNA


title: S1393Nr11_H23_K2


title: S1393Nr12_H23_K3


title: Veh_5 (t=week0)

description: 16S rRNA


title: S1393Nr10_H23_K1


title: Veh_10 (t=week0)

description: 16S rRNA


title: HL60_CAS9-ATRA-1_RNASeq


title: Veh_4 (t=week0)

description: 16S rRNA


title: 100 cGy IR, 72 hr, replicate 2

city: Gainesville

first: Jeremy

middle: Robert Barker

last: Newman

state: FL

address: 2033 Mowry Road

department: Genetics Institute

institute: University of Florida

data_processing:
Raw RNA-seq reads were trimmed using Trimmomatic (version 0.32; Bolger et al., 2014) to remove adapters and low-quality reads. A Phred-33 quality score of 20 was used for quality trimming of ends of reads (parameters LEADING:20 TRAILING:20). Sliding-window trimming was also performed with a window size of 4 nt and a minimum average quality of 15 (parameter SLIDINGWINDOW:4:15). Reads that were less than 80 nt after trimming were removed from further analysis (parameter MINLEN:80).
Trimmed reads were then aligned paired-end to the A. thaliana TAIR10 genome assembly (http://www.arabidopsis.org/; Lamesch et al., 2012) using the STAR aligner (version  2.5.2b; Dobin et al., 2013),
Resulting alignments were then passed to RSEM (version 1.2.28; Li & Dewey, 2011) using the rsem-calculate-expression program with parameter --alignments to estimate the abundances of TAIR10-annotated transcripts and genes
Gene expression abundance estimates were expressed as copies per million (CPM). A gene was considered detected if it had CPM > 0 in at least 2 biological replicates for a given treatment group. The data were then log-transformed
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file that includes gene expression estimates as CPM for each TAIR10 gene and each biological replicate
Supplementary files format and content: tab-delimited text file that includes gene expression estimates as log-transformed CPM for each TAIR10 gene and each biological replicate

organism: Arabidopsis thaliana

source_name: Whole rosette

growth_protocol: Arabidopsis thaliana (Col-0 ecotype) seeds were sown in autoclaved soil and cold-treated at 4°C for 3 days to promote uniform germination (Zhou et al., 2017). Plants were grown under a short-day condition (8 hr light, 16 hr dark) at 22°C for 1 week, followed by transplantation of each seedling to individual cells in 36-cell trays.

extract_protocol:
Total RNA was extracted from approximately 0.1 g whole rosette tissues using the RNeasy Plant Mini Kit (Qiagen). RNA samples were quantified using a NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed using an Agilent 2100 Bioanalyzer.
RNA-seq library construction was performed by the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR, RRID:SCR_019152), using poly(A) selection and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: At 4 weeks of growth, plants were placed in a 137Cs irradiator and exposed to gamma IR at 1.4 cGy per second. Plants were irradiated for 7 sec (10 cGy equivalent), 71 sec (100 cGy equivalent) or not exposed (0 cGy or “Mock”).

value: Whole rosette

value: 100 cGy IR

tag: exposure time


title: 100 cGy IR, 72 hr, replicate 3


title: S1393Nr9_H23_M3


title: Veh_2 (t=week0)

description: 16S rRNA


title: S1393Nr7_H23_M1


title: Veh_1 (t=week0)

description: 16S rRNA


title: Veh_3 (t=week0)

description: 16S rRNA


title: S1393Nr6_H23_P3

value: mut. TP53


title: 10 cGy IR, 72 hr, replicate 3

value: 10 cGy IR


title: 10 cGy IR, 72 hr, replicate 2


title: S1393Nr16_H1299_M1

value: Lung Cancer


title: S1393Nr4_H23_P1


title: S1393Nr5_H23_P2


title: 10 cGy IR, 72 hr, replicate 1


title: embryo, TBBPA_2hpf_replicate3

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

description:
CU76
gene_fpkm-CU-70-77.txt

data_processing:
Raw data (raw reads) in fastq format was firstly processed throughin-house perl scripts. In this step, clean data (clean reads) was obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. A
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene.
Differential expression analysisof two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: GRZ11
Supplementary files format and content: Excel file contains FPKM values for each sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were spawned and maintained in system water

extract_protocol:
At each time point, embryos were collected in RNA zol, homogenized and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit (Zymo). RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification(
For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(

treatment_protocol: Embryos were exposed to 0 or 40 uM TBBPA in 0.1% DMSO from 0.75 to 2, 3.5 or 4.5 hpf

value: whole embryo

value: wildtype

value: TBBPA

tag: time

value: 2 hpf


title: Mock, 72 hr, replicate 3

value: Mock


title: embryo, TBBPA_2hpf_replicate2

description:
CU75
gene_fpkm-CU-70-77.txt


title: S1393Nr3_H23_C3

value: non-specific gRNA control


title: embryo, TBBPA_2hpf_replicate1

description:
CU74
gene_fpkm-CU-70-77.txt


title: Mock, 72 hr, replicate 2


title: S1393Nr8_H23_M2


title: 100 cGy IR, 72 hr, replicate 1


title: embryo, DMSO_2hpf_replicate4

description:
CU73
gene_fpkm-CU-70-77.txt

value: DMSO


title: S1393Nr1_H23_C1


title: S1393Nr2_H23_C2


title: Mock, 72 hr, replicate 1


title: embryo, DMSO_2hpf_replicate3

description:
CU72
gene_fpkm-CU-70-77.txt


title: 100 cGy IR, 24 hr, replicate 2


title: embryo, DMSO_2hpf_replicate2

description:
CU71
gene_fpkm-CU-70-77.txt


title: Astrocyte (D40), cytokine stimulated, rep 2

city: San Antonio

first: Uchit

last: Bhaskar

state: Texas

address: One, UTSA Circle

department: Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

data_processing:
Quality check and preprocessing - fastp
Read Mapping - Hisat2
Raw Counts generation - featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for Fibroblasts and Astrocyte (D40) healthy, control samples
Supplementary files format and content: tab-delimited text file includes raw counts for Astrocyte (D40) samples only, with and without cytokine stimulation.

growth_protocol: Fibroblasts were maintained in DMEM-F12 with 15% FBS, FdiAs were maintained in Astrocyte maturation media in 37C, 5% CO2 prior to total RNA extraction.

extract_protocol:
RNA was extracted using Qiagen All Prep DNA/RNA mini kit.
RNA libraries were prepared by Novogene Co., Ltd. (UC Davis, CA).

treatment_protocol: For neuroinflammatory conditions, FdiAs (D40) were stimulated with IL-1B, TNF-alpha and complement C1q in astrocyte maturation media for 24 hours at 37C, 5% CO2.

value: Fibroblast-derived induced Astrocyte

value: Astrocyte differentiation + Cytokine Stimulation


title: 100 cGy IR, 24 hr, replicate 1


title: embryo, TBBPA_2hpf_replicate4

description:
CU77
gene_fpkm-CU-70-77.txt


title: 10 cGy IR, 24 hr, replicate 3


title: embryo, DMSO_2hpf_replicate1

description:
CU70
gene_fpkm-CU-70-77.txt


title: Astrocyte (D40), cytokine stimulated, rep 1


title: embryo, TBBPA_4.5hpf_replicate4

description:
CU67
gene_fpkm-CU-50-67.txt

value: 4.5 hpf


title: Astrocyte (D40), control, rep 3

value: Astrocyte differentiation


title: Astrocyte (D40), control, rep 2


title: 10 cGy IR, 24 hr, replicate 1


title: 10 cGy IR, 24 hr, replicate 2


title: embryo, TBBPA_4.5hpf_replicate3

description:
CU66
gene_fpkm-CU-50-67.txt


title: embryo, TBBPA_4.5hpf_replicate2

description:
CU65
gene_fpkm-CU-50-67.txt


title: Mock, 24 hr, replicate 3


title: Mock, 24 hr, replicate 2


title: embryo, TBBPA_4.5hpf_replicate1

description:
CU64
gene_fpkm-CU-50-67.txt


title: embryo, DMSO_4.5hpf_replicate4

description:
CU63
gene_fpkm-CU-50-67.txt


title: Fibroblast, healthy, rep 2

value: Fibroblast

value: WT


title: embryo, DMSO_4.5hpf_replicate3

description:
CU62
gene_fpkm-CU-50-67.txt


title: Fibroblast, healthy, rep 1


title: Golph3 sh3

city: Bunkyo-ku

first: Junya

last: Arai

state: Tokyo

address: Clinical reserch center A #422 7-3-1 Hongo

country: Japan

institute: University of Tokyo

data_processing:
RaNA (https://ranaseq.eu/contact)
Read count extraction and normalization were performed with RaNa website.
Assembly: mm10
Supplementary files format and content: Tab-delimited tsv file included raw counts for each samples.

growth_protocol: Grown in RPMI1640 supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was harvested using the isogen with spin column kit (NIPPON-GENE).
RNA libraries for RNA sequence were prepared using TruSeq Stranded mRNA Library Prep kit.

value: Golph3 shRNA adenoivirus treatment


title: Golph3 sh2


title: Astrocyte (D40), cytokine stimulated, rep 3


title: S1393Nr50_LoVo_C2

value: Colon Cancer

value: LoVo

value: epithelial cells


title: 10 cGy IR, 3 hr, replicate 3

value: Whole rosette

value: 10 cGy IR

value: 3 h


title: 100 cGy IR, 3 hr, replicate 1

value: 100 cGy IR


title: embryo, TBBPA_3.5hpf_replicate4

description:
CU57
gene_fpkm-CU-50-67.txt

value: whole embryo

value: wildtype

value: TBBPA

value: 3.5 hpf


title: Golph3 sh1


title: embryo, DMSO_4.5hpf_replicate1

description:
CU60
gene_fpkm-CU-50-67.txt

value: DMSO


title: embryo, TBBPA_3.5hpf_replicate3

description:
CU56
gene_fpkm-CU-50-67.txt


title: 100 cGy IR, 3 hr, replicate 2


title: shcont3

value: Control shRNA adenoivirus treatment


title: Fibroblast, healthy, rep 3


title: 10 cGy IR, 3 hr, replicate 1


title: shcont2


title: Astrocyte (D40), control, rep 1

value: Fibroblast-derived induced Astrocyte

value: Astrocyte differentiation


title: shcont1


title: embryo, TBBPA_3.5hpf_replicate1

description:
CU54
gene_fpkm-CU-50-67.txt


title: Mock, 24 hr, replicate 1

value: Mock


title: 100 cGy IR, 3 hr, replicate 3


title: embryo, DMSO_4.5hpf_replicate2

description:
CU61
gene_fpkm-CU-50-67.txt

value: 4.5 hpf


title: Mock, 3 hr, replicate 2


title: Mock, 3 hr, replicate 3


title: embryo, DMSO_3.5hpf_replicate4

description:
CU53
gene_fpkm-CU-50-67.txt


title: p53KO, Day 29 rep 2

city: New York

first: Rei

last: Kudo

state: NY

address: 417 E 68th Street

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol: RNA was extracted by using Rneasy Mini kit (Qiagen).

treatment_protocol: MCF7 cells were treated with 50 nM abemaciclib (Selleck) for indicated days.

value: breast cancer cell

value: TP53 knockout

value: abemaciclib

value: day 29


title: HepG2,formononetin,rep3 [FMNTc3]

city: luzhou

first: chun

last: li

state: sichuan

address: No. 182 Chunhui Road, Longmatan District

institute: the Affiliated Traditional Chinese Medicine  Hospital of Southwest Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Trimmed sequence were Mapped to GRCh38 whole genome using STAR(2.5.3a) with parameters --twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5.
Raw counts were calculated using StringTie(v1.3.1c).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal calf serum, 100 U/ml penicillin, and 100 mg/ml streptomycin at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng totalRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA-seq Kit following manufacturer's protocols.

treatment_protocol: Cells were intervened with 625μm formononetin for 72h.

value: liver

value: human hepatoma

value: WT

value: formononetin


title: HepG2,formononetin,rep2 [FMNTc2]


title: embryo, DMSO_3.5hpf_replicate3

description:
CU52
gene_fpkm-CU-50-67.txt

value: whole embryo

value: wildtype


title: embryo, DMSO_3.5hpf_replicate2

description:
CU51
gene_fpkm-CU-50-67.txt

value: 3.5 hpf


title: p53KO, Day 29 rep 1


title: embryo, DMSO_3.5hpf_replicate1

description:
CU50
gene_fpkm-CU-50-67.txt

value: DMSO


title: Mock, 3 hr, replicate 1

value: Whole rosette

value: 3 h


title: 100 cGy IR, 1 hr, replicate 3

value: 100 cGy IR

value: 1 h


title: HepG2,control,rep3 [Cona3]

value: DMEM


title: 10 cGy IR, 3 hr, replicate 2

value: 10 cGy IR


title: HepG2,formononetin,rep1 [FMNTc1]


title: embryo, TBBPA_3.5hpf_replicate2

description:
CU55
gene_fpkm-CU-50-67.txt

value: TBBPA


title: p53KO, Day 21 rep 1

value: breast cancer cell

value: TP53 knockout

value: abemaciclib

value: day 21


title: Vis5-4B

city: Bethesda

first: Neelam

last: Sinha

state: Maryland

address: 4998, BATTERY LN, APT 206

department: NHGRI

institute: NIH

description: Leica DMi8 brightfield/widefield

data_processing:
We used Spaceranger version 2.1.1 with default parameters, software made by 10X genomics, to process the raw Visium Spatial Gene Expression data and generate quality-controlled gene expression values associated with each spatial location (“Spatial Transcriptomics - 10x Genomics,” n.d.). We then employed SpotClean to correct for the INS bleed that we observed in the original visualization (Ni et al., 2022).
Supplementary files format and content: h5
Library strategy: Spatial transcriptomics

source_name: Pancreas

extract_protocol: 10X Genomics Visium Spatial Gene Expression protocol

treatment_protocol: tissue flash frozen with isopentane and stored in liquid nitrogen

value: Pancreas


title: 100 cGy IR, 1 hr, replicate 2


title: HepG2,control,rep2 [Cona2]

value: liver

value: human hepatoma

value: WT


title: 100 cGy IR, 1 hr, replicate 1


title: p53KO, Day 5 rep 2

value: day 5


title: Vis5-4A

description: Leica DMi8 brightfield/widefield


title: HepG2,control,rep1 [Cona1]


title: p53KO, Day 5 rep 1


title: 10 cGy IR, 1 hr, replicate 3


title: Vis5-3B

description: Leica DMi8 brightfield/widefield

value: NGT


title: 10 cGy IR, 1 hr, replicate 2

value: Whole rosette


title: p53KO, Day 3 rep 2

value: day 3


title: GSC11 dbcAMP  rep3

city: Guangzhou

first: Zixi

last: Qin

address: Department of Pathology, Medical College, Jinan University, Guangzhou, 510632, P. R. China

institute: Jinan university

data_processing:
Illumina Casava1.4 software used for basecalling.
Data were filtered the low-quality sequences, including adapter sequence and low-quality bases (mass value ≤20) using the software FASTP.
Reads were referenced to the genome using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software.
Reads were calculated using fragments per kilobaseof exon per million fragments mapped (FPKM) software.
Genome_build: mm10

source_name: glioma stem cell

growth_protocol: GSC11 were cultured under clonal conditions in low-adherence plates (Corning) and maintained in DMEM/F12 medium supplemented with 2% B27 (Gibco), 20 ng/mL basic fibroblast growth factor (bFGF) (Gibco), and 10 ng/mL epidermal growth factor (EGF) (Gibco) at 37℃ under 5% CO2. Tumor spheres were reseeded every 4 days after dissociation with Accutase (Innovative Cell Technologies).

extract_protocol:
GSC11 were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSC11 cells were treated with dbcAMP for 24 hours. cAMP expression levels were detected by ELILSA analysis after dbcAMP treatment.

value: brain

tag: tumor stage

value: Glioblastoma (Grade Ⅳ)

value: glioma stem cell

value: treated with dbcAMP for 48 hours


title: 10 cGy IR, 1 hr, replicate 1

value: 10 cGy IR

value: 1 h


title: Vis5-3A

description: Leica DMi8 brightfield/widefield


title: GSC11 dbcAMP  rep2


title: p53KO, Day 21 rep 2

value: breast cancer cell

value: TP53 knockout


title: p53KO, Day 3 rep 1

value: abemaciclib


title: Vis5-2B

description: Leica DMi8 brightfield/widefield

value: Pancreas


title: Mock, 1 hr, replicate 3

value: Mock


title: GSC11 control  rep3

value: untreated


title: Vis5-2A

description: Leica DMi8 brightfield/widefield


title: p53KO, Day 1 rep 2

value: day 1


title: Vis5-1B

description: Leica DMi8 brightfield/widefield


title: p53KO, Day 1 rep 1


title: Mock, 1 hr, replicate 2


title: Vis5-1A

description: Leica DMi8 brightfield/widefield


title: Vis3-D

description: Leica DMi8 brightfield/widefield


title: GSC11 control  rep1


title: p53KO, Day 0 rep 1

value: day 0


title: D105T72 culture 3h

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using DESeq2.

source_name: human monocytes

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.
Sequencing was performed in 13 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end) with an average depth of 40 millions of clusters per sample.

treatment_protocol: Human CD14+ monocytes were cultured with or without IL-4, in presence of AhR inhibitor or agonist, for 3h or 6h.

tag: donor

tag: agent

tag: time point

value: culture 3h


title: GSC11 control  rep2


title: MCF7 parental, Day 29 rep 2

value: WT

value: day 29


title: Vis3-C

description: Leica DMi8 brightfield/widefield


title: D105T71 culture 3h


title: Vis3-B

description: Leica DMi8 brightfield/widefield

value: NGT


title: MCF7 parental, Day 29 rep 1


title: GSC11 dbcAMP  rep1

value: brain

value: Glioblastoma (Grade Ⅳ)


title: MCF7 parental, Day 21 rep 2

value: day 21


title: Vis3-A

description: Leica DMi8 brightfield/widefield


title: D105T69 culture 3h

value: FICZ


title: Mock, 1 hr, replicate 1

value: Whole rosette

value: 1 h


title: MCF7 parental, Day 21 rep 1

value: breast cancer cell


title: Vis2-D

description: Leica DMi8 brightfield/widefield


title: D105T68 culture 3h


title: Vis2-C

description: Leica DMi8 brightfield/widefield


title: p53KO, Day 0 rep 2

value: TP53 knockout

value: abemaciclib


title: MCF7 parental, Day 5 rep 1

value: day 5


title: D105T60 culture 3h


title: Vis2-B

description: Leica DMi8 brightfield/widefield

value: Pancreas


title: Vis2-A

description: Leica DMi8 brightfield/widefield


title: MCF7 parental, Day 5 rep 2


title: D105T59 culture 3h


title: D105T70 culture 3h


title: MCF7 parental, Day 3 rep 1

value: day 3


title: Age-matched Xenopus embryo, stage 35, sample 1

city: Medford

first: Vaibhav

middle: P

last: Pai

state: MA

address: 200 Boston Ave suite 4600

department: Biology

institute: Tufts University

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
06_Emb

data_processing:
Trim adapter and polyX tails: The RNAseq raw reads are single-end reads. The reads were trimmed for adapter “CTGTCTCTTATACACATCTCCGAGCCCACGAGAC” and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp (Chen et al., 2018).
Generating genome indexes: Xenopus laevis genome sequences and gene annotation were downloaded from the NCBI genome database, version 10.1. GenomeGenerate module of the STAR aligner (Dobin et al., 2013) was used to generate the genome indexes. STAR aligner option was set to sjdbOverhang = 75 for 76-bp reads, as was ideal.
Aligning reads to the genome: Adapter-trimmed reads were aligned to the genome using STAR aligner with the two-pass option. Reads were mapped across the genome to identify novel splice junctions in the first-pass. These new annotations were then incorporated into the reference indexes and reads were re-aligned with this new reference in the second pass. While more time-intensive, this step could aid in aligning across these junctions, especially in organisms where the transcriptome was not as well annotated. The resulting gene count table is at rsem_gene_count.tsv
Estimate expression: Gene expression was estimated from the gene alignments using RSEM tool for accurate quantification of gene and isoform expression from RNA-Seq data (Li and Dewey, 2011).The resulting gene count table is at rsem_gene_count.tsv
Filtering, normalization, and transformation: To filter out low expressing genes, we kept genes that had counts per million (CPM) more than 0.6 in at least 3 samples. There were 28009 genes after filtering. We then normalized counts by weighted trimmed mean of M-values (TMM) (Robinson and Oshlack 2010). If no normalization is needed, all the normalization factors would be 1. Here the normalization factors were between 0.78 and 1.28. To use linear models in the following analysis, we performed Voom transformation (Law et al. 2014) to transform counts into logCPM.
Differential expression analysis: To discover the differential genes, we uselimma, an R package that powers differential expression analyses(Ritchie et al. 2015). We performed moderated t-tests to detect genes that were differentially expressed
Assembly: Xenopus laevis (NCBI genome database, version 10.1)
Supplementary files format and content: tab-delimited file includes a gene count table
Supplementary files format and content: tab-delimited file includes logCPM normalized values

organism: Xenopus laevis

growth_protocol: Xenopus laevis embryos were fertilized in vitro according to standard protocols in 0.1X Marc's Modified Ringer's (MMR) solution and kept at 14oC. At stage 9 a subset of embryos were transferred to 0.75X MMR solution and the ectodermal animal cap tissue was cut out of the embryos. This tissue was allowed to heal and develop in 0.75X MMR at 14oC into autonomously-moving Xenobots by day 7.  Intact sibling embryos kept in 14oC for 7 days (reaching stage 35) were used as age-matched embryos.

extract_protocol:
A sample of Xenobot consisted of 50 pooled Xenobots and each was repeated 3 times. A sample of age-matched Xenopus embryos consisted of 10 pooled stage 35 Xenopus embryos and each was repeated 3 times. Tissue was extracted using TRI Reagent (Molecular Research Center, Inc - MRC) as per the manufacturer’s protocol, and total RNA quality and quantity was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
RNA library preparation was done with the Illumina Stranded Total RNA with Ribo-Zero Plus. Libraries were then multiplexed, and an rRNA depletion run using single-end, 75-nucleotide sequencing was performed on NextSeq 550 High Output 75 cycles.

value: whole embryo


title: shCsde1_1

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

organism: Mus musculus

source_name: Dorsal root ganglion(DRG) neuron

extract_protocol:
For Ribotag-RNA sequencing, lysate from the freshly collected cultured DRG neurons were immunoprecipitated with an anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using Rneasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (Nanopore, cDNA-PCR barcoding kit(SQK-PCB111.24))

value: Dorsal root ganglion(DRG) neuron

tag: strain

tag: developmental stage

value: adult

value: Preconditioning(Sciatic nerve injury)

tag: in vitro_viral_gene_delivery

tag: ip antibody

value: Anti-HA tag(abcam, #ab9110)


title: Age-matched Xenopus embryo, stage 35, sample 3

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
18_Emb

tag: tissue

tag: genotype

value: WT

tag: treatment


title: Control_3

description: control.tsv

tag: cell type

value: AAV-control

value: Anti-HA tag(abcam, #ab9112)


title: Control_2

description: control.tsv

value: Anti-HA tag(abcam, #ab9111)


title: shCsde1_2


title: Age-matched Xenopus embryo, stage 35, sample 2

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
12_Emb


title: shCsde1_3


title: Control_1

description: control.tsv


title: D105T58 culture 3h

value: culture 3h


title: MCF7 parental, Day 1 rep 2

tag: cell line

value: day 1


title: Xenobot, day 7, sample 3

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
13_Ctrl

source_name: derived from ectoderm

value: derived from ectoderm


title: si-USP30-AS1

city: SHENZHEN

first: Yapei

last: JIANG

state: Guangdong

address: Tsinghua University campus, Shenzhen University Town, Xili Street,  Nanshan District，Shenzhen city，Guangdong

institute: Tsinghua University

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: GRCh38 release-102
Supplementary files format and content: FASTQ Sequence Trace (.fq)

source_name: Triple-negative breast cancer

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: Triple-negative breast cancer

value: Breast cancer cell

value: USP30-AS1 Knockdown


title: D105T67 culture 3h

value: medium


title: Xenobot, day 7, sample 2

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
07_Ctrl


title: si-NC

value: Negative control


title: si-HnRNPF

value: HnRNPF Knockdown


title: MCF7 parental, Day 1 rep 1

value: breast cancer cell

value: abemaciclib


title: D105T57 culture 3h

value: FICZ


title: D105T56 culture 3h


title: Xenobot, day 7, sample 1

description:
rsem_gene_count.tsv
sv_adj_logCPM_for_plotting.tsv
01_Ctrl


title: D105T55 culture 3h


title: MCF7 parental, Day 0 rep 1

value: day 0


title: MIA PaCa-2/R treated with AMG510

city: Shanghai

first: yafang

last: Wang

address: 393 Middle Huaxia Road

institute: Shanghaitech University

data_processing:
The python toolkit bcbio: (https://bcbio-nextgen.readthedocs.io/en/latest/) was used to implement the RNA-seq analysis pipeline using human hg38 reference genome and hg38 Ensembl transcripts (Ensembl version 79).
FASTQ files were aligned to the human reference genome
Clean reads were separately aligned to the reference genome in orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software and converted into binary alignment map (BAM) files.
The value of the exon model per kilobase base fragment per million gene location fragments (FPKM) for each identified gene was calculated using Stringtie’s default parameters.
Subsequently, DESeq2 was used to identify significantly differentially expressed genes (DEGs) based on the following criteria: multiple variations and corrected p value were >2 and <0.05, respectively.
Assembly: hg38 (GRCh38) & hg38 Ensembl transcripts
Supplementary files format and content: gene.count.matrix.annot.xls
Supplementary files format and content: gene.tpm.matrix.annot.xls

source_name: pancreas

growth_protocol: MIA PaCa-2 cells were cultured in Dulbecco's modified Eagle medium (DMEM) with 10% FBS, 2.5% horse serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from MIA PaCa-2 parental and resistant treated with DMSO or AMG510 for 24 hr using TRIzol® Reagent (Invitrogen)
An RNA-seq transcriptome library was generated with a TruSeqTM RNA sample preparation kit from Illumina (San Diego, CA) using 1 μg of total RNA and sequenced by Majorbio Company (Shanghai, China)

treatment_protocol: MIA PaCa-2 parental and resistant cells were treated with DMSO or 100nM AMG510 for 24h.

value: pancreas

value: MIA PaCa-2

value: Cancer cell line


title: MK pancreas, biol rep 2

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mouse genome mm10 and sorted by coordinate using STAR v2.7.9a
BigWig files of mapped reads for each sample was generated from Bam files using deepTools bamCoverage
Assembly: mm10
Supplementary files format and content: BigWig files of mapped reads for each sample

extract_protocol:
Total RNA was extracted using Trizol followed by Invitrogen's Pure link kit following manufacturer’s instructions
Illumina NextSeq High Output 150 cycle sequencing kit was used for library making following rRNA reduction.

value: Pancreas

value: Tamoxifen oral gavage


title: D105T48 culture 3h

value: culture 3h


title: MK pancreas, biol rep 1


title: D105T47 culture 3h


title: MIA PaCa-2/R treated with DMSO

value: DMSO


title: D105T46 culture 3h


title: WT pancreas, Input, biol rep 3

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mm10 mouse genome using Bowtie2
Peak calling was performed using Homer FindPeaks tools with the "histone" mode, which takes into account both local background and corresponding input samples.
Assembly: mm10
Supplementary files format and content: bed files (identified peaks)

extract_protocol:
Chromatin was extracted from pancreatic tissue of mice 22 days after tamoxifen gavage. ChIP-seq protocol was followed as described in Fazio EN et al. (Mol Biol Cell, 2017)
Illumina NextSeq High Output 150 cycle sequencing kit was used

value: Wildtype

tag: chip antibody


title: WT pancreas, H3K04me3, biol rep 3

value: H3K4me3 (Millipore Sigma #04-745)


title: WT pancreas, H3K27me3, biol rep 3

value: H3K27me3 (Millipore Sigma #07-449)


title: D105T45 culture 3h


title: MCF7 parental, Day 3 rep 2

value: WT

value: day 3


title: HPAF-II cells, AZD4573 8 h

growth_protocol: HPAF-II cells were cultured in Eagle's Minimum Essential Medium (EMEM) with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from HPAF-II control-, or AZD4573-treated cells for 4 or 8 hr using TRIzol® Reagent (Invitrogen)
An RNA-seq transcriptome library was generated with a TruSeqTM RNA sample preparation kit from Illumina (San Diego, CA) using 1 μg of total RNA and sequenced by Majorbio Company (Shanghai, China)

treatment_protocol: HPAF-II cells were treated with vehicle or AZD4573 for short periods of time (0h, 4h, and 8h) at appropriate concentration for target engagement.

value: HPAF-II

value: KRAS G12D


title: D105T44 culture 3h


title: HPAF-II cells, AZD4573 4 h


title: MIA PaCa-2 treated with DMSO


title: D105T43 culture 3h

value: medium


title: WT pancreas, Input, biol rep 2


title: HPAF-II cells, 0 h


title: MCF7 parental, Day 0 rep 2

value: breast cancer cell

value: abemaciclib


title: WT pancreas, H3K27me3, biol rep 2


title: Th1 EM WT D18 rep1 batch1

city: North Adelaide

first: Simon

last: Barry

state: SA

address: Women’s and Children’s Hospital, Clarence Rieger Building, floor 2, 72 King William Rd

department: Robinson Research Institute

institute: University of Adelaide

data_processing:
RNA-seq raw data in FASTQ format were uploaded to the Phoenix High Performance Compute Server at The University of Adelaide. Quality control was assessed using FastQC, followed by the removal of low-quality bases and adapters with AdapterRemoval (version 2.3.2).
Expression levels were quantified using Salmon (version 1.2.1) against a decoy-aware transcriptome index constructed from GENCODE (GRCh38, Human Release 34) transcript sequences and genome assemblies.
Differential expression (DE) was analyzed using edgeR and RUVseq. Gene-level counts were derived from transcript-level data, with normalization performed using calcNormFactors. Genes with >1 count per million (CPM) in at least the minimum number of samples per group were analyzed. Unwanted variation was addressed using RUVg with k=3, incorporating negative control genes and experimental groupings into the design matrix for refined DE analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each sample.

source_name: PBMC

growth_protocol: Purified CD4+ Th1 cells were activated with anti-CD3/CD28 coated magnetic beads (Dynabeads® Human T-Activator CD3/CD28; Life Technologies), at a 1:1 bead-to-cell ratio in X-VIVO™ supplemented with 2% 1M Gibco™ N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid (HEPES; Thermo Fisher Scientific Inc.), 1% L-Glutamine (Merck, German), 5% Human Serum (Merck, German) henceforth called Complete X-VIVO (CX-VIVO) with the addition of 100 units/mL IL-2 (proleukine; Novaris, Basel, Switzerland). Cells were incubationed at 37°C with 5% CO₂ for 3 days.

extract_protocol:
RNA was extracted using miRNeasy Micro Kit (Qiagen). 10ng - 1ug of total RNA was used for the construction of sequencing libraries.
Poly-A-tailed messenger RNA (mRNA) was selected (NEBNext® Poly(A) mRNA Magnetic Isolation Module) from total RNA.  NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used to generate cDNA libraries from the isolated Th1 EM WT and KO RNA (RIN score ≥ 7). All procedures were performed according to manufacturer’s protocols. NEBNext® Multiplex Oligos for Illumina (NEB) was used for barcoding individual RNA libraries, and SPRIselect (Beckman Coulter) was used for size selection and purification.

treatment_protocol: Three sgRNAs targeting exon 3 of ZEB2 (KO) and a control sgRNA (WT) were combined with Cas9 to form ribonucleoproteins, which were then electroporated into pre-activated CD4+ Th1 cells. Subsequently, live cells were sorted into Th1 EM (CD62L-) and Th1 CM (CD62L+) for RNA extraction.

value: PBMC

value: CD4+ Th1 Tconv

tag: library batch

tag: memory status

value: EM


title: D105T36 culture 3h


title: WT pancreas, H3K04me3, biol rep 2

value: Pancreas


title: Th1 EM KO D18 rep1 batch1

value: KO


title: 100 cGy IR, 24 hr, replicate 3

extract_protocol:
Total RNA was extracted from approximately 0.1 g whole rosette tissues using the RNeasy Plant Mini Kit (Qiagen). RNA samples were quantified using a NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed using an Agilent 2100 Bioanalyzer.
RNA-seq library construction was performed by the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR, RRID:SCR_019152), using poly(A) selection and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

value: Whole rosette

value: 100 cGy IR

tag: exposure time


title: D105T35 culture 3h

value: culture 3h


title: WT pancreas, Input, biol rep 1

value: Wildtype

value: Tamoxifen oral gavage


title: WT pancreas, H3K27me3, biol rep 1

value: H3K27me3 (Millipore Sigma #07-449)


title: Th1 EM WT D16 rep1 batch2

value: WT


title: KE pancreas, Input, biol rep 3


title: Th1 CM KO D16 rep1 batch2

value: CM


title: D105T31 culture 3h


title: D105T32 culture 3h


title: D105T34 culture 3h


title: miRNAs in plasma from healthy women control Pool G21

city: Buenos Aires

first: Adriana

last: De Siervi

address: Vuelta de Obligado 2490

institute: CONICET

description: miRNAs

hyb_protocol: The hybridization protocol was performed by the service provided by the Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA)-CONICET (Dr. Patricia Demkura)

scan_protocol: The scan protocol was performed by the service provided by the Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA)-CONICET (Dr. Patricia Demkura)

data_processing: Data normalization and analysis were performed using Expression Console™ Software 1.3.1 and Affymetrix® Transcriptome Analysis Console (TAC) Software.

label: Biotin

source_name: Plasma from healthy women without MeSL

label_protocol: Samples were labeled using Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit

extract_protocol: Total RNA isolation was performed using Tri Reagent (Molecular Research Center). Before extraction 40 fmol of cel-39 synthetic miRNA was spiked to 400 µl of plasma.

tag: gender

value: female

value: plasma

tag: clinical

value: healthy women


title: KE pancreas, H3K27me3, biol rep 3


title: miRNAs in plasma from healthy women control Pool G20

description: miRNAs


title: miRNAs in plasma from healthy women with MeSL -  Pool G23

description: miRNAs

source_name: Plasma from healthy women with MeSL

value: women with MeSL


title: OPC, Slit1_1

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

data_processing:
RNA from control and Slit1 overexpression OPCs were subjected to 50-bp single-end sequencing with a BGISEQ-500 sequencer
At least 20 million clean reads of sequencing depth were obtained for each sample
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include fpkm and tpm values for each Sample

source_name: OPC

extract_protocol:
Total RNA fraction was extracted using Eastep®Super Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
vector was transfected into OPC by Lonza Kit
Slit1 was transfected into OPC by Lonza Kit

value: OPC

value: Wild type


title: OPC, DNA_1

value: control


title: miRNAs in plasma from patients with breast cancer stage IIB

description: miRNAs

source_name: Plasma from women with breast cancer

value: breast cancer; stage IIB


title: miRNAs in plasma from patients with breast cancer stage IIIA

description: miRNAs

value: breast cancer; stage IIIA


title: Th1 EM WT D10 rep1 batch2

value: PBMC

value: CD4+ Th1 Tconv

tag: donor

value: EM


title: KE pancreas, H3K04me3, biol rep 3

value: Pancreas

value: H3K4me3 (Millipore Sigma #04-745)


title: D105T24 culture 3h

tag: agent

tag: time point

value: culture 3h


title: miRNAs in plasma from healthy women with MeSL -  Pool G22

description: miRNAs


title: miRNAs in plasma from patients with breast cancer stages IIIB, IIIC and IV

description: miRNAs

value: breast cancer; stages IIIB, IIIC and IV


title: miRNAs in plasma from patients with breast cancer stage IIA

description: miRNAs

value: breast cancer; stage IIA


title: WT pancreas, H3K04me3, biol rep 1

value: Wildtype

value: Tamoxifen oral gavage


title: D105T33 culture 3h

value: FICZ


title: Th1 EM KO D16 rep1 batch2

value: KO


title: D105T23 culture 3h


title: Th1 EM KO D10 rep2 batch2


title: KE pancreas, Input, biol rep 2


title: D105T22 culture 3h


title: KE pancreas, H3K27me3, biol rep 2

value: H3K27me3 (Millipore Sigma #07-449)


title: Th1 CM WT D16 rep1 batch2

value: CM

value: WT


title: D105T21 culture 3h


title: KE pancreas, H3K04me3, biol rep 2


title: Th1 EM KO D10 rep1 batch2


title: Th1 CM WT D10 rep1 batch2


title: FTA_1_84_B_liver

city: Gainesville

last: Martyniuk

state: Florida

address: 2063 Mowry

department: Physiological Sciences

institute: University of Florida

description:
fathead minnow (Pimephales promelas)
Field study using mobile lab

scan_protocol: Microarrays were scanned using an Agilent G2505 C Microarray Scanner and Agilent Feature Extraction Software v. 10.1.1.1 was used to extract raw signal intensities from microarray images (Agilent Technologies). All quality evaluation metrics reported by the scanner were within normal ranges.

data_processing: Raw signal intensities were quantile normalized and log2 transformed. The intensities of spike-in and “dark spot” Agilent controls were used to determine the lower limit of detection for this assay (Agilent Technologies).

organism: Pimephales promelas

label_protocol: Each array contained 61,718 individual probes. RNA extracts were prepared for microarray hybridization using Agilent One-color Low Input Quick Amp Labeling kits (Agilent Technologies v. 6.9.1). Six-hundred nanograms of labeled RNA per sample were fragmented and hybridized on microarray slides for 17 hr. Slides were then washed according to the manufacturer’s instructions.

extract_protocol: RNA was extracted from tissue using Trizol Reagent and the Qiagen RNeasy plus mini kits according to the manufacturer's instructions (Qiagen LLC, Germantown, MD, USA).

value: Male

value: Liver

tag: group


title: Th1 CM KO D10 rep2 batch2

value: PBMC


title: D105T20 culture 3h


title: KE pancreas, Input, biol rep 1


title: miRNAs in plasma from patients with breast cancer stages 0 and IA

description: miRNAs

value: female

value: plasma

value: breast cancer; stages 0 and IA


title: FTA_2_REF_80_liver

hyb_protocol: Slides were then washed according to the manufacturer’s instructions.


title: FTA_2_75_liver


title: D105T19 culture 3h

value: medium


title: KE pancreas, H3K27me3, biol rep 1

value: Pancreas


title: REF_110_liver

value: REF


title: Th1 CM KO D10 rep1 batch2

value: CD4+ Th1 Tconv


title: Th1 EM WT D8 rep1 batch2

value: EM


title: REF_85_liver


title: Th1 EM KO D8 rep2 batch2


title: KE pancreas, H3K04me3, biol rep 1

value: Tamoxifen oral gavage

value: H3K4me3 (Millipore Sigma #04-745)


title: KR pancreas, Input, biol rep 3


title: D105T12 culture 3h

value: culture 3h


title: D105T11 culture 3h


title: Th1 EM KO D8 rep1 batch2

value: KO


title: D105T09 culture 3h

value: FICZ


title: Th1 CM WT D8 rep1 batch2

value: CM

value: WT


title: D105T10 culture 3h


title: KR pancreas, H3K27me3, biol rep 3

value: H3K27me3 (Millipore Sigma #07-449)


title: KR pancreas, H3K04me3, biol rep 3


title: D105T08 culture 3h


title: KR pancreas, Input, biol rep 2


title: Th1 CM KO D8 rep2 batch2

value: PBMC


title: FTA_2_74_liver

value: Male

value: Liver


title: D105T07 culture 3h


title: FTA_1_107_liver


title: FTA_1_105_liver


title: Th1 CM KO D8 rep1 batch2


title: D105T06 monocyte (time 0)

value: time 0


title: Cntl_66_liver

value: cntl


title: REF_109_liver


title: KR pancreas, H3K04me3, biol rep 2

value: Pancreas


title: KR pancreas, H3K27me3, biol rep 2


title: H3K27ac ChIP-STARR-seq output replicate 2

city: Singapore

first: Lee

last: Siggens

address: 14 medical drive, MD6, level 8

country: Singapore

institute: National University of Singapore

data_processing:
alignment with bwa to GRC38
Assembly: hg38
Supplementary files format and content: processed data are H3K27ac input and H3K27ac ChIP-STARR-seq output enriched regions across H3K27ac peaks. Scores are given as rpm for the respective data-sets. Loci are listed as genomic coordinates for GRC38 and the closest gene with gene names and ENSEMBL IDs.

growth_protocol: DMEM, sodium pyruvate, 10% FBS, 37C temprature, 5% CO2, penicillin and streptomycin

extract_protocol:
H3K27ac ChIP, Trizol and DirectZol RNA miniprep kit
PCR using overhang adaptors and susbequent NGS library prep with NEB Ultra II
Plasmid and cDNA samples amplified with primers by PCR

treatment_protocol: transfection with plasmid DNA using Jetprime

value: Human Embryonic Kidney

tag: antibody

tag: library type

value: cDNA library


title: H3K27ac ChIP-seq library cloned into modified STARR-seq vector

value: Plasmid library


title: H3K27ac ChIP-STARR-seq output replicate 1


title: D105T04 monocyte (time 0)


title: KR pancreas, H3K04me3, biol rep 1

tag: tissue

value: Tamoxifen oral gavage


title: D105T05 monocyte (time 0)


title: D105T02 monocyte (time 0)


title: Nontargetingcontrol siRNA 5_2

city: Boston

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing: raw counts

source_name: Lonza, HUCLS, ID:180767

growth_protocol: Primary human hepatic stellate cells (HSCs) were cultured routinely on coated plastic tissue culture dishes in DMEM medium supplemented with 10% FBS and 1% Pennicillin/Streptomycin.

extract_protocol:
total RNA was harvested using Direct-zol RNA Miniprep Kits (Zymo Research)
Stranded libraries were prepared from polyA-selected RNA, and paired end sequencing was performed at 150 nt (PE150). Libraries were prepared from total RNA samples with RIN scores greater than 9.

treatment_protocol: Hepatic stellate cells (HSCs) were transfected with NTC si5 (shControl), ABHD17B si1, or ABHD17B si4 for 3 days using Dharmafect-1 (Horizon Discovery).

value: Lonza, HUCLS, ID:180767

value: Hepatic Stellate Cell

tag: genotype

value: wildtype

value: siRNA5 negative control

tag: time

value: 3 days


title: KR pancreas, Input, biol rep 1

tag: treatment


title: Cntl_72_liver


title: FTA_1_82_liver


title: KR pancreas, H3K27me3, biol rep 1


title: EZ pancreas, H3K27me3, biol rep 3


title: Nontargetingcontrol siRNA 5_3

source_name: Lonza, HUCLS, ID:180768

tag: cell line

value: Lonza, HUCLS, ID:180768

tag: cell type


title: D105T03 monocyte (time 0)


title: Nontargetingcontrol siRNA 5_1

source_name: Lonza, HUCLS, ID:180766

value: Lonza, HUCLS, ID:180766


title: MFH 9N

city: Chongqing

first: Hongzhong

last: Zhou

institute: ChongQing Medical University/.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: MFH 9N adjacent nontumoral  tissue

growth_protocol: The tissue specimens were snap-frozen in liquid nitrogen and stored at −80°C for further investigation.

extract_protocol:
Total RNA was extracted from HCC tissues using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 9 pairs of primary HCC tissues with extrahepatic metastasis (EHMH) and 9 pairs of metastasis-free HCC tissues (MFH) were sequenced.

tag: metastasis status

value: Metastasis-free HCC tissues

value: adjacent nontumoral  tissue


title: EZ pancreas, H3K04me3, biol rep 3

tag: chip antibody

value: H3K4me3 (Millipore Sigma #04-745)


title: MFH 8N

source_name: MFH 8N adjacent nontumoral  tissue


title: EZ pancreas, Input, biol rep 3

source_name: Pancreas


title: EZ pancreas, H3K27me3, biol rep 2

value: H3K27me3 (Millipore Sigma #07-449)


title: FTA_2_REF_103_liver

source_name: liver

value: Male

value: Liver


title: FTA_2_98_liver


title: FTA_2_99_liver


title: REF_86_liver

value: REF


title: FTA_2_REF_78_liver


title: ABHD17B depletion with siRNA 4_3

source_name: Lonza, HUCLS, ID:180765

value: Lonza, HUCLS, ID:180765

value: ABHD17B siRNA4


title: D105T01 monocyte (time 0)

source_name: human monocytes

value: time 0


title: EZ pancreas, H3K04me3, biol rep 2

value: Pancreas

value: Tamoxifen oral gavage


title: ABHD17B depletion with siRNA 1_2

source_name: Lonza, HUCLS, ID:180761

value: Lonza, HUCLS, ID:180761

value: Hepatic Stellate Cell

value: wildtype

value: ABHD17B siRNA1


title: EZ pancreas, Input, biol rep 1


title: REF_87_liver


title: FTA_1_106_liver


title: MFH 4N

source_name: MFH 4N adjacent nontumoral  tissue


title: ABHD17B depletion with siRNA 4_2

source_name: Lonza, HUCLS, ID:180764

value: Lonza, HUCLS, ID:180764

value: 3 days


title: ABHD17B depletion with siRNA 4_1

source_name: Lonza, HUCLS, ID:180763

value: Lonza, HUCLS, ID:180763


title: MFH 7N

source_name: MFH 7N adjacent nontumoral  tissue

value: Metastasis-free HCC tissues

value: adjacent nontumoral  tissue


title: sampleno5

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Raw sequencing data were processed using Guppy basecaller (v6.5.7, Oxford Nanopore Technologies) using the high accuracy settings to generate high-quality reads. Subsequent data analysis, including alignment, transcript quantification, and differential expression analysis, was performed using Minimap2 for alignment and DESeq2 for differential expression analysis. Quality control of the sequencing data was assessed using FastQC.
Assembly: hg38

source_name: tumour

extract_protocol:
Total RNA was extracted from cell lines and tumour samples from treated mice using TRIzol reagent, followed by purification with the Direct-zol RNA Miniprep Kit (Zymo Research), which includes an on-column DNase I digestion step to remove genomic DNA
Library preparation was conducted using the cDNA-PCR Barcoding Kit V14 (SQK-PCB114.24, Oxford Nanopore Technologies) according to the manufacturer’s protocol

treatment_protocol: The antitumor activity of DMSO control and halofuginone  was tested in a Patient-Derived Xenograft (PDX) model, designated SF8894

value: tumour

value: DMSO


title: MFH 2N

source_name: MFH 2N adjacent nontumoral  tissue


title: FTA_2_97_liver

value: Male

value: Liver


title: ABHD17B depletion with siRNA 1_3

source_name: Lonza, HUCLS, ID:180762

value: Lonza, HUCLS, ID:180762


title: MFH 6N

source_name: MFH 6N adjacent nontumoral  tissue


title: REF_88_liver

value: REF


title: ABHD17B depletion with siRNA 1_1


title: EZ pancreas, Input, biol rep 2

value: Pancreas


title: EZ pancreas, H3K27me3, biol rep 1

value: Tamoxifen oral gavage

value: H3K27me3 (Millipore Sigma #07-449)


title: MFH 1N

source_name: MFH 1N adjacent nontumoral  tissue


title: FTA_2_100_B_liver


title: MFH 5N

source_name: MFH 5N adjacent nontumoral  tissue


title: Cntl_68_liver

value: cntl


title: MFH 3N

source_name: MFH 3N adjacent nontumoral  tissue


title: EZ pancreas, H3K04me3, biol rep 1

value: H3K4me3 (Millipore Sigma #04-745)


title: MFH 9T

source_name: MFH 9T HCC tissue

value: HCC tissues


title: MKE pancreas, biol rep 1

source_name: Pancreas


title: sampleno30

value: Halofuginone


title: sampleno3


title: MFH 8T

source_name: MFH 8T HCC tissue


title: MKE pancreas, biol rep 3


title: sampleno33


title: Cntl_64_liver

source_name: liver


title: sampleno2


title: MFH 7T

source_name: MFH 7T HCC tissue


title: KE pancreas, biol rep 2


title: FTA_2_REF_79_liver


title: Cntl_67_liver


title: sampleno29


title: KE pancreas, biol rep 1


title: sampleno28


title: MKE pancreas, biol rep 2


title: MFH 4T

source_name: MFH 4T HCC tissue


title: FTA_2_REF_77_liver


title: sampleno31


title: Cntl_70_liver


title: sampleno1


title: MFH 3T

source_name: MFH 3T HCC tissue


title: KE pancreas, biol rep 3


title: Cntl_71_liver


title: MFH 2T

source_name: MFH 2T HCC tissue


title: myocardial infarction Sham full length

city: Beijing

first: Xia

last: Binbin

state: Beijing

address: NO.1 Beichen West  Road, Chaoyang District

institute: The Institute of Microbiology of the Chinese Academy of Sciences

description:
MISham-FL
raw_count_gene.tsv
tpm_transcript.csv

data_processing:
Fast5 files were basecalled by Guppy (version 5.0.11) to generate fastq files
Pychopper (version 2.5.0) was used to identify full-length sequences. Nanopore data removes low quality (Q<7) and relatively short sequences (L<500)
For the alignment of short-read data, we applied Hisat2 (version 2.2.1) and Samtools (version 1.7) was used to convert sam files to bam files. Next, we used featureCounts (version 2.0.1) to quantify gene expression (with parameter "-g gene_id") and excluded rare transcripts with the sum of the reads below 10.
Transcripts (either annotated or novel) were quantified using kallisto (version 0.50.1).
Assembly: GENCODE M26 (GRCm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text files include TPM values for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated from the samples using Trizol reagents (Invitrogen, 15596018CN), where infarct core and peripheral regions were used in the MI and MISham groups, and infarct core tissue was used in the IR and IRSham groups.
The SQK-PCB109 (Oxford Nanopore Technologies) kit was used to prepare a full-length transcriptome sequencing library. In detail, 2 μM VN Primer (VNP) and 10 mM dNTPs were added and incubated at 65° C for 5 min. Then snap cooled the samples and add 5xRT Buffer, RNaseOUT, and 10 μM Strand-Switching Primer (SSP) at 42℃ for 2 min. Next, 1 μl of Maxima H Minus Reverse Transcriptase was added, which allowed the full-length transcript to be reversely transcribed into cDNA in vitro for further PCR. Sequencing uses PromethION (FLO-PRO002) to generate fast5 files and the sequencing was scheduled to run for 72 hr or stop early when there are less than 10 active pores. Reads with quality score (Q score) < 7 were filtered out to ensure the quality of sequencing. Next-generation sequencing (Illumina)-based RNAseq was applied to the same samples. In total, 16 samples were sequenced for four groups (MI, IR, MI-Sham, and IR-Sham) with four samples in each group.

value: heart

value: same as MI group


title: REF_85

source_name: excised testis

value: Testis


title: MFH 6T

source_name: MFH 6T HCC tissue

value: Metastasis-free HCC tissues


title: FTA_2_REF_103


title: EZ pancreas, biol rep 2


title: REF_110


title: MFH 5T

source_name: MFH 5T HCC tissue


title: EZ pancreas, biol rep 3


title: FTA_2_REF_101_liver


title: EZ pancreas, biol rep 1


title: Aim22_M1CD45pos_F1CD45neg and Aim23_M2CD45pos_F2CD45neg

first: Vijay

last: Kuchroo

address: 25 Shattuck Street

institute: Harvard Medical School

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Kallisto software (https://pachterlab.github.io/kallisto/)
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Lung

extract_protocol:
Following euthanization and perfusion with cold PBS through the right ventricle to clear blood and circulating immune cells, C57Bl6 mouse lungs were removed and inflated with 1-2mL of protease solution containing Collagenase Type I (catalog #17100–017, 450 U/mL; Gibco), Elastase (catalog #LS002279, 4 U/mL; Worthington Biochemical Corporation), Dispase (catalog #354235, 5 U/mL; BD Biosciences), DNaseI (catalog #10104159001, 0.33 U/mL; Roche) in DMEM/F12 (#11320033, ThermoFisher Scientific). Lungs were then diced into small pieces (<2 mm2), and incubated in 1–2 mL protease solution for 25 min at 37°C with frequent gentle agitation. Protease solution was neutralized with DMEM/F12 (#11320033, ThermoFisher Scientific) + 10% fetal bovine serum (#A3840001, ThermoFisher Scientific) and the tissue was further disrupted by gentle pipetting. Following an additional wash with DMEM/F12, the tissue was incubated for 10 min at 37°C in 2 mL Trypsin-EDTA (#59429C, Millipore Sigma) + 0.325 mg DNaseI with intermittent agitation. Trypsin was neutralized with an equal volume of DMEM-F12 + 10% FBS, and dissociated by pipetting, filtered through a 40-μm strainer, centrifuge, and resuspended in DMEM + 2% BSA. After washing, cells were stained with antibodies (CD11b (clone: M1/70), CD11c (clone: N418), CD45 (clone: 30-F11), Ep-CAM (clone: G8.8), Podoplanin (clone: 8.1.1) from BioLegend) and Fixable Viability Dye (eBioscience) for 20 minutes on ice, washed, then sorted on a BD FACSAria (BD Biosciences). For droplet-based scRNA-seq, cells were sorted into an Eppendorf tube containing 50 μl of 0.4% BSA in PBS and stored on ice until proceeding to the Single Cell Platform.
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: Lung


title: EHMH 9N

source_name: EHMH 9N adjacent nontumoral  tissue

value: HCC tissues with extrahepatic metastasis

value: adjacent nontumoral  tissue


title: ischemic reperfusion full length

description:
IR-FL
raw_count_gene.tsv
tpm_transcript.csv

value: infarct core region

value: LCA for 40 min, succeeded by reperfusion for 72 hr


title: Aim27_M2CD45neg_F2CD45pos and Aim28_M2CD45neg_F2CD45pos


title: EHMH 8N

source_name: EHMH 8N adjacent nontumoral  tissue


title: CNTL_66

value: Male

value: CNTL


title: myocardial infarction full length

description:
MI-FL
raw_count_gene.tsv
tpm_transcript.csv

value: infarct core and peripheral regions

value: 72 hr post-surgery


title: CNTL_65


title: MFH 1T

source_name: MFH 1T HCC tissue


title: Cntl_65_liver

value: Liver

value: cntl


title: Aim24_M2CD45pos_F2CD45neg and Aim26_M1CD45neg_F1CD45pos


title: sampleno27

source_name: tumour

value: tumour


title: FTA_2_76


title: ischemic reperfusion Sham full length

description:
IRSham-FL
raw_count_gene.tsv
tpm_transcript.csv

value: same as IR group


title: CFS, Estrus3

city: Karnal

first: Suneel

middle: Kumar

last: Onteru

state: HARYANA

address: Lab No 154, Animal Biochemistry Division, NDRI, Karnal

department: Animal Biochemistry

country: India

institute: NDRI

data_processing:
miRNA Seq data was analyzed through various open-source softwares as described previously [34]. Reference mature miRNA file was downloaded from mirBase whereas genome fasta and GFF files were downloaded from NCBI. Reference indexes were created using bowtie build command. FastQC tool was used to assess the overall quality of each sample. UMIs were extracted from the reads and adaptors were removed using UMI_tools as mentioned previously [34]. UMI extracted and adaptor removed reads were filtered to retain reads for downstream miRNA analysis with read length >15 bp and <30 bp using Cutadapt tool. Filtered reads were aligned initially to known bta mature miRNA sequences from miRBase (v22) using Bowtie (with parameters -n 1 -l 19 --norc --best --strata -a). Unaligned reads from the previous step were aligned to the Bos Taurus reference genome GCF_002263795.3 using Bowtie (with parameters -n 1 -l 19 --norc --best --strata -m 1). Samtools view option were used to sort and convert the SAM file into BAM file. BAM files were deduplicated using the UMI_tools dedup option –method=unique. Samtools idxstats were used to count each miRNA in every sample aligned to miRNAs whereas featurecounts tools were used to count reads aligned to miRNA coordinates in the reference genome using miRNA subset of GFF annotation file. Both mature miRNA-based counts and genome-based miRNA counts were combined into one file using R. DESeq2 was used to identify differentially expressed miRNAs and pheatmap function was used to create heatmap of log2 normalized counts.
Assembly: Bos Taurus reference genome GCF_002263795.3
Supplementary files format and content: Normalized_Counts in csv format

organism: Bubalus bubalis

source_name: cell free Saliva

extract_protocol:
Total RNA was extracted from CFS using TRIzol LS (Life Technologies, USA) as per the manufacturer's protocol. In brief, the mix of CFS and TRIzol LS was thawed on ice and kept at room temperature for 5 min. 200ul chloroform was added per 1ml of Trizol LS used and the mixture was vortexed for 20 secs followed by incubation at room temperature for 5 minute and then centrifuged at 12000g for 15 minutes. Aqueous layer containing RNA was transferred to fresh Eppendorf tube and added 1ul of linear polyacrylamide, 0.1X of 3M NaOAc and 2.5X of absolute ethanol and kept at -80 O/N and finally centrifuged at 14000g for 30 minutes to get RNA pellet. Further processing of total RNA was performed as per manufacturer instructions and finally the extracted total RNA was DNaseI digested, purified using Zymo Columns, and final RNA elution was done in 10 μL of nuclease-free water and stored at −80°C. Total RNA was sent to Genotypic Pvt Ltd, Bangalore, India for custom NGS Library preparation and subsequent generation of miRNA Seq data. RNA purity and concentrations were determined using Nanodrop spectrophotometer, Qubit and Bioanalyzer available at Genotypic Pvt Ltd, Bangalore, India.
Small RNA sequencing libraries were prepared with QIAseq® miRNA Library Kit (Cat: 331502) protocol (Qiagen, Maryland, USA). In brief, 5 ul of total RNA was used as starting material. 3’ adapters were ligated to the specific 3’OH group of miRNAs followed by ligation of 5’ adapter. Adapter ligated fragments were reverse transcribed with Unique Molecular Index (UMI) assignment by priming with reverse transcription primers. cDNA thus formed was enriched and barcoded by PCR amplification (22cycles). The 5’ and 3’ adapters sequences used in the protocol are 5’-GTTCAGAGTTCTACAGTCCGACGATC-3’ and 5’-AACTGTAGGCACCATCAAT-3’ respectively. Universal Illumina adapter sequence used in the protocol is 5’-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’. Qubit fluorometer (Thermo Fisher Scientific, MA, USA) was used to quantify sequencing library. Agilent 2100 Bioanalyzer was used to analyze the fragment size distribution. The raw miRNA Seq data of Bubalus Bubalis cell free saliva samples were deposited in National Center for Biotechnology Information (NCBI) GEO database with accession no XXXXXXX. All libraries were sequenced through Illumina Next Seq with 75 bp reads in order to generate greater than 10 million SE reads per sample as per manufacturer's instructions.

value: cell free Saliva

tag: animal id

value: Wildtype

tag: phase

value: Estrus


title: EHMH 6N

source_name: EHMH 6N adjacent nontumoral  tissue


title: EHMH 7N

source_name: EHMH 7N adjacent nontumoral  tissue


title: Aim21_M1CD45pos_F1CD45neg


title: CFS, Estrus2


title: EHMH 4N

source_name: EHMH 4N adjacent nontumoral  tissue


title: P7 whole mouse heart r6

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

institute: Montreal Heart Institute

description: Drop-seq library. R1 files contain cell barcodes, R2 files contain cDNA sequences.

data_processing:
Base calls and demultiplexing was performed using bcl2fastq (v2.17).
Raw FASTQ files for each sample were processed using kallisto and bustools (kb-python, v0.24.4, https://www.kallistobus.tools) against the ensemble reference release 98 for Mus musculus (GRCm38, primary assembly).
We utilized emptyDrops from the DropletUtils package in R (v.1.4.3, https://doi.org/10.1186/s13059-019-1662-y) to call single-cells from the raw, unfiltered digital gene expression (DGE) matrices (FDR threshold <= 1%).
Potential cell doublets were identified using the scrublet package (v.0.2.1,https://github.com/AllonKleinLab/scrublet) on a per sample basis and cells with a predicted scrublet score >= 0.25 were removed from furhter analysis.
Cells with more than 10.000 UMIs, less than 500 genes and more than 15% mitochondrial genes expressed, were further filtered out.
Genes expressed in less than 5 cells were also excluded from final analysis.
We fruther excluded red blood cells, contaminating lung cells and a potential multiplet cell cluster from the final dataset.
Genome_build: GRCm38
Supplementary_files_format_and_content: perinatheart.raw_umi_counts.final_cells.tsv: Flat tab-serparated text file with raw UMI counts for 67264 cells and 23245 genes for 36 samples (including 6 samples for E14.5 from GSE109247) used for analysis in the manuscript. Cells were filtered as descripted in data processing to remove any potential cell doublets and low quality cells.
Supplementary_files_format_and_content: perinatheart.metadata.final_cells.tsv: Metadata for all cells in perinatheart.raw_umi_counts.final_cells.tsv.

source_name: Heart

extract_protocol:
Hearts were extracted by cutting the abdominal aorta using scissors and subsequently utilizing fine tweezers and carefully pulling out the lungs together with the connected heart. Any remaining lung tissue, trachea, fat or non-cardiac tissue was carefully removed. The pulmonary veins and the inferior vena cava were cut as close to the base of the heart as possible and the pulmonary artery and aorta were cut close to the pulmonary valve and ascending aorta, respectively, to exclude the majority of these two large vessels from the tissue dissociation. Hearts were dissociated using gentleMACS C-tubes (Miltenyi Biotec, Cat-Nr:130-093-237) containing enzymatic digestion solution according to manufacturer’s protocol from the Neonatal Heart Dissociation Kit (Miltenyi Biotec, Cat-Nr: 130-098-373) using a gentleMACS Octo Dissociator (Miltenyi Biotec, Cat-Nr: 130-095-937). Single cells were co-encapsulated with barcoded microbeads to produce single cell transcriptomes attached to microparticles (STAMPS) according to the Drop-seq protocol. STAMPS were counted and PCR amplified for 13 cycles. Amplified cDNA was measured using Bioanalyzer and used for library preparation.
A modified Nextera-XT protocol as described in Macosko et al. 2015 was used to construct libraries. Illumina i7 primer were used in combination with a custom i5 primer.
scRNA-seq with Illumina i7 and custom i5 primer.

tag: strain

tag: developmental time point

tag: replicate

tag: Sex

value: M

tag: illumina flowcell

tag: litter id


title: P7 whole mouse heart r5

value: F


title: CFS, Diestrus2

value: Diestrus


title: CFS, Diestrus1


title: P7 whole mouse heart r4


title: P7 whole mouse heart r2


title: EHMH 5N

source_name: EHMH 5N adjacent nontumoral  tissue

value: HCC tissues with extrahepatic metastasis

value: adjacent nontumoral  tissue


title: FTA_2_97

tag: gender

value: Testis

tag: group


title: FTA_2_98

value: Male

tag: tissue


title: P7 whole mouse heart r3


title: CNTL_68

value: CNTL


title: CFS, Diestrus3

tag: genotype


title: EHMH 2N

source_name: EHMH 2N adjacent nontumoral  tissue


title: EHMH 3N

source_name: EHMH 3N adjacent nontumoral  tissue


title: CNTL_64


title: gl2_As_1.30h_4

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Raw reads were aligned to the Arabidopsis Information resource (TAIR10) genome using STAR (v2.5.4) with default parameters
Mapped reads were counted by HTSeq (v0.6.0)
Normalization and differential expression analysis with EdgeR
Assembly: TAIR10
Supplementary files format and content: Text format with two columns: geneID and FPKM per gene

source_name: Roots

growth_protocol: Plants were grown on horizontal plates with 0.5X MS medium for 9 days. Then, they were treated with liquid 0.5X MS medium supplemented with 60 µM As(III) for 1.5h. Each sample consisted on 30 seedlings

extract_protocol:
Total RNA was isolated using High Pure RNA Isolation kit (Roche)
Stranded mRNA-seq libraries were generated using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions.
Libraries were sequenced at single-end 50 bp in the Illumina Hi-Seq 2500 System at the Salk In stitute’s Next Generation Sequencing Core Facility

treatment_protocol: Liquid 0.5X MS media supplemented with 60 µM As(III) for 1.5h

value: Roots

tag: ecotype

tag: treatment

value: AsV

tag: time point

value: 1.5 hours


title: CFS, Estrus1


title: FTA_2_REF_104

source_name: excised testis


title: FTA_2_75


title: gl2_As_1.30h_3


title: CNTL_71


title: P7 whole mouse heart r1


title: P4 whole mouse heart r6


title: CNTL_69


title: gl2_As_1.30h_2


title: P4 whole mouse heart r4


title: P4 whole mouse heart r5


title: EHMH 9T

source_name: EHMH 9T HCC tissue

tag: metastasis status

value: HCC tissues


title: gl2_control_1.30_3

value: mock


title: gl2_As_1.30h_1


title: EHMH 8T

source_name: EHMH 8T HCC tissue


title: EHMH 7T

source_name: EHMH 7T HCC tissue


title: P4 whole mouse heart r3


title: EHMH 1N

source_name: EHMH 1N adjacent nontumoral  tissue


title: gl2_control_1.30_1


title: gl2_control_1.30_2


title: col_As_1.30h_4

value: wildtype


title: P4 whole mouse heart r1


title: FTA_2_100


title: EHMH 3T

source_name: EHMH 3T HCC tissue


title: P0 whole mouse heart r5


title: col_As_1.30h_3


title: REF_87

value: REF


title: EHMH 4T

source_name: EHMH 4T HCC tissue


title: CNTL_67


title: FTA_2_REF_78


title: REF_112


title: FTA_2_REF_79


title: P0 whole mouse heart r3


title: EHMH 5T

source_name: EHMH 5T HCC tissue


title: myocardial infarction Sham rep3

description:
MISham3
raw_count_gene.tsv
tpm_transcript.csv

source_name: heart

value: heart

tag: cell line

value: same as MI group


title: P0 whole mouse heart r2


title: EHMH 2T

source_name: EHMH 2T HCC tissue


title: P0 whole mouse heart r4


title: EHMH 6T

source_name: EHMH 6T HCC tissue


title: P4 whole mouse heart r2

value: M


title: EHMH 1T

source_name: EHMH 1T HCC tissue


title: col_As_1.30h_2


title: KO1 - Cells

city: Salt Lake City

first: Gregory

last: Ducker

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

description: Total RNA extracted from HepG2 BHMT KO cells

data_processing:
Kallisto quant - used for alignment to transcriptome GRCh38 and to quantify abundances of RNA-Seq transcripts (Galaxy Version 0.46.0.4). PARAMETERS: Perform sequence based bias correction: Yes Number of bootstrap samples: 0 Seed for the bootstrap sampling: 42 Search for fusions: No Library strandness information: Unstranded
DeSeq2 - used to measure differential expression between groups. DeSeq2 version 1.33.1 was used on R version 4.1.0.
Genome_build: GRCh38 (Homo sapiens)
Supplementary_files_format_and_content: Matrix Table with DeSeq2 output - both normalized and raw counts

source_name: HepG2 Cells

growth_protocol: HepG2 BHMT Overexpression (OE) and KO cells were grown for 48 hours in 6cm dishes in full HPLM

extract_protocol:
RNA was extracted from cells using the Qiagen RNAeasy Mini Kit.
Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus

treatment_protocol: 1 week before extraction, BHMT OE cells were treated with blasticidin for 48 hours to drive expression of BHMT.

tag: mouse strain

value: Cells

tag: cell strain

value: BHMT KO


title: KO2 - Cells


title: REF_88


title: FTA_2_REF_77


title: myocardial infarction Sham rep4

description:
MISham4
raw_count_gene.tsv
tpm_transcript.csv


title: E18.5 whole mouse heart r6

source_name: Heart

tag: strain


title: OE3 - Cells

description: Total RNA extracted from HepG2 BHMT OE cells

value: BHMT OE


title: KO3 - Cells


title: col_control_1.30h_1


title: P0 whole mouse heart r6

tag: developmental time point

value: F


title: myocardial infarction Sham rep2

description:
MISham2
raw_count_gene.tsv
tpm_transcript.csv


title: col_control_1.30h_4


title: myocardial infarction rep2

description:
MI2
raw_count_gene.tsv
tpm_transcript.csv

value: infarct core and peripheral regions

tag: cell type

value: 72 hr post-surgery


title: P0 whole mouse heart r1

tag: replicate

tag: Sex


title: myocardial infarction Sham rep1

description:
MISham1
raw_count_gene.tsv
tpm_transcript.csv


title: E18.5 whole mouse heart r3

tag: illumina flowcell

tag: litter id


title: KO5 - Tumor

description: Nude mouse injected with BHMT KO cells, total RNA extracted from tumor

source_name: Mouse Xenograft Tumor

extract_protocol:
Tumors were harvested from the nude mouse. RNA was homogenized using a Cryomill and extracted using the Qiagen RNAeasy Fibrous Mini Kit.
Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus

value: Nude

value: Solid tumor


title: E18.5 whole mouse heart r5


title: col_control_1.30h_2

value: Roots


title: col_control_1.30h_3

value: 1.5 hours


title: myocardial infarction rep3

description:
MI3
raw_count_gene.tsv
tpm_transcript.csv


title: E18.5 whole mouse heart r1


title: SH-SY5Y cells_2-AB pre-treatment_No LPS induction rep2

city: Tsukuba

first: sharmin

last: Aktar

state: Ibaraki Prefecture

department: Life and Environmental Science

institute: University of Tsukuba

description: Gene expression data from SH-SY5Y cells, maintained in culture medium for 24 h and no LPS-induced for 24h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, human; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).
RMA (SST-RMA, Transcriptome Analysis Console, version 4)

source_name: SH-SY5Y cells were maintained in culture medium for 24h and then induced with LPS solution (0 ng/mL) for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: SH-SY5Y cells  were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). SH-SY5Y cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Bio West, Nuaillé, France) and 1penicillin-streptomycin solution (Merck KGaA) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: BBEE was extracted with 70% Ethanol (1 mL) at room temperature under the dark for 2 weeks. After the extraction was completed, it was centrifuged at 1000 xg for 10 minutes and collected the supernatant. The supernatant of the extracted sample was filtered by using a 0.22 µm filter unit and stored at -20 ºC in the dark until use. Lipopolysaccharide (LPS; E. coli O111:B4) was purchased from EMD Millipore Co. (Billerica, MA USA). 5 mg of LPS was dissolved in 2 ml of PBS (-), and stored at -80 ℃ under the dark until use. SH-SY5Y cells were seeded into a 96-well plate at density of 2.0×105 cells/mL and incubated at 37 °C for 24 h. The cells were treated with or without BBEE at 37 °C for 24 h. After the BBEE treatment, the LPS solution (1 ng/ml) was added to each well and incubated for 24h and 24 h at 37 °C.

value: SH-SY5Y cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: SH-SY5Y cells _2-AB pre-treatment 24h_LPS induction 24h_rep1

description: Gene expression data from SH-SY5Y cells, pre-treated with 2-AB for 24 h and then LPS-induced for 24h

source_name: SH-SY5Y cells were treated with 0.2 mg/mL BBEE for 24 h and then induced with LPS solution (1 ng/mL) for 24 h


title: SH-SY5Y cells_2-AB  pre-treatment 24h_LPS induction 24h_rep2


title: E16.5 whole mouse heart r5


title: col_As_1.30h_1

source_name: Roots

value: AsV


title: E18.5 whole mouse heart r4


title: KO1 - Tumor


title: OE1 - Cells


title: myocardial infarction rep1

description:
MI1
raw_count_gene.tsv
tpm_transcript.csv


title: KO4 - Tumor


title: myocardial infarction rep4

description:
MI4
raw_count_gene.tsv
tpm_transcript.csv


title: OE5 - Tumor

description: Nude mouse injected with BHMT OE cells, total RNA extracted from tumor


title: SH-SY5Y cells_BBEE pre-treatment 24h_LPS induction 24h_rep2

description: Gene expression data from SH-SY5Y cells, pre-treated with BBEE for 24 h and then LPS-induced for 24h


title: ischemic reperfusion Sham rep2

description:
IRSham2
raw_count_gene.tsv
tpm_transcript.csv

value: same as IR group


title: ischemic reperfusion Sham rep3

description:
IRSham3
raw_count_gene.tsv
tpm_transcript.csv


title: KO3 - Tumor


title: OE2 - Cells


title: SH-SY5Y cells_BBEE pre-treatment 24h_LPS induction 24h_rep1


title: E16.5 whole mouse heart r6

description: Drop-seq library. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: E18.5 whole mouse heart r2


title: ischemic reperfusion Sham rep4

description:
IRSham4
raw_count_gene.tsv
tpm_transcript.csv


title: ischemic reperfusion Sham rep1

description:
IRSham1
raw_count_gene.tsv
tpm_transcript.csv


title: ischemic reperfusion rep2

description:
IR2
raw_count_gene.tsv
tpm_transcript.csv

value: infarct core region

value: LCA for 40 min, succeeded by reperfusion for 72 hr


title: OE3 - Tumor


title: ischemic reperfusion rep1

description:
IR1
raw_count_gene.tsv
tpm_transcript.csv

value: heart


title: E16.5 whole mouse heart r1

value: M


title: ischemic reperfusion rep3

description:
IR3
raw_count_gene.tsv
tpm_transcript.csv


title: E16.5 whole mouse heart r4


title: ischemic reperfusion rep4

description:
IR4
raw_count_gene.tsv
tpm_transcript.csv


title: OE4 - Tumor