title: Unirradiated Carnosine-treated LT-HSCs, rep3

city: Chongqing

first: Mengjia

last: Hu

address: Gaotanyan Street 30

institute: Third Military Medical University

description: Isolation of hematopoietic stem cells from the bone marrow of unirradiated mice after carnosine treatment

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 GRCm38 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）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

treatment_protocol: Isolation of hematopoietic stem cells from the bone marrow of unirradiated mice after saline or carnosine treatment

value: Bone marrow

value: Hematopoietic stem cells

value: Stem cells

value: Wild type

value: carnosine


title: Media_pDC_NRF2_Rep1

status: Public on Nov 28 2024

type: SRA

city: New York

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

country: USA

institute: Hospital for Special Surgery

description:
Library name: Media_pDC_NRF2_D2
CUT&RUN

library_source: genomic

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and peaks called using MACS2
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes filtered raw counts and merged peaks file
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: pDC

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. pDCs were isolated using BDCA4+ positive selection (Miltenyi Biotec: 130-090-532). pDCs were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS, penicillin/streptomycin (Invitrogen), and L-glutamine (Invitrogen).

extract_protocol: Epicypher CUT and RUN Protocol was followed

treatment_protocol: pDCs were cultured at 40,000 cells (for HDs) or at 10,000-20,000 cells (for patients with SSc and SLE) per well in a 96-U bottom plate and incubated at 37°C, 5% CO2 and 95% humidity. For TLR7 and TLR9 activation assays, pDCs were stimulated with either heat- inactivated H1N1 VR-95 influenza A virus (ATCC) at a concentration of 2 MOI/cells or with CpG C274 at 0.075μM (Guiducci et al., 2006) respectively

tag: cell type

value: pDC

tag: treatment

value: Media


title: Human_lung_normal_16

city: Barcelona

first: Ivan

last: Milenkovic

state: Catalonia

address: Dr. Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

library_source: transcriptomic

data_processing:
Basecalling using Guppy.
Demultiplexing using deeplexicon.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: EpiNano output with basecalling errors per-site, corresponding to the RNA modification levels.

molecule: total RNA

source_name: Lung

extract_protocol:
RNA was extracted using TRIzol.
dRNA libraries were done following ONT instruction manuals.

tag: tissue

value: Lung

tag: genotype

value: WT


title: Unirradiated Carnosine-treated LT-HSCs, rep2

country: China

organism: Mus musculus

tag: cell line


title: Human_lung_normal_15


title: Media_pDC_NRF2_Rep2

description:
Library name: Media_pDC_NRF2_D3
CUT&RUN


title: Unirradiated Carnosine-treated LT-HSCs, rep1


title: Human_lung_normal_14


title: Human_lung_normal_13


title: Media_pDC_NRF2_Rep3

description:
Library name: Media_pDC_NRF2_D4
CUT&RUN


title: Human_lung_normal_12


title: Human_lung_normal_10


title: Human_lung_normal_9


title: Unirradiated Saline-treated LT-HSCs, rep2

description: Isolation of hematopoietic stem cells from the bone marrow of unirradiated mice after saline treatment

value: saline


title: human hepatoma cells_rep 2

city: Iksan-Si  Jeonbuk

first: Hee-Jeong

last: Han

country: South Korea

institute: Korea Zoonosis Research Institute  Jeonbuk National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Corning® Gentest™ Plateable Human CryoHepatocytes

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) , 1x NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37°C. PHH were thawed and transferred in Cryopreserved Hepatocyte Recovery Medium (CM7000, GIBCO). Then cells were seeded on Collagen I, rat tail Coated 6-well Plates with Williams E Medium (A1217601, GIBCO). After 12 h incubation, medium was changed with long term culture media (Williams’ medium E containing B27, Glutamax (Gibco), Forskolin (20 μM), SB431542 (10 μM), IWP2 (0.5 μM), DAPT (5μM), LDN193189 (0.1 μM) and penicillin/ streptomycin).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: primary human hepatocyte cells


title: human hepatoma cells_rep 1

value: epithelial-like, tumorigenic cells


title: Human_lung_normal_20


title: Human_lung_normal_6


title: Human_lung_normal_7


title: Unirradiated Saline-treated LT-HSCs, rep1


title: primary human hepatocyte cells_rep 2


title: Human_lung_normal_5


title: Flight group Low 5mC, S17_S16

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

data_processing:
The sequence reads were mapped to the designated reference genome using STAR (Spliced Transcripts Alignment to a Reference). To evaluate the quality of the RNA-seq data, the number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes were determined with bamUtils.
Assembly: mm10
Supplementary files format and content: excel, raw counts and analyzed data

source_name: whole skin

extract_protocol:
For targeted RNA sequencing, total RNA was extracted using ABI Picopure RNA isolation kit and quality assessment was performed using Agilent 2100 Bioanalyzer.
Agilent SureSelect Custom cDNA Conversion Module, plus SSEL XTHS reagent Kit with Mouse All Exon V2 (67.1Mb).
The paired-end library was prepared with 30-200ng of RNA using Agilent SureSelect Custom cDNA Conversion Module, plus SSEL XTHS reagent Kit with Mouse All Exon V2 (67.1Mb). Sequencing was performed using NovaSeq 6000 S2 kit on Illumina NovaSeq 6000 platform with a read length of 100bp.

value: hind limb skin

value: Flight group Low 5mC


title: Human_lung_normal_4


title: Flight group Low 5mC, S16_S15


title: Human_lung_normal_3


title: Unirradiated Saline-treated LT-HSCs, rep3


title: primary human hepatocyte cells_rep 1


title: Human_lung_normal_11


title: Human_lung_normal_2


title: Human_lung_normal_8


title: human hepatoma cells_rep 3

value: Corning® Gentest™ Plateable Human CryoHepatocytes


title: Flight group Low 5mC, S14_S13


title: Human_lung_normal_1


title: Human_lung_tumor_20


title: Human_lung_tumor_19


title: Human_lung_tumor_18


title: Flight group High 5mC, S12_S11

value: Flight group High 5mC


title: Human_lung_tumor_14


title: Human_lung_tumor_16


title: Human_lung_tumor_13


title: EndMTed HUVEC 1

city: Tsu

first: Takumi

last: Kageyama

state: Mie

address: 2-174 Edobashi

department: Department of Nephro-Urologic Surgery and Andrology

country: Japan

institute: Mie University Graduate School of Medicine

description:
added_1
D01-added1.bam

data_processing:
Sequencing adaptors, low-quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.9a. The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Santa Clara, CA). The read counts allocated for each gene and transcript (Ensembl Genes 2016.12.01) were quantified using a Transcripts Per Million (TPM) method.
Statistical analysis of between two groups ("added" and "control") were performed by moderated t-test. The differentially expressed genes (DEGs) were estimated to be significant if FDR (False Discovery Rate) – corrected q-value < 0.05 and FC (Fold Change) > 1.5.
Assembly: GRCm38
Supplementary files format and content: counts.txt

source_name: HUVEC

growth_protocol: HUVECs were cultured in a medium prepared using an endothelial cell growth medium (Lonza Bioscience, CC-3162, Basel, Switzerland). Cells were cultured at 37°C in a humidified incubator with 5% CO2 and passaged at a ratio of 1:3 after reaching confluency.

extract_protocol:
otal RNA from HUVEC, and EndMT-induced HUVEC were extracted using an RNeasy Mini Kit (Qiagen Inc., #74104, Venlo, Netherlands) following the manufacturer's instructions and prepared for high-throughput sequencing. The integrity and quantity of the total RNA were measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Total RNA obtained from each sample was subjected to a sequencing library construction using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA) according to the manufacturer’s protocols.

treatment_protocol: HUVECs were seeded and allowed to reach confluence. The culture medium was replaced with endothelial cell basal medium (Lonza Bioscience, CC-3156, Basel, Switzerland), and then, to induce EndMT, cells were treated with IL-1β and TGF-β2.Human recombinant interleukin-1β and human transforming growth factor beta 2 (Thermo Fisher Scientific Inc., #200-01B and #100-35B, Waltham, MA) were used to stimulate the EndMT process at a concentration of 10 ng/mL in all experiments for 96 hours. The medium and supplements were replaced once at 48 hours.

value: HUVEC

value: Endothelial Cells

value: IL-1β + TGF-β2 treatment


title: normal HUVEC 2

description:
control_2
D05-control2.bam

value: no treatment


title: EndMTed HUVEC 3

description:
added_3
D03-added3.bam


title: Human_lung_tumor_12


title: EndMTed HUVEC 2

description:
added_2
D02-added2.bam


title: Human_lung_tumor_15


title: Flight group High 5mC, S13_S12


title: Human_lung_tumor_11


title: Flight group Low 5mC, S15_S14


title: Human_lung_tumor_10


title: Flight group High 5mC, S9_S8


title: Flight group High 5mC, S11_S10


title: Human_lung_tumor_9


title: Flight group High 5mC, S8_S7


title: Human_lung_tumor_17


title: Human_lung_tumor_8


title: Ground Control, S7_S6

value: Ground Control


title: BxPC3,plusIFNγ, Replicate6, H3K27ac HiChIP

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

data_processing:
We mapped HiChIP paired end reads to hg38 using HiC-Pro (Servant, 2015). Default settings were using to remove duplicate reads, identify valid interactions, and generate contact maps.
Valid pair files were binned to 5kb resolutions and filtered for loops that had 3 or more contacts.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
We prepared HiChIP cell libraries using H3K27ac AQuA-HiChIP method (Gryder, Khan and Stanton, 2020). We cultured BxPC-3 cells in RPMI media supplemented with 10% Serum Plus-II (Thermo Fisher) only or in RPMI media supplemented with 10% Serum Plus-II (Thermo Fisher) and 100 IU/mL IFNγ (BioLegend) for 2 days. For absolute quantification (AQuA-HiChIP), we grew 3T3 mouse fibroblasts in DMEM media (supplemented with 10% Serum Plus-II (Thermo Fisher Scientific) with no IFNγ. Then, we fixed cells in 1% formaldehyde (Sigma-Aldrich) for 10 mins and quenched to a final concentration of 125nM glycine (Sigma-Aldrich). We spiked in 2 million fixed mouse cells (with no IFNγ treatment) with 10 million of fixed treated-BxPC-3 cells or non-treated cells. The cells were lysed in 0.5% SDS (Sigma-Aldrich), quenched with 10% Triton X-100 (Sigma-Aldrich), and digested with MboI (NEB R0147M). Next, the DNA overhangs were blunted, biotinylated (ThermoFisher 19524016), and ligated. Nuclei were spun down, resuspended in nuclear lysis buffer and sonicated using a Covaris LE220 program: Fill level 10, PIP 450, Duty factor 30, CPB 200. We incubated the sheared DNA with Dynabeads Protein A (ThermoFisher 10001D) for 2 hours at 4 °C to preclear the samples. We then placed the tubes on a magnet and the supernatant was kept. We performed immunoprecipitation with a cross-species reactive H3K27ac antibody (Active Motif 39133). The samples were incubated with the antibody and Dynabeads Protein A overnight at 4 °C. We then washed, eluted and treated the samples with Proteinase K (New England Biolabs). We purified the samples using Zymo DNA Clean & Concentrator.
Biotin capture was performed with Dynabeads M-280 Streptavidin (ThermoFisher 11205D), followed by library preparation as previously described (Gryder, Khan and Stanton, 2020). We purified the amplified libraries with Illumina Sample Purification Beads. We sequenced the libraries using paired-end reads with NovaSeq 6000 S1 2x100 kit to generate 100-200 million read pairs per sample.
H3K27ac HiChIP

treatment_protocol: For IFNγ-stimulated conditions, cells were cultured in medium supplemented with 100 IU/mL human IFNγ (BioLegend) for 48 hours.

value: PDAC

value: IFNg treatment


title: HJ-4-1

city: lianyungang

first: Luyao

last: Zhang

address: tongguan

institute: Jiangsu Ocean University

description: Library name: B1

data_processing:
Raw data quality assessed with FastQC.
Quality trimming using Trimmomatic.
Alignment with HISAT2.
Redundancy and insertion fragment distribution analysis with RSeQC.Uniformity and genome structure distribution analysis with Qualimap.
Gene coverage and sequencing distribution analysis with BEDTools.
Assembly: HISAT2
Supplementary files format and content: The counts matrices provide gene expression counts across different samples. RSEM quantification files contain estimated expression levels for each gene and transcript. Quality control reports from FastQC are also included to visualize and assess the sequencing data quality.

source_name: Colorectal Carcinoma

growth_protocol: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 32µM HJ-4 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: Colorectal Carcinoma

value: Colorectal cells

value: HJ-4, 32 μM, 24 hours


title: BxPC3,plusIFNγ, Replicate5, H3K27ac HiChIP


title: DMSO-2

description: Library name: D2

extract_protocol:
One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer.
Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: WT

value: DMSO, 0.1%, 24 hours


title: DMSO-1

description: Library name: D1


title: normal HUVEC 3

description:
control_3
D06-control3.bam


title: Flight group High 5mC, S10_S9


title: Human_lung_tumor_7

value: Lung


title: Ground Control, S6_S5

value: hind limb skin


title: normal HUVEC 1

description:
control_1
D04-control1.bam


title: SFN_5_S46

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Read-count normalization and differentially expressed analyses were performed using the edgeR package from Bioconductor.
Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City CA) was used to identify and interactively explore significantly altered pathways, functional sets and gene networks, enriched among the set of DE genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: rawCounts.txt: tab delimited text file with raw counts per gene per sample

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SFN

tag: time


title: BxPC3,plusIFNγ, Replicate2, H3K27ac HiChIP


title: Human_lung_tumor_6


title: Ground Control, S5_S4


title: BxPC3,plusIFNγ, Replicate3, H3K27ac HiChIP


title: SFN_4_S45


title: BxPC3,plusIFNγ, Replicate1, H3K27ac HiChIP


title: SFN_3_S44


title: Ground Control, S4_S3


title: Human_lung_tumor_4


title: Human_lung_tumor_5


title: SFN_2_S43


title: Ground Control, S2_S1


title: Human_lung_tumor_3


title: BxPC3,noIFNγ, Replicate6, H3K27ac HiChIP


title: SFN_1_S42


title: F_7BAB_072921_blood_Control (long-term)

type: genomic

city: Cambridge

first: Sinisa

last: Hrvatin

state: MA

address: 455 Main Street

department: Whitehead Institute

institute: MIT

hyb_protocol: A Tecan liquid handler was used to automate the process from Hybridization to X-Stain

scan_protocol: Samples were scanned on the Illumina iScan System

data_processing:
The SeSaMe normalization method was used to estimate methylation levels (B-values) for each CpG site.
processed value definition: B-values provide the average methylation levels for each CpG site.  Detection P-values represent the probability of a detected signal being background fluorescence

label: Cy3 and Cy5

source_name: blood

extract_protocol: Genomic DNA was extracted using Dneasy blood and tissue kit  (QIAGEN #69506). DNA samples were normalized to between 12.5-25 ng/μL in 30 μL. DNA was bisulfite converted using the Zymo EZ DNA methylation kit (D5004).

value: blood

tag: strain

value: Control (long-term)


title: BxPC3,plusIFNγ, Replicate4, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate5, H3K27ac HiChIP


title: Human_lung_tumor_2


title: DMSO_5_S41

value: DMSO


title: Flight group Low 5mC, FLLAR01

data_processing:
Quality control of sequencing reads obtained was performed using FastQC version 0.11.8. Adapter removal was perfomed using Trim Galore! version 0.4.1. Reads were then aligned to the mouse reference genome GRCm38/mm10 using bismark v0.20.0. The spike-in control sequences were used at this step to check the bisulfite conversion rates and to validate the efficiency of the bisulfite treatment. Methylkit v1.7.0, a R/Bioconductor package, was used to perform the differential methylation analysis.
The CpG data set was filtered for low coverage (CpGs with coverage less than 10X in all samples per comparative group were discarded) and for extremely high coverage to discard reads with possible PCR bias (CpGs with coverage higher than the 99.9th percentile were discarded).
The data was then normalized for read coverage distribution between samples. A pairwise comparison was performed between groups to identify differentially methylated regions (DMRs), with a window and step size of 1000bp using logistic regression. After the p-values have been computed, methylkit uses the sliding window model (SLIM) to correct P-values to q-values for multiple comparison tests.
Statistically significant DMRs were identified with a q-value cutoff < 0.01 and a methylation difference higher than 25%. All DMRs were annotated with the R/Bioconductor package annotatr, with the refGene and CpG island annotations from UCSC.
Assembly: mm10
Supplementary files format and content: tsv files, converted cytosine detected, output for methylKit
Supplementary files format and content: csv files with differentially methylated regions

extract_protocol:
Reduced representation bisulfite sequencing (RRBS) analysis was performed using Diagenode Epigenomics Services (Diagenode, Cat# G02020000) on total DNA isolated from murine skin samples using the DNeasy Blood & Tissue Kit (Qiagen, Cat# 69504)
RRBS libraries were prepared using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030033).
100ng of genomic DNA were used to start library preparation. Following library preparation, samples were pooled together. PCR clean-up after the final library amplification was performed using a 1.45x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). RRBS library pools were sequenced on a NovaSeq6000 (Illumina) using 50 bp paired-end read sequencing (PE50).

value: Flight group Low 5mC


title: BxPC3,noIFNγ, Replicate4, H3K27ac HiChIP


title: DMSO_4_S40


title: Flight group Low 5mC, FLLAR18


title: Human_testis_tumor

source_name: Testis

value: Testis


title: Human_testis_normal


title: BxPC3,noIFNγ, Replicate1, H3K27ac HiChIP

value: no treatment


title: DMSO_3_S39


title: Ground Control, S3_S2

value: Ground Control


title: Human_lung_tumor


title: Flight group Low 5mC, FLISS02


title: DMSO_2_S38


title: Flight group High 5mC, FLLAR13

value: Flight group High 5mC


title: Flight group High 5mC, FLLAR17


title: Human_lung_normal


title: Nuclear RNA-Seq EXOSC3-dTAG plus dTAGv-1 rep 2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

data_processing:
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 to ensembl GRCh38 (default settings)
Removal of unmapped, multimapped and discordant mapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates

molecule: nuclear RNA

growth_protocol: HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
Nuclear RNA for RNA-Seq was extracted from isolated nuclei using Trizol
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: colorectal carcinoma

value: plus dTAGv-1


title: DMSO_1_S37


title: Human_lung_tumor_1


title: Flight group Low 5mC, FLISS07


title: Classical-CD45-C01

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.C01

data_processing:
DSS files with raw count data were imported into R, QC filtered according to Nanostring protocols, and normalized using GeomxTools package from Bioconductor.
Normalized data were coerced into a Seurat object and standard subsequent analyses, comprising SCTransform data integration over all patients, PCA/UMAP/tSNE dimensionality reduction and clustering, was performed using the integrated pipeline of Seurat R package.
Mixed cell deconvolution in each ROI, estimating ROI dominant cell type identity, was performed using the SpatialDecon R Package and both primary and granular matrices derived from cell profiles defined in the Human Cell Atlas (HCA) intestine dataset. Relative percentage distribution and enrichment of cell types across clusters, disease type and Pan-CK/CD45 condition was studied with Correspondence Analysis tools.
Using reverse deconvolution, genes with cell-type abundance-independent expression variation were filtered for downstream differential analysis. Identification of conserved cell type markers within each cluster and differential expression analysis between ROI conditions and NEC subtypes relied on Seurat function FindMarkers.
Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City CA) was used to identify and interactively explore significantly altered pathways, functional sets and gene networks, enriched among the set of DE genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: countsSCT.txt.gz: tab delimited text file with raw counts per gene per sample
Supplementary files format and content: AllDataHumanProtein.xlsx :  Excel file containing raw and normalized concentration values for 77 proteins for a subset of patients (n = 2 cardiac NEC, n = 2 classical NEC, ~6 ROIs/patient) used to validate transcriptomics
Supplementary files format and content: CS16_1492_1D_CS18_190_1C.png : Hi-res images of cardiac (CS16-1492-1D) and classical (CS18-190-1C) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS17_128_3B_CS19_1149_1B.png : Hi-res images of cardiac (CS17-128-3B) and classical (CS19-1149-1B) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS13_1240_CS15_843.png : Hi-res images of classical (CS13-1240 and CS15-843) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS15_1579_CS15_1962.png : Hi-res image of classical (CS15-1579) NEC tissue immunofluorescent morphological staining and ROI selection
Library strategy: Spatial Transcriptomics

extract_protocol:
Archived formalin-fixed, paraffin-embedded ileal tissue blocks were sectioned (5 µm) and stained with fluorescent antibody morphological markers, bound to UV-photocleavable oligos, for epithelial (panCK)- and immune (CD45)-rich regions.
Spatial transcriptome sequencing libraries were prepared for NanoString Digital Spatial Profiling using the human GeoMx® Whole Transcriptome Atlas kit and reagents, according to manufacturer's instructions.

tag: nec subtype

value: Classical

tag: cell subtype

tag: cluster

tag: patient


title: Nuclear RNA-Seq EXOSC3-dTAG plus dTAGv-1 rep 1


title: BxPC3,noIFNγ, Replicate3, H3K27ac HiChIP

value: PDAC


title: Flight group High 5mC, FLLAR06


title: Classical-PanCK-B12

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B12

value: PanCK+

value: PanPre


title: Nuclear RNA-Seq HCT116 minus dTAGv-1 rep 2

value: HCT116 Unmodified

value: minus dTAGv-1


title: Human_liver_normal

source_name: Liver

value: Liver

value: WT


title: BxPC3,noIFNγ, Replicate2, H3K27ac HiChIP


title: Human_liver_tumor


title: Classical-PanCK-B11

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B11


title: Nuclear RNA-Seq HCT116 minus dTAGv-1 rep 1


title: Flight group High 5mC, FLISS10

value: hind limb skin


title: Human_colon_tumor

source_name: Colon

value: Colon


title: Classical-CD45-B10

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B10

source_name: Macrophage

value: CDPre

value: Macrophage


title: Flight group High 5mC, FLISS04


title: 3' QUANT-Seq XRN2-dTAG plus dTAGv-1 plus EPAP rep 2

description:
XRN2_EPAP_antisense.bw
XRN2_EPAP_sense.bw

data_processing:
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings)
Removal of unmapped and multimapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Aligned read lengths were reduced to the 3'-most aligned nucleotide
Bigwig files were generated from split strand BAM files of the 3'-most aligned nucleotide using the bamCoverage of Deeptools, scaling samples based on aligned Drosophila S2 spike-in reads
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution S2 spike-in scaled RPKM bigwig coverage was generated from split strand merged replicates

extract_protocol:
Nuclear RNA was extracted from isolated nuclei using Trizol reagent
DNA-free & rRNA-free nuclear RNA libraries were constructed using QUANT-Seq mRNA 3′ end library preparation kit (Lexogen)

value: 4sU labelled, plus dTAGv-1, plus EPAP


title: Cardiac-PanCK-B09

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B09

value: Cardiac

value: PanCar


title: CMC_adult_liver_untreated_rep2

data_processing:
Basecalling using Guppy.
Demultiplexing using Guppy.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: CMC scores for the nanoCMC sequencing (they are calculated by comparing the treated vs untreated sample, that is why there is only one processed file per 2 raw files), as well as the EpiNano outputs for the rest of the cDNA runs;  they contain the values for mismatches, insertions and deletions per site for all cytosolic rRNA molecules, which we used to infer the presence/absence of modifications and SNPs.

extract_protocol:
RNA was extracted using TRIzol.
cDNAlibraries were done following ONT instruction manuals.


title: Ground Control, HGCISS03

value: Ground Control


title: Flight group High 5mC, FLISS01

value: Flight group High 5mC


title: 3' QUANT-Seq XRN2-dTAG plus dTAGv-1 plus EPAP rep 1

value: colorectal carcinoma


title: Cardiac-CD45-B08

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B08

value: CDCar


title: Cardiac-PanCK-B07

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B07

source_name: DC

value: PanCK+

value: DC


title: Human_colon_normal


title: Ground Control, HGCISS02


title: CMC_adult_liver_untreated_rep1


title: 3' QUANT-Seq XRN2-dTAG plus dTAGv-1 minus EPAP rep 1

description:
XRN2_antisense.bw
XRN2_sense.bw

value: 4sU labelled, plus dTAGv-1, minus EPAP


title: Cardiac-CD45-B06

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B06

source_name: Monocyte

value: Monocyte


title: Ground Control, HGCISS01


title: 3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 plus EPAP rep 2

description:
EXOSC3_EPAP_antisense.bw
EXOSC3_EPAP_sense.bw


title: Ground Control, HCLAR17


title: CMC_adult_liver_treated_rep1

value: Liver


title: 3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 plus EPAP rep 1


title: Cardiac-PanCK-B05

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B05


title: CMC_adult_brain_untreated_rep2

source_name: Brain

value: Brain

value: WT


title: Cardiac-CD45-B04

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B04


title: Ground Control, HCLAR13

value: hind limb skin


title: 3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 minus EPAP rep 2

description:
EXOSC3_antisense.bw
EXOSC3_sense.bw


title: Cardiac-PanCK-B03

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B03


title: CMC_adult_liver_treated_rep2


title: Ground Control, HCLAR01


title: 3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 minus EPAP rep 1

description:
EXOSC3_antisense.bw
EXOSC3_sense.bw


title: CMC_adult_brain_treated_rep2


title: CMC_adult_brain_untreated_rep1


title: 3' QUANT-Seq XRN2-dTAG plus dTAGv-1 minus EPAP rep 2

description:
XRN2_antisense.bw
XRN2_sense.bw


title: 3' QUANT-Seq HCT116 plus dTAGv-1 plus EPAP rep 2

description:
cont_EPAP_antisense.bw
cont_EPAP_sense.bw

value: HCT116 unmodified


title: Cardiac-CD45-B02

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B02


title: Classical-PanCK-B01

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B01

value: Classical


title: CMC_adult_brain_treated_rep1


title: Classical-CD45-A12

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A12

value: CDPre

value: Macrophage


title: CON，H3K9me3

city: beijing

first: Xuejia

last: He

address: 2 yabao road

institute: Capital Institute of Pediatrics

description: CUT&Tag

data_processing:
1 Clean Reads Filtering  Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Raw reads would be processed to get high quality clean reads according to three stringent filtering standards:  i Removing reads containing adapters;  ii Removing reads containing more than 10% of unknown nucleotides (N);  iii Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.  2 Reads Alignment  BWA[1] (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak scanning.  3 Strand Cross Correlation  Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and  binding characteristics. It is based on the fact that a high quality IP-seq experiment produces  significant clustering of enriched DNA sequence tags at locations bound by the protein of interest,  and that the sequence tag density accumulates on forward and reverse strands centered around the  binding site. SPP R package was used to calculate the correlation between forward and reverse  strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.  4 Peak Detection  MACS[2] (version: macs14)( -p 1e-3 -m 10,30) is a computational method that was designed to  identify read-enriched regions from ChIP-seq data. Dynamic Possion Distribution was used to  calculated p-value of the specific region based on the unique mapped reads. The region would be  defined as a peak when p-value<1e-5. Then, the distribute of chromosome distribution, peak width,  fold enrichment, significant level and peak summit number were displayed.  5 Peak Related Genes Annotation  According to the genomic location information and gene annotation information of peak, peak  related genes can be confirmed. Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream2k, upstream2k and exons) was performed.
Assembly: mouse genome (mm10)
Supplementary files format and content: According to the genomic location information and gene annotation information of peak, peak
Supplementary files format and content: related genes can be confirmed. Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream2k, upstream2k and exons) was performed.
Library strategy: CUT&Tag

source_name: brain

growth_protocol: Constructing a low-folate cell line. Mouse embryonic stem cells (mESCs) Sv/129 were maintained in Dulbecco’s modifed Eagle’s medium (DMEM, Gibco, USA) supplemented with 0.1  mM β-mercaptoethanol (Invitrogen, Carlsbad, USA), 0.1  mM non-essential amino acids (Invitrogen, Carls_x0002_bad, USA), 0.1  mM glutamate (Invitrogen, Carlsbad, USA), 15% fetal bovine serum (Gibco, USA), and 1000 U/ml mouse leukemia inhibitory factor (Millipore, Bill_x0002_erica, USA), cultured in culture dishes coated with 0.2% gelatin (Invitrogen, Carlsbad, USA). Constructing a low-folate cell line.After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily.

extract_protocol:
Cells/tissues crosslinked with 1% formaldehyde for 10 minutes.CUT& Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-01) in accordance with the manufacturer’s instructions.
Briefly, cells were gathered and bound to beads coated with concanavalin A, permeabilized by digitonin, and then incubated with H3K9me3 antibodies (CST, 13969).pA-Tn5 transposase was then incubated with the samples. TheDNA was extracted, amplified, and purified following transposon activation and tagmentation to create a library

treatment_protocol: 1.Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group.

value: brain

value: Brain tissue

tag: cut&tag antibody

value: normal saline


title: FA0，H3K9me3

description: CUT&Tag

value: Mouse embryonic stem cells (mESCs)

value: low folic acid(FA=0）


title: CMC_embryo_brain_untreated_rep2


title: 3' QUANT-Seq HCT116 plus dTAGv-1 minus EPAP rep 2

description:
cont_antisense.bw
cont_sense.bw

value: colorectal carcinoma


title: 3' QUANT-Seq HCT116 plus dTAGv-1 minus EPAP rep 1

description:
cont_antisense.bw
cont_sense.bw


title: CMC_embryo_brain_treated_rep2


title: Classical-PanCK-A11

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A11

value: PanCK+


title: NTD，H3K9me3

description: CUT&Tag

value: MTX


title: Classical-PanCK-A10

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A10


title: PAH_PASMC_5

city: Quebec city

first: Francois

last: Potus

address: 2725 Ch Ste-Foy

country: Canada

institute: IUCPQ-Laval university

data_processing:
Sequenced reads were mapped to the human genome assembly (GRCh38) with STAR v2.6.1a
The quantification of the transcriptome-mapped reads was perfomred using rsem
The raw counts generated from rsem were normalized using DESEQ2 and the differentially expressed genes were identified using the same software
Assembly: hg38
Supplementary files format and content: CSV files including raw or normalized counts for each sample

source_name: Pulmonary artery smooth muscle cell (PASMC)

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer’s instructions. RNA quality was checked, and RNA was quantified using a NanoDrop spectrophotometer.
RNA libraries were prepared using the TruSeq® Stranded mRNA Library

value: PAH PASMC

value: No treatment


title: CMC_embryo_brain_treated_rep1

value: Brain


title: EedKO_HNF4_rep2

city: Los Angeles

first: Unmesh

last: Jadhav

state: California

address: 1425 San Pablo Street

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

data_processing:
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Samtools version 1.17
Tracks for libraries were generated by converting bam files to  to BigWig by Deeptools for display on the UCSC browser.
Assembly: GRCm38, GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Intestine

growth_protocol: Mouse intestinal epithelial cell.

extract_protocol:
CUT&RUN was performed using EpiCypher CUTANA kit according to manufacturer protocol with the following changes. Cells were resuspended in the permeabilization buffer (CUTANA Wash Buffer, 0.01% Digitonin, and 1X protease inhibitor) directly after isolation. Cells were incubated on ice for 5 minutes and bound to Concanavalin A Beads at room temperature for 10 minutes. Bead-bound cells were resuspended in 180ul of antibody buffer (permeabilization buffer, 2mM EDTA) with 0.5 ug antibody of interest, and incubated overnight. Digestion was done at 4C for 30minutes on a nutator. Fragment release postdigestion was done at 4C for 30 minutes and purified using SeraMag beads with 30% PEG-8000.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol:
Mouse small intestine was disected from Fetus at E12.5 and E16.5. Intestine was cut into pieces. Single cell suspension was generated by 10mM Trypsin. Epithelial cells were isolated using EasySep Release beads and Antibody againt EpCAM.
Adult Villi Cells: Fetus Intestine Epithelial: Mouse intestine was dissected and cut into 1cm pieces and treated with 5mM EDTA for 30 minutes with vigurous shaking. Villi were isolated by using 70um filter. Villi were treated by 4X TrypLE to generate single cell suspension.
HCT116: Cells were treated with DMSO or 10uM GSK-3484862 for 6 days. After 6 days cells were grwon without any DMSO or GSK-3484862 for 3 days.

value: Intestine

value: Epithelial

value: Eed fl/fl Villin-CreER-T2

value: Tamoxifen

tag: antibody

value: HNF4 (Santa Cruz Biotechnology:Catalogue # sc-374229)


title: EedKO_HNF4_rep1


title: Classical-CD45-A09

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A09

value: Classical

value: CDPre


title: PAH_PASMC_4

value: Pulmonary artery smooth muscle cell (PASMC)


title: Classical-CD45-A08

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A08


title: adult_liver_rep2

value: Liver

value: WT


title: EedKO_CTCF_rep2

value: CTCF(Diagenode:Catalogue# C15410210)


title: 3' QUANT-Seq HCT116 plus dTAGv-1 plus EPAP rep 1

value: colorectal carcinoma

value: HCT116 unmodified

value: 4sU labelled, plus dTAGv-1, plus EPAP


title: adult_liver_rep1


title: PAH_PASMC_3

value: PAH PASMC


title: PAH_PASMC_2

value: No treatment


title: Cardiac-PanCK-A07

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A07

value: Cardiac

value: PanCK+

value: PanCar


title: EedKO_CDX2_rep2

value: Intestine

value: Epithelial

value: Eed fl/fl Villin-CreER-T2

value: CDX2(Cell Signalling:Catalogue # D11D10)


title: adult_brain_rep1

value: Brain


title: PAH_PASMC_1

value: Pulmonary artery smooth muscle cell (PASMC)


title: Cardiac-CD45-A06

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A06

value: CDCar

value: Macrophage


title: CMC_embryo_brain_untreated_rep1

value: WT


title: Cardiac-PanCK-A05

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A05


title: CTRL_PASMC_4


title: E15.5_liver_embryo_rep2

value: Liver


title: CTRL_PASMC_3


title: Adult_HNF4_rep2

value: Wild Type

value: HNF4 (Santa Cruz Biotechnology:Catalogue # sc-374229)


title: Cardiac-CD45-A04

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A04

value: Monocyte


title: E15.5_liver_embryo_rep1


title: Adult_HNF4_rep1


title: Cardiac-CD45-A03

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A03


title: E15.5_brain_embryo_rep2


title: Adult_CTCF_rep2

value: CTCF(Diagenode:Catalogue# C15410210)


title: CTRL_PASMC_2

value: No treatment


title: E15.5_brain_embryo_rep1


title: CTRL_PASMC_1


title: Classical-PanCK-H09

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H09

value: Classical

value: PanCK+

value: PanPre


title: EedKO_CTCF_rep1

value: Intestine

value: Epithelial

value: Tamoxifen


title: adult_brain_rep2

value: Brain


title: PAH_PASMC_siSCRAM_3

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH PASMC

value: siSCR


title: E9.5_whole_embryo_rep2

source_name: Whole embryo

value: Whole embryo

value: WT


title: EedKO_CDX2_rep1

value: Eed fl/fl Villin-CreER-T2

value: CDX2(Cell Signalling:Catalogue # D11D10)


title: Classical-PanCK-H08

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H08


title: PAH_PASMC_siSCRAM_2


title: Adult_CDX2_rep2

value: Wild Type


title: Adult_CTCF_rep1

value: CTCF(Diagenode:Catalogue# C15410210)


title: Adult_CDX2_rep1


title: Neurons_Snord90_KO

source_name: Neurons

value: Neurons

value: Snord90 KO


title: Classical-PanCK-H06

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H06

value: Classical

value: PanCK+


title: E9.5_whole_embryo_rep1


title: PAH_PASMC_siSCRAM_1


title: E16.5_CTCF_rep2

value: Intestine


title: Neurons_WT


title: E16.5_CTCF_rep1

value: Epithelial


title: PAH_PASMC_siFOXM1_3


title: PAH_PASMC_siFOXM1_2


title: Classical-PanCK-H05

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H05

value: PanPre


title: Cardiac-PanCK-A02

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.A02

value: Cardiac

value: PanCar


title: PAH_PASMC_siFOXM1_1

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH PASMC


title: Classical-PanCK-H04

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H04


title: E16.5_CDX2_rep2


title: Classical-PanCK-H03

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H03


title: PAH_PASMC_Veh_4

value: DMSO


title: mESC_WT

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells

value: WT


title: PAH_PASMC_Veh_3


title: Classical-PanCK-H02

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H02


title: E12.5_CDX2_rep2

value: CDX2(Cell Signalling:Catalogue # D11D10)


title: Neurons_rep1


title: E12.5_CTCF_rep1

value: Wild Type


title: Neurons_rep2


title: Classical-PanCK-H01

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H01


title: NPC_rep2

source_name: NPC

value: NPC


title: Classical-PanCK-H07

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.H07


title: Classical-PanCK-G12

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G12


title: PAH_PASMC_Veh_2


title: E12.5_CDX2_rep1


title: PAH_PASMC_Veh_1


title: NPC_rep1


title: EedKO_H2AK119Ub

data_processing:
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Samtools version 1.17
Tracks for libraries were generated by converting bam files to  to BigWig by deeptools for display on the UCSC browser.
Assembly: GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol: Mouse intestine was dissected and cut into 1cm pieces and treated with 5mM EDTA for 30 minutes with vigurous shaking. Villi were isolated by using 70um filter. Villi were treated by 4X TrypLE to generate single cell suspension.

value: Eed fl/fl Villin-CreER-T2

value: Tamoxifen


title: mESC_Snord90_KO

data_processing:
Basecalling using Guppy.
Demultiplexing using deeplexicon.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: EpiNano output with basecalling errors per-site, corresponding to the RNA modification levels.

extract_protocol:
RNA was extracted using TRIzol.
dRNA libraries were done following ONT instruction manuals.

value: Snord90 KO


title: PAH_PASMC_siSCR_4

value: siSCR


title: mESC_rep2


title: EedKO_H3K36me3

value: Intestine


title: PAH_PASMC_siSCR_3


title: Classical-CD45-G10

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G10

source_name: Neutrophils

value: Classical

value: CDPre

value: Neutrophils


title: mESC_rep1


title: E16.5_CDX2_rep1

value: Epithelial


title: EedKO_H3K36me2


title: Classical-PanCK-G09

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G09

value: PanCK+

value: Monocyte


title: PAH_PASMC_siSCR_2

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH PASMC


title: Classical-PanCK-G08

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G08

value: DC


title: Adult_testis_rep3

value: Testis

value: WT


title: PAH_PASMC_siSCR_1


title: Classical-CD45-G07

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G07


title: PAH_PASMC_siAURKB_4

value: siAURKB


title: Adult_testis_rep1


title: Adult_testis_rep2


title: EedKO_H3K27me1

value: Eed fl/fl Villin-CreER-T2


title: EedKO_H3K27me2

value: Tamoxifen


title: Classical-CD45-G06

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G06


title: Adult_liver_rep3

value: Liver


title: PAH_PASMC_siAURKB_3


title: PAH_PASMC_siAURKB_2


title: Adult_liver_rep2


title: Classical-CD45-G11

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G11

source_name: Gametocytes

value: Gametocytes


title: Adult_H3K36me3

value: Intestine

value: Wild Type


title: Classical-CD45-G04

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G04

value: Classical

value: CDPre

value: Macrophage


title: PAH_PASMC_siAURKB_1


title: Adult_H2AK119Ub

value: Epithelial


title: Adult_liver_rep1


title: PAH_PASMC_Barasertib_4

value: Barasertib


title: Adult_H3K36me2


title: Classical-CD45-G02

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G02

source_name: Platelets

value: Platelets


title: EedKO_H3K27me3


title: Adult_H3K27me3


title: Adult_heart_rep3

source_name: Heart

value: Heart


title: Adult_heart_rep2


title: Classical-PanCK-G03

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G03

value: PanCK+

value: PanPre


title: PAH_PASMC_Barasertib_2

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH PASMC


title: Classical-CD45-F12

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F12

source_name: Erythroblast

value: Erythroblast


title: PAH_PASMC_Barasertib_3


title: Adult_H3K27me2


title: Adult_H3K27me1


title: Adult_brain_rep3

value: Brain

value: WT


title: PAH_PASMC_Barasertib_1


title: Carnosine-treated LT-HSCs, rep3

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 GRCm38 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）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: Hematopoietic stem cells

value: Stem cells

value: Wild type

value: Isolation of hematopoietic stem cells from the bone marrow of irradiated mice after carnosine treatment


title: Adult_heart_rep1


title: Classical-PanCK-G01

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G01

value: Classical


title: 10ug_Recovery_Rep2

value: CRC

value: CDX2(Cell Signalling:Catalogue # D11D10)


title: Classical-PanCK-G05

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.G05


title: Classical-PanCK-F11

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F11


title: Adult_brain_rep2


title: Classical-CD45-F10

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F10

source_name: Myelocyte

value: CDPre

value: Myelocyte


title: FA4，H3K9me3

description: CUT&Tag

value: Mouse embryonic stem cells (mESCs)

value: normal folic acid(FA=4）


title: 10ug_Recovery_Rep1


title: Adult_brain_rep1


title: Carnosine-treated LT-HSCs, rep1


title: Classical-PanCK-F09

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F09

value: PanCK+

value: PanPre


title: Carnosine-treated LT-HSCs, rep2


title: Newborn_testis_rep2

source_name: Testis

value: Testis


title: Saline-treated LT-HSCs, rep3

value: Isolation of hematopoietic stem cells from the bone marrow of irradiated mice after saline treatment


title: Newborn_testis_rep1

value: WT


title: Classical-PanCK-F08

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F08


title: 10ug_Rep1


title: Classical-CD45-F07

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F07

source_name: Astrocyte

value: Astrocyte


title: Saline-treated LT-HSCs, rep2

value: Bone marrow

value: Hematopoietic stem cells


title: DMSO_Recovery_Rep2

value: DMSO


title: Newborn_liver_rep2

source_name: Liver

value: Liver


title: Saline-treated LT-HSCs, rep1

value: Stem cells

value: Wild type


title: Newborn_liver_rep1


title: DMSO_Rep2

value: CRC

value: CDX2(Cell Signalling:Catalogue # D11D10)


title: Newborn_heart_rep2

value: Heart


title: nTg_S13_RHMC_5

city: Urbana

first: Thomas

last: Gaj

state: IL

address: 1406 W. Green St.

department: Bioengineering

institute: University of Illinois Urbana-Champaign

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Mus musculus Annotation Release 109 transcripts. Because reads from the mouse study contained a higher proportion of retained introns, both spliced and un-spliced transcripts from Annotation Release 109 (NCBI) were used with the three main human C9ORF72 transcript variants and EGFP-KASH with the GRCm39 reference genome as the decoy sequence for the Salmon index. Quasi-mapping was then performed with Salmon (v1.10.0) with additional arguments: --seqBias and –gcBias, which were used to correct for sequence- and GC-specific biases, --numBootstraps=30, which was used to compute bootstrap transcript abundance estimates, and –validateMappings and –recoverOrphans, which were used to improve the accuracy of mappings.
The transcript-levels counts were then read into R (v.4.3.1) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.28.0)
Assembly: GRCm39, NCBI Annotation Release 109
Supplementary files format and content: McCallister_C9BACexp_rawcounts.txt (gene level annotations and counts in tab-delimited text format)

source_name: Brain tissue

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% anti-anti at 37 C for 48 hr after transfection, at which point they were harvested.

extract_protocol:
RNA was extracted from FACS-enriched neuronal nuclei using the RNeasy Plus Mini Kit (Qiagen) and converted to complementary DNA (cDNA) using the iScript cDNA Synthesis Kit (Bio-Rad).
RNA-seq libraries were prepared with the Universal Plus Total RNAseq from Tecan. R1 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one S2 lane for 101 cycles from one end of the fragments on a NovaSeq 6000 with V1.5 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Cells were transfected with plasmids encoding the CRISPR effector protein, with either a C0ORF72-targeting crRNA or a non-targeting crRNA, via transient transfection.

value: Brain tissue

value: EGFP-KASH+ nuclei from motor cortex

value: Primary neuron

value: RfxCas13d-N2V8/S13 + EGFP-KASH


title: Classical-CD45-F06

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F06

value: Classical

value: CDPre

value: Platelets


title: DMSO_Recovery_Rep1


title: nTg_S13_RHMC_1


title: DMSO_Rep1


title: Classical-CD45-F03

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F03


title: nTg_S13_RHMC_2


title: ASO4_3

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Annotation Release 109.2020112 (NCBI)  along with the GRCh38 reference genome as the decoy sequence for the Salmon index. Quasi-mapping was then performed  with Salmon (v1.5.2) with additional arguments: --seqBias and –gcBias, which were used to correct for sequence- and GC-specific biases, --numBootstraps=30, which was used to compute bootstrap transcript abundance estimates, and –validateMappings and –recoverOrphans, which were used to improve the accuracy of mappings.
The transcript-levels counts were then read into R (v.4.2.2) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.26.1)
Assembly: GRCm39, NCBI Annotation Release 109.2020112
Supplementary files format and content: McCallister_HEK293T_rawcounts.txt: gene level annotations and counts in tab-delimited text format

source_name: Kidney

extract_protocol:
RNA was extracted from HEK293T cells using the PureLink RNA Mini Kit (Invitrogen) and converted to complementary DNA (cDNA) using the iScript cDNA Synthesis Kit (Bio-Rad).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche).  The libraries were pooled; quantitated by qPCR and sequenced on one S1 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000 with V1.5 sequencing kits.

value: Kidney

value: HEK293T cells

value: Human embyronic kidney cells

value: Wild-type

value: ASO treated cells, used as a reference sample for pairwise comparisons


title: Newborn_heart_rep1

value: WT


title: nTg_NTG_RHMC_5

value: RfxCas13d/NTG + EGFP-KASH


title: 10ug_Rep2

value: CRC


title: Newborn_brain_rep2

source_name: Brain

value: Brain


title: Classical-CD45-F02

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F02


title: Newborn_brain_rep1


title: mouse 2-29th week after HFD diet

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

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

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing: Taxonomic classification was assigned to OTU representative sequences using the Ribosomal Database Project's Naïve Bayesian Classifier v2.2 (RDP-NBC).

source_name: stool

extract_protocol:
Mouse feces were collected at different time points during the entire experiment and stored at -80 °C before extraction. Stool genomic DNA was extracted using the QIAamp PowerFecal DNA Kit (QIAGEN) and analyzed by bacterial tag-encoded 16S rDNA amplicon pyrosequencing (Beijing Genomics Institute, Shenzhen, China) according to standard protocols.
The qualified raw sequences were sent to paired-end reads merging to tags using Fast Length Adjustment of Short reads, v1.2.11 (FLASH). The tags were clustered to OTUs at 97% sequence similarity using USEARCH (v7.0.1090) and UPARSE.

value: stool


title: nTg_NTG_RHMC_4

value: Brain tissue


title: ASO4_1


title: nTg_NTG_RHMC_3

value: EGFP-KASH+ nuclei from motor cortex


title: mouse 2-20th week after HFD diet


title: Classical-CD45-F05

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F05

source_name: MSC

value: MSC


title: ASO2_3


title: E9.5_rep1

source_name: Whole embryo

value: Whole embryo


title: Classical-CD45-F04

description:
Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1001660012684.C.F04

value: Classical


title: mouse 2-16th week after HFD diet


title: nTg_NTG_RHMC_2

value: Primary neuron


title: nTg_NTG_RHMC_1


title: ASO2_1


title: mouse 2-8th week after HFD diet


title: Embryo_liver_rep1

value: Liver


title: Embryo_liver_rep2


title: N2V8_S7_2

value: Kidney

value: RfxCas13d-N2V8 with an additional crRNA, used as a reference sample for pairwise comparisons


title: N2V8_S7_3

value: HEK293T cells

value: Human embyronic kidney cells


title: nTg_GFP_RHMC_5

value: EGFP-KASH only


title: mouse 1-29th week after HFD diet


title: ASO4_2

value: Wild-type

value: ASO treated cells, used as a reference sample for pairwise comparisons


title: mouse 2-2nd week after HFD diet


title: Embryo_heart_rep1

value: Heart

value: WT


title: nTg_GFP_RHMC_4


title: nTg_GFP_RHMC_3


title: E9.5_rep2


title: Embryo_brain_rep2

value: Brain


title: N2V8_S7_1


title: nTg_GFP_RHMC_2

value: Brain tissue


title: N2V8_S4_3


title: mouse 1-16th week after HFD diet

value: stool


title: ASO2_2


title: Tg_S13_RHMC_7

value: EGFP-KASH+ nuclei from motor cortex

value: RfxCas13d-N2V8/S13 + EGFP-KASH


title: Embryo_brain_rep1


title: mouse 1-8th week after HFD diet


title: N2V8_S4_2


title: Embryo_heart_rep2


title: Tg_S13_RHMC_6


title: N2V8_S4_1


title: Tg_S13_RHMC_4


title: sprague-Dawley,phosphatase inhibitor Lats-1,Day7_y5

city: Suzhou

first: min

last: wang

address: 242 Guangji Road

institute: Affiliated Suzhou Hospital of Nanjing Medical University

data_processing:
Quality control, Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel transcripts prediction.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: Rattus_norvegicus.Rnor_6.0.97
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: myocardium

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ®spectrophotometer(IMPLEN, CA, USA) . ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system(Agilent Technologies, CA, USA）.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: myocardium

value: sprague-Dawley


title: N2V8_S3_3


title: Tg_S13_RHMC_3

value: Primary neuron


title: sprague-Dawley,phosphatase inhibitor Lats-1,Day7_y4


title: sprague-Dawley,phosphatase inhibitor Lats-1,Day7_y2


title: mouse 1-20th week after HFD diet


title: N2V8_S3_2

value: Kidney


title: Tg_S13_RHMC_2


title: rRNA depleted Drosophila brain tissue sample 1

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology

description: Library name: rRNA_1

data_processing:
Sequenced files in FASTQ format were initially assessed for quality using FastQC.
Trimmomatic was used to trim the reads as per the following parameters: -phred33 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:25 MINLEN:19.
Once high-quality reads were confirmed, alignment was performed against the Drosophila dm6 reference genome, using STAR.
Count matrix was generated using featureCounts package
Assembly: Drosophila dm6 reference genome
Supplementary files format and content: The processed data file contains the counts for PolyA enriched and rRNA depleted samples

organism: Drosophila melanogaster

extract_protocol:
5-day old adult Drosophila adult brains (N=15) of desired genotypes were dissected in 1X PBS and RNA was extracted using TRIzol method (Thermo Fisher Scientific) following the manufacturer's protocol. Quality of RNA was assessed using Agilent Tapestation 4200 before proceeding for Library preparation and sequencing.
For Poly(A)-enrichment of mRNA, Illumina libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit (E7765L) and sequenced with Illumina NovaSeq 6000 system.rRNA-depletion was performed as recommended by NEBNext RNA Depletion Core Reagent protocol. Briefly, the RNA integrity was confirmed on an Agilent Tapestation 4200 and samples with at least 7.0 RIN values were used for experiments. The total RNA (500-1000 ng), 2 μL of the 2μM probe pool, 2 μL of the 2μM NEBNext probe hybridisation buffer and nuclease free water were mixed to a total volume of 15 μL. This mixture was then incubated at 95°C for 2 min, a touchdown from 95°C to 22°C (0.1°C/sec) and a 5-min hold at 22°C.  We then added 2 μL NEBNext RNase H Reaction Buffer, 2 μL NEBNext Thermostable RNase H and 1 μL nuclease free water and incubated for 30 min at 50°C. Then RNase H treated sample was digested with DNase I and purified using NEBNext RNA Sample Purification Beads as recommended by NEBNext RNA Depletion Core Reagent protocol. The concentrations of purified RNA samples were measured using the Qubit HS RNA Assay. The purified rRNA depleted samples were taken for library preparation using NEBNext Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalogue no-E7765L) as per the manufacturer's protocol. The libraries were sequenced on Illumina NovaSeq 6000 platform with 2x100bp read length. Similarly, rRNA-depletion was performed as recommended by QIAseq FastSelect – rRNA Fly Kits protocol (Cat. No. / ID:  333262) using total RNA from Drosphila S2 cells. The rRNA-depleted samples were processed using similar protocol as described above.


title: rRNA depleted S2 cells sample

description: Library name: Qiagen_rRNA

source_name: rRNA depleted S2 cells sample

value: S2 cells


title: N2V8_S3_1

value: HEK293T cells

value: RfxCas13d-N2V8 with an additional crRNA, used as a reference sample for pairwise comparisons


title: PolyA enriched Drosophila brain tissue sample 2

description: Library name: PolyA_2


title: sprague-Dawley,phosphatase inhibitor Lats-1,Day7_y1


title: PolyA enriched S2 cells sample

description: Library name: Qiagen_PolyA

source_name: PolyA enriched S2 cells sample


title: Tg_S13_RHMC_1


title: N2V7_S7_3

value: Human embyronic kidney cells

value: RfxCas13d-N2V7 with an additional crRNA, used as a reference sample for pairwise comparisons


title: PolyA enriched Drosophila brain tissue sample 1

description: Library name: PolyA_1


title: sprague-Dawley,S282A,Day7_s7


title: Tg_NTG_RHMC_6

value: RfxCas13d/NTG + EGFP-KASH


title: N2V7_S7_2

value: Wild-type


title: sprague-Dawley,S282A,Day7_s6


title: Tg_NTG_RHMC_5


title: EedKO_H3K9me3

source_name: Intestine

extract_protocol:
~1x106 cells were fixed in 1% formaldehyde for 25 min at room temperature immediately after isolation. The reaction was stopped by addition of Glycine to a final concentration of 0.13 M.  Cells were lysed using a buffer containing 30 mM Tris-HCl (pH 8), 1% SDS, 10 mM EDTA, and protease inhibitors (Roche), and the chromatin was sonicated for 50 min using a Covaris sonicator (5-min on/off cycles at 4 °C). Debris were removed using centrifugation and the chromatin was incubated overnight at 4°C with antibody against H3K9me3 (Abcam, Ab8898). Antibody-bound chromatin was captured using magnetic beads (Themo Fisher, 10001D) and washed using low-salt (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% TritonX-100), high-salt (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% TritonX-100), and lithium chloride (10 mM Tris pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholate) buffers. Chromatin was treated with 1% SDS and 0.1 M NaHCO3 for 6 h at 65°C to reverse the cross-links and DNA was purified using columns
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

value: Intestine

value: Epithelial

value: Eed fl/fl Villin-CreER-T2

value: Tamoxifen


title: rRNA depleted Drosophila brain tissue sample 2

description: Library name: rRNA_2

value: Brain


title: sprague-Dawley,S282A,Day7_s4


title: N2V7_S4_3


title: Tg_NTG_RHMC_3

value: Brain tissue

value: EGFP-KASH+ nuclei from motor cortex


title: EedKO_rep1

extract_protocol:
50,000  cells were lysed in 50 µl cold ATAC lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) followed by centrifugation at 500 g at 4°C to isolate nuclei. Nuclei were resuspended in 50 µl transposition reaction mix with Nextera Tn5 Transposase (Illumina, FC-121-1030) and incubated for 30 min at 37°C. Transposed DNA was purified using columns (Qiagen, 28004) and amplified using high-fidelity 2X PCR Master Mix
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.


title: sprague-Dawley,S282A,Day7_s1

value: myocardium

value: sprague-Dawley


title: N2V7_S4_2

value: Kidney


title: Adult_H3K9me3

value: Wild Type


title: N2V7_S4_1

value: HEK293T cells


title: BxPC3, IgG, Replicate3, CUT&RUN

data_processing:
The fastq files were trimmed and quality-controlled with Trim Galore (version 0.6.10 with the default options in a pair-end mode. The resulting reads were aligned to hg38 using bowtie2 (version 2.4.4) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 (Langmead & Salzberg, 2012). The alignment files were sorted by coordinate, then unpaired reads were removed, and indexed with samtools (version 1.14) (Danecek et al., 2021).
For reads visualization on genome tracks, the processed bam files were merged with samtools and visualized via the Integrative Genomics Viewer (version 2.16.1) (Robinson et al., 2011).
For peak identification, peaks and summits were called with MACS2 (version 2.2.7.1) using all three individual bam files for all replicates targeting the protein of interest (-t) and all three targeting IgG as controls (-c) with options --format BAMPE --gsize 2.7e9 --keep-dup all (Zhang et al., 2008).sortRegions descend (Ramirez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
We performed CUT&RUN in BxPC-3 cells using CUTANA ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol (Skene & Henikoff, 2017). In brief, 500,000 cells were trypsinized, washed, and bound to activated Concanavalin A-conjugated paramagnetic beads (EpiCypher). The cell-bead conjugates were then resuspended in recommended buffer with 0.5 μg antibody targeting the protein of interest: Anti-BPTF (ThermoFisher Scientific A300-973A), Anti-SRF (Cell Signaling Technology 5147S), Anti-H3K4me3 (EpiCypher 13-0041k) as positive control, and Anti-IgG (EpiCypher 13-0042k) as negative control. The suspensions were incubated overnight at 4 °C with gentle shaking. Then, the cell-bead conjugates were washed twice with the kit’s permeabilization buffer, and incubated with pAG-MNase (Epicypher 15-1016) for 10 min at room temperature. Subsequently, the unbound pAG-MNase was washed away, and the MNase was activated by adding CaCl2 to a final concentration of 2 mM. The reaction was stopped after the pAG-MNase was allowed to digest and release the antibody-bound chromatin for 2 hours at 4 °C. Finally, the released DNA was purified with the spin columns provided by the kit (EpiCypher).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). The libraries were sequenced on a Illumina NextSeq 500 using 2x75bp reads.

value: PDAC

tag: cut&run antibody

value: IgG (EpiCypher 13-0042k)


title: Tg_GFP_RHMC_5

value: Primary neuron

value: EGFP-KASH only


title: N2V7_S3_3

value: Human embyronic kidney cells

value: Wild-type

value: RfxCas13d-N2V7 with an additional crRNA, used as a reference sample for pairwise comparisons


title: TAK1 inhibitor-treated immune cells

city: Strasbourg

first: Julien

last: Moehlin

address: 3 Rue Koeberlé

country: France

institute: Institute for Translational Medicine and Liver Disease (ITM)

library_source: transcriptomic single cell

data_processing:
Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the reference transcriptome Homo sapiens hg38 (including mitochondrial genes) with BWA-MEM (Anders et al. Genome Biol. 2010).
Data was demultiplexed as described in Grün et al. Nat Methods. 2014.
Mapping and generation of count tables were automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Unsupervised clustering and differential gene expression analysis was performed in R with Seurat 3.2.27 (Butler et al. Cell 2019).
Assembly: hg38
Supplementary files format and content: Comma-separated values files and matrix files

molecule: polyA RNA

source_name: Pancreatic ductal adenocarcinoma tumorspheroids

growth_protocol: Patient-derived tumorspheroids were generated from patient adenocarcinoma pancreatic tissues undergoing surgical resection. Tissue was dissociated using gentleMACS™ Octo Dissociator with Heaters and Human tumor dissociation kit (Miltenyi Biotec). CD45+ immune cells were grown in complete Mammocult medium. Other cell types were grown in 3D tumorspheroids (see Method section)

extract_protocol:
CD45+ cells were sorted by flow cytometry into 384 well cell capture plates (Single Cell Discovery, https://www.scdiscoveries.com) using SH800 cell sorter (Sony).
SORT-seq (partially robotized version of the CEL-seq2 protocol).

treatment_protocol: TAK1 inhibitor 5Z-7-oxozeaenol 25 µM or DMSO control on patient-derived tumorspheroid

value: CD45+ immune cells

value: 5Z-7-oxozeaenol or DMSO


title: Tg_NTG_RHMC_1

value: RfxCas13d/NTG + EGFP-KASH


title: sprague-Dawley,Cx43-wt,Day7_w5


title: sprague-Dawley,Cx43-wt,Day7_w3


title: sprague-Dawley,Cx43-wt,Day7_w1


title: N2V7_S7_1


title: mouse 1-2nd week after HFD diet

value: stool


title: sprague-Dawley,Cx43-wt,Day7_w4


title: Tg_GFP_RHMC_2

value: Brain tissue

value: EGFP-KASH+ nuclei from motor cortex


title: Tg_NTG_RHMC_4


title: WT_S7_3

value: RfxCas13d with an additional crRNA, used as a reference sample for pairwise comparisons


title: Tg_NTG_RHMC_2


title: N2V7_S3_1

value: Kidney


title: BxPC3, IgG, Replicate1, CUT&RUN


title: sprague-Dawley,control,Day7_v4

value: myocardium

value: sprague-Dawley


title: BxPC3, H3K4me3, Replicate3, CUT&RUN

value: PDAC

value: H3K4me3 (EpiCypher 13-0041k)


title: EedKO_rep2

value: Intestine

value: Epithelial

value: Eed fl/fl Villin-CreER-T2

value: Tamoxifen


title: sprague-Dawley,control,Day7_v3


title: BxPC3, H3K4me3, Replicate2, CUT&RUN


title: 3-Drd2

city: Wuhan

first: Youming

last: Lu

state: Hu Bei

address: No. 13, Hangkong Road, Qiaokou District

department: School of Basic Medicine and Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Paired-end sequencing was performed on cDNA library using HiSeq 6000 instrument (Illumina).
The qualified reads were mapped to human reference genome hg38 (GRCh38) using STAR split mapping algorithm.
The expression level of genes was determined based on the value of FPKM
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: Mus brain

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

treatment_protocol: The MM slices were prepared and digested in buffer that contained 10 mM Tris-Cl (pH 7.6), 50 mM NaF, 1 mM Na3VO4, 1 mM edetic acid, 1 mM benzamidine, 1 mM PMSF, 1 mg/10 ml papain, and a mixture of aprotinin, leupeptin, and pepstatin A (10 mg/ml each) for 30 min.Aspiration of fluorescent cells with glass electrodes

tag: Sex

value: male

value: Mus brain

value: neuron


title: 2-Drd2


title: WT_S7_1

value: HEK293T cells

value: Human embyronic kidney cells

value: Wild-type


title: WT_S7_2


title: sprague-Dawley,control,Day7_v2


title: N2V7_S3_2

value: RfxCas13d-N2V7 with an additional crRNA, used as a reference sample for pairwise comparisons


title: BxPC3, IgG, Replicate2, CUT&RUN

value: IgG (EpiCypher 13-0042k)


title: 1-Drd2


title: BxPC3, BPTF, Replicate3, CUT&RUN

value: BPTF (ThermoFisher Scientific A300-973A)


title: BxPC3, H3K4me3, Replicate1, CUT&RUN


title: sprague-Dawley,control,Day7_v1

value: myocardium


title: WT_S4_3

value: Kidney

value: RfxCas13d with an additional crRNA, used as a reference sample for pairwise comparisons


title: Tg_GFP_RHMC_3

value: Brain tissue

value: EGFP-KASH+ nuclei from motor cortex

value: Primary neuron

value: EGFP-KASH only


title: 8 pv

value: PV-positive


title: 7 pv

value: male


title: POINT-Seq INTS1 plus IAA rep 3

data_processing:
Adapters removed from sequencing reads using Trim Galore (paired-end mode), discarding read with length <10 bases and quality below Phred score <20.
Alignment with STAR to reference human genome GRCh38 (default settings)
Extract uniquely mapped concordant reads (MAPQ <30) using SAMTools
Merge biological replicates using and separate into forward and reverse strands using SAMTools bitwise flags.
Generate BPM normalised coverage using genomeCoveragebed from Bedtools
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution bins per million (BPM) bigwig coverage was generated from split strand merged replicates

extract_protocol:
RNA for POINT-Seq was extracted using a protocol designed by Sousa-Luis et al., 2021.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: colorectal carcinoma

value: plus IAA


title: WT_S4_2

value: HEK293T cells


title: BxPC3, BPTF, Replicate2, CUT&RUN

value: PDAC


title: POINT-Seq INTS1 plus IAA rep 2


title: WT_S4_1

value: Human embyronic kidney cells

value: Wild-type


title: BxPC3, BPTF, Replicate1, CUT&RUN


title: 6 pv

value: Mus brain

value: neuron


title: BxPC3, SRF, Replicate3, CUT&RUN

value: SRF (Cell Signaling Technology 5147S)


title: POINT-Seq INTS1 plus IAA rep 1


title: WT_S3_3

value: Kidney


title: AKK

description: 10X Chromium Next GEM 3’ v3 chemistry Single Cell kit

data_processing:
cellranger-5.0.1
Assembly: mm10

source_name: liver tumor

extract_protocol:
Tumors were cut into small pieces in ice-cold perfusion buffer and transferred to gentleMACS C tubes with four rounds of dissociation in digestion buffer with 0.5 mg/ml Collagenase IV and 0.1 mg/ml DNaseI using gentleMACS dissociator according to the manufacturer’s instructions. The cell suspensions were passed through 70 µm cell strainers prior to loading to the Percoll gradient mix to create a gradient. After centrifugation, the pellets were subjected to red blood cell lysis and resuspended in 2% FBS-PBS FACS buffer. Isolated cells were stained with an anti-CD45-APC antibody  for 45 minutes on ice. LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit was used to exclude dead cells. Isolated cells were analyzed. CD45+ cells were sorted on a BD FASCAriaIII Flow Cytometer. The cells were gated on viability (without doublets via SSC-A SSC-H gating and dead cells) for subsequent scRNA-sequencing.
The sorted live CD45+ cells stored in ice-cold FACS buffer were immediately processed according to manufacturer’s instructions by encapsulation into single cell gel beads (GEMs) and unique molecular identifier (UMI) barcoding using the Chromium Next GEM 3’ v3 chemistry Single Cell kit (10× Genomics) at The Beijing Genomics Institute. Libraries were prepared and sequenced on a NovaSeq platform (Illumina)

value: liver tumor


title: POINT-Seq INTS1 minus IAA rep 3

value: minus IAA


title: WT_S3_2

value: RfxCas13d with an additional crRNA, used as a reference sample for pairwise comparisons


title: BxPC3, SRF, Replicate2, CUT&RUN


title: PBS


title: WT_S3_1


title: BxPC3, SRF, Replicate1, CUT&RUN


title: POINT-Seq INTS1 minus IAA rep 1


title: AKK treatment, biological replicate 2

data_processing: For each sample, there is an average throughout of 24.2Gb and a total throughput of 96.9Gb. An average of 94% of the bases achieved a quality score of Q30 where Q30 denotes the accuracy of a base call to be 99.9%. STAR 2.5.2, RSEM 1.2.31 and EBSeq 1.18.0 were used to proceed alignment, expression estimation and tests for differential expression.

source_name: tumor

extract_protocol:
Total RNA was harvested from liver tumors by using the RNease Plus Mini Kit (QIAGEN).
The qualified RNA was subjected to Illumina NovaSeq 6000 sequencer, indexed library construction, Illumina sequencing run (pair-end sequencing of 151bp)

value: tumor


title: UT_3

value: Untransfected Negative Control


title: AKK treatment, biological replicate 1


title: POINT5-Seq INTS1 plus IAA rep 3

data_processing:
Adapters removed from sequencing reads using Trim Galore (paired-end mode), discarding read with length <10 bases and quality below Phred score <20.
Alignment with STAR to reference human genome GRCh38 (default settings)
Extract uniquely mapped concordant reads (MAPQ <30) using SAMTools
The 5’ end of each read in POINT-5 was extracted alongside their directionality using an adaptation of the script created for mNET-seq (Nojima et al., 2015)
Merge biological replicates using and separate into forward and reverse strands using SAMTools bitwise flags.
Generate BPM normalised coverage using genomeCoveragebed from Bedtools.
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution bins per million (BPM) bigwig coverage was generated from split strand merged replicates


title: UT_2


title: BxPC3,plusIFNγ, Replicate9, ATAC-seq

description: Ultima Genomics

data_processing:
For Illumina data, adaptors were trimmed with trimmomatic (version 0.39) with the options ILLUMINACLIP:Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:24 (Bolger, Lohse and Usadel, 2014). For Ultima data, cram files were converted to fastq using samtools (version 1.9), and trimmed using cutadapt (version 4.0) (Danecek et al., 2021; Martin, 2011).
Reads from both sequencing platforms were aligned to GRCh38 with bowtie2 (version 2.4.4) (Langmead and Salzberg, 2012), deduplicated with picard through gatk MarkDuplicates (version 4.2.5.0), and downsampled to the sample with the lowest reads using samtools, then peaks were called with MACS2 callpeak (version 2.2.7.1) with default parameters (Zhang.,2008).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
ATAC-seq was performed using homemade transposomes with minor modifications that are detailed below (Buenrostro et al.,2013; Picelli et al., 2014)). For each replicate, we trypsinized, washed, and resuspended 250,000 cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% tween-20, 0.01% digitonin) and lysed for 10 minutes on ice (Corces et al., 2017). After lysis, 50,000 cells were resuspended in transposase reaction mix (1ul Tn5 (0.5 µM), 4ul 5X TD-TAPS (50mM TAPS-NaOH, 25mM MgCl2, 50% DMF), 5ul dilution buffer (10mM Tris-HCl, pH 7.4, 100mM NaCl, 1mM DTT, 50% glycerol), 2ul 10% Tween, and 8ul PBS) and tagmentation was performed at 37°C for 30 minutes. Next, samples were purified using the Zymo Clean and Concentrate kit.
For the library preparation, DNA was amplified with NEBNext High-Fidelity 2× PCR Master Mix as previously described (Buenrostro et al.,2013). The PCR program was as followed: 72 °C for 5 minutes, 98 °C for 30 seconds, (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds) x 12 cycles. Samples were sequenced on both Illumina NextSeq 500 and Ultima Genomics platforms.

value: IFNgamma treatment


title: BxPC3,plusIFNγ, Replicate8, ATAC-seq

description: Ultima Genomics


title: PBS treatment, biological replicate 2


title: POINT5-Seq INTS1 plus IAA rep 2


title: BxPC3,plusIFNγ, Replicate7, ATAC-seq

description: Ultima Genomics


title: POINT5-Seq INTS1 plus IAA rep 1


title: PBS treatment, biological replicate 1


title: N2V8_S13_3

value: RfxCas13d-N2V87 with crRNA 13


title: BxPC3,plusIFNγ, Replicate6, ATAC-seq

description: Ultima Genomics


title: POINT5-Seq INTS1 minus IAA rep 3

value: colorectal carcinoma


title: N2V8_S13_2


title: BxPC3,plusIFNγ, Replicate5, ATAC-seq

description: Ultima Genomics


title: POINT5-Seq INTS1 minus IAA rep 2


title: BxPC3,plusIFNγ, Replicate4, ATAC-seq

description: Ultima Genomics


title: N2V8_S13_1


title: POINT-Seq INTS1 minus IAA rep 2


title: N2V8_NTG_3

value: RfxCas13d-N2V8 with NTG crRNA


title: POINT5-Seq INTS1 minus IAA rep 1


title: Circular RNA_Before IP_biological rep2

type: RNA

city: Daejeon

first: Sung Ho

last: Boo

address: 291, Daehak-ro

institute: Korea Advanced Institute of Science and Technology

description: Circular RNA_Before IP_biological rep2

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The signals were scanned using the Agilent Scanner G2505C

data_processing: Quantification was performed by Feature Extraction Software (Agilent Technology, Palo Alto, CA), and analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA)

source_name: HeLa

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3 labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (QIAGEN)

growth_protocol: HeLa cells were grown with Dulbecco’s Modified Eagles Medium (Sigma-aldrich) supplemented with 10% (vol/vol) fetal bovine serum (Sigma-aldrich) and 1% (vol/vol) penicillin/streptomycin (Sigma-aldrich)

extract_protocol: Total RNAs associated with eIF4A3 were extracted using Trizol by manufacturer's recommendations

treatment_protocol: RNA immunoprecipitations were performed using either α-eIF4A3 antibodies.

tag: gender

value: Female

value: no IP


title: BxPC3,plusIFNγ, Replicate2, ATAC-seq

description: Illumina NextSeq 500

value: PDAC


title: VSMCs, KO3

city: Guangzhou

first: Xiaoyu

last: Liu

address: 253 Industrial Avenue, Guangzhou, 510280, China

department: Department of Cardiology

institute: Zhujiang Hospital, Southern Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(parameter;default)
Clean reads were mapped to  human GRCm39.108 genome using by Hisat2（v2.2.0）
The expression level of genes were calculated by StringTie （v2.1.2） and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads.
Assembly: GRCm39.108.
Supplementary files format and content: xlsx file includes read counts for each sample

source_name: vascular smooth muscle cells

growth_protocol: mouse vascular smooth muscle cells were from wild type (WT) mice or STING-/- (KO) mice.

extract_protocol:
Total RNA of mouse vascular smooth muscle cells were extracted using TRIzol regents and RNA quality was determined using Agilent 2100 Bioanalyser.
mRNA molecules were purified from total RNA using oligo (dT)-attached magnetic beads. Then, mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperature. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesis cDNA was subjected to end-repair and then was 3'-adenylated. Adapters were ligated to the ends of these 3'-adenylated cDNA fragments. PCR was used to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 Bioanalysers.

treatment_protocol: mouse vascular smooth muscle cells were cultured in calcifying medium (CM).

value: vascular smooth muscle cells

value: KO

value: calcifying medium


title: BxPC3,plusIFNγ, Replicate1, ATAC-seq

description: Illumina NextSeq 500


title: N2V8_NTG_2

value: HEK293T cells

value: Human embyronic kidney cells

value: Wild-type


title: N2V8_NTG_1

value: Kidney


title: UT_1


title: VSMCs, KO2


title: VSMCs, KO1


title: Circular RNA_Before IP_biological rep1

description: Circular RNA_Before IP_biological rep1


title: N2V7_S13_3

value: RfxCas13d-N2V7 with crRNA 13


title: Circular RNA_eIF4A3 IP_biological rep2

description: Circular RNA_eIF4A3 IP_biological rep2

value: eIF4A3 IP


title: N2V7_S13_2


title: BxPC3,noIFNγ, Replicate8, ATAC-seq

description: Ultima Genomics

value: no treatment


title: BxPC3,noIFNγ, Replicate9, ATAC-seq

description: Ultima Genomics


title: VSMCs, WT3

value: WT


title: VSMCs, WT2


title: Circular RNA_eIF4A3 IP_biological rep1

description: Circular RNA_eIF4A3 IP_biological rep1


title: Circular RNA_siControl_BeforeIP_biological rep2

extract_protocol: Total RNAs associated with CBP80 or eIF4E were extracted using Trizol by manufacturer's recommendations

treatment_protocol: RNA immunoprecipitations were performed using either α-CBP80 or α-eIF4E antibodies.

value: siControl + Before IP


title: N2V7_NTG_3

value: RfxCas13d-N2V7 with NTG cRNA


title: VSMCs, WT1


title: N2V7_S13_1


title: BxPC3,noIFNγ, Replicate6, ATAC-seq

description: Ultima Genomics


title: BxPC3,noIFNγ, Replicate7, ATAC-seq

description: Ultima Genomics


title: BxPC3,plusIFNγ, Replicate3, ATAC-seq

description: Illumina NextSeq 500

value: IFNgamma treatment


title: Circular RNA_siControl_BeforeIP_biological rep1

value: Female


title: Circular RNA_siSMG6_BeforeIP_biological rep1

value: siSMG6 + Before IP


title: BxPC3,noIFNγ, Replicate5, ATAC-seq

description: Ultima Genomics

value: PDAC


title: N2V7_NTG_2


title: BxPC3,noIFNγ, Replicate4, ATAC-seq

description: Ultima Genomics


title: Circular RNA_siSMG6_CBP80IP_biological rep2

value: siSMG6 + CBP80 IP


title: BxPC3,noIFNγ, Replicate3, ATAC-seq

description: Illumina NextSeq 500


title: Murine skin, Healthy, Day4, Biological replicate 6, Mouse 16

city: Copenhagen

first: Kristian

middle: Kåber

last: Pedersen

address: Bispebjerg Bakke 23

department: Department of Dermatology

country: Denmark

institute: Copenhagen University Hospital – Bispebjerg

data_processing:
The raw reads were cleaned with SOAPnuke version 1.5.2 (RRID:SCR_015025, parameters: -l 15 -q 0.2 -n 0.05).
The reads were mapped to the murine genome (GRCm39, version GCA_000001635.9) with Bowtie 2 version v2.2.5 (RRID:SCR_016368; parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200).
The mapped reads were quantified using RSEM version v1.2.8 (parameters: -p 8 --forward-prob 0 --paired-end). The final result is the processed count matrix. The count matrix include gene counts with decimals because RSEM return probabilistically-weighted read alignments.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

source_name: Skin

extract_protocol:
Tissue samples were homogenized in TRIzol and RNA isolated with chloroform. Total RNA was harvested using the Nucleospin RNA kit which includes DNAse treatment (Machery-Nagel).
Library preparation was performed using the MGIEasy RNA Directional Library Prep Set, which uses oligo dT primers for mRNA enrichment

treatment_protocol:
To induce basal cell carcinoma in the murine skin we gave the mice Tamoxifen (3 i.p. injections with 300 µg tamoxifen) and treated them with x-ray (1 irradiation, 4 Gy over 2.05 minutes)
Induced skin then received one of the following treatments: no treatment; ablative fractional laser (1 treatment; 5% density, 40 mJ/microbeam, 1 pass); vismodegib (8 treatments, twice daily)

value: Skin

value: Ptch1+/- K14-CreER2 p53fl/fl

tag: time from_treatment

tag: age (days)

tag: disease

tag: tumor state

tag: group

tag: tumor induction

value: No treatment


title: Murine skin, Healthy, Day4, Biological replicate 3, Mouse 14

tag: tissue

tag: treatment