title: Caco-2,Mimic ISO-miR-1246_G, repl5

value: Mimic ISO-miR-1246_G


title: A66 [LARC]

status: Public on Feb 26 2024

type: SRA

city: Guangzhou

first: Peng

last: Deng

address: Panyu

country: China

institute: SYSUCC

library_source: transcriptomic

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT/csv file contain counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: LARC

growth_protocol: DLD-1 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: DLD-1 cells were plated into 6-well plate 20 h before treatment and harvest cells for RNA extraction at 48h.

tag: tissue

value: locally advanced rectal cancer (LARC) tissue


title: Caco-2,Mimic ISO-miR-1246_G, repl4

city: Kaunas

first: Jurgita

last: Skiecevičienė

address: Eiveniu str. 4

department: Institute for Digestive Research

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Quality trimming and adapter sequences removal using DDBuk program from BBmap v38.87.
Trimmed reads were aligned to human reference genome GRCh38.p13 using STAR v2.7.9 Gencode v34 annotations
Counts per gene were detected using Verse v0.1.5.
ComBat-seq was applied for batch effect.
Further analysis was performed using DESeq2 v1.32.0
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene id,  gene  name, gene  type along with  gene count  values for each sample

molecule: polyA RNA

extract_protocol:
RNA from tansfected cells was extracted using miRNeasy Mini Kit (Qiagen, MD, USA) 48h post-transfection, according to manufacturer recommendations.
Polyadenylated RNA sequencing libraries were generated with 1 µg of total RNA input per sample applying a standard Illumina TrueSeq Stranded mRNA protocol.

treatment_protocol: Reverse transfection with miRNA mimic of ISO-miR-1246_G, ISO-miR-1246_a and  WT-miR-1246  as well  as negative control  was performed using Lipofectamine 3000 reagent.

tag: cell line

tag: passage index

tag: treatment


title: uninjured Slc34a1 expressing PTECs, Tamoxifen-labeled, FACS-enriched, biol rep 2

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

country: USA

institute: Cedars Sinai Medical Center

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20(Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR(version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) withdefault parameters, using a custom MOUSE GRCh38 transcriptome reference downloaded fromhttp://www.gencodegenes.org, containing all protein coding and long non-coding RNA genesbased on MOUSE GENCODE version 33 annotation. Expression counts for each gene in allsamples were normalized by a modified trimmed mean of the M-values normalization method andthe unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version1.26.0 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model,and the Wald test was applied to assess the differential expressions between two sample groups byDESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing,and differential expression gene candidates were selected with a false discovery rate less than 0.05.
Further filtering of candidate differentially expressed genes to false discovery rate less than 0.01and an absolute log 2 fold-change greater than 1 was applied to the studies comparing normaluninjured PTEC vs. Sox9:48h IRI vs. Sox9: day14 post IRI. GO term enrichment was conductedwith DAVID retaining only terms with a p-value for enrichment less than 0.01. After manuallymerging redundant biological process GO terms, relevant terms among the top 20 were plottedusing custom scripts in R and the ggplot2 (version 3.3.3) package. For visualization of coordinatedgene expression in samples, a two-way hierarchical clustering with Pearson correlation distancematrix was performed with samples and DEG candidates using the Bioconductor g-plots package(version 3.0.3) in R. MA plots, and PCA plots were created using custom R scripts and theBioconductor FactoMineR package (version 2.4).
Assembly: mm10
Supplementary files format and content: tab-deliminited text files include raw files for each sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer. RNA was extracted from TdTomato positive enriched sorted cells were processed following the manufacture instruction mRNA easy, Qiagen). Briefly, total RNA samples were assessed for concentration using a Nanodrop (Nanodrop 504 ND8000, Thermo Fisher Scientific, Carlsbad, CA) and quality using the TapeStation 505 (4200 TapeStation, Agilent Technologies, Santa Clara, CA). Up to 30 ng of total RNA per sample was used for poly-A mRNA selection.
Libraries for RNA-Seq were prepared with Nugen Universal plus mRNA-Seq Kit (part number: 0508) to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library. Different index adaptors were used for multiplexing samples in one sequencing lane. The concentration of the amplified library was measured with a Qubit fluorometer and an aliquot of the library was resolved on a Bioanalyzer.

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. To obtain control uninjured PTECs, tamoxifen was administered to Slc34a1IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.To obtain cells that activated Sox9 at 48h after kidney IRI, tamoxifen was administered at induction of kidney IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.To obtain cells that continued to express Sox9 at d14 post-kidney IRI, tamoxifen was administered at d10 and d12 after IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.

value: Kidney

tag: cell type

value: Cre induced TdT+ cells

tag: genotype

tag: age

value: 9-12 weeks


title: 10d-2_H3K4me3_Cut&Run

library_source: genomic

data_processing:
Libraries were analyzed with Partek Flow software v10.
unaligned reads were filtered out of contaminants using default parameter in the Filter contaminants (Bowtie 2) -2.2.5 Partek task then aligned with the Bowtie algorithm
Peaks calling was carried out using MACS3 using the input datasets as background peaks and a Cutoff q-value of 0.01 and the mm10 mouse genome version, additionally, scale was adjusted to the larger dataset in the Partek parameters for the MACS3 algorithm.
Genomic regions were quantified with the defaults parameter in Partek flow and normalized to transcripts per million counts in each library to explore the samples with PCA analysis accounting by feature variability.
Differential region enrichment was analyzed with Partek Flow’s version of the GSA algorithm.
Motif enrichment was studied within the positively enriched regions of the GSA analysis at 10 and 2 days against the JASPAR vertebrate database of binding motifs with a following manual curation of transcript factor motifs present in mouse.
The enriched genesets between 48 hours and 10 days Sox9 CUT&RUN datasets were used for pathway analysis against the Gene Ontology (GO) database on Partek.
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeaks (Except for Input files)
Library strategy: Cut&Run

molecule: genomic DNA

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer.
Cells pellets of around 100.000 cells from 2 or 10 days post injury were lighly fixed in 0.2% PFA and freeze at –80 for storage until all samples were collected. Each sample was split in 3 aliquots for subsequent processing with  Sox9 antibody (#AB5535, Millipore), as a positive control with H3K4me3 (#9751, Cell signaling) or as an input control. CUT&RUN assays were carried out with the Cell Signalling assay kit and protocol (Catalog number #86652, Cell Signaling) and next-generation sequencing libraries were generated from the immuno-enriched DNA samples using the DNA Library Prep Kit for Illumina with the Multiplex Oligos for Illumina Systems (Dual Index Primers) kits (#56795 and #47538, Cell Signaling, respectively). The final libraries quality was assessed by fragment size in a TapeStation before sequencing.

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. .To obtain Sox9 lineage cells, tamoxifen was administered at induction of kidney IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated at 48h and day10 post-IRI as stated in the below stated extract protocol.

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 2

tag: cut&run antibody

value: H3K4me3 (#9751, Cell signaling)


title: A60 [LARC]


title: Caco-2,Mimic ISO-miR-1246_G, repl3


title: B74

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R scripts were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: locally advanced rectal cancer

growth_protocol: 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy were harvested for RNA-seq.

extract_protocol:
Total RNA of patient samples were harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

value: locally advanced rectal cancer


title: Caco-2,Mimic ISO-miR-1246_G, repl2


title: uninjured Slc34a1 expressing PTECs, Tamoxifen-labeled, FACS-enriched, biol rep 1


title: tdTnegGFPpos cells at d6 post-IRI, Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 3

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20(Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR(version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) withdefault parameters, using a custom MOUSE GRCh38 transcriptome reference downloaded fromhttp://www.gencodegenes.org, containing all protein coding and long non-coding RNA genesbased on MOUSE GENCODE version 33 annotation. Expression counts for each gene in allsamples were normalized by a modified trimmed mean of the M-values normalization method andthe unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version1.26.0 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model,and the Wald test was applied to assess the differential expressions between two sample groups byDESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing,and differential expression gene candidates were selected with a false discovery rate less than 0.05.
Further filtering of candidate differentially expressed genes to false discovery rate less than 0.01and an absolute log 2 fold-change greater than 1 was applied to the studies comparing normaluninjured PTEC vs. Sox9:48h IRI vs. Sox9: day14 post IRI. GO term enrichment was conductedwith DAVID retaining only terms with a p-value for enrichment less than 0.01. After manuallymerging redundant biological process GO terms, relevant terms among the top 20 were plottedusing custom scripts in R and the ggplot2 (version 3.3.3) package. For visualization of coordinatedgene expression in samples, a two-way hierarchical clustering with Pearson correlation distancematrix was performed with samples and DEG candidates using the Bioconductor g-plots package(version 3.0.3) in R. MA plots, and PCA plots were created using custom R scripts and theBioconductor FactoMineR package (version 2.4).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer. RNA was extracted from the above desired cells following the manufacture instruction (mRNA easy, Qiagen). Briefly, total RNA samples were assessed for concentration using a Nanodrop (Nanodrop 504 ND8000, Thermo Fisher Scientific, Carlsbad, CA) and quality using the TapeStation 505 (4200 TapeStation, Agilent Technologies, Santa Clara, CA). Up to 30 ng of total RNA per sample was used for poly-A mRNA selection.
Libraries for RNA-Seq were prepared with Nugen Universal plus mRNA-Seq Kit (part number: 0508) to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library. Different index adaptors were used for multiplexing samples in one sequencing lane. The concentration of the amplified library was measured with a Qubit fluorometer and an aliquot of the library was resolved on a Bioanalyzer.

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. To obtain WRCs,  tamoxifen was administered at d2, and d4 to Axin2CreERT2/+:R26RtdT/+:Acta2-GFP animals, and at d6 dual positive (tdT positive and GFP positive) and their tdT negative, GFP positive counterparts were enriched via FACS.  The cells were isolated as stated in the below stated extract protocol.

value: endogenous GFP cells only from kidney-3

value: Axin2CreERT2/+:R26RtdT/+ :Acta2-GFP


title: 10d-1_Input_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 1


title: tdTnegGFPpos cells at d6 post-IRI, Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 2

value: endogenous GFP cells only from kidney-2


title: 10d-1_H3K4me3_Cut&Run


title: 10d-1_Sox9_Cut&Run

value: Sox9 (#AB5535, Millipore)


title: A50 [LARC]


title: A44 [LARC]


title: tdTnegGFPpos cells at d6 post-IRI, Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 1

value: endogenous GFP cells only from kidney-1


title: Caco-2,Mimic ISO-miR-1246_a, repl5

value: Mimic ISO-miR-1246_a


title: A47 [LARC]


title: cells activating Axin2 at d6 post-IRI (tdTposGFPpos cells), Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 3

value: TdT+ cells and endogenous GFP cells from kidney-3


title: P7 OE, Amigo1neo/neo, rep3

city: Montreal

first: Jean-François

last: Cloutier

state: Quebec

address: 3801 University

department: Neurology and Neurosurgery

country: Canada

institute: The Neuro

description:
Sample name: A1.1.1.20180703.9
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35[1] and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b[2]
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM[3] in order to obtain gene and transcript level expression , either in TPM or FPKM values, for these stranded RNA libraries.
Assembly: GRCmm38, mm10
Supplementary files format and content: .txt file includes normalized gene readcounts computed by DESeq2 version 1.18.1[4]
Supplementary files format and content: .txt file includes gene expression readcount directly from STAR
Supplementary files format and content: .txt file includes gene expression readcount computed using RSEM[3] to obtain gene expression in FPKM values
Supplementary files format and content: .txt file includes gene expression readcount computed using RSEM[3] to obtain gene expression in TPM values
Supplementary files format and content: .txt file includes gene expression readcount computed using RSEM[3] to obtain transcript level expression in FPKM values
Supplementary files format and content: .txt file includes gene expression readcount computed using RSEM[3] to obtain transcript level expression in TPM values

source_name: olfactory epithelium

extract_protocol:
Total RNA was collected from 3 Amigo1neo/neo OE and 3 Amigo1-/- OE using the RNeasy mini kit (QIAGEN) and 4μg of each sample was sent for RNA sequencing and Bioinformatics at the Genomics Platform at the Institute for Research in Immunology and Cancer (IRIC)
KAPA RNA Hyperprep (Roche), using a PolyA capture (Thermo)

value: olfactory epithelium

value: Amigo1 knock-out with neomycin cassette


title: Caco-2,Mimic ISO-miR-1246_a, repl4


title: A43 [LARC]

value: locally advanced rectal cancer (LARC) tissue


title: Caco-2,Mimic ISO-miR-1246_a, repl3


title: A40 [LARC]


title: P7 OE, Amigo1neo/neo, rep1

description:
Sample name: A1.1.1.20180703.4
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt


title: cells activating Axin2 at d6 post-IRI (tdTposGFPpos cells), Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 2

value: TdT+ cells and endogenous GFP cells from kidney-2


title: Caco-2,Mimic ISO-miR-1246_a, repl2


title: cells activating Axin2 at d6 post-IRI (tdTposGFPpos cells), Tamoxifen at d2 and d4 post-IRI, FACS-enriched, biol rep 1

value: TdT+ cells and endogenous GFP cells from kidney-1


title: P7 OE, Amigo1-/-, rep3

description:
Sample name: A1.5.1.20180601.12
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt

value: Amigo1 knock-out


title: A36 [LARC]


title: Caco-2,Mimic ISO-miR-1246_a, repl1


title: Caco-2,Mimic ISO-miR-1246_G, repl1

value: Mimic ISO-miR-1246_G


title: Mst1/2 KO sample 5

city: Shanghai

first: Yongchun

last: Zhang

state: Shanghai

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong university

description: fpkm_gene expression matrix.txt for all  RNA-seq samples

data_processing:
The raw sequencing data were processed by Cutadapt to obtain high-quality clean reads.The reads were then mapped to a reference genome (Mouse: UCSC/mm9) using HISAT2 (v2.0.1). Gene expression levels were estimated by HTSeq (v0.6.1) and presented in read counts or Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
Assembly: UCSC/mm9
Supplementary files format and content: tab-delimited text files include RPKM values for all Sample

source_name: esophagus

growth_protocol: Esophageal epithelium was obtained from mouse esophagus

extract_protocol:
The esophagus was dissected from the mice and muscle layers and adventitia were stripped away using forceps. Subsequently, the esophagus was incubated with 0.5 U/ml of Dispase I at room temperature for 10 minutes, allowing the separation of mesenchymal layers from the epithelium. The mesenchyme layers were then removed from the epithelium under a dissection microscope, and the epithelium was then washed with sterile 1X PBS and lysed with RNA lysis buffer. Total RNA was extracted from the lysate using the Qiagen RNeasy Plus Universal Mini Kit.
Libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) and size-selected with VAHTS DNA Clean Beads (Vazyme Biotech) according to the manufacturer’s instructions. The libraries were sequenced by Illumina NovaSeq 6000 using a paired-end (150 bp for each end of the fragment) configuration.

treatment_protocol: Mice were administered 3 doses (100 mg/kg) of tamoxifen every 2 weeks

value: esophagus

value: Esophageal epithelium

value: Mst1 and Mst2 knockout

value: Tamoxifen


title: P7 OE, Amigo1-/-, rep2

description:
Sample name: A1.5.1.20180601.7
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt


title: A34 [LARC]


title: 308_D28

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing raw Kallisto gene count from individual samples

source_name: Whole blood

extract_protocol:
RNA recovered from Paxgene tubes using the Qiagen PAXgene Blood RNA isolation Kit
Libraries created using Illumina Stranded Total RNA Prep with Ribo-Zero Plus
Final sequencing libraries generated using the IDT-Ilmn RNA UD Indexes SetA, and QC performed prior to sequencing using the Bioanalyzer and DNA 1000 reagents

value: Whole blood

tag: subject

tag: infection

tag: study day


title: P7 OE, Amigo1-/-, rep1

description:
Sample name: A1.5.1.20180601.2
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt


title: Mst1/2 KO sample 4


title: 307_D10


title: A32 [LARC]


title: Mst1/2 KO sample 3


title: P7 OE, Amigo1+/+, rep1

description:
Sample name: A1.5.1.20180601.6
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt

value: Wild Type


title: Mst1/2 KO sample 2


title: P7 OE, Amigo1neo/neo, rep2

description:
Sample name: A1.1.1.20180703.8
DESeq2 version 1.18.1[4] was then used to normalize gene readcounts.
A_vs_B_DESEQ.txt
star_genes_readcount.stranded.annotated.txt
genes_FPKM.annotated.txt
genes_TPM.annotated.txt
isoforms_FPKM.annotated.txt
isoforms_TPM.annotated.txt


title: A28 [LARC]


title: mESC_Dppa24DKO_c53_reChIP_K27K4

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_bivalent_K27K4_Annotated Probe Report for All Probes.txt
53_K27K4

data_processing:
Single-end reads in fastqs were trimmed (illumina adapters), filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore v0.6.6 in single-end mode. (trim_galore --phred33 --quality 20 --length 20)
Trimmed reads were then aligned to the mm10 mouse genome (GRCm38.p6) using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and idexed using samtools v1.9.
Duplicate alignments were then marked with using MarkDuplicates (picard v2.6.0) and re-indexed with samtools.
bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked BAM files using bamCoverage (DeepTools v3.5.0) whilst excluding ENCODE blalcklisted genomic regions for the mm10 genome (v2). (bamCoverage --of bigwig -bs 1 -bl mm10-blacklist.v2.bed  --normalizeUsing CPM --effectiveGenomeSize 2652783500 --extendReads 147).
Duplicate marked BAM files were loaded into seqmonk v1.48.1 using standard parameters (no deduplication, MAPQ>20, primary alignments only) and extending reads by 200bp.Peak calling for datasets was performed using two biological replicates or clones per ChIP with the IgG-IgG serving as the input control using MACS2 (p-value<1e-5, fragment size 300).
Assembly: GRCm38.p6
Supplementary files format and content: MACS2 peak files (except for IgG-IgG controls)
Supplementary files format and content: CPM/bp normalised bigWig files.

source_name: E14 mESC

growth_protocol: Cells were cultured at 37 degrees celsius with 5% CO2 on gelatin-coated plates in serum/LIF mESC media (DMEM, 15% FBS, 1x penicillin/streptomycin, 1x NEAA, 1x glutamine, mLIF, beta-mercaptoethanol)

extract_protocol:
Cells were fixed with 1% formaldehyde in prewarmed DMEM for 8 minutes at room temperature. After quenching with 1M glycine, cells were washed by ice cold 1X PBS and resuspend in chromatin resuspension buffer (PBS + 0.5M EDTA). Chromatin pellets were snap-freeze on dry ice and store at -80 degree freezer before use.
ChIP-re-ChIP was performed on 2 million cell pellets. Briefly, cell pellets were gently lysed and treated with MNAse to generate predominantly mononucleosomes then chromatin pre-cleared to reduce non-specific binding by incubating with washed dynabeads for 3 hours at 4 degrees celcius. During this time, three sets of antibody-dynabeads are formed for the IgG control, H3K4me3 and H3K27me3 immunoprecipitations. 5% of the precleared chromatin was set aside as an input control and the remainder split across the three antibody-dynabead reactions for the first overnight immunoprecipitation.  Following the first immunoprecipitation, the chromatin-antibody-dynabead complexes are thoroughly washed to remove any non-specific binding, prior to chromatin elution with SDS at 37 degrees. SDS was removed and chromatin concentrated with a buffer exchange using  Amicon 3KDa molecular weight filters, setting aside 10% of this sample that represents in-line total H3K4me3 or total H3K27me3 controls. The second immunoprecipitation was then performed overnight using the opposing antibody such that the reChIP was performed in both orientations (H3K4me3 followed by H3K27me3, K4K27 or vice-versa K27K4) with IgG followed by IgG (IgG-IgG) as a negative control.  Chromatin is then eluted, treated with RNAse A and proteinase K, crosslinks reversed and enriched DNA fragments purified. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit.

value: E14 mESC

value: embryonic stem cell

tag: strain

value: DPPA2/4 DKO

tag: clone

value: clone 53

tag: antibody

value: H3K27me3 (CST 9733) followed by H3K4me3 (Millipore 07-473)

tag: sequencing batch

value: C


title: A16 [LARC]

value: locally advanced rectal cancer (LARC) tissue


title: Mst1/2 KO sample 1


title: mESC_Dppa24DKO_c53_reChIP_K4K27

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_bivalent_K4K27_Annotated Probe Report for All Probes.txt
53_K4K27

value: H3K4me3 (Millipore 07-473) followed by H3K27me3 (CST 9733)


title: 303_H2


title: A15 [LARC]


title: WT sample 5

value: WT


title: 302_D6


title: mESC_Dppa24DKO_c53_H3K27me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_H3K27me3_Annotated Probe Report for All Probes.txt
53_totalK27


title: A12 [LARC]


title: WT sample 4


title: A35 [LARC]


title: 308_PD3


title: A9 [LARC]


title: mESC_Dppa24DKO_c53_H3K4me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_H3K4me3_Annotated Probe Report for All Probes.txt
53_totalK4

value: H3K4me3 (Millipore 07-473)


title: mESC_Dppa24DKO_c43_reChIP_K27K4

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_bivalent_K27K4_Annotated Probe Report for All Probes.txt
43_K27K4

value: clone 43


title: WT sample 3

value: esophagus


title: 307_D8


title: 306_D6


title: WT sample 2

value: Esophageal epithelium


title: 304_D28


title: A6 [LARC]


title: A8 [LARC]


title: WT sample 1


title: mESC_Dppa24DKO_c43_H3K27me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_H3K27me3_Annotated Probe Report for All Probes.txt
43_totalK27


title: 304_PD3


title: A3 [LARC]


title: KO2_in vitro

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
The clean reads were aligned to Mus musculus genome (mm10) by bowtie2 with default parameter, and uniquely mapping reads were summarized by featureCounts (from Subread package)
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by DESeq2 with a cut-off threshold of 1.5-fold change and FDR adjusted p-value 0.05.
Assembly: mm10
Supplementary files format and content: txt file included FPKM values

source_name: thymus

growth_protocol: For in vitro samples: sorted WT and KO CD4+CD8+ DP thymocytes in vitro cultured in complete RPMI1640 culture medium, and stimulated with a-CD3(8μg/ml)+a-CD28(8μg/ml) for 24h, then sorted DN cells. For in vivo samples: sorted CD4-CD8-CD5+TCRb+ thymocytes (agonist-p) from Bcl6-wt and Bcl6-cko mice.

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol (Invitrogen, cat#15596018) according to the manufacturer’s protocol.
RNA-seq library was constructed for deep sequencing by BGI Genomics (in vivo) or Novogene (in vitro).

value: thymus

value: Bcl6fl/fl Cd4cre


title: mESC_Dppa24DKO_c43_H3K4me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_H3K4me3_Annotated Probe Report for All Probes.txt
43_totalK4


title: 303_H1

value: Whole blood


title: KO1_in vitro


title: A1 [LARC]


title: 302_D0


title: WT2_in vitro


title: Palb_Oxa_1 [DLD-1]

value: Colorectal adenocarcinoma cell line DLD-1


title: 309_D28


title: WT1_in vitro


title: mESC_WT_c58_reChIP_K4K27

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_bivalent_K4K27_Annotated Probe Report for All Probes.txt
58_K4K27

value: E14 mESC

value: clone 58


title: Palb_2 [DLD-1]


title: 308_H2


title: mESC_WT_c58_H3K27me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_H3K27me3_Annotated Probe Report for All Probes.txt
58_totalK27

value: embryonic stem cell


title: 306_D0


title: mESC_WT_c58_H3K4me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_H3K4me3_Annotated Probe Report for All Probes.txt
58_totalK4


title: mESC_Dppa24DKO_c43_reChIP_K4K27

description:
chromatin immunoprecipitated genomic DNA
Dppa_DKO_bivalent_K4K27_Annotated Probe Report for All Probes.txt
43_K4K27

value: DPPA2/4 DKO


title: PFF_Fexo_1

city: Suwon-si

first: Sang Myun

last: Park

state: Gyeonggi-do

address: 164, Worldcup-ro, Yeongtong-gu

department: Pharmacology

country: South Korea

institute: Ajou University School of Medicine

data_processing:
RNA sequencing data were generated using an Illumina NovaSeq 6000 platform with paired-end reads
Quality control steps including FASTQC (version 0.11.9) and the low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore (version 0.6.6).
Alignment to the mouse genome reference (GRCm38) was performed using STAR (version 2.7.3a).
RNA abundance was estimated by as the FPKM values according to GENCODE database (version 25) using Cufflinks tool
Assembly: GRcm38
Supplementary files format and content: Tab-delimited text files include log2(FPKM+1) values for all sample
Supplementary files format and content: Tab-delimited text files include log2(FPKM+1) values for each sample

source_name: cortex

extract_protocol:
Total RNA was extracted from each sample using the Qiagen Rneasy mini kit according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Kit).

value: cortex

value: Heterozygous

value: 10μg PFF intrastriatal inoculation and 20mg/kg/day fexofenadine oral Injection

tag: time


title: 305_D28


title: 307_D6


title: PBS_Fexo_2

value: 1x PBS intrastriatal inoculation and 20mg/kg/day fexofenadine oral Injection


title: PFF_Fexo_2


title: Oxa_1 [DLD-1]


title: 304_H4


title: mESC_WT_c57_reChIP_K27K4

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_bivalent_K27K4_Annotated Probe Report for All Probes.txt
57_K27K4

value: WT

value: clone 57

value: H3K27me3 (CST 9733) followed by H3K4me3 (Millipore 07-473)

value: C


title: Oxa_2 [DLD-1]


title: mESC_WT_c58_reChIP_K27K4

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_bivalent_K27K4_Annotated Probe Report for All Probes.txt
58_K27K4


title: Ctrl_2 [DLD-1]


title: Palb_Oxa_2 [DLD-1]


title: ICN1 T-ALL, KO mouse 3

city: Bethesda

first: Stanley

last: Adoro

state: MD

address: Center Dr

department: CCR

institute: NCI

description: CD45.2+NGFR+ cells were sorted by FACS

data_processing:
Alignment STAR version=2.7.9a -sjdbOverhang 150
Read counts htseq 0.11.4
Differential Expression Analysis: DESeq2_1.38.3
Assembly: GRCm39 Gencode_mouse release M27
Supplementary files format and content: HTSeq counts file tab delimeted

source_name: spleen

growth_protocol: Mice were maintained in SPF conditions on uniprim antibiotic food. Once extracted, the cells were kept in complete RPMI +10% FBS before/after sorting on ice until put in TRIzol.

extract_protocol:
RNA was extracted using TRIzol reagent
Illumina Nextera XT library preparation kit

treatment_protocol: Spleens were lysed with ACK and filtered through a 70um filter before FACS sorting for CD45.2 and NGFR. Cells were sorted into cRPMI and put into TRIzol

value: spleen

value: T-ALL

value: Chmp5f/f CD4 cre+


title: mESC_WT_c57_reChIP_K4K27

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_bivalent_K4K27_Annotated Probe Report for All Probes.txt
57_K4K27

value: H3K4me3 (Millipore 07-473) followed by H3K27me3 (CST 9733)


title: 303_D6

value: Whole blood


title: PBS_Fexo_1


title: mESC_WT_c57_reChIP_IgGIgG

description:
chromatin immunoprecipitated genomic DNA
57_IgGIgG

value: E14 mESC

value: IgG (invitrogen) followed by IgG (Invitrogen)


title: Palb_1 [DLD-1]

value: Colorectal adenocarcinoma cell line DLD-1


title: 301_D28


title: mESC_WT_c57_total_H3K27me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_H3K27me3_Annotated Probe Report for All Probes.txt
57_totalK27

value: embryonic stem cell


title: mESC_WT_c57_total_H3K4me3

description:
chromatin immunoprecipitated genomic DNA
Dppa_WT_H3K4me3_Annotated Probe Report for All Probes.txt
57_totalK4

value: H3K4me3 (Millipore 07-473)


title: Ctrl_1 [DLD-1]


title: ICN1 T-ALL, KO mouse 1

description: CD45.2+NGFR+ cells were sorted by FACS


title: E14_mESC_reChIP_K27K4_3_R2

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14_K27K4_peaks.txt
E14-R2-K27K4

value: non-clonal

value: B


title: 308_H1


title: E17_H3K4me3

city: Philadelphia

first: Rexxi

middle: Diptya

last: Prasasya

state: PA

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
CUT&RUN reads were trimmed using TrimGalore with default parameters
CUT&RUN reads were aligned to mm10 using Bowtie2 version 2.5.0 with parameters: --N, 1 -sensitive -local
Low quality read (QMAP <= 10) and non-primary alignments were removed using SAMtools version 1.16.1 with parameters: view -q 10 -F 256
Duplicated reads were removed using SAMtool rmdup and mitochondrial reads were removed using grep function. Blacklisted regions were removed usign BEDtools version 2.27.1
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were prepared using deepTools version 3.5.1 with function bamCoverage and parameters -bs 1 --normalizeUsing CPM
Assembly: mm10
Supplementary files format and content: bigWig (normalized to counts per 10 million), narrowPeak (except for IgG sample), bedGraph (normalized to counts per million spike in sacCer3 reads)
Library strategy: CUT&RUN

source_name: Oct-GFP+ prospermatogonia

extract_protocol:
Freshly sorted cells were bound to concanavalin A-coated magenetic beads and wash and permeabilize using C&R Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, with 1x Roche complete protease inhibitor EDTA Free) with 0.05% Digitonin and 2 mM EDTA
CUT&RUN libraries were prepared using KAPA HyperPrep Kit and was ammplified using KAPA HiFi Hot Start Ready mix. All of DNA that was recovered following Phenol:Chloroform extraction was used as input.

tag: developmental stage

value: Oct-GFP+ prospermatogonia

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology, 9751)


title: ICN1 T-ALL, WT mouse 3

description: CD45.2+NGFR+ cells were sorted by FACS

tag: tissue

value: Chmp5f/f CD4 cre-


title: E14_mESC_reChIP_K4K27_1_R2

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14_K4K27_peaks.txt
E14-R2-K4K27

tag: cell line

value: WT


title: Col_input

first: Wenhao

last: Xie

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The RNA-seq reads with high quality score were aligned to the genome of Arabidopsis thaliana (TAIR10) using Hisat2.The ChIP-seq filtered reads were mapped to Arabidopsis thaliana genome (TAIR10) using Bowtie2 (v.2.4.5). We then used SAMtools (v.1.13) to remove the PCR duplicates and the low mapped quality reads.
SAMtools was used to obtain high mapping quality reads.
FeatureCounts was used to calculate the reads count of genes.
bamCoverage (v.3.5.1) was used to normalize the reads using RPKM, and computeMatrix (v.3.5.1) was used to calculate the enrichment signals.
Assembly: TAIR10
Supplementary files format and content: bigwig and featurecounts matirx

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana seedlings were grown on MS medium under 16-h light/8-h dark conditions at 22°C for 14 days.

extract_protocol:
The total RNA was extracted using the RNAprep Pure Plant Kit (DP432; Tiangen, Beijing, China).Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The RNA-seq was constructed using the KAPA stranded RNA-seq kit (kk8401; Roche, Basel, Switzerland). The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

value: seedlings

value: wild-type

tag: treatment

value: keep in 22°C


title: E14_mESC_total_H3K27me3_R2

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14 H3K27me3.txt
E14-R2-totalK27

tag: cell type


title: 305_PD7


title: ICN1 T-ALL, WT mouse 2

description: CD45.2+NGFR+ cells were sorted by FACS

value: spleen

value: T-ALL

tag: genotype


title: 304_H2

value: Whole blood


title: E14_mESC_total_H3K4me3_R2

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14 H3K4me3.txt
E14-R2-totalK4

value: E14 mESC


title: Col_H3K4me2


title: PFF_Efa_2

value: cortex

value: Heterozygous

value: 10ug PFF intrastriatal inoculation and 123mg/kg/day efavirenz I.P Injection


title: PFF_Efa_1


title: E14_mESC_reChIP_K27K4_R1

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14_K27K4_peaks.txt
E14-R1-K27K4

value: embryonic stem cell

value: H3K27me3 (CST 9733) followed by H3K4me3 (Millipore 07-473)

value: A


title: 303_D0


title: 301_D14


title: Col_H3K4me1


title: ICN1 T-ALL, KO mouse 2

description: CD45.2+NGFR+ cells were sorted by FACS

value: Chmp5f/f CD4 cre+


title: Col_RNA_rep3


title: PFF_Control_2

value: 10ug PFF intrastriatal inoculation


title: 309_PD7


title: 309_PD3


title: E14_mESC_reChIP_K4K27_R1

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14_K4K27_peaks.txt
E14-R1-K4K27

value: non-clonal

value: H3K4me3 (Millipore 07-473) followed by H3K27me3 (CST 9733)


title: Col_RNA_rep2

value: seedlings


title: PFF_Control_1


title: 308_D6


title: E14_mESC_total_H3K27me3_R1

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14 H3K27me3.txt
E14-R1-totalK27

value: WT


title: 307_D0


title: Col_RNA_rep1

value: wild-type

value: keep in 22°C


title: ICN1 T-ALL, WT mouse 1

description: CD45.2+NGFR+ cells were sorted by FACS

value: spleen

value: T-ALL

value: Chmp5f/f CD4 cre-


title: Col_H3K4me3


title: 306_D28

value: Whole blood


title: E14_mESC_reChIP_IgGIgG_R1

description:
chromatin immunoprecipitated genomic DNA
E14-R1-IgGIgG

value: E14 mESC

value: IgG (invitrogen) followed by IgG (Invitrogen)


title: PBS_Efa_1

value: cortex

value: Heterozygous

value: 1x PBS intrastriatal inoculation and 123mg/kg/day efavirenz I.P Injection


title: DMED4

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters.
Assembly: The reference genome was mRatBn7.2
Supplementary files format and content: Count martrix

organism: Rattus norvegicus

source_name: corpus cavernosum

extract_protocol:
Fresh CC tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before cDNA library preparation.
Standard protocol of RD  Rhapsody

value: corpus cavernosum

value: all CC cells

value: DMED


title: E14_mESC_total_H3K4me3_R1

description:
chromatin immunoprecipitated genomic DNA
Annotated Probe Report for E14 H3K4me3.txt
E14-R1-totalK4

value: embryonic stem cell

value: non-clonal

value: H3K4me3 (Millipore 07-473)

value: A


title: DMED3

description: BD Rhapsody


title: PBS_Control_2

value: 1x PBS intrastriatal inoculation


title: 305_PD3


title: Het_491

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

data_processing:
Data were analyzed using the Bluebee pipeline (Illumina, 117UG228V0200 version).
De-multiplexing was performed using the unique molecular identifiers included in the adapters to correct for possible amplification biases. Sequence reads passing the quality control (fastQC; %Q30 > 93.) were  trimmed  from  adapter  sequences  and  mapped using the STAR aligner.
Assembly: Mouse  genome (GRCm38/mm10 version Dec 2011)
Supplementary files format and content: Count tables

source_name: Cochlea

extract_protocol:
RNA was extracted from isolated cochlea using TRI Reagent (Sigma-Aldrich, Life Science), or RNeasy microkit. RNA was quantified with Qubit (Thermo Fisher Scientific), and qualities were controlled by microelectrophoresis (TapeStation 4200, Agilent).
cDNA libraries were prepared using the CORALL RNA-seq Library Prep Kit (Lexogen).
Paired-end sequencing (2 × 80 nucleotides) was performed using a NextSeq500 sequencer (Illumina).

treatment_protocol: No treatment

value: Cochlea

value: Opa1+/- heterozygous

value: No


title: DMED2

description: BD Rhapsody


title: 304_D6

value: Whole blood


title: 302_D28


title: PBS_Control_1


title: CAF01*2 + CAF16*4, scRNAseq

city: Copenhagen

first: Katharina

last: Wørzner

address: Artillerivej 5

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

data_processing:
BCL files were converted to FASTQ files with bcl2fastq (Illumina) and data were then processed with the use of BD Rhapsody™ Targeted Analysis Pipeline aligning to the mm10 genome using SevenBridges Genomics.
The raw transcript count matrix was loaded into R (v4.2.3) and the R-package Seurat (v.4.3.0) was used for analysis
Assembly: mm10
Supplementary files format and content: Csv and fastq

source_name: Spleen

extract_protocol:
Cells from the spleen of IL-17A fate reporter mice immunized with either CAF01:H56 two times with two weeks in between (n = 10) or followed by four immunizations with CAF16:H56 were processed and stimulated with H56 (1 µg/ml) for 6 hours at 37 oC. Next, CD4+ T cells were isolated using the EasySep mouse CD4+ T cell isolation kit (STEMCELL Technologies Inc., Canada) according to the manufacturer’s recommendation. Live YFP+ cells were sorted using a BD FACSAria™ Cell Sorter (BD BioSciences).
Cells were prepared for sequencing using the BD Rhapsody™ Immune Response Panel Mm (Cat.no: 633753, 397 genes, BD BioSciences) and the BD Rhapsody™ Scanner (BD BioSciences) according to the manufacture’s recommendations.

value: Spleen

value: YFP+ cells


title: Het_2


title: 301_D10


title: NC2

description: BD Rhapsody

value: normal


title: CAF01*2, scRNAseq

description: BD Rhapsody™ Immune Response Panel Mm (Cat.no: 633753, 397 genes, BD BioSciences)


title: 309_H2


title: PBS_Efa_2

value: cortex

value: Heterozygous


title: NC1

description: BD Rhapsody

value: corpus cavernosum


title: WT_6

value: Wild-type


title: 308_D0


title: CAF01*2 + CAF16*4, biol rep 3, scRNAseq

data_processing:
Raw reads were validated using fastQC (v0.11.9) and trimmed using AdapterRemoval (v2.3.1), with a Phred score of 20 and a minimum length of 30bp.
The reads were mapped to the mouse genome (GCR 000001635.26 GRCm38.p6) using hisat2 (v2.1.0), and the read count was produced using HTSeq (v0.9.1).
The raw read counts were filtered with a threshold of 10 and normalized by rlog to construct the principle component analysis.
Assembly: mm10
Supplementary files format and content: text files includes raw counts for each sample

extract_protocol:
RNA was extracted from the cell samples using RNeasy Micro Kit (Qiagen). RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
The SMART-Seq v4 ultra-low input kit was used to synthesize cDNA. Library construction was performed based on the manufacturer’s recommendation for Nextera XT kit.


title: Heart,Treatment, 7d,rep2

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

description:
Treatment_7d_2_ATACseq
t_7_2

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the danRer11 reference genome using Bowtie2.
Assembly: danRer11 genome
Supplementary files format and content: one csv file containing raw count values for ATAC-seq peaks of WT and treatment samples

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish were raised and maintained under standard laboratory conditions.

extract_protocol: ATAC-seq libraries were prepared for each sample by Active Motif Inc.

treatment_protocol: freshly isolated noncardiomyocytes nonCMs from injury area of adult zebrafish hearts were used as input.

value: Heart

value: wild type

value: amputation


title: CAF01*2 + CAF16*4, biol rep 2, scRNAseq


title: WT_5


title: E17_IgG

value: Oct-GFP+ prospermatogonia

value: Rabbit IgG (Cell Signaling Technology 2729)


title: Het_484


title: CAF01*2 + CAF16*4, biol rep 1, scRNAseq


title: Het_7


title: Heart,Treatment, 7d,rep1

description:
Treatment_7d_1_ATACseq
t_7_1


title: 305_H2


title: WT_4


title: Heart,WT,7d,rep2

description:
WT_7d_2_ATACseq
W_7_2


title: CAF01*2, biol rep 3, bulk RNAseq


title: Heart,WT,7d,rep1

description:
WT_7d_1_ATACseq
W_7_1


title: DMED1

description: BD Rhapsody

value: all CC cells

value: DMED


title: 304_D0


title: IL-12/18 Neonate [scRNA-seq]

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description: 10x Genomics

data_processing:
The raw FASTQ data was processed using Cell Ranger v3.0.1
Count matrixes were filtered using Seurat v2.3.3 to remove cell barcodes with less than 200 genes and with more than 5% mitochondrial counts
Seurat v2.2.3 was used to normalize, scale, regress out variation in UMI counts and mitochondrial content, perform dimensionality reduction and generate UMAP projections.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files; containing cell barcodes, genes, and matricies which can be combined to form a Barcodes X Features sparse count matrix for each sample.

extract_protocol:
Murine cells were isolated from isolated from spleen and 4-6 neonatal tissues were pooled per biological sample. Single cell suspensions from spleen were obtained by manual dissociation and filtration through a 40uM strainer. CD8+ T cells were isolated by positive magnetic separation using anti-CD8a microbeads. 2x105 cells were plated per well in round-bottomed 96 well plates. Cells were incubated in RPMI supplemented with 10% fetal bovine serum, L-glutamine, penicillin-streptomycin, 2-mercaptoethanol (RP-10) and 10 ng/ml recombinant human IL-2 (Thermo Fisher Scientific) for 18-22 hours. For bystander-activated samples, media was additionally supplemented with recombinant murine IL-12p70 (Thermo Fisher Scientific) and recombinant murine IL-18 (Thermo Fisher Scientific) at 1 ng/ml. 1.5 mg/ml Brefeldin A (Millipore Sigma; St. Louis, MO) was added to the cells for the final 4 hours of incubation prior to antibody labeling for flow cytometry analysis. Live Va2+CD8+ cells were sorted into 0.04% BSA in PBS.
Cells were counted and 3-8k cells per sample were loaded in the Chromium controller for the formation of gel bead-in-emulsions (GEMs) following the manufacturer's instructions (10X Genomics). The single-cell RNA-seq libraries were prepared using Chromium Single Cell 3′ Reagent Kit v2 following the accompanied protocol and were sequenced on Illumina NextSeq500.

value: CD8+ T-cells

value: gBT-I WT

tag: age

value: Neonate (5 to 7 days)

value: IL-12/18 (bystander activation)


title: 302_PD3

value: Whole blood


title: IL-2 Neonate [scRNA-seq]

description: 10x Genomics

value: Spleen

value: IL-2 (control)


title: CAF01*2, biol rep 2, bulk RNAseq

value: YFP+ cells


title: H3K27ac differentiated B

city: Evanston

first: Stephenie

last: Droll

state: IL

address: Hogan 2-100 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
the following processing steps were performed within Nextflow
quality control by FASTQC
adaptor trimming by Trimgalore
alignment with BWA-MEM
Peak calling with MACS2
Assembly: hg38
Supplementary files format and content: Called peaks in bed format (.narrowPeak)

source_name: epidermis

growth_protocol: Keratinocytes were maintained in SFM and Medium 154 with human keratinocyte growth supplement, antimycotic, penicillin streptomycin. Progenitor cells were cultures at < 60% confluency. Differentiation was induced by seeding at confluency with 1.2 mM caclium chloride for four days. Incubator set at 37 C, 5% CO2.

extract_protocol:
Keratinocytes were fixed for 10 minutes in 1% formaldehyde, quenched with glycine, nuclei extracted, and sonicated with a Bioruptor Pico (Diagenode).
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: epidermis

value: primary, neonatal keratinocytes

value: differentiated

value: Active Motif 39034


title: WT_8

value: Cochlea

value: Wild-type

value: No


title: CAF01*2, biol rep 1, bulk RNAseq


title: IL-12/18 Adult [scRNA-seq]

description: 10x Genomics

value: Adult (2 to 4 months)


title: 301_D8


title: H3K27ac differentiated A


title: HFHS_4

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

data_processing:
these cDNA libraries were then sequenced using an Illumina Novaseq6000 platform
Following sequencing, the obtained reads were subjected to a filtering process to remove any low-quality reads,
and the remaining clean reads were aligned to a reference genome using the HISAT2 software (version 2.2.4)
Differentially expressed genes were identified with the P-value<0.05 and fold change>1.5 between the two groups.
Supplementary files format and content: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ovary

growth_protocol: the C57BL/6J mice were fed a high-fat high-sucrose diet (45% kcal fat, 35% kcal carbohydrate, Research Diets) for 12 weeks

extract_protocol:
Total RNAs of ovaries from mice subjected to either a NCD or a HFHS diet were extracted using Trizol.
The extracted RNAs were used to construct RNA libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina from New England Biolabs.

value: ovary

value: WT

value: HFHS diet


title: IL-2 Adult [scRNA-seq]

description: 10x Genomics

value: CD8+ T-cells

value: gBT-I WT


title: 309_D6

value: Whole blood


title: 306_D14


title: HFHS_3


title: H3K27ac progenitor B

value: progenitor


title: HFHS_2


title: 307_D28


title: 306_D10


title: HFHS_1


title: 305_H1


title: H3K27ac progenitor A


title: 303_D28


title: p63 differentiated B

value: Cell Signaling 1309T


title: Ctrl_4

value: normal diet


title: p63 progenitor B

value: epidermis


title: IL-2 Adult [scATAC-seq]

description: 10x Genomics

data_processing:
The raw FASTQ data was processed using Cell Ranger v3.0.1
ArchR v1.0.2 was used to remove barcodes if their TSS enrichment score was lower than 4.0 or if there were fewer than 1000 unique nuclear fragments generated.
ArchR v1.0.2 was used to perform dimensionality reduction and generate UMAP projections.
Assembly: mm10
Supplementary files format and content: Tab-separated values fragment file where each line represents a unique ATAC-seq fragment captured by the assay and is matched to a cell barcode.
Supplementary files format and content: scATAC_Clusters.tsv: Tab-separated values file containing Cell Barcodes matched to assigned cluster identities reported in the study.
Supplementary files format and content: scATAC_Peaks.tsv: Tab-separated values file containing the ATAC-Seq merged peakset
Supplementary files format and content: scATAC_Summarized_Experiment.tsv: Tab-separated values file containing metadata for each of the samples.

extract_protocol:
FACS-sorted cells were permeabilized and nuclei were isolated using a lysis buffer containing 0.1% Igepal CA-630, 5mM Tris-Cl pH 8.0, 150mM sucrose, 5mM NaCl, 1mM MgAc2 and 3mM CaCl2
Cells were counted and 3-8k isolated nuclei per sample were loaded in the Chromium controller for the formation of gel bead-in-emulsions (GEMs) following the manufacturer's instructions (10X Genomics). The single-cell ATAC-seq libraries were prepared using Chromium Next GEM Single Cell ATAC Kit v2 following the accompanied protocol and were sequenced on Illumina NextSeq500.

treatment_protocol: Murine cells were isolated from isolated from spleen and 4-6 neonatal tissues were pooled per biological sample. Single cell suspensions from spleen were obtained by manual dissociation and filtration through a 40uM strainer. CD8+ T cells were isolated by positive magnetic separation using anti-CD8a microbeads. 2x105 cells were plated per well in round-bottomed 96 well plates. Cells were incubated in RPMI supplemented with 10% fetal bovine serum, L-glutamine, penicillin-streptomycin, 2-mercaptoethanol (RP-10) and 10 ng/ml recombinant human IL-2 (Thermo Fisher Scientific) for 18-22 hours. For bystander-activated samples, media was additionally supplemented with recombinant murine IL-12p70 (Thermo Fisher Scientific) and recombinant murine IL-18 (Thermo Fisher Scientific) at 1 ng/ml. 1.5 mg/ml Brefeldin A (Millipore Sigma; St. Louis, MO) was added to the cells for the final 4 hours of incubation prior to antibody labeling for flow cytometry analysis. Live Va2+CD8+ cells were sorted into 0.04% BSA in PBS.

value: Spleen

value: IL-2 (control)


title: IL-12/18 Neonate [scATAC-seq]

description: 10x Genomics

value: Neonate (5 to 7 days)

value: IL-12/18 (bystander activation)


title: p63 progenitor A

value: primary, neonatal keratinocytes


title: Ctrl_3


title: 302_D10


title: p63 differentiated A

value: differentiated


title: Lin28b IL-12/18 rep 1 [ATAC-seq]

description:
ATAC-seq analysis of Lin28b Tg IL-12/18 cells
peaks.bed
read_counts.tsv

data_processing:
Illumina pipeline software was used for base calling.
The raw reads were trimmed using cutadapt (parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -e 0.06 -m 15) and were aligned to the mouse genome (mm10) using bowtie2 (parameters: -X 2000 -p 16). The read alignments were filtered to remove PCR duplicates and low-quality alignments using PICARD (MarkDuplicates parameters: TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All REMOVE_DUPLICATES=true ASSUME_SORT_ORDER=coordinate READ_NAME_REGEX=null) and samtools (parameters: -f 0x2 -q 30). These bam files were uploaded to GEO.
The peaks of ATAC-seq reads were called using macs2 (parameters: -f BAMPE -g mm -B -q 0.05) and the reproducible peaks were obtained using Irreproducibility discovery rate (IDR) analysis. The peaks from all samples were merged using bedtools to generate a unified set of peaks. The accessibility at these peaks was estimated by counting the number of ATAC-seq reads that map to peak regions using featureCounts.
The differential accessibility analysis was performed using edgeR. The ATAC-seq peaks were mapped to the nearest gene using bedtools and were classified into promoter-proximal peaks or enhancer peaks based on whether they were within the promoter region of the nearest transcription start site (TSS) or not; the promoter region was defined as 1kb upstream and 500bp downstream of a TSS.
For generating bigwig files, the read alignments to the unified set of peaks were extracted, converted to BEDPE format and the alignment ends were adjusted for Tn5-gapping. The resulting bed files were converted to bedgraph format using genomeCoverageBed while normalizing for the total peak-mapped reads  (params: -pc -bg -scale <scalling factor>) and were converted to bigwig format using bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated count file, containing counts of ATAC-seq reads mapping to unified set of peaks
Supplementary_files_format_and_content: edgeR output files; tab-separated edgeR output files for ATAC-seq data
Supplementary_files_format_and_content: Bigwig files for the ATAC-seq data
Supplementary_files_format_and_content: Bed file containing the unified set of peaks, with three extra columns: 1) peak_id; 2) whether a peak is promoter-proximal (promoter) or distant (enhancer); 3) gene name for the nearest transcription start site

source_name: Splenic CD8+ T-cells

growth_protocol: Spleens were harvested from TCR Tg gBT-I adult, neonate or Lin28b Tg adult mice, and 4-6 neonatal spleens were pooled per biological sample. Single cell suspensions from spleen were obtained by manual dissociation and filtration through a 40uM strainer and CD8+ T cells were isolated by positive magnetic separation using anti-CD8a microbeads (Miltenyi Biotec) according to the manufacturer’s instructions.

extract_protocol:
The FACS sorted cells were permeabilized and nuclei were isolated using a lysis buffer containing 0.1% Igepal CA-630, 5mM Tris-Cl pH 8.0, 150mM sucrose, 5mM NaCl, 1mM MgAc2 and 3mM CaCl2.
The ATAC-seq libraries were prepared following the published protocols (PMID: 25559105; PMID: 28846090), by the Transcriptional Regulation and Expression Facility at Cornell University and sequenced on Illumina NextSeq500.

treatment_protocol: Total of 200,000 cells were plated per well in round-bottomed 96 well plates and cells were incubated in RPMI supplemented with 10% fetal bovine serum, L-glutamine, penicillin-streptomycin, 2-mercaptoethanol (RP-10) and 10 ng/ml recombinant human IL-2 (Thermo Fisher Scientific) for 18-22 hours. For bystander-activated samples, media was additionally supplemented with recombinant murine IL-12p70 (Thermo Fisher Scientific) and recombinant murine IL-18 (Thermo Fisher Scientific)at 1 ng/ml.

value: Splenic CD8+ T-cells

value: Adult (2 to 4 months)

value: gBT-I Lin28b Tg


title: SW620_sEV/Exos_3

city: Bundoora

first: Wittaya

last: Suwakulsiri

state: Victoria

address: Plenty Road and, Kingsbury D

department: Biochemistry and Chemistry

institute: La Trobe University

data_processing:
Raw reads were cleaned by removing adaptor sequences, low quality reads containing >50% bases with quality [QA] ≤15 and reads with >2% undefined nucleotides
Clean reads were aligned using HISAT and StringTie
Aligned reads were counted using featureCount
Transcripts were classified into four categories: i) protein-coding, ii) long non-coding, iii) pseudogene transcripts, and iv) other including short non-coding from ENSEMBL human database using BiomaRT
Assembly: Ensembl GRCh38
Supplementary files format and content: csv file shown raw counts of transcripts for each sample
Supplementary files format and content: csv file shown fragment counts of fusion genes for each sample

source_name: Colon

growth_protocol: RPMI1640 with 1% ITS and 1%Pen/Strep

extract_protocol:
Trizol protocol
HiSeq 3000/4000 PE Cluster Kit
Ribo-Zero depletion kit (Illumina). Total RNA was fragmented and transcribed to be single strand DNA

value: Colon

value: cancer cell

value: WT

tag: group

value: sEV/Exos


title: Ctrl_1

value: ovary


title: Lin28b IL-2 rep 2 [ATAC-seq]

description:
ATAC-seq analysis of Lin28b Tg IL-2 cells
peaks.bed
read_counts.tsv


title: Lin28b IL-2 rep 1 [ATAC-seq]


title: 307_D14

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing raw Kallisto gene count from individual samples

extract_protocol:
RNA recovered from Paxgene tubes using the Qiagen PAXgene Blood RNA isolation Kit
Libraries created using Illumina Stranded Total RNA Prep with Ribo-Zero Plus
Final sequencing libraries generated using the IDT-Ilmn RNA UD Indexes SetA, and QC performed prior to sequencing using the Bioanalyzer and DNA 1000 reagents

value: Whole blood

tag: subject


title: IL-2 Neonate [scATAC-seq]

description: 10x Genomics

value: CD8+ T-cells

value: gBT-I WT


title: SW620_lEV/sMB-Rs_3

value: lEV/sMB-Rs


title: SW620_lEV/MPs_3

value: lEV/MPs


title: IL-12/18 Adult [scATAC-seq]

description: 10x Genomics

value: Spleen


title: E10.5 otocyst Control (no primary antibody), CUT&Tag

city: Ann Arbor

first: Donna

last: Martin

address: 1150 Medical Center Dr

institute: University of Michigan

description: microdissected developing mouse E10.5 otocyst

data_processing:
CUT&Tag reads were aligned to the mm10 genome using bowtie2.
bigwig files were generated using deeptools. Reads were normalized to reads per kilobase per million (RPKM).
Peaks were called using SEACR norm stringent mode.
Assembly: mm10
Supplementary files format and content: bigwig, read tracks
Supplementary files format and content: SEACR , genomic coordinates for peaks

source_name: E10.5 otocyst

growth_protocol: Developing mouse otocyst from E10.5 embryos

extract_protocol:
Cells were equally divided into three samples and subjected to CUT&Tag. Cells were incubated with either anti-CHD7 or anti-SOX2 antibodies, while the no primary antibody control did not receive any antibodies. DNA libraries were prepared from samples and 150 bp paired end sequencing performed on an Illumina NovaSeq6000 S4 Flowcell at the University of Michigan
Tn5-mediated tagmentation using the CUT&Tag-It kit (Active Motif).

treatment_protocol: 34 microdissected otocysts were pooled and digested in Accutase at room temperature for 30 minutes with gentle agitation.

value: E10.5 otocyst

value: developing inner ear

value: wild-type


title: Ctrl_2

value: normal diet


title: 309_D0

tag: infection


title: 306_D8

tag: study day


title: E10.5 otocyst SOX2, CUT&Tag


title: Neonate IL-12/18 rep 2 [ATAC-seq]

description:
ATAC-seq analysis of Neonate IL-12/18 cells
peaks.bed
read_counts.tsv

value: Splenic CD8+ T-cells

value: Neonate (5 to 7 days)

value: IL-12/18 (bystander activation)


title: Lin28b IL-12/18 rep 2 [ATAC-seq]

value: Adult (2 to 4 months)

value: gBT-I Lin28b Tg


title: Neonate IL-12/18 rep 3 [ATAC-seq]


title: 305_D0


title: SW480_sEV/Exos_3

value: Colon

value: cancer cell

value: WT

value: sEV/Exos


title: 303_PD7

value: Whole blood


title: E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 3

data_processing:
Libraries were subjected to 151-bp paired-end sequencing on an Illumina NovaSeq machine following the manufacturer’s protocol (Illumina, San Diego, CA).
Bcl2fastq2 Conversion software was used to create de-multiplexed FastQ files (Illumina).
Sequencing reads were trimmed with Cutadapt v2.3 (2) and read quality was assessed using FastQC v0.11.8 (3).
Reads were aligned to the mouse reference genome GRCm38 (ENSEMBL) with STAR v2.7.8a (4) and RSEM v1.3.3 was used to assign count estimates to aligned genes (5).
Quality control metrics from this pipeline were integrated and evaluated using multiQC v1.7 (6)
Assembly: mm9
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

growth_protocol: Timed pregnancies were established to generate litters of embryos, with the morning of seminal plug detection marking E0.5. The day of birth was defined as Postnatal day 0 (P0).

extract_protocol:
Otocysts were collected from E10.5 embryos in ice-cold PBS and RNALater (Ambion AM7021). RNA was isolated from pairs of otocysts from three embryos of each genotype (WT, Chd7Gt/+, Sox2CreER/+ and Chd7Gt/+;Sox2CreER/+) using the RNAqueous Micro Scale RNA Isolation kit according to the manufacturer’s instructions (Ambion AM1931, Austin, TX).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions (NEB E7760, Ipswich, MA).


title: E10.5 otocyst Chd7Gt/+ replicate 3


title: Neonate IL-12/18 rep 1 [ATAC-seq]

value: gBT-I WT


title: Neonate IL-2 rep 3 [ATAC-seq]

description:
ATAC-seq analysis of Neonate IL-2 cells
peaks.bed
read_counts.tsv

value: IL-2 (control)


title: 302_D8


title: Neonate IL-2 rep 2 [ATAC-seq]


title: 301_D0


title: 301_D6


title: SW480_Cell lysate_3

value: Cell lysate


title: E10.5 otocyst wild type replicate 3

value: E10.5 otocyst


title: Neonate IL-2 rep 1 [ATAC-seq]


title: E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 2


title: SW480_lEV/MPs_3

value: lEV/MPs


title: Serum,MCI,63

city: Maastricht

first: Qingfeng

last: Wen

state: Limburg

address: Universiteitssingel 40

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

description:
Memories_HB04750_Serum_S159_R1_001.fastq
miR.Counts_serum.csv

data_processing:
We used cutadapt (version 1.8.1) to trim adapters and random bases
Data were processed with miRge2 with the latest release of miRbase
Supplementary files format and content: For miR.Counts_serum.csv, each row represents one miRNA, each column represents one serum sample.
Supplementary files format and content: For miR.Counts_plasma.csv, each row represents one miRNA, each column represents one plasma sample.

source_name: Serum

extract_protocol:
RNAs were isolated using the tRNA/YRNA Depletion Protocol.
Libraries were prepared for sequencing with the automated Gel-Free option in the NEXTFLEX® Small RNA-Seq Kit v3.

value: Serum

tag: Sex

value: Female

tag: disease state

value: MCI


title: SW620_sEV/Exos_2


title: E10.5 otocyst Chd7Gt/+ replicate 2


title: E10.5 otocyst CHD7, CUT&Tag

value: developing inner ear

value: wild-type


title: Adult IL-12/18 rep 6 [ATAC-seq]

description:
ATAC-seq analysis of Adult IL-12/18 cells
peaks.bed
read_counts.tsv

value: Splenic CD8+ T-cells

value: Adult (2 to 4 months)

value: IL-12/18 (bystander activation)


title: SW620_Cell lysate_3

value: Colon

value: cancer cell


title: SW620_lEV/sMB-Rs_2

value: WT

value: lEV/sMB-Rs


title: Serum,Control,21

description:
Memories_HB04749_Serum_S112_R1_001.fastq
miR.Counts_serum.csv

value: Control


title: Adult IL-12/18 rep 5 [ATAC-seq]

value: gBT-I WT


title: SW480_lEV/sMB-Rs_3


title: SW620_lEV/MPs_2


title: E10.5 otocyst Sox2CreER/+ replicate 2


title: Serum,Control,19

description:
Memories_HB04686_Serum_S40_R1_001.fastq
miR.Counts_serum.csv

value: Male


title: Serum,Control,20

description:
Memories_HB04690_Serum_S135_R1_001.fastq
miR.Counts_serum.csv


title: Adult IL-12/18 rep 4 [ATAC-seq]


title: SW620_Cell lysate_2

value: Cell lysate


title: Adult IL-12/18 rep 3 [ATAC-seq]


title: Serum,Control,18

description:
Memories_HB04685_Serum_S183_R1_001.fastq
miR.Counts_serum.csv


title: E10.5 otocyst Sox2CreER/+ replicate 3

value: E10.5 otocyst


title: SW480_sEV/Exos_2

value: sEV/Exos


title: E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 1


title: Adult IL-12/18 rep 2 [ATAC-seq]


title: SW480_lEV/sMB-Rs_2


title: Serum,MCI,62

description:
Memories_HB04671_Serum_S134_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Female


title: E10.5 otocyst Chd7Gt/+ replicate 1


title: SW480_lEV/MPs_2

value: lEV/MPs


title: Serum,Control,17

description:
Memories_HB04662_Serum_S132_R1_001.fastq
miR.Counts_serum.csv


title: SW480_Cell lysate_2


title: Adult IL-2 rep 6 [ATAC-seq]

description:
ATAC-seq analysis of Adult IL-2 cells
peaks.bed
read_counts.tsv

value: IL-2 (control)


title: Serum,Control,16

description:
Memories_HB04661_Serum_S88_R1_001.fastq
miR.Counts_serum.csv


title: E10.5 otocyst Sox2CreER/+ replicate 1


title: Adult IL-2 rep 5 [ATAC-seq]

value: Splenic CD8+ T-cells


title: E10.5 otocyst wild type replicate 2


title: Serum,AD,28

description:
Memories_HB04635_Serum_S209_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: SW620_sEV/Exos_1


title: DKO, replicate1, scRNAseq

city: Heidelberg

first: Kai

last: Breuhahn

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University

description: 10x Genomics

data_processing:
Sequence data were applied to Cell Ranger (version 6.0.1, 10X Genomics) to align reads and to generate the barcode unique molecular identifier (UMI) gene expression matrices based on the mouse reference genome mm10 with default parameters.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: liver

extract_protocol:
Frreshly primary liver cells were isolated according to the two-step isolation protocol.
cells were loaded onto the Chromium (10x Genomics, Leiden, Netherlands) using the Chromium Next GEM Single Cell 3’ kit v3.1 (10x Genomics). The single cell suspension was processed as described in the manufacturer's protocol. After cDNA synthesis, the samples were initially quantified with the Qubit High Sensitivity Assay (Invitrogen/Thermo Fisher) and were diluted for a quality check on the Agilent Bioanalyzer using a High Sensitivity Assay (Agilent Biotechnologies, Waldbronn, Germany). Libraries were then generated for NGS sequencing. Sequencing was performed at Novogene on the Illumina NovaSeq with 150 PE read output (Illumina, San Diego, USA).

value: liver

value: primary liver cells

value: dko

value: no


title: Adult IL-2 rep 4 [ATAC-seq]

value: Adult (2 to 4 months)


title: Adult IL-2 rep 3 [ATAC-seq]


title: TAZKO, replicate1, scRNAseq

description: 10x Genomics

value: tazko


title: E10.5 otocyst wild type replicate 1

value: WT


title: Adult IL-12/18 rep 1 [ATAC-seq]

value: IL-12/18 (bystander activation)

value: gBT-I WT


title: YAPKO, replicate1, scRNAseq

description: 10x Genomics

value: yapko


title: Serum,MCI,61

description:
Memories_HB04623_Serum_S16_R1_001.fastq
miR.Counts_serum.csv

value: MCI


title: Serum,Control,14

description:
Memories_HB04628_Serum_S127_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Male

value: Control


title: SW620_Cell lysate_1

value: Colon

value: cancer cell

value: Cell lysate


title: SW620_lEV/MPs_1

value: lEV/MPs


title: WT, replicate1, scRNAseq

description: 10x Genomics

value: liver

value: primary liver cells

value: wildtype


title: Serum,Control,15

description:
Memories_HB04642_Serum_S182_R1_001.fastq
miR.Counts_serum.csv


title: SW620_lEV/sMB-Rs_1

value: lEV/sMB-Rs


title: SW480_sEV/Exos_1

value: sEV/Exos


title: Old, snRNAseq

city: Bronx

first: Kosaku

last: Shinoda

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
10x Genomics
Young_vs_MidAge_vs_Old_barcodes.tsv.gz
Young_vs_MidAge_vs_Old_features.tsv.gz
Young_vs_MidAge_vs_Old_matrix.mtx.gz
Young_vs_MidAge_vs_Old.cloupe

data_processing:
FASTQ files were aligned against the mouse mm10 reference, and converted to gene expression on the basis of Unique Molecular Identifier (UMI) using Cell Ranger Software (version 6.1.2) with “--force-cells 10000”.
Obtained single cell data were normalized with sctransform, integrated for batch effect correction, and mapped to two-dimensional uniform manifold approximation and projection (UMAP) space using Seurat (version 4.1.0). Cellular populations were delineated by FindClusters function in Seurat with “resolution = 0.3”.
To remove multiplets and low-quality droplets, barcodes that did not have a number of detected UMIs between 200 and 2,000 and a number of detected genes between 100 and 3,000 were filtered out.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and combined loupe files
Supplementary files format and content: WT_KO_barcodes.tsv.gz (barcode-1 represents WT, barcode-2 represents KO)
Supplementary files format and content: Young_vs_MidAge_vs_Old_barcodes.tsv (barcode-1 represents young, barcode-2 represents middle age, barcode-3 represents old)

source_name: interscapular BAT

extract_protocol:
In preparation for snRNA-seq, harvested mouse interscapular brown adipose tissues were minced in nuclear preparation buffer (10mM HEPES, 1.5mM MgCl2, 10mM KCl, 250mM Sucrose, 0.1% NP-40, 0.6U/μl Rnase inhibitor), and then fully homogenized in a Dounce homogenizer. The homogenate was passed through a 100uM filter and centrifuged at 750xg for 5min. The pellet was resuspended in 2% BSA/PBS, filtered again and sorted using a MoFloXDP Cell Sorter using the gating strategy previously described (PMID: 32597862).
Nuclei lysis, RNA extraction, and cDNA synthesis were performed using the Single Cell 3' v3.1 Dual Index Gene Expression Reagent kit (10x Genomics) following the manufacturer’s instructions. The quality and size of the cDNA library were determined by TapeStation. Sequencing of the library was performed using Illumina NovaSeq at 20,000 read pairs per cell.

value: Brown adipocytes

value: interscapular BAT

tag: strain

value: 24 month old


title: Adult IL-2 rep 1 [ATAC-seq]

value: Splenic CD8+ T-cells

value: Adult (2 to 4 months)

value: IL-2 (control)

value: gBT-I WT


title: Serum,MCI,60

description:
Memories_HB04619_Serum_S107_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Male

value: MCI


title: Lin28b IL-12/18 rep 2 [RNA-seq]

description:
RNA-seq analysis of Lin28b Tg IL-12/18 cells
read_counts.tsv

data_processing:
Illumina pipeline software was used for base calling.
Raw reads were trimmed to remove adapters using cutadapt and were mapped to the mouse genome (mm10) using tophat (--no-novel-juncs --library-type fr-firststrand).
The reads mapping to each gene were counted using featureCounts (-s 0 -Q 50).
The differential expression analysis of RNA-seq was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated count file, containing counts of RNA-seq reads mapping to exons
Supplementary_files_format_and_content: edgeR output files; tab-separated edgeR output files for RNA-seq data

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
RNA-seq libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation, by the Transcriptional Regulation and Expression Facility at Cornell University.

value: IL-12/18 (bystander activation)

value: gBT-I Lin28b Tg


title: Middle age, snRNAseq

value: 12 month old


title: SW480_lEV/sMB-Rs_1

value: Colon

value: cancer cell

value: WT


title: Lin28b IL-12/18 rep 1 [RNA-seq]


title: SW480_lEV/MPs_1

value: lEV/MPs


title: Serum,Control,12

description:
Memories_HB04614_Serum_S208_R1_001.fastq
miR.Counts_serum.csv

value: Control


title: Serum,Control,13

description:
Memories_HB04615_Serum_S62_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: SW480_Cell lysate_1

value: Cell lysate


title: Serum,MCI,59

description:
Memories_HB04613_Serum_S206_R1_001.fastq
miR.Counts_serum.csv


title: Young adult, snRNAseq

value: Brown adipocytes

value: interscapular BAT

value: 2 month old


title: Lin28b IL-2 rep 2 [RNA-seq]

description:
RNA-seq analysis of Lin28b Tg IL-2 cells
read_counts.tsv

value: Splenic CD8+ T-cells

value: Adult (2 to 4 months)

value: IL-2 (control)


title: Lin28b IL-2 rep 1 [RNA-seq]


title: Adult IL-2 rep 2 [ATAC-seq]

value: gBT-I WT


title: UCP1-Stx4KO, snRNAseq

description:
10x Genomics
WT_KO_barcodes.tsv.gz
WT_KO_features.tsv.gz
WT_KO_matrix.mtx.gz
WT_KO_cloupe.cloupe

value: 3 month old


title: Mouse 5 at 10 days IRI

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

institute: Cedars Sinai Medical Center

description:
E114
5

data_processing:
Sequencing reads were demultiplexed, quantified, and filtered for empty droplets with CellRanger v6.0.2
Using Seurat v4.0.5 poor quality droplets (>45% mitochondrial counts, <1000 UMIs, and >300 or <7000 genes) were removed.
Samples's gene expression was normalized with SCtransform and samples were integrated in Seurat (v4.0.5) with IntegrateData().
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Expression data for individual samples and the combined data set are provided as three gzipped files (or a single gzipped TAR file) consisting of a sparse matrix of raw counts ("_matrix.mtx") and corresponding lists of cell barcodes ("_barcodes.tsv") and gene names ("_features.tsv"). Metadata for the combined matrix is provided as a CSV file with UMAP and PCA coordinates, QC metric, time points, and cell type identification.

source_name: Mouse Kidney

extract_protocol: 10x Genomics Single Cell 3′ v3.1 Kit

tag: time point

value: kidney


title: Neonate IL-12/18 rep 2 [RNA-seq]

description:
RNA-seq analysis of Neonate IL-12/18 cells
read_counts.tsv

value: Neonate (5 to 7 days)

value: IL-12/18 (bystander activation)


title: Serum,Control,10

description:
Memories_HB04604_Serum_S86_R1_001.fastq
miR.Counts_serum.csv

value: Serum


title: Serum,Control,11

description:
Memories_HB04610_Serum_S158_R1_001.fastq
miR.Counts_serum.csv

value: Male


title: Serum,MCI,58

description:
Memories_HB04600_Serum_S59_R1_001.fastq
miR.Counts_serum.csv

value: MCI


title: Littermate control, snRNAseq

value: control (WT)


title: Neonate IL-12/18 rep 1 [RNA-seq]


title: Keratinocytes, CASZ1 siRNA A

description:
Salmon_CASZ1_RNA-seq.tsv
DESeq_CASZ1_RNA-seq.csv

data_processing:
the following processing steps were performed within Nextflow
quality control by FASTQC
adaptor trimming by Trimgalore
alignment to hg38 by STAR
quantification gene expression by Salmon using the counts per gene option
differential expression by DESeq2, p < 0.05 and log2 fold-change +/- 1
Assembly: hg38
Supplementary files format and content: Salmon gene counts output tsv, DESeq output csv

extract_protocol:
RNA was extracted by the Quick-RNA Miniprep Kit with DNase treatment. For ChIP, keratinocytes were fixed for 10 minutes in 1% formaldehyde, quenched with glycine, nuclei extracted, and sonicated with a Bioruptor Pico (Diagenode).
RNA-sequencing: NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit. ChIP-sequencing: NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: For siRNA treatment, 3 million keratinocytes were electroporated with 1 nm siRNA (purchased from Horizon) with a 4D Nucleofector and the P3 Primary Cell 4D-Nucleofector X Kit according to manufacturer's instructions.

value: epidermis

value: primary, neonatal keratinocytes

value: CASZ1 siRNA

tag: condition

value: differentiated


title: Serum,Control,9

description:
Memories_HB04596_Serum_S153_R1_001.fastq
miR.Counts_serum.csv

value: Female

value: Control


title: Mouse 4 at 10 days IRI

description:
E113
4


title: Neonate IL-2 rep 2 [RNA-seq]

description:
RNA-seq analysis of Neonate IL-2 cells
read_counts.tsv

value: Splenic CD8+ T-cells


title: Keratinocytes, control siRNA B

value: control siRNA


title: Mouse 3 at 10 days IRI

description:
E112
3


title: Serum,MCI,57

description:
Memories_HB04595_Serum_S204_R1_001.fastq
miR.Counts_serum.csv


title: Keratinocytes, control siRNA A


title: Adult IL-12/18 rep 6 [RNA-seq]

description:
RNA-seq analysis of Adult IL-12/18 cells
read_counts.tsv

value: Adult (2 to 4 months)

value: gBT-I WT


title: Mouse 2 at 48 hours IRI

description:
E111
2

value: kidney


title: Serum,MCI,56

description:
Memories_HB04592_Serum_S13_R1_001.fastq
miR.Counts_serum.csv


title: Adult IL-12/18 rep 5 [RNA-seq]


title: Mouse 1 at 48 hours IRI

description:
E110
1


title: Keratinocytes, CASZ1 siRNA B


title: PHH Donor 3 72h plated Replicate 2 [GC131312]

city: Leuven

first: Gert

last: Vanmarcke

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing: RNA was extracted and quality control was performed as mentioned above. Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system. Single-end reads were generated, with an average of 4 million reads obtained per sample. Alignment was performed with Hisat2. Raw counts were log2 transformed before performing downstream analyses. Principal component analysis (PCA) was done using the ggplot2 package in R, written in Jupyter Notebook. Differentially expressed genes were calculated with the DESeq2 package in R among different pairwise comparisons. The threshold criteria of p-value and false discovery rate were ≤ 0.05 and for fold change ≥ 2 in gene expression to identify differentially expressed genes. Further enrichment analyses for biological processes or pathways were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment.

source_name: Liver

growth_protocol: Briefly, cell culture plates were coated with a rigid collagen solution (50 μg collagen in 1 mL 0.02N acetic acid) and incubated overnight. Plates were washed with phosphate buffered saline solution before seeding. After thawing, cells were plated with a density of 0.25 x 106viable cells/well and 0.1 x 106viable cells/well in a 48- or 96- well plate, respectively. Plating medium consisted of William’s E medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 IU/mL penicillin and 100 µg/mL streptomycin, 4 μg/mL insulin, 1 μM dexamethasone and 20 µM Z-VAD-FMK. After cell attachment (±3 hours after seeding), cell medium was replaced by plating medium without Z-VAD-FMK. The hepatocyte monolayers were overlaid 24 hours after seeding with Matrigel (0.25 mg Matrigel® in 1 mL ice-cold culture medium). Culture medium consisted of William’s E medium supplemented with 2 mM L-glutamine, 100 IU/mL penicillin and 100 µg/mL streptomycin, 0.1 μM dexamethasone and 1% (v/v) ITS+™ Premix. Every 24 hours, medium was changed and 3 days after cell seeding, an extra layer of Matrigel was added.

extract_protocol:
We performed RTqPCR, using progeny from 3 wells of 96 well plates for RNA extraction using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions with addition of DNAseI from the On-Column DNase I Digestion kit (Sigma-Aldrich).
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Liver

value: Donor S1557T

value: cryopreserved plateable primary human hepatocytes

value: female, 24 years old

tag: gender

value: female

value: 24 years old


title: Serum,MCI,55

description:
Memories_HB04581_Serum_S38_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: MCI


title: PHH Donor 3 72h plated Replicate 3 [GC131313]

description: Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: Serum,Control,8

description:
Memories_HB04577_Serum_S201_R1_001.fastq
miR.Counts_serum.csv

value: Male


title: Adult IL-12/18 rep 4 [RNA-seq]

value: IL-12/18 (bystander activation)


title: testis at differentiating stage

city: Qingdao

first: Chaofan

last: Jin

address: Yushan 5 road

institute: Ocean University of China

data_processing:
The raw sequencing data was processed using CellRanger (v2.20). Fastq files were run through the count application with default settings, conducting alignment (using STAR aligner) based on black rockfish reference genome (CNGB, CNP0000222), as well as filtering and UMI counting. The resulting UMI count matrices were employed for further analysis.
Assembly: CNGB, CNP0000222
Supplementary files format and content: matrix files

organism: Sebastes melanops

source_name: testis

extract_protocol:
the tunica albuginea of the testis was removed, and the testis was incubated in 10 ml Leibovitz-15 medium (Gibco Invitrogen, Grand Island, NY) containing 20 mg/ml collagenase H (Roche Diagnostics, Mannheim, Germany), 0.25% trypsin (Worthing- ton Biochemical, Lakewood, NJ), 5% fetal bovine serum (Gibco), and 0.05% DNase I (Roche Diagnostics) for 4 hours at 28℃. Cell suspensions were fertilized through 40 μm strainers. Following three rounds of centrifugation at 200 rpm, and discarding the supernatant after each centrifugation, the testicular cells were suspended in 1ml PBS.
cells were diluted following manufacturer’s instructions, and 33.8 μl of total mixture buffer along with cells were loaded into the 10x Chromium Controller using Chromium Single Cell 3′ v2 reagents.

value: testis


title: Adult IL-12/18 rep 3 [RNA-seq]


title: testis at regenerating stage


title: PHH Donor 2 72h plated Replicate 3 [GC131310]

value: Donor S1510T

value: male, 70 years old, CYP3A4-dependant metabolization of 11404.8 pmol / mg protein / min

value: male

value: 70 years old


title: Neonate IL-2 rep 1 [RNA-seq]

value: Splenic CD8+ T-cells

value: Neonate (5 to 7 days)

value: IL-2 (control)

value: gBT-I WT


title: Serum,MCI,54

description:
Memories_HB04568_Serum_S179_R1_001.fastq
miR.Counts_serum.csv


title: testis at regressed stage


title: PHH Donor 3 72h plated Replicate 1 [GC131311]

value: Liver

value: Donor S1557T

value: cryopreserved plateable primary human hepatocytes


title: Adult IL-12/18 rep 2 [RNA-seq]

value: Adult (2 to 4 months)


title: Serum,MCI,53

description:
Memories_HB04559_Serum_S177_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Female


title: Adult IL-12/18 rep 1 [RNA-seq]


title: PHH Donor 2 72h plated Replicate 2 [GC131309]


title: PHH Donor 2 72h plated Replicate 1 [GC131308]


title: Serum,Control,7

description:
Memories_HB04540_Serum_S35_R1_001.fastq
miR.Counts_serum.csv

value: Male

value: Control


title: Adult IL-2 rep 6 [RNA-seq]

description:
RNA-seq analysis of Adult IL-2 cells
read_counts.tsv


title: Serum,Control,6

description:
Memories_HB04537_Serum_S156_R1_001.fastq
miR.Counts_serum.csv


title: Adult IL-2 rep 5 [RNA-seq]


title: MsNxCO2_085

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

data_processing:
Raw reads were filtered for low quality reads using BBDuk (BBtools, Joint Genome Institute)
Reads were aligned to the chromosome-level haploid genome (Zhongmu-1) (Shen et al. 2020).
Gene-level counts were obtained using featureCounts (Liao et al. 2014)
Supplementary files format and content: tab delimited file contains raw counts for each sample

organism: Medicago sativa

source_name: Agate, Effective, Low nitrogen, Ambient CO2, Replicate 4

growth_protocol: Seeds were germinated on plates in sterile water and at room temperature for 3 days before sowing. Plants were transferred to two inch square pots containing equal parts (by weight) of calcined clay and coarse sand. The soil substrate was mixed, washed, autoclaved, and cooled before use. To each pot, 10 mL of rhizobium was added from a 1 L bacterial culture grown in modified arabinose-gluconate media for 5 days. Plants were grown in growth chambers with 500 µmol m-2 s-2 light, 8hr/16hr day/night cycles, and 22 C. Plants were bottom-watered with an equal volume of distilled water every 2-3 days

extract_protocol: Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: Plants split between chambers maintained at either ambient (420 ppm) or elevated (600 ppm) CO2. Plants were fertilized with 500 mL of either 6, 10 or 16 mM KNO3 in 0.5X Hoagland solution once a week

value: Leaf

tag: cultivar

value: Agate

tag: nitrogen fixation_capability

value: effective

tag: kno3 treatment

value: 6 mM KNO3

tag: co2 treatment

value: 420 ppm CO2


title: PHH Donor 1 72h plated Replicate 3 [GC131307]

tag: tissue

value: Donor S1448T

tag: cell type

value: male, 49 years old, CYP3A4-dependant drug metabolization of 9100.8 pmol / mg protein / min

value: male

value: 49 years old


title: Serum,MCI,51

description:
Memories_HB04530_Serum_S130_R1_001.fastq
miR.Counts_serum.csv

tag: age

value: MCI


title: PHH Donor 1 72h plated Replicate 2 [GC131306]

value: Liver


title: Adult IL-2 rep 4 [RNA-seq]

value: Splenic CD8+ T-cells

tag: treatment

value: IL-2 (control)

tag: genotype

value: gBT-I WT


title: MsNxCO2_084

source_name: Agate, Effective, Low nitrogen, Ambient CO2, Replicate 3


title: PHH Donor 1 72h plated Replicate 1 [GC131305]

tag: subject

value: cryopreserved plateable primary human hepatocytes


title: Adult IL-2 rep 3 [RNA-seq]

value: Adult (2 to 4 months)


title: Serum,MCI,50

description:
Memories_HB04524_Serum_S84_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Male


title: Serum,MCI,52

description:
Memories_HB04531_Serum_S109_R1_001.fastq
miR.Counts_serum.csv


title: PHH Donor 3 Freshly thawed [GC131286]

value: Donor S1557T

value: female, 24 years old

value: female

value: 24 years old


title: MsNxCO2_087

source_name: Saranac, Ineffective, Low nitrogen, Ambient CO2, Replicate 4

value: Leaf

value: Saranac

value: ineffective

value: 6 mM KNO3

value: 420 ppm CO2


title: Adult IL-2 rep 2 [RNA-seq]


title: Serum,MCI,49

description:
Memories_HB04519_Serum_S106_R1_001.fastq
miR.Counts_serum.csv

value: MCI


title: Adult IL-2 rep 1 [RNA-seq]

value: Splenic CD8+ T-cells


title: PHH Donor 2 Freshly thawed [GC131285]

value: Liver

value: Donor S1510T

value: male, 70 years old, CYP3A4-dependant metabolization of 11404.8 pmol / mg protein / min

value: male

value: 70 years old


title: MsNxCO2_081

source_name: Saranac, Effective, Low nitrogen, Ambient CO2, Replicate 4

value: effective


title: MsNxCO2_082

source_name: Agate, Effective, Low nitrogen, Ambient CO2, Replicate 1

value: Agate


title: dpi14_scATACseq

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the danRer11 reference genome using Cell Ranger ATAC.
Assembly: danRer11 genome
Supplementary files format and content: one csv file containing raw count values for scATAC-seq peaks of all the samples

source_name: Heart

extract_protocol:
Isolated noncardiomyocytes were used as input for nuclei preparation following the 10X Genomics Chromium single-cell ATAC-seq solution protocol
scATAC-seq libraries were prepared for sequencing as outlined in the 10X Genomics single-cell ATAC-seq solution protocol.

treatment_protocol: Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. After apex resection, fish were returned to a recovery tank with fresh system water.

value: Heart

value: wild type


title: MsNxCO2_080

source_name: Saranac, Effective, Low nitrogen, Ambient CO2, Replicate 3


title: Serum,MCI,48

description:
Memories_HB04518_Serum_S199_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Female


title: PHH Donor 1 Freshly thawed [GC131284]

value: Donor S1448T

value: cryopreserved plateable primary human hepatocytes

value: male, 49 years old, CYP3A4-dependant drug metabolization of 9100.8 pmol / mg protein / min

value: 49 years old


title: MsNxCO2_086

source_name: Saranac, Ineffective, Low nitrogen, Ambient CO2, Replicate 2

value: Leaf

value: Saranac

value: ineffective

value: 6 mM KNO3

value: 420 ppm CO2