title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: TT-44

status: Public on Dec 31 2021

type: SRA

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

country: USA

institute: Tenaya Therapeutics Inc.

library_source: transcriptomic

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl mus musculus annotations (GRCm38, Apr 2020) release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Cardiac Tissue

growth_protocol: iPSC culture, iPSC-CM differentiation, and blasticidin selection:   WTC iPSCs and derivative lines were fed daily with E8 medium (STEMCELL Technologies) and cultured under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences). iPSCs were dissociated non-enzymatically using 0.5 μM ethylenediaminetetraacetic acid (EDTA) (Thermo Fisher Scientific) and passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10 μM; Selleckchem). iPSCs were frozen in BamBanker human iPSC Freeze Media (Thermo Fisher Scientific). Differentiation of iPSCs was induced through the Wnt modulation method with 7 μM of glycogen synthase kinase 3 b (GSK3b) inhibitor CHIR99021 (Selleckchem) and 5 μM of inhibitor of WNT production 2 (IWP2) (Sigma). Basal Media was composed of RPMI media supplemented with B27 (Thermo Fisher Scientific). As previously described, we generated a blasticidin-selectable iPSC line to purify our iPSC-CMs using 1 μM blasticidin (Thermo Fisher Scientific). Eighteen days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum with 10% dimethyl sulfoxide (DMSO).

extract_protocol:
RNA extraction: Left ventricular cardiac tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TYA-018 (highly selective HDAC6 inhibitor) was administered daily by oral gavage at 15 mg/kg starting when mice were 2 months old.

tag: genotype

tag: treatment

value: Vehicle

tag: tissue

value: Cardiac Tissue


title: SE.IL4IL13 sam11_L001

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description:
SE.IL4IL13
column sam11_L001 in counts.matrix

data_processing:
The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth.
Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited gene expression data of each sample

molecule: total RNA

organism: Homo sapiens

source_name: Keratinocyte

growth_protocol: Primary normal human epidermal keratinocytes, adult (HEKa; Invitrogen, Carlsbad, CA) were cultured in the EpiLife medium supplemented with a defined growth supplement (Thermo Fisher Scientific, Waltham, MA). Cells were used in fewer than four passages in all experiments.

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA), according to the manufacture instructions.

treatment_protocol: HEKa (2 x 10^5 cells per well) were plated in a 12 well plate and adhered overnight. After that, cells were treated with the following cytokines: IL-4/IL-13/IL-4 + IL-13/IL-22 (50 ng/ml) or IFN-γ (10 ng/ml; all from R&D systems, Minneapolis, MN) for 24 h. Then, cells were stimulated in the presence or absence  heat-killed S. aureus or S. epidermidis (both from InvivoGen, San Diego, CA) at 1 ´ 10⁸ cells per ml for 3 h (gene expression analysis except for S100A7 and CCL22) or 24 h (gene expression analysis for S100A7 and CCL22 or measurement cytokines in the culture supernatants).

tag: cell type

value: skin, primary

tag: age

value: adult

value: treated with IL-4 + IL-13 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: D3 WT CHIR FGF INPUT ChIP-seq biological replicate 1

city: London

last: Briscoe

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: ChIP-seq

library_source: genomic

data_processing:
The nf-core/chipseq pipeline (version 1.1.0; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3529400) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --input design.csv --genome mm10 --gtf refseq_genes.gtf --single_end --narrow_peak --min_reps_consensus 2 -profile crick -r 1.1.0".
All data was processed relative to the human UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on December 11th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using from the nf-core/chipseq pipeline command defined above.

molecule: genomic DNA

source_name: In vitro differentiated epiblast-like cells

growth_protocol: WT and SOX2 TetON ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. 1ug/ml doxycycline was included in the culture medium of SOX2 TetON ES cells . To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then N2B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 until day 3. ES cells were reverted to naive pluripotency by culturing in 2i medium (N2/B27 containing basal medium supplemented with 3uM CHIR and 500nM PD0325901).

extract_protocol:
Approximately 5*10^6 cells were transferred to a Diagenode TPX tube and resuspended in ice cold shearing buffer (1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6), 0.3% SDS + protease inhibitors). Chromatin was sheared using a Bioruptor plus: 25 cycles of 30s On/30s Off on high setting. Sheared lysates were diluted to 0.15% SDS  prior to immunoprecipitation.
The DNA library for sequencing was prepared from Qiagen column purified DNA. DNA fragmentation of IP and input samples was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: Adherent cells were fixed  for 45min at room temperature with 2mM Di(N-succinimidyl) glutarate, then fixed for an additional 10min at room temperature with 1% PFA. Fixation was quenched by addition of 250mM glyceine for 5 minutes.

tag: strain

value: wild-type

tag: time point


title: TT-49


title: none.IL4IL13 sam10_L001

description:
none.IL4IL13
column sam10_L001 in counts.matrix

value: treated with IL-4 + IL-13 for 24 hrs


title: bulk_RNA-seq_HS1_day_14_replicate_2

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

country: Sweden

institute: Lund University

description:
hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt
pantro6.s2.multi.Gencode27.Exon.sjdb.v2.txt

data_processing:
bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the genome (GRCh38 and PanTro6) using STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
The Subread package FeatureCounts was used to quantify the reads overlapping Gencode v27 gene annotations. The human Gencode annotation was lifted over to PanTro6 using UCSC LiftOver tool.
single cell fastqs:
I1 Technical: Index read
R1 Technical: 16 bp Barcode and 10bp UMI
R2 Biological
Genome_build: GRCh38 and PanTro6
Supplementary_files_format_and_content: matrix.mat: raw read counts
Supplementary_files_format_and_content: Exon.sjdb.txt: featureCounts

source_name: forebrain neural progenitors

growth_protocol: iPS cells were differentiated into forebrain neural progenitor cells using the following protocol: The iPSCs were plated at 10.000 cells/cm2 in N2 medium (1:1 DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), 0.2% penicillin/streptomycin (Gibco)) with dual SMAD-inhibition (10 µM SB431542 (Axon), 100 ng/ml noggin (Miltenyi)) as well as ROCK inhibitor (10 µM Y27632) on LN111 coated Nunc delta surface multidishes (1.14 µg/cm2; Biolamina). The media was changed every 2-3 days to N2 medium with SMAD-inhibitors up until day 9 of differentiation when only N2 medium was used. On day 11 the cells were dissociated using StemPro accutase (75  µl/cm2; Gibco) and replated at 800,000 cells/cm2 on LN111-coated Nunc plates in B27 medium (Neurobasal supplemented with 1% B28 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) supplemented with 10 µM ROCK inhibitor, BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2mM; Sigma-Aldrich). The cells were then harvested at day 13, 14, 15, or 16.

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen) for bulk RNA-seq
Libraries for bulk RNA-seq were prepared withTruSeq RNA Library prep kit v2 (Illumina). Single cell libraries were prepared with Chromium Single Cell 3' Library & Gel Bead kit v2 (10x Genomics)

value: iPSC-derived forebrain neural progenitors


title: TT-43


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 3

description: ChIP-seq

tag: chip antibody

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: SA.IL13 sam9_L001

description:
SA.IL13
column sam9_L001 in counts.matrix

value: treated with IL-13 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: SE.IL13 sam8_L001

description:
SE.IL13
column sam8_L001 in counts.matrix

value: treated with IL-13 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: A1-3

city: Guangzhou

first: Yinxiong

last: Li

address: Kaiyuan street 190

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
quanlity check,fastQCV0.10.1, cutadaptV1.9.1
readsmapping, hisat2v2.0.1
Gene expression level analysis, HTSEQv0.6.1
Differential expression analysis, DESeq2 V1.6.3
Go enrichment,GOSeq v1.34.1
Genome_build: ENSEMBL  GRCm38.100
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Asgr1 knockout

value: 13 week

value: liver


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 2

description: ChIP-seq


title: bulk_RNA-seq_HS1_day_13_replicate_2


title: A1-2


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 1

description: ChIP-seq


title: A1-1


title: bulk_RNA-seq_HS1_day_15_replicate_1


title: bulk_RNA-seq_HS1_day_13_replicate_1


title: WT-3

value: wild type


title: SE.IL4 sam5_L001

description:
SE.IL4
column sam5_L001 in counts.matrix

value: treated with IL-4 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: none.IL13 sam7_L001

description:
none.IL13
column sam7_L001 in counts.matrix

value: treated with IL-13 for 24 hrs


title: D3 SOX2 CHIR FGF TCF4 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: TCF4 (Santa Cruz sc-8631 goat)

value: Doxycycline withdrawn during differentiation


title: H231

city: Canberra

first: Yeu-Yang

last: Tseng

state: ACT

address: 131 Garran Rd

country: Australia

institute: ANU

description: MRC5, 8hpi-1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped to hg38 whole genome using TopHat2
Aligned BAM files were further processed using featureCounts to get read summarization based on hg38 genome annotations.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include  raw reads for each sample

source_name: lung

growth_protocol: Both HFF and MRC5 were routinely cultured (typically 2–3 × 106 cells in a T75 flask) in DMEM supplemented with 10% FCS.

extract_protocol:
Infected cells were sorted and total RNA was extracted using RNAqueous™ Total RNA Isolation Kit. llumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with HSV-1 expressing GFP at an MOI of 0.5 for 4 or 8 hours.

tag: cell line

value: MRC-5 (ATCC, CCL-171)

tag: hiv-1 infection

value: lung


title: H232

description: MRC5, 8hpi-2


title: H233

description: MRC5, 8hpi-3


title: D3 SOX2 CHIR FGF TCF4 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: D3 SOX2 CHIR FGF TCF4 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SA.none sam3_L001

description:
SA.none
column sam3_L001 in counts.matrix

value: skin, primary

value: adult

value: treated with Staphylococcus aureus for 3 hrs


title: bulk_RNA-seq_HS1_day_14_replicate_1

value: iPSC-derived forebrain neural progenitors


title: H223

description: MRC5, 4hpi-3


title: SA.IL4 sam6_L001

description:
SA.IL4
column sam6_L001 in counts.matrix

value: treated with IL-4 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: SE.none sam2_L001

description:
SE.none
column sam2_L001 in counts.matrix

value: treated with Staphylococcus epidermidis for 3 hrs


title: D3 SOX2 CHIR FGF TCF3 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: TCF3 (Santa Cruz sc-8635 goat)


title: D3 SOX2 CHIR FGF TCF3 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: none.IL4 sam4_L001

description:
none.IL4
column sam4_L001 in counts.matrix

value: treated with IL-4 for 24 hrs


title: H222

description: MRC5, 4hpi-2


title: D3 SOX2 CHIR FGF TCF3 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: none.none sam1_L001

description:
none.none
column sam1_L001 in counts.matrix

value: untreated


title: WT-2

value: 13 week

value: liver


title: SG_Wound_H3K4me3

city: Gangnam-gu

first: Seok-Hyung

last: Kim

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

country: South Korea

institute: Samsung Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic
trimmed sequenced reads then mapped to mm9 whole genome using Bowtie
Peak calling were performed using MACS2
Deeptools takes an alignment of reads or fragments as input and generates a coverage track (bigWig) as output
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, bed

growth_protocol: All primary mouse fibroblasts (MEFs, MMTV-CAFs, Mouse wound healing fibroblasts) were immortalized by overexpression of HPV E6/E7. All cells were grown in DMEM medium containing 10% FBS and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).

extract_protocol:
DNA was purified with phenol chloroform extraction and ethanol precipitation.
The construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions. Briefly, the chipped DNA was ligated with adaptors. After purification, PCR reaction was done with adaptor-ligated DNA and index primer for multiplexing sequencing. Library was purified by using magnetic beads to remove all reaction components. The size of library was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). High-throughput sequencing was performed as paired-end 100 sequencing using HiSeq 2500 (Illumina, Inc., USA).

treatment_protocol: Mouse wound healing fibroblasts were isolated from fresh tissue of dorsal wound area at day 10 post-wound in mice. MMTVCAFs from MMTV-PyMT breast cancer mice models. SgPrrx1(Prrx1 deletion) cells were generated using sgRNA against Prrx1 (CRISPR/Cas9 technology). SgNS(WT) was used as a control. MEFs (Mouse embryonic fibroblasts) were isolated from embryos (WT and 129S-Prrx1tm1Jfm/Mmmh (Prrx1 mutant mice) harvested at E10-13. All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence. Cells were cross-linked for 10 min at room temperature by the addition of one-tenth of the volume of fresh 11% formaldehyde solution. The cell pellets were resuspended with nuclei lysis buffer and sonicated. Whole cell lysates were incubated overnight at 4'C with agarose A/G beads that had been pre-incubated with a-H3K27Ac, a-H3K4me3 or a-Prrx1. 50ul of agarose A/G beads were blocked with 0.1% BSA(w/v) in PBS. Beads were bound with 5ug of the indicated antibody.

value: H3K4me3 (Abcam, Cat# :ab8580)


title: H221

description: MRC5, 4hpi-1


title: SG_Wound_H3K27ac

value: H3K27ac (Abcam, Cat# :ab4729)


title: WT_Wound_PRRX1

value: PRRX1 (LS-bio, LS-C336798)


title: WT-1

value: wild type


title: D3 SOX2 CHIR FGF SOX2 IP ChIP-seq biological replicate 2

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)

value: Doxycycline withdrawn during differentiation


title: sh1.DNMT3B.rep2

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p13 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (³|2.0|-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Genome_build: human genome assembly NCBI GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files includeTMM normalized counts per million (CPM) values for each Sample ...

source_name: Derived from 2102EP

growth_protocol: All cells were cultured in DMEM with 10% FBS and antibiotic in incubator (5% CO2; 37°C)

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the NovaSeq 6000 sequencing kit version 1, according to the manufacturer’s instructions.

value: Embryonic carcinoma

tag: tissue origin

value: testis

tag: dnmt3b knockdown

value: DNTM3B sh1 Knockdown


title: H211

description: MRC5, mock-1

value: MRC-5 (ATCC, CCL-171)

value: mock

value: lung


title: WT_Wound_Input

value: None (Santa Cruz Biotechnology, Cat# sc-2025)


title: D3 SOX2 CHIR FGF SOX2 IP ChIP-seq biological replicate 3

description: ChIP-seq


title: sh1.DNMT3B.rep3


title: H212

description: MRC5, mock-2


title: D3 SOX2 CHIR FGF SOX2 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: SG_Wound_Input


title: PLK0.control.rep1

value: PLKO.1 Control


title: sh1.DNMT3B.rep1


title: PLK0.control.rep3


title: D3 SOX2 CHIR FGF LEF1 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: D3 SOX2 CHIR FGF LEF1 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: D3 SOX2 CHIR FGF LEF1 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: WT_Wound_H3K27ac


title: SG_MMTV_Input

value: FVB/NJ


title: SG_MMTV_H3K4me3


title: PLK0.control.rep2


title: H133

description: HFF, 8hpi-3

source_name: skin

value: HFF-1 (ATCC SCRC-1041)

value: skin


title: WT_Wound_H3K4me3

value: H3K4me3 (Abcam, Cat# :ab8580)


title: H131

description: HFF, 8hpi-1


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2B9_rep3

tag: cisplatin sensitivity

value: 5-aza deoxy-cytosine acquired resistant


title: H132

description: HFF, 8hpi-2


title: H123

description: HFF, 4hpi-3


title: SG_MMTV_H3K27ac

value: H3K27ac (Abcam, Cat# :ab4729)


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2B9_rep2


title: H213

description: MRC5, mock-3


title: H122

description: HFF, 4hpi-2


title: D3 SOX2 CHIR FGF DOX TCF4 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: TCF4 (Santa Cruz sc-8631 goat)

value: Doxycycline maintained during differentiation


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2B9_rep1

value: Embryonic carcinoma


title: WT_MMTV_PRRX1

value: PRRX1 (LS-bio, LS-C336798)


title: H121

description: HFF, 4hpi-1


title: WT_MMTV_Input


title: D3 SOX2 CHIR FGF DOX TCF4 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: D3 SOX2 CHIR FGF INPUT ChIP-seq biological replicate 1

description: ChIP-seq

value: Doxycycline withdrawn during differentiation


title: H113

description: HFF, mock-3


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2A2_rep3

value: testis


title: H112

description: HFF, mock-2

value: mock


title: D3 SOX2 CHIR FGF DOX TCF3 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: TCF3 (Santa Cruz sc-8635 goat)


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2A2_rep2


title: D3 SOX2 CHIR FGF DOX TCF3 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: H111

description: HFF, mock-1


title: WT_MMTV_H3K27ac


title: SG_MEF_H3K4me3

value: MEF


title: D3 SOX2 CHIR FGF DOX SOX2 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)


title: D3 SOX2 CHIR FGF DOX TCF4 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SG_MEF_Input

value: None (Santa Cruz Biotechnology, Cat# sc-2025)


title: M09_Skin_12M_F0_3

city: Chicago

first: Alexander

last: Misharin

address: SQBRC 303 E Superior St 5-404

department: Medicine (Pulmonary Division)

institute: Northwestern University

description: mRNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.36) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (GRCm38.p3y) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

growth_protocol: Male C57BL/6J mice were provided by NIA NIH

extract_protocol:
RNA was isolated using an RNeasy DNA/RNA kit after homogenization and lysis in guanidine thiocyanate buffer supplemented with β-mercaptoethanol. RNA concentration and quality were assessed using an Agilent TapeStation. RNAseq libraries were prepared using an NEB Next RNA Ultra kit with polyA enrichment module using an Agilent Bravo NGS Automated fluidics handling platform as described elsewhere (Misharin et al., 2017, J Exp Med 214). Libraries were multiplexed and sequenced on an Illumina NextSeq 500 platform using 75 cycles of high-output flow cells and a dual indexing strategy.
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) using 75 cycles of high-output flow cells and a dual indexing strategy.

treatment_protocol: Mice were housed at Northwestern University Feinberg School of Medicine Center for Comparative Medicine for 4 weeks prior to sacrifice.

tag: Sex

value: male

tag: organ

value: Skin

tag: age (months)

tag: pfu (influenza)


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH1A5_rep2


title: M09_SI_12M_F0_3

description: mRNA-seq

value: Small intestine


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH2A2_rep1


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH1A5_rep1


title: D3 SOX2 CHIR FGF DOX SOX2 IP ChIP-seq biological replicate 2

description: ChIP-seq

tag: genotype

tag: treatment


title: SG_MEF_H3K27ac

tag: cell type


title: M09_MuscSat_12M_F0_3

description: mRNA-seq

value: Muscle


title: KI_MEF_Input


title: D3 SOX2 CHIR FGF DOX SOX2 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: 5-aza deoxy-cytosine sensitive 2102EP_rep3

source_name: Testicular embryonal carcinoma cell lines derived from retroperitoneal lymph node

value: 5-aza deoxy-cytosine sensitive


title: D3 SOX2 CHIR FGF DOX TCF3 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: M09_Lung_12M_F0_3

description: mRNA-seq

value: Lung


title: KI_MEF_H3K4me3

value: H3K4me3 (Abcam, Cat# :ab8580)


title: WT_MMTV_H3K4me3

value: FVB/NJ


title: D3 SOX2 CHIR FGF DOX LEF1 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: LEF1 (Millipore CS200635)

value: Doxycycline maintained during differentiation


title: 5-aza deoxy-cytosine sensitive 2102EP_rep2

value: Embryonic carcinoma


title: 5-aza deoxy-cytosine acquired resistant 2102EP-AH1A5_rep3

value: testis

value: 5-aza deoxy-cytosine acquired resistant


title: 5-aza deoxy-cytosine sensitive 2102EP_rep1


title: KI_MEF_H3K27ac

value: H3K27ac (Abcam, Cat# :ab4729)


title: M09_Liver_12M_F0_3

description: mRNA-seq

value: Liver


title: D3 SOX2 CHIR FGF DOX LEF1 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: WT_MEF_PRRX1

value: MEF

value: PRRX1 (LS-bio, LS-C336798)


title: CAF9_None

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic
trimmed sequenced reads then mapped to mm9 whole genome using Bowtie
Peak calling were performed using MACS2
Deeptools takes an alignment of reads or fragments as input and generates a coverage track (bigWig) as output
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, bed

source_name: Human CAF

growth_protocol: All primary human colon CAFs were immortalized with SV40-large T antigen (pHIV7-CNPO-Tag) and hTERT (pHIV7-CNPO-hTERT). All cells were grown in DMEM medium containing 10% FBS and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).

treatment_protocol: All Human colon CAFs were incubated at 37°C in 5% CO2 and grown to 80-90% confluence. Cells were cross-linked for 10 min at room temperature by the addition of one-tenth of the volume of fresh 11% formaldehyde solution. The cell pellets were resuspended with nuclei lysis buffer and sonicated. Whole cell lysates were incubated overnight at 4'C with agarose A/G beads that had been pre-incubated with a-H3K27Ac. 50ul of agarose A/G beads were blocked with 0.1% BSA(w/v) in PBS. Beads were bound with 5ug of the a-H3K27Ac.

value: colon cancer associated fibroblasts (CAF)

value: IgG (vendor :Santa Cruz Biotechnology, catalog :sc-2025)


title: M09_GutEP_12M_F0_3

description: mRNA-seq

value: male

value: Gut epithelium


title: M09_LI_12M_F0_3

description: mRNA-seq

value: Large intestine


title: M09_Kidney_12M_F0_3

description: mRNA-seq

value: Kidney


title: D3 SOX2 CHIR FGF DOX BCATENIN IP ChIP-seq biological replicate 3

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: WT_MEF_Input

value: None (Santa Cruz Biotechnology, Cat# sc-2025)


title: M09_Cerebellum_12M_F0_3

description: mRNA-seq

value: Cerebellum


title: D3 SOX2 CHIR FGF DOX BCATENIN IP ChIP-seq biological replicate 1

description: ChIP-seq

value: Doxycycline maintained during differentiation


title: D3 SOX2 CHIR FGF DOX INPUT ChIP-seq biological replicate 1

description: ChIP-seq


title: WT_MEF_H3K4me3

value: H3K4me3 (Abcam, Cat# :ab8580)


title: M09_Esophagus_12M_F0_3

description: mRNA-seq

value: Esophagus


title: CAF8_None


title: CAF8_H3K27ac

value: H3K27ac (vendor :Abcam, catalog :ab4729)


title: M09_Blood_12M_F0_3

description: mRNA-seq

value: Blood


title: CAF9_H3K27ac


title: D3 SOX2 CHIR FGF DOX BCATENIN IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SG_Wound_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic
trimmed sequenced reads then mapped to mm10 whole genome using STAR
Read count extraction were performed using htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: All primary mouse fibroblasts (MEFs, MMTV-CAFs, Mouse wound healing fibroblasts) were immortalized by overexpression of HPV E6/E. All cells were grown in DMEM medium containing 10% FBS and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).

extract_protocol:
Total RNA ((including gDNA removal) was extracted using by RNeasy plus mini kit (Cat no.#74134, Qiagen).
Sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (Illumina).  After pooled libraries were denatured, sequencing of each library was carried out using the 100 bp. paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit with HiSeq 2500 (Illumina Technologies., USA).

treatment_protocol: Mouse wound healing fibroblasts were isolated from fresh tissue of dorsal wound area at day 10 post-wound in mice. MMTVCAFs from MMTV-PyMT breast cancer mice models. SgPrrx1(Prrx1 deletion) cells were generated using sgRNA against Prrx1(CRISPR/Cas9 technology). SgNS(WT) was used as a control. MEFs (Mouse embryonic fibroblasts) were isolated from embryos (WT and 129S-Prrx1tm1Jfm/Mmmh (Prrx1 mutant mice) harvested at E10-13. All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence.


title: WT_MEF_H3K27ac

value: H3K27ac (Abcam, Cat# :ab4729)


title: SG_Wound_2


title: D3 SOX2 CHIR FGF BCATENIN IP ChIP-seq biological replicate 3

description: ChIP-seq

value: Doxycycline withdrawn during differentiation


title: D3 SOX2 CHIR FGF DOX LEF1 IP ChIP-seq biological replicate 1

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: M09_BAT_12M_F0_3

description: mRNA-seq

value: Brown adipose tissue


title: SG_Wound_1


title: WT_Wound_3


title: M09_Adrenal_12M_F0_3

description: mRNA-seq

value: Adrenal Gland


title: M08_WAT_12M_F0_2

description: mRNA-seq

value: male

value: White adipose tissue


title: CAF6_None

value: colon cancer associated fibroblasts (CAF)

value: IgG (vendor :Santa Cruz Biotechnology, catalog :sc-2025)


title: CAF6_H3K27ac


title: CAF7_H3K27ac


title: CAF7_None


title: M08_Stomach_12M_F0_2

description: mRNA-seq

value: Stomach


title: CAF5_None


title: WT_Wound_2


title: WT_Wound_1


title: WT NAIVE TCF4 IP ChIP-seq biological replicate 1

description: ChIP-seq

source_name: Undifferentiated naïve pluripotent embryonic stem cells

value: TCF4 (Santa Cruz sc-8631 goat)

value: wild-type


title: SG_MMTV_3

value: FVB/NJ


title: CAF4_None


title: M08_Skin_12M_F0_2

description: mRNA-seq

value: Skin


title: WT NAIVE TCF3 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: TCF3 (Santa Cruz sc-8635 goat)


title: SG_MMTV_2


title: WT NAIVE TCF4 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: CAF4_H3K27ac

value: H3K27ac (vendor :Abcam, catalog :ab4729)


title: SG_MMTV_1


title: M08_SI_12M_F0_2

description: mRNA-seq

value: Small intestine


title: D3 SOX2 CHIR FGF BCATENIN IP ChIP-seq biological replicate 2

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: M08_MuscSat_12M_F0_2

description: mRNA-seq

value: Muscle


title: WT NAIVE TCF3 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: D3 SOX2 CHIR FGF BCATENIN IP ChIP-seq biological replicate 1

description: ChIP-seq

value: Doxycycline withdrawn during differentiation


title: CAF3_None


title: M08_Lung_12M_F0_2

description: mRNA-seq

value: Lung


title: WT NAIVE TCF3 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: WT_MMTV_3


title: WT NAIVE TCF4 IP ChIP-seq biological replicate 3

description: ChIP-seq


title: CAF5_H3K27ac


title: M08_Liver_12M_F0_2

description: mRNA-seq

value: Liver


title: WT_MMTV_2


title: CAF3_H3K27ac


title: CAF2_None


title: WT_MMTV_1


title: M08_LI_12M_F0_2

description: mRNA-seq

value: male

value: Large intestine


title: CAF2_H3K27ac

value: colon cancer associated fibroblasts (CAF)


title: WT NAIVE SOX2 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)


title: WT NAIVE SOX2 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SG_MEF_3

value: MEF


title: CAF1_None

value: IgG (vendor :Santa Cruz Biotechnology, catalog :sc-2025)


title: SG_MEF_2


title: WT NAIVE LEF1 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: LEF1 (Millipore CS200635)

value: wild-type


title: M08_GutEP_12M_F0_2

description: mRNA-seq

value: Gut epithelium


title: WT NAIVE SOX2 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: M08_Esophagus_12M_F0_2

description: mRNA-seq

value: Esophagus


title: WT NAIVE LEF1 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: KI_MEF_3


title: M08_Cerebellum_12M_F0_2

description: mRNA-seq

value: Cerebellum


title: WT NAIVE LEF1 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: KI_MEF_2


title: M08_Brain_12M_F0_2

description: mRNA-seq

value: Frontal cortex


title: WT NAIVE INPUT ChIP-seq biological replicate 1

description: ChIP-seq


title: PI-IBS PI-IBS082

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: PI-IBS

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
Paired end reads were aligned using STAR-2.6.1c
Gene counts were generated using subread-1.5.1 featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file which includes raw counts and FPKM values for each gene per sample

source_name: Colonic Epithelieum

extract_protocol:
Colonic biopsies were collected from volunteers and flash frozen using liquid nitrogen. RNA was extracted using Qiagne, miRNeasy Mini Kit per manufacture guidelines. Total RNA was then used using Illumina TruSeq RNA to build sequencing libraries.
Created unique dual-indexed (UDI) TruSeq stranded mRNA libraries. All libraries pooled and sequenced on a NovaSeq 2x150-bp Charter-Service RNA-Seq run, generating ≥20 Million reads for each library with mean quality scores for all libraries ≥Q30.

tag: condition

value: High PA


title: PI-IBS PI-IBS090

description: PI-IBS

value: Low PA


title: M08_Blood_12M_F0_2

description: mRNA-seq

tag: strain

value: Blood


title: KI_MEF_1


title: WT NAIVE BCATENIN IP ChIP-seq biological replicate 3

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)

tag: time point


title: PI-IBS PI-IBS077

description: PI-IBS


title: M08_Kidney_12M_F0_2

description: mRNA-seq

value: Kidney


title: Healthy PI-IBS076

description: Healthy

value: Healthy Low PA


title: WT_MEF_3


title: Healthy PI-IBS052

description: Healthy


title: WT_MEF_2


title: WT NAIVE BCATENIN IP ChIP-seq biological replicate 2

description: ChIP-seq

tag: chip antibody


title: CAF1_H3K27ac

value: H3K27ac (vendor :Abcam, catalog :ab4729)


title: M08_BAT_12M_F0_2

description: mRNA-seq

value: male

value: Brown adipose tissue


title: SG_MEF_1

value: MEF


title: M08_Adrenal_12M_F0_2

description: mRNA-seq

value: Adrenal Gland


title: WT_MEF_1


title: WT NAIVE BCATENIN IP ChIP-seq biological replicate 1

description: ChIP-seq


title: D3 WT CHIR FGF ATAC-seq

description: ATAC-seq

data_processing:
The nf-core/atacseq pipeline (version 1.0.0; Ewels et al., 2020; https://doi.org/10.5281/zenodo.2634133) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/atacseq --design design.csv --genome mm10 --gtf refseq_genes.gtf -profile crick -r 1.0.0".
All data was processed relative to the human UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on December 11th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/atacseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 broadPeak files generated using from the nf-core/atacseq pipeline command defined above.

growth_protocol: WT and SOX2 TetON ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. 1ug/ml doxycycline was included in the culture medium of SOX2 TetON ES cells . To induce differentiation cells were cultured in  N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then N2B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 until day 3.

extract_protocol:
Cells were pelleted and resuspended in lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). Following a 10min centrifugation at 4 C, nucleic extracts were resuspended in transposition buffer for 30min at 37 C and purified using a QIAGEN MinElute PCR Purification kit following manufacturer’s instructions.
Transposed DNA was eluted in a 10mL volume and amplified by PCR with Nextera primers to generate single-indexed libraries. A maximum of 12 cycles of PCR was used to prevent saturation biases

treatment_protocol: Adherent cells were treated with StemPro Accutase (A1110501) to obtain a single cell suspension. Cells were counted and resuspended to obtain 50,000 cells per sample in ice-cold PBS


title: PI-IBS PI-IBS041

description: PI-IBS


title: Healthy PI-IBS039

description: Healthy


title: M07_WAT_12M_F0_1

description: mRNA-seq

value: White adipose tissue


title: PI-IBS PI-IBS032

description: PI-IBS


title: coculture_1681_SG_3

source_name: cancer cell line

growth_protocol: To establish Hanging drop spheroid coculture system, Cancer cells and fibroblasts were detached and resuspend with complete medium. The lid of the 60mm Petri dish was inverted. We used an auto-pipettor to deposit drop onto the bottom of the lid of dish and Inverted the lid onto prepared PBS-bottom of dish and incubated at 37'C, 5% CO2 humidity culture incubator. GFP tagged cancer cells and   fibroblasts (1:3 ratio) were in each drop, at least 20~25 drops per dish. After a day (~24 hours), the droplets were monitored and cell aggregates formed. The aggregated spheroids were collected using complete medium, transferred to 100mm petri dish, incubated for a week on a shaker in 37'C, 5% CO2 culture incubator.

treatment_protocol: Mouse wound healing fibroblasts were isolated from fresh tissue of dorsal wound area at day 10 post-wound in mice. MMTVCAFs from MMTV-PyMT breast cancer mice models. SgPrrx1(Prrx1 deletion) cells were generated using sgRNA against Prrx1(CRISPR/Cas9 technology). SgNS(WT) was used as a control. The aggregated spheroids were incubated at 37'C, 5% CO2 humidity culture incubator.

value: 168_FARN; Breast cancer cell line

tag: co-cultured cells

value: MMTV-CAF

value: PRRX1 deletion


title: D3 SOX2 CHIR FGF ATAC-seq

description: ATAC-seq

value: Doxycycline withdrawn during differentiation


title: M07_Skin_12M_F0_1

description: mRNA-seq

value: Skin


title: M07_Stomach_12M_F0_1

description: mRNA-seq

value: Stomach


title: D3 SOX2 CHIR FGF DOX ATAC-seq

description: ATAC-seq

value: Doxycycline maintained during differentiation


title: M07_SI_12M_F0_1

description: mRNA-seq

value: Small intestine


title: PI-IBS PI-IBS027

description: PI-IBS

value: High PA


title: D3 WT FGF RNA-seq biological replicate 2

description: RNA-seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.16; Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”, and for paired-end data “-A AGATCGGAAGAGC” was appended to the command.
The RSEM package (version 1.3.0; Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a; Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 11th December 2017. The parameters passed to the “rsem-calculate-expression” command were “--star --star-gzipped-read-file --star-output-genome-bam --forward-prob 0”, and for paired-end data “--paired-end” was appended to the command.
Differential expression analysis was performed with the DESeq2 package (version 1.16.1; Love et al., 2014) within the R programming environment (version 3.4.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

growth_protocol: WT and SOX2 TetON ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. 1ug/ml doxycycline was included in the culture medium of SOX2 TetON ES cells . To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then either N2/B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 or N2/B27 + 10ng/ml bFGF + 5uM LGK974 until day 3.

extract_protocol:
Total RNA was extracted from cells using a QIAGEN RNeasy kit in RLT buffer, following the manufacturer’s instructions. Extracts were digested with DNase I to eliminate genomic DNA.
The total RNA samples were quality controlled to determine RNA integrity and concentration using Agilent Tapestation prior to library preparation. Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) and sequenced as 76bp single-end, stand-specific reads on the Illumina HiSeq 4000 platform (Francis Crick Institute).

value: wild-type


title: coculture_1681_SG_2

tag: cell line


title: coculture_1681_SG_1


title: M07_MuscSat_12M_F0_1

description: mRNA-seq

value: Muscle


title: PI-IBS PI-IBS021

description: PI-IBS

value: Low PA


title: M07_Lung_12M_F0_1

description: mRNA-seq

value: male

value: Lung


title: HDAC4 3SA_CFA_rep2

city: Heidelberg

first: Daniela

last: Mauceri

address: Im neuenheimer Feld 366

department: Neurobiology

country: Germany

institute: Heidelberg University

data_processing:
Illumina sequencing was performed by GATC Biotech, Constance, Germany.
Illumina sequencing was performed using 50 bp single-end reads in FastQ format with at least 30 million reads. Gene expression was analyzed using the Bowtie, TopHat, Cufflinks, Cuffmerge, Cuffdiff software suite.
Genome_build: Mus musculus, mm10 / GRCm38, v85 Ensembl reference genome
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include a unique identifier describing the transcript (test_id), the name, RefSeq ID and genomic coordinates of the identified transcript, average FPKM values per condition, comparative gene expression changes between two conditions (log2 fold change), uncorrected pvalue and FDR adjusted pvalue.

source_name: Dorsal spinal cord

extract_protocol:
Spinal cord tissue was dissected and frozen. RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions and 0.3µg of total RNA was used for library preparation.
Libraries were prepared according to Illumina instructions (performed by GATC Biotech, Constance, Germany).

tag: tissue

value: Dorsal spinal cord

tag: age

value: 3 months

tag: intraspinal injection

value: rAAV-HDAC4 3SA

value: intraplantar CFA


title: Healthy PI-IBS016

description: Healthy

value: Healthy Low PA


title: coculture_1681_WT_3

value: 168_FARN; Breast cancer cell line

value: MMTV-CAF

value: WT


title: coculture_1681_WT_2


title: HDAC4 3SA_CFA_rep3


title: coculture_1681_WT_1


title: coculture_1681_3


title: HDAC4 3SA_Saline_rep2

value: intraplantar saline


title: HDAC4 3SA_Saline_rep3


title: PI-IBS PI-IBS005

description: PI-IBS


title: Healthy PI-IBS011

description: Healthy


title: coculture_1681_2


title: M07_Kidney_12M_F0_1

description: mRNA-seq

value: Kidney


title: M07_LI_12M_F0_1

description: mRNA-seq

value: Large intestine


title: M07_Liver_12M_F0_1

description: mRNA-seq

value: Liver


title: HDAC4 wt_CFA_rep3

value: rAAV-HDAC4 wt


title: coculture_1681_1


title: HDAC4 3SA_Saline_rep1


title: PI-IBS PI-IBS002

description: PI-IBS

value: High PA


title: coculture_LLC1_SG_3

value: LLC1; Lung cancer cell line

value: Wound healing fibroblast

value: PRRX1 deletion


title: M07_GutEP_12M_F0_1

description: mRNA-seq

value: male

value: Gut epithelium


title: M07_Esophagus_12M_F0_1

description: mRNA-seq

value: Esophagus


title: PI-IBS PI-IBS020

description: PI-IBS

value: Low PA


title: coculture_LLC1_SG_2


title: HDAC4 3SA_CFA_rep1

value: Dorsal spinal cord

value: 3 months

value: rAAV-HDAC4 3SA

value: intraplantar CFA


title: HDAC 4wt_CFA_rep2


title: PI-IBS PI-IBS001

description: PI-IBS


title: M07_Cerebellum_12M_F0_1

description: mRNA-seq

value: Cerebellum


title: coculture_LLC1_SG_1


title: HDAC4 wt_Saline_rep3

value: intraplantar saline


title: M07_Brain_12M_F0_1

description: mRNA-seq

value: Frontal cortex


title: coculture_LLC1_WT_3

value: WT


title: HDAC4 wt_Saline_rep2

value: rAAV-HDAC4 wt


title: M07_Blood_12M_F0_1

description: mRNA-seq

value: Blood


title: M07_Heart_12M_F0_1

description: mRNA-seq

value: Heart


title: Transplanted organoids-day 10_rep2

first: Yi

last: Xiao

address: No. 253, Industrial Avenue, Haizhu District

institute: Southern Medical University

description:
For days 10 organoid single cells, we set the 90 % threshold of total RNA counts was set in each single cell, only cells with more than 91 % RNA counts belong to rat or human were regarded as rat or human cells.The home build reference genome for GRCh38 and Rnor6 using cellranger mkref function was used to align inserted cDNA from days 10  organoid single cells.
Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read9.

data_processing:
Illumina Hiseq Novaseq PE150 for base-calling
The quality of the raw reads data for each sample was  evaluated using FastQC
Trimmomatic reads filtering with a minimum length of 16 nucleotides for quality score  and  a clean database was generated.
The quality of the clean data for each sample was  evaluated using FastQC
Genome_build: GRCh38,Rnor6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Umbilical cord

extract_protocol:
organoids were removed, flash frozen on dry ice, and then constructed the sequencing libraries.Cell number and viability were measured by Countess II.DNA was quantified using Qubit dsDNA BR Assay.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Umbilical cord-derived mesenchymal stem cells

tag: disease state

value: post-transplantation


title: Transplanted organoids-day 10_rep1

description:
For days 10 organoid single cells, we set the 90 % threshold of total RNA counts was set in each single cell, only cells with more than 91 % RNA counts belong to rat or human were regarded as rat or human cells.The home build reference genome for GRCh38 and Rnor6 using cellranger mkref function was used to align inserted cDNA from days 10  organoid single cells.
Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read8.


title: Transplanted organoids-day 3_rep2

description:
For days 3 organoid single cells, we set the 90 % threshold of total RNA counts was set in each single cell, only cells with more than 91 % RNA counts belong to rat or human were regarded as rat or human cells.The home build reference genome for GRCh38 and Rnor6 using cellranger mkref function was used to align inserted cDNA from days 3  organoid single cells.
Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read6.


title: Transplanted organoids-day 3_rep3

description:
For days 3 organoid single cells, we set the 90 % threshold of total RNA counts was set in each single cell, only cells with more than 91 % RNA counts belong to rat or human were regarded as rat or human cells.The home build reference genome for GRCh38 and Rnor6 using cellranger mkref function was used to align inserted cDNA from days 3  organoid single cells.
Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read7.


title: M07_BAT_12M_F0_1

description: mRNA-seq

tag: Sex

value: male

value: Brown adipose tissue


title: HDAC4 wt_Saline_rep1


title: coculture_LLC1_WT_2

value: LLC1; Lung cancer cell line

value: Wound healing fibroblast


title: coculture_LLC1_WT_1


title: Transplanted organoids-day 3_rep1

description:
For days 3 organoid single cells, we set the 90 % threshold of total RNA counts was set in each single cell, only cells with more than 91 % RNA counts belong to rat or human were regarded as rat or human cells.The home build reference genome for GRCh38 and Rnor6 using cellranger mkref function was used to align inserted cDNA from days 3  organoid single cells.
Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read5.


title: M07_Adrenal_12M_F0_1

description: mRNA-seq

tag: organ

value: Adrenal Gland


title: LacZ_CFA_rep3

value: Dorsal spinal cord

value: 3 months

value: rAAV-LacZ


title: LacZ_CFA_rep2

value: intraplantar CFA


title: coculture_LLC1_2


title: coculture_LLC1_3


title: M06_WAT_18M_F0_3

description: mRNA-seq

value: White adipose tissue

tag: age (months)


title: Original organoid_rep3

description: Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read4.

value: pre-transplantation


title: HDAC4 wt_CFA_rep1


title: coculture_LLC1_1


title: Original organoid_rep1

description: Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read2.


title: M06_Stomach_18M_F0_3

description: mRNA-seq

value: Stomach

tag: pfu (influenza)


title: LacZ_Saline_rep3

value: intraplantar saline


title: decidualized endometrial stromal cells (dESCs), si-SCRIB, rep3

city: Shanghai

first: Yaoming

last: Peng

state: 上海

address: Shanghai Medical College Fudan University

department: obstetric and gynecology

institute: Fudan university

data_processing:
Raw data (raw reads) were processed using Trimmomatic version 0.36.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome (GRCh38) using hisat2 version2.2.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: human genome hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM file include FPKM values for every gene and every sample
counts file with raw gene counts for every gene and every sample

source_name: endometrial stromal cells (ESCs)

growth_protocol: ESCs were cultured in Dulbecco modified Eagle’s medium (DMEM)/F12 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and 1% penicillin-streptomycin mix (Gibco, USA) at 37℃ in a humidified chamber with 5% CO2.

extract_protocol:
Total RNA was extracted from decidualized ESCs transfected with si-Ctrl and si-SCRIB using the TRIzol reagent (Invitrogen, USA). Isolated RNA was quantified by the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and the RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ESCs were transfected with scrambled siRNA (si-Ctrl) or SCRIB targeting siRNA (si-SCRIB) and then subjected to hormone treatment (1 μM medroxyprogesterone and 0.5 mM cyclic adenosine monophosphate) for 6 days to induce decidualization

value: emdometrium-derived primary human endometrial stromal cells

tag: menstrual cycle

value: mid-secretory phase

value: healthy woman

value: transfected with SCRIB-targeting siRNA (si-SCRIB), then subjected to hormone treatment (1 μM medroxyprogesterone and 0.5 mM cyclic adenosine monophosphate) for 6 days

tag: genotype

value: reduced SCRIB expression


title: decidualized endometrial stromal cells (dESCs), si-SCRIB, rep2

tag: cell type

tag: treatment


title: M06_SI_18M_F0_3

description: mRNA-seq

tag: strain

value: male

value: Small intestine


title: decidualized endometrial stromal cells (dESCs), si-SCRIB, rep1


title: LacZ_Saline_rep1


title: MS3_HF_A3

city: Lexinton

first: Analia

middle: S

last: Loria

state: KY

address: 900 S Limestone

department: Pharmacology

institute: U of Kentucky

data_processing:
Quality control- raw reads of FASTQ formats were processed. Reads containing adapter and poly-N sequences were removed. Q20, Q30 and GC content of clean data were calculated at this time.
Mapping to reference using STAR (v2.6.1d).
Quantification using feature counts (v1.5.0-p3).
Differential analysis using DESeq2 (v1.20.0) and EdgeR (v3.24.3).
Enrichment analysis using cluster profiler (v3.8.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: fpkm_genename.txt: Tab-delimited text file containing FPKM.
Supplementary_files_format_and_content: readcount_genename.txt: Tab-delimited text file containing read counts.

source_name: gonadal white adipose tissue mature adipocyte

extract_protocol:
Fresh gonadal white adipose tissue was harvested after euthanasia and subjected to collagenase digestion. Tissue was centrifuged and filtered to separate the mature fraction from the stromal vascular fraction. Magnetic Activated Cell Sorting (MACs) was used to further isolate adipocytes from other cell types. Pre-and mature adipocytes were collected and saved in Purezol at -80oC for later RNA extraction using the Promega ReliaPrep RNA miniprep systems. Total RNA was sent to Novogene for RNAseq analysis.
Novogene’s RNA-Seq: Illumina Novaseq 6000, S4 flowcell, PE150 seq parameter.

treatment_protocol: Maternal Separation and Early Weaning (MSEW) was performed separating the pups from the dam everyday from postnatal day (PD) 2-16. The mice were also weaned early on PD 17. This differs from control pups which remained undisturbed until their weaning day on PD21.

value: female

value: maternal separation & early weaning

tag: diet

value: high-fat diet

value: gonadal white adipose tissue

value: mature adipocyte


title: MS2_HF_A


title: M06_Lung_18M_F0_3

description: mRNA-seq

value: Lung


title: decidualized endometrial stromal cells (dESCs), si-Ctrl, rep3

value: transfected with scrambled siRNA (si-Ctrl), then subjected to hormone treatment (1 μM medroxyprogesterone and 0.5 mM cyclic adenosine monophosphate) for 6 days

value: control


title: Young-Sed-3

city: Boston

first: Yuteng

last: Zhang

state: MA

address: 20 Shattuck St

department: Surgery

institute: Brigham and Women's Hospital

data_processing:
Base-calling used bcl2fastq v2.20.0.422 with additional “--barcode-mismatches 1 --ignore-missing-positions --ignore-missing-controls --ignore-missing-filter --ignore-missing-bcls” and “ --use-bases-mask=y150n*,I8,I8,y150n*” parameters.
Sequence reads for the sample were trimmed with Trimmomatic 0.36 with the leading and trailing trimming set to 3, the sliding window size was 4 bp, and the required quality was set to 15. Seed mismatches set to 2, palindrome clip set to 30, simple clip to 10, minimum adapter length to 1.
Alignment was performed using STAR aligner v.2.5.2b with default parameters to the Mus musculus GRCm38 reference genome available on ENSEMBL.
Generation of gene level hit counts was performed using featureCounts from the Subread package v.1.5.2. Read counting was performed based on largest overlap of exons for each gene feature (as determined by the gene_id field from the ENSEMBL genome annotation). Corresponding exon-level hit counts were also calculated independently of the gene-level hit counting based on the exon fields from the ENSEMBL genome annotation.
Normalization and transformation of the gene-level hit counts was performed using the DESeq2 R package using default recommended parameters. Differential gene expression was calculated based on the normalized and transformed gene hit counts using DESeq2, with genes having absolute log fold change values greater than 1 and adjusted p-values less than 0.05 were labelled significantly differentially expressed.
Differential splice variant expression was similarly performed using the DEXSeq R package.
Genome_build: Mus musculus GRCm38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: raw counts

source_name: Young-Sed-Quadriceps femoris

extract_protocol:
Quadriceps femoris were harvested and snap-frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Pre-made library – no library preparation performed

treatment_protocol: Both young and old mice were subjected to a sedentary activity (no regimented running) or treadmill running exercise regime at an increasing speed from 8-12 m/min for 40 minutes, three times weekly, over the course of 8 weeks.

value: 18 weeks

value: 8 weeks of sedentary activity

value: Quadriceps femoris


title: Original organoid_rep2

description: Each sample has four different indexes when building the libraries and the data of each sample is divided into 4 files according to the index,  which contains two Fastq files, namely Read1 and Read3.

value: Umbilical cord-derived mesenchymal stem cells

value: pre-transplantation


title: C3_HF_A


title: Young-Sed-2


title: LacZ_CFA_rep1

value: Dorsal spinal cord

value: 3 months

value: rAAV-LacZ

value: intraplantar CFA


title: decidualized endometrial stromal cells (dESCs), si-Ctrl, rep2

value: emdometrium-derived primary human endometrial stromal cells

value: mid-secretory phase

value: healthy woman


title: C2_HF_A

value: female

value: high-fat diet

value: gonadal white adipose tissue


title: M06_Liver_18M_F0_3

description: mRNA-seq

value: male

value: Liver


title: C1_HF_A

value: control

value: mature adipocyte


title: Young-Sed-1

value: 18 weeks

value: 8 weeks of sedentary activity

value: Quadriceps femoris


title: Young-Exer-10

source_name: Young-Exer-Quadriceps femoris

value: 8 weeks of treadmill running exercise regimen


title: decidualized endometrial stromal cells (dESCs), si-Ctrl, rep1

value: transfected with scrambled siRNA (si-Ctrl), then subjected to hormone treatment (1 μM medroxyprogesterone and 0.5 mM cyclic adenosine monophosphate) for 6 days


title: M06_LI_18M_F0_3

description: mRNA-seq

value: Large intestine


title: M06_Kidney_18M_F0_3

description: mRNA-seq

value: Kidney


title: Young-Exer-8


title: MS4_HF_P

source_name: gonadal white adipose tissue preadipocyte

value: maternal separation & early weaning

value: preadipocyte


title: C1

city: Tianjin

first: xuan

last: zhou

address: West huanhu road

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Initial processing was done using Cell Ranger(3.0.2)
data analysis including standardization, cell subpopulation, difference of gene expression, and marker gene screening were achieved by Seurat software
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx, matrix file exported by cellranger
Supplementary_files_format_and_content: genes.tsv, features file exported by cellranger
Supplementary_files_format_and_content: barcodes.tsv, barcode file exported by cellranger

source_name: human

extract_protocol:
primary tumors from two treatment naive patients, and fresh HNSCC tissues were dissociated with the Gentle MACS Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Next, single cells were counted using automated cell counter and adjusted to the concentration of 1000 cells/μL and we retained single-cell transcriptomes for 13,903 cells after initial quality controls. Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs)
Cells were lysed, and the RNAs were reverse-transcribed into cDNAs. Libraries were generated from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1

value: tongue


title: LacZ_Saline_rep2

value: Dorsal spinal cord

value: 3 months

value: rAAV-LacZ

value: intraplantar saline


title: M06_GutEP_18M_F0_3

description: mRNA-seq

value: male

value: Gut epithelium


title: M06_MuscSat_18M_F0_3

description: mRNA-seq

value: Muscle


title: M_2uM_3

first: Mengping

last: Xi

address: 197 Rui Jin Er Road

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Human Peripheral blood

data_processing:
The reads were aligned on the hg19 UCSC genome using the ultrafast universal RNAseq aligner STAR (Dobin et al. 2013, doi: 10.1093/bioinformatics/bts635)
The counts were computed into Reads Per Kilobase of transcript, per Million mapped reads (RPKM) using HTseq (Anders et al. 2015, doi.org/10.1093/bioinformatics/btu638)
Normalized with the SARTools (Statistical Analysis of RNA-Seq data Tools) DESeq2- R pipeline (Varet et al. 2016, https://doi.org/10.1371/journal.pone.0157022).
Genome_build: hg19 UCSC genome

source_name: T-cell acute lymphoblastic leukemia cell lines

growth_protocol: Jurkat and Molt-4 were both incubated in RPMI 1640 (Gibco, Billings, MT, USA) supplemented with 10% Fetal bovine serum (Sigma, USA) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Cells were collected and washed with cold PBS, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: without chidamide treated or with Chidamide treated in 2uM for 48 hours

value: with Chidamide treated in 2uM for 50 hours


title: MS1_HF_A

value: female

value: high-fat diet

value: gonadal white adipose tissue

value: mature adipocyte


title: M_2uM_2

description: Human Peripheral blood

value: with Chidamide treated in 2uM for 49 hours


title: MS3_HF_P


title: M06_Esophagus_18M_F0_3

description: mRNA-seq

value: Esophagus


title: M06_Cerebellum_18M_F0_3

description: mRNA-seq

value: Cerebellum


title: M_2uM_1

description: Human Peripheral blood

value: with Chidamide treated in 2uM for 48 hours


title: MS2_HF_P

value: maternal separation & early weaning

value: preadipocyte


title: MS1_HF_P


title: Old-Sed-5

source_name: Old-Sed-Quadriceps femoris

value: 28 months

value: 8 weeks of sedentary activity

value: Quadriceps femoris


title: Young-Exer-7

value: 18 weeks

value: 8 weeks of treadmill running exercise regimen


title: M06_Brain_18M_F0_3

description: mRNA-seq

value: male

value: Frontal cortex


title: C4_HF_P

value: female

value: control


title: M_CTR_2

description: Human Peripheral blood

value: without chidamide treated


title: M06_Blood_18M_F0_3

description: mRNA-seq

value: Blood


title: C3_HF_P

value: high-fat diet

value: gonadal white adipose tissue


title: Old-Sed-4


title: Old-Exer-6

source_name: Old-Exer-Quadriceps femoris


title: M_CTR_1

description: Human Peripheral blood


title: M06_BAT_18M_F0_3

description: mRNA-seq

value: Brown adipose tissue


title: C2_HF_P


title: M06_Adrenal_18M_F0_3

description: mRNA-seq

value: Adrenal Gland


title: C1_HF_P


title: Old-Exer-5


title: M05_WAT_18M_F0_2

description: mRNA-seq

value: White adipose tissue


title: MS1_LF_P

value: maternal separation & early weaning

value: low-fat diet

value: preadipocyte


title: p75KO_prol_rep4

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

description:
RNA-Seq on p75NTR-/- (p75KO) neuronal stem/progenitor cells  at E12.5, replicate 4
MUC9820

data_processing:
Data quality was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Transcript-level quantification was performed with Salmon version 0.10.2. Settings were: -libType A, -gcBias, -biasSpeedSamp 5 using the mm10 (GRCm38.p6) reference transcriptome provided by Ensembl.
Gene count normalization and differential expression analysis was performed with DESeq2 version 1.22.0 in R version 3.6.1.
For gene annotation, Ensembl gene Ids were mapped to MGI symbols using the Bioconductor package “biomaRt” version 2.38 and genome information was provided by Ensembl (GRCm38.p6).
Genes with a minimal mean count across samples (baseMean) of 50, fold change of 1.5x and Benjamin-Hochberg-adjusted p-value<0.05 were called significantly changed.
Genome_build: mm10
Supplementary_files_format_and_content: _results_allGenes.txt file contains the unfiltered results from the DESeq2 analysis for differential expression between wildtype (p75+/+) and p75KO (p75-/-) neuronal stem/progenitor cells.

source_name: neuronal stem/progenitor cells

growth_protocol: Embryonic NSPCs   from  E12.5  embryos  were  cultured  under  proliferation  conditions  in  Neurobasal-A   medium supplemented with GlutaMAX (1%), glutamine (0.5%), Penicillin/Streptomycin   (1%), rhFGF-2 (20 ng/ml), B-27 minus Vitamin A (2%) (all from Invitrogen) and rhEGF   (20 ng/ml, Sigma-Aldrich).

extract_protocol:
RNA was extracted using the Quiagen Rneasy Mini Kit according to manufacture's manual.
The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies). Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.
stranded mRNA-Seq

value: E12.5 embryo


title: J_2uM_1

description: Human Peripheral blood

value: with Chidamide treated in 2uM for 48 hours


title: M05_Stomach_18M_F0_2

description: mRNA-seq

value: Stomach


title: J_2uM_2

description: Human Peripheral blood

value: with Chidamide treated in 2uM for 49 hours


title: M_CTR_3

description: Human Peripheral blood


title: Old-Sed-6

value: 28 months

value: 8 weeks of sedentary activity

value: Quadriceps femoris


title: C1_LF_P

value: female

value: control


title: J_CTR_3

description: Human Peripheral blood

value: without chidamide treated


title: M05_Skin_18M_F0_2

description: mRNA-seq

value: male

value: Skin


title: p75KO_prol_rep2

description:
RNA-Seq on p75NTR-/- (p75KO) neuronal stem/progenitor cells  at E12.5, replicate 2
MUC9814


title: wt_prol_rep4

description:
RNA-Seq on wildtype neuronal stem/progenitor cells (p75NTR-/- litter mates) at E12.5, replicate 4
MUC9819


title: J_CTR_2

description: Human Peripheral blood


title: colon, WD2

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed(smart-seq2 public primer) sequence for adaptor sequence, and masked for low-quality sequence and reads reads whose N base more than 5% for total bases, then mapped to Mus_musculus.GRCm38.90.chr using HISAT2 2.1.0 -with parameters-dta –t –p 4.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments   Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes   in each sample.
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample.

source_name: colon

extract_protocol:
Colons were removed, flash frozen in liquid nitrogenon, and RNA was harvested using the E.Z.N.A Total RNA Kit(OMEGA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight-week old Gm31629-/- and littermate WT mice were treated with 3% DSS in drinking water for 7 days and sacrificed on day 8.

value: colon

value: eight-week old

value: WT


title: colon, WD3

value: treated with 3% DSS in drinking water for 7 days


title: M05_SI_18M_F0_2

description: mRNA-seq

value: Small intestine


title: J_CTR_1

description: Human Peripheral blood


title: p75KO_prol_rep1

description:
RNA-Seq on p75NTR-/- (p75KO) neuronal stem/progenitor cells  at E12.5, replicate 1
MUC9808

value: E12.5 embryo


title: J_2uM_3

description: Human Peripheral blood

value: with Chidamide treated in 2uM for 50 hours


title: M05_MuscSat_18M_F0_2

description: mRNA-seq

value: Muscle


title: Wt_prol_rep1

description:
RNA-Seq on wildtype neuronal stem/progenitor cells (p75NTR-/- litter mates) at E12.5, replicate 1
MUC9807


title: colon, KD3


title: CTRL_4_in_UN-KC6141

city: La Jolla

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

description: established cell line

data_processing:
esATAC pipeline v1.4 was used for all below processing steps, calling other software with their default parameters
adapter removal was done with AdapterRemoval v1
read mapping was done with RBowtie2
peaks were identified using F-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files listing peak coordinates and closest genes

source_name: cell line derived from PDAC tumors of KrasG12D/PEC/IkkαΔPEC mice

growth_protocol: The UN-KC-6141 cell line were generated in Dr. Surinder K. Batra lab at the University of Nebraska Medical Center (Omaha, NE). (Torres et al., 2013, PLoS One 8, e80580)

extract_protocol:
Cells were resuspended in nuclei permeabilization buffer followed by gentle Dounce homogenization on ice to release the nuclei from cells. The nuclei suspension was filtered through 40 µm BD Falcon Cell Strainers (Cat. # 352340), spun down and resuspended in the tagmentation buffer from Illumina Nextera DNA Sample Preparation Kit (FC-121-1031). The nuclei number was determined by quantification using a hemocytometer and 20000 to 50000 nuclei were used to perform the tagmentation reaction. The tagmented DNA was purified with the Qiagen DNA purification kit and amplified using NEBNext PCR MasterMix (M0541 NEB).
DNA fragments of 200-500 bp size were selected using Ampure XP beads (A63880, Beckman Coulter).  After Qubit DNA quantification (Qubit dsDNA HS Assay Kit, Cat. # Q32851) and DNA ScreenTape Analysis, the bulk ATAC-Seq libraries were sequenced on Illumina HiSeq4000 system sequencer.

treatment_protocol: Cell lines were trasfected using Lipofectamine 3000 (Thermo Fisher Scientific, L3000015) with the following CRISPR/Cas9 KO HDR plasmid according to manufacturer’s instructions: ENX-1 Crispr/Cas9 KO plasmid (m) (Santa Cruz Biotechnology, sc-420259), ENX-1 HDR plasmid (m) (Santa Cruz Biotechnology, sc-420259-HDR),  and control CRISPR/Cas9 plasmid (Santa Cruz Biotechnology, sc-418922). To obtain stable expression, cells were selected 96 hrs after the transfection with puromycin (InvivoGen Cat# ant-pr-1).

value: PDAC

tag: original genotype

tag: additional genotype

value: ctrl


title: M05_Lung_18M_F0_2

description: mRNA-seq

value: Lung


title: P97_Avoidance_CD137

city: Cambridge

first: Ang

middle: Andy

last: Tu

address: 500 Main Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: scRNA + TCR-Seq
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: hg19
Supplementary_files_format_and_content: gene expression count (genes by cells)

source_name: Transcriptome of single cells

extract_protocol: Seq-Well

tag: timepoint

value: Avoidance

value: Treatment failure

tag: sequencing platform

value: NovaSeq S2 100 cycles


title: colon, WD1

tag: tissue

tag: age


title: P97_Maintenance_CD137

value: Maintenance


title: M05_Liver_18M_F0_2

description: mRNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.36) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (GRCm38.p3y) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

value: male

value: Liver


title: colon, KD2

value: colon


title: Old-Exer-4

value: 28 months

value: 8 weeks of treadmill running exercise regimen

value: Quadriceps femoris


title: M05_LI_18M_F0_2

description: mRNA-seq

value: Large intestine


title: EZH2KO_3_in_UN-KC6141

description: established cell line

tag: cell line


title: colon, KD1

value: eight-week old

value: treated with 3% DSS in drinking water for 7 days


title: P97_Baseline_CD137

value: Baseline


title: EZH2KO_1_in_UN-KC6141

description: established cell line

value: PDAC


title: P97_Avoidance_CD154


title: PB-GPC4-rep2

first: Qin

last: Shen

address: Chifeng Street, Siping Road, Yangpu District

institute: Tongji University

data_processing:
Illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the clean data were further processed on https://usegalaxy.org/ online website. Firstly, sequence reads were trimmed for low-quality sequence using Trimmomatic with parameters LEADING 20/TRAILING 20/SLIDING WINDOW bases 4 quality 20/MINLEN 35, then mapped to mm10 whole genome using HISAT2 with default parameters. Finally, the output BAM file were calculated to counts using featurecounts with parameters only count primary alignments TRUE.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and abundance for every gene and every sample

source_name: PB-GPC4_cerebral cortex

extract_protocol:
500-1000ng total RNA were extracted following the TRIzol® reagent protocol (Cat#15596018, Invitrogen)
The mRNA library preparation including mRNA capturing, fragmentation (200-300bp), adaptor (Cat#E7775, NEB) ligation, and library amplification and purification was finished following the manufacturer’s protocols of KAPA Hyper Prep Kit (Cat#KK8504, Kapa Biosystems).

treatment_protocol: For C57BL/6 mice, 3μg/μl PiggyBac transposase expression plasmid plus 1.5μg/μl PB-Ctrl plasmid were injected into the lateral ventricle of brains, which were then electroporated at embryonic (E) 14.5,  the embryos were placed back into the abdorminal of the pregnant mice for normal development, the cortices were dissociated at E17.5; for ICR mice, 3μg/μl PiggyBac transposase expression plasmid plus 1.5μg/μl PB-Ctrl, PB-CCN1, or PB-GPC4 plasmid, respectively, were injected into the lateral ventricle of brains, which were then electroporated at E13.5, the cortces were dissociated at E15.5.

tag: strain background

value: ICR

value: wildtype

value: Embryonic day 15.5

value: brain; cerebral cortex


title: M05_GutEP_18M_F0_2

description: mRNA-seq

extract_protocol:
RNA was isolated using an RNeasy DNA/RNA kit after homogenization and lysis in guanidine thiocyanate buffer supplemented with β-mercaptoethanol. RNA concentration and quality were assessed using an Agilent TapeStation. RNAseq libraries were prepared using an NEB Next RNA Ultra kit with polyA enrichment module using an Agilent Bravo NGS Automated fluidics handling platform as described elsewhere (Misharin et al., 2017, J Exp Med 214). Libraries were multiplexed and sequenced on an Illumina NextSeq 500 platform using 75 cycles of high-output flow cells and a dual indexing strategy.
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) using 75 cycles of high-output flow cells and a dual indexing strategy.

tag: Sex

tag: organ

value: Gut epithelium


title: PB-GPC4-rep1


title: M05_Esophagus_18M_F0_2

description: mRNA-seq

value: Esophagus

tag: age (months)

tag: pfu (influenza)


title: P97_Maintenance_CD154

value: Maintenance

value: Treatment failure

value: NovaSeq S2 100 cycles


title: P97_Buildup_CD154

value: Buildup


title: KO_rep3 (CL100072790_L1_WHMARqncEAAKRAAPEI-559)

first: Bo

last: Xu

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

data_processing:
Reads (FASTQ) were aligned to the Marchantia polymorpha genome sequence v3 using STAR v2.5.1b in 2-pass mode with 0.95 similarity cutoff and 0.9 length cutoff.
Quantification of gene expression was performed with featureCounts v1.5 based on the Phytozome annotation v3.1.
Calculation of CPMs and FPKMs was performed based on customized Python scripts (Haak et al., 2018).
Genome_build: Marchantia polymorpha v3 (Phytozome)
Supplementary_files_format_and_content: matrix of raw counts

organism: Marchantia polymorpha

source_name: Thalli of 10-day-old Marchantia polymorpha plants

growth_protocol: Gemmae were grown on half strength Gamborg’s B5 media with vitamins (pH5.8) containing 1% (w/v) agar at 22°C under 16 h-white light and 8 h-dark regime.

extract_protocol: About 100mg of fresh thalli from 10-day-old plants was ground frozen using a Tissue Lyer II homogenizer (Qiagen). RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen), and DNA contamination was removed using the TURBO DNA-free Kit (Ambion).

tag: genotype

value: KO

value: Thalli

value: male


title: KO_rep2 (CL100072790_L1_WHMARqncEAAJRAAPEI-535)


title: PB-CCN1-rep2

source_name: PB-CCN1_cerebral cortex


title: M05_Cerebellum_18M_F0_2

description: mRNA-seq

value: Cerebellum


title: PB-CCN1-rep1


title: KO_rep1 (CL100072790_L1_WHMARqncEAAIRAAPEI-507)


title: P97_Baseline_CD154


title: M05_Blood_18M_F0_2

description: mRNA-seq

value: Blood


title: CTRL_3_in_UN-KC6141

description: established cell line

value: ctrl


title: PB-Ctrl-rep2

source_name: PB-Ctrl_cerebral cortex


title: OX_rep3 (CL100072790_L1_WHMARqncEAAHRAAPEI-503)

value: OX


title: P97_Buildup_CD137


title: P96_Maintenance_CD137

value: Placebo


title: PB-Ctrl-rep1

value: ICR

value: wildtype


title: OX_rep2 (CL100072790_L1_WHMARqncEAAGRAAPEI-594)


title: M05_BAT_18M_F0_2

description: mRNA-seq

value: Brown adipose tissue


title: M05_Kidney_18M_F0_2

description: mRNA-seq

value: Kidney


title: P96_Buildup_CD137


title: M05_Adrenal_18M_F0_2

description: mRNA-seq

value: Adrenal Gland


title: OX_rep1 (CL100072790_L1_WHMARqncEAAFRAAPEI-573)


title: PB-Ctrl-NCKO-rep2

source_name: PB-Ctrl-NCKO_cerebral cortex

value: Ccn1 conditional knockout (Nestin-Cre, Ccn1fl/fl)

value: Embryonic day 17.5

value: brain; cerebral cortex


title: P96_Baseline_CD137

value: Baseline

value: NovaSeq S2 100 cycles


title: PB-Ctrl-NCKO-rep1


title: M04_WAT_18M_F0_1

description: mRNA-seq

value: White adipose tissue


title: P96_Maintenance_CD154

value: Maintenance


title: M04_Stomach_18M_F0_1

description: mRNA-seq

value: male

value: Stomach


title: P96_Buildup_CD154

value: Buildup


title: M04_Skin_18M_F0_1

description: mRNA-seq

value: Skin


title: WT_rep1 (CL100072790_L1_WHMARqncEAACRAAPEI-529)

value: WT

value: Thalli


title: PB-Ctrl-WT-rep1

source_name: PB-Ctrl-WT_cerebral cortex

value: wildtype


title: P96_Baseline_CD154

value: Placebo


title: WT_rep2 (CL100072790_L1_WHMARqncEAADRAAPEI-570)


title: P95_Avoidance_Double_negative

value: Avoidance

value: Treatment failure


title: CAV-5

city: Beijing

first: Congcong

address: Anzhen Road 2

institute: Beijing Institute of Heart Lung and Vascular Disease

data_processing:
Software SOAPnuke to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases (N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). SOAPnuke: version: v1.5.2 parameters: -l 15 -q 0.5 -n 0.1
We map clean reads to reference genome using HISAT. HISAT2: Version: v2.0.4 Parameters: -p 8 --phred64 --sensitive -I 1 -X 1000
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM. Bowtie2: Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k200 RSEM: Version: v1.2.12
We detect DEGs with DEGseq as requested. DEGseq: Parameters: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: Homo_sapiens_9606.NCBI.GCF_000001405.38_GRCh38.p12. v1904
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file includes FPKM values for every gene in each Sample.

source_name: Aortic valve

extract_protocol:
Aortic valves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We use Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC, RNA concentration, RIN value, 28S/18S and the fragment length distribution.
RNA libraries were prepared for sequencing using standard BGISEQ-500 platform.

tag: disease state

value: calcified aortic valve

value: Aortic valve


title: CAV-4


title: P95_Maintenance_Double_negative


title: ES-TS-XEN_XEN_d3_rep2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Base calling was performed using bcl2fastq v2.20.0.422 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: plain text (tab-separated values)

source_name: XEN coculture ES-TS-XEN

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.

extract_protocol:
RNA was extracted follwing Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were observed in monoculture (without different cells) or co-culture conditions.

tag: cell type

value: XEN


title: CAV-3


title: ES-TS-XEN_TS_d3_rep2

source_name: TS coculture ES-TS-XEN

value: TS

tag: strain


title: M04_Lung_18M_F0_1

first: Alexander

address: SQBRC 303 E Superior St 5-404

institute: Northwestern University

description: mRNA-seq

value: Lung


title: M04_MuscSat_18M_F0_1

description: mRNA-seq

value: Muscle


title: ES-TS-XEN_ES_d3_rep2

source_name: ES coculture ES-TS-XEN

value: ES


title: M04_Liver_18M_F0_1

description: mRNA-seq

value: male

value: Liver


title: P95_Buildup_Double_negative

value: Buildup

value: NovaSeq S2 100 cycles


title: ES-TS-PrES_PrES_d3_rep2

source_name: PrES coculture ES-TS-PrES

value: PrES


title: CAV-2


title: WT_rep3 (CL100072790_L1_WHMARqncEAAERAAPEI-571)

value: WT

value: Thalli


title: M04_LI_18M_F0_1

description: mRNA-seq

value: Large intestine


title: PB-Ctrl-WT-rep2

value: wildtype

value: Embryonic day 17.5

value: brain; cerebral cortex


title: ES-TS-PrES_TS_d3_rep2

source_name: TS coculture ES-TS-PrES


title: P95_Baseline_Double_negative

value: Baseline

value: Treatment failure


title: P95_Avoidance_CD137

value: Avoidance


title: M04_GutEP_18M_F0_1

description: mRNA-seq

value: Gut epithelium


title: CON-3

value: non-calcified aortic valve

value: Aortic valve


title: ES-TS-PrES_ES_d3_rep2

source_name: ES coculture ES-TS-PrES

value: ES


title: P95_Maintenance_CD137

value: Maintenance


title: M04_Esophagus_18M_F0_1

description: mRNA-seq

value: male

value: Esophagus


title: CAV-1

value: calcified aortic valve


title: M04_SI_18M_F0_1

description: mRNA-seq

value: Small intestine


title: TS-XEN_TS_d3_rep2

source_name: TS coculture TS-XEN

value: TS


title: M04_Cerebellum_18M_F0_1

description: mRNA-seq

value: Cerebellum


title: P95_Buildup_CD137

value: Buildup

value: NovaSeq S2 100 cycles


title: CON-1


title: CON-2


title: M04_Brain_18M_F0_1

description: mRNA-seq

value: Frontal cortex


title: M04_Blood_18M_F0_1

description: mRNA-seq

value: Blood


title: Tumor-infiltrating Tc9 cells_2

city: Houston

first: Liuling

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata.
Then we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
Then we map those clean reads onto reference genome (mm10).
Finally, we identify gene expression in samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with Fragments Per Kilobase of transcript per Million mapped reads (fpkm) for every gene and every sample

source_name: Subcutaneous B16 tumor

extract_protocol:
Tumor tissue was removed and Tc1 or Tc9 cells in tumors were sorted by flow cytometry sorter. Total RNA of sorted cells was extracted with the RNeasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard DNB protocols

treatment_protocol: Thy1.1+ Pmel-1 Tc1 or Tc9 cells were in vitro polarized for 5 days and then intravenously (i.v.) injected into Thy1.2+ B6 mice bearing 10-day s.c. B16 tumor. 14 days after adoptively transfer, tumor-infiltrating Tc1 and Tc9 cells were sorted by flow cytometry sorter to detect their gene expresssion.

value: Subcutaneous B16 tumor

value: in vitro polarized Tc9 cells

tag: treatment

value: in vitro polarized Tc9 cells were adoptively transferred in vivo


title: ES-XEN_XEN_d3_rep2

source_name: XEN coculture ES-XEN

value: XEN


title: ES-XEN_ES_d3_rep2

source_name: ES coculture ES-XEN


title: P95_Avoidance_CD154

source_name: Transcriptome of single cells

value: Avoidance

value: Treatment failure


title: Tumor-infiltrating Tc9 cells_1


title: P95_Baseline_CD137

value: Baseline


title: M04_BAT_18M_F0_1

description: mRNA-seq

value: male

value: Brown adipose tissue


title: P95_Buildup_CD154


title: Tumor-infiltrating Tc1 cells_2

value: in vitro polarized Tc1 cells

value: in vitro polarized Tc1 cells were adoptively transferred in vivo


title: TS-PrES_PrES_d3_rep2

source_name: PrES coculture TS-PrES

value: PrES


title: M04_Adrenal_18M_F0_1

description: mRNA-seq

value: Adrenal Gland


title: TS-PrES_TS_d3_rep2

source_name: TS coculture TS-PrES

value: TS


title: P95_Maintenance_CD154

value: Maintenance

value: NovaSeq S2 100 cycles


title: TS-XEN_XEN_d3_rep2

source_name: XEN coculture TS-XEN


title: P93_Avoidance_CD137

value: Partial tolerance


title: viviparous species N. micrantha denoted as X-species, Leaf X4 rep2 [X4-2]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. colorata genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Genome_build: Nymphaea_colorata_Nym_GWHAAYW00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Nymphaea micrantha

growth_protocol: The plants of two Nymphaea species N. micrantha (X) and N. colorata (L) (Figure 1A and 1B) were grown in a planting container of 100 cm diameter and 60 cm depth, with 30 cm soil thickness at Water Lily Resource Garden of the Floriculture Institute of Guangxi Academy of Agricultural Sciences, Guangxi, China during the growth season of 2019. Six disease free plants with robust growth for each genotype were selected for the transcriptome study

extract_protocol:
The total RNA was extracted by CTAB method from leaf tissues of each sample using the three biological repeats.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: The harvested leaves were immediately frozen in liquid nitrogen and stored at -80 °C.

value: viviparous species

value: wild type

tag: developmental stage

value: Maturity stage

value: the leaves are fully unfolded with obvious viviparous traces/mark in the center of X-species while absent in L-species

value: leaf


title: ES-PrES_ES_d3_rep2

source_name: ES coculture ES-PrES

value: ES


title: Tumor-infiltrating Tc1 cells_1

value: Subcutaneous B16 tumor


title: P93_Maintenance_CD137


title: viviparous species N. micrantha denoted as X-species, Leaf X4 rep1 [X4-1]


title: M03_Skin_24M_F0_3

last: Misharin

description: mRNA-seq

value: male

value: Skin


title: viviparous species N. micrantha denoted as X-species, Leaf X3 rep2 [X3-2]

value: Development stage

value: the leaves are half rolled and the with tip is in contact with water surface


title: ES-TS_TS_d3_rep2

source_name: TS coculture ES-TS


title: P93_Buildup_CD137

value: Buildup


title: ES-TS_ES_d3_rep2

source_name: ES coculture ES-TS


title: M03_SI_24M_F0_3

description: mRNA-seq

value: Small intestine


title: P93_Baseline_CD137

value: Baseline


title: XEN_only_XEN_d3_rep2

source_name: XEN monoculture

value: XEN


title: P93_Avoidance_CD154

value: Avoidance

value: NovaSeq S2 100 cycles


title: P93_Maintenance_CD154

value: Maintenance

value: Partial tolerance


title: viviparous species N. micrantha denoted as X-species, Leaf X2 rep2 [X2-2]

value: viviparous species

value: wild type

value: the leaves are submerged and completely rolled leaves with 4-6 cm length


title: PrES_only_PrES_d3_rep2

source_name: PrES monoculture

value: PrES


title: P95_Baseline_CD154

value: Treatment failure


title: ES-PrES_PrES_d3_rep2

source_name: PrES coculture ES-PrES


title: M03_WAT_24M_F0_3

description: mRNA-seq

value: male

value: White adipose tissue


title: TS_only_TS_d3_rep2

source_name: TS monoculture

value: TS


title: M03_Lung_24M_F0_3

description: mRNA-seq

value: Lung


title: M03_Liver_24M_F0_3

description: mRNA-seq

value: Liver


title: viviparous species N. micrantha denoted as X-species, Leaf X1 rep2 [X1-2]

value: Development stage

value: the leaves are submerged and completely rolled with 1-2 cm length

value: leaf


title: viviparous species N. micrantha denoted as X-species, Leaf X3 rep1 [X3-1]

value: the leaves are half rolled and the with tip is in contact with water surface


title: P93_Buildup_CD154

value: Buildup

value: NovaSeq S2 100 cycles


title: M03_LI_24M_F0_3

description: mRNA-seq

value: Large intestine