title: Pancreas, KPC ASC KO, mouse 388

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed using Dragen BCLConvert (v3.7.4).
RNA-seq read alignment and UMI counting was performed in R (v4.1.2). The scPipe package (v1.14.0) was employed to process the data. Multiplex RNA-seq FASTQ files had already been demultiplexed and contained the I1 index and UMI sequences in the read header, but headers were reordered using awk for compatibility with scPipe.
Read alignment was performed using the RSubread package (v2.6.4). An index was built using the Ensembl Mus musculus GRCm38 primary assembly genome file and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm38 v100 GFF3 genome annotation file. BAM files were processed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
Additional gene annotation was obtained using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed, grouping samples by mouse genotype. Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the eBayes function. Differentially expressed genes were determined using a false discovery rate (FDR)-adjusted p-value < 0.05. In addition, genes were ranked by confident effect size at this adjusted p-value threshold using the limma_confects function from the topconfects package (v1.10.0).
Assembly: mm10
Supplementary files format and content: Comma-separated text fiile with UMI-corrected counts for every gene and every sample

source_name: Pancreas

growth_protocol: Mice were aged under SPF conditions to 20 weeks.

extract_protocol:
Total RNA (~1µg) was isolated from snap-frozen mouse pancreas tissues using TRI Reagent® Solution (Sigma) followed by on-column RNeasy® Mini Kit RNA clean-up and DNase treatment (Qiagen).
Libraries were generated using an in-house multiplex RNA-seq method (MHTP, Medical Genomics Facility). Libraries were prepared using 20 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. Illumina P5 was added by tagmentation by Nextera transposase and PCR and Illumina P7 was added by PCR. The library was designed so that the forward read (R1) used the standard R1 primer to sequence the cDNA in the sense direction for transcript identification. The index read (I1) used the standard i7 primer to sequence directly into the sample index and then the 10 bp UMI. Sequencing (R1 101 bp; I1 18 bp) was performed on a NextSeq 2000 (Illumina) P3 100 cycle run.

value: Pancreas

value: KPC ASC KO

tag: donor


title: d05A112, d05A113, mESC, Mouse

status: Public on Jan 01 2026

type: SRA

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

country: China

institute: Peking University

description:
Library name: d05A112_d05A113
d05

library_source: genomic

data_processing:
Samples with more than 50,000 remaining contacts were retained for downstream analysis. For diploid samples, the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

extract_protocol:
We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036). Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C.

tag: cell type

value: mESC

tag: strain

value: C57BI6/J(female)x CAST/EiJ(male)


title: WT(Col-0)_NAA_Bio3

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

description: Library name: WT(Col-0)_NAA_3

library_source: transcriptomic

data_processing:
using Galaxy Belgium platform
Trimmomatic to remove adaptors
Salmon quant to align reads
tximport to count read
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy (for Arabidopsis thaliana), Genome Selaginella moellendorffii v1.0 (for Selaginella moellendorffii)
Supplementary files format and content: tab-delimited file of count read for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: 1/2 MS  plates 22°C constant light 4d old root of Arabidopsis thaliana, and 14d old root of Selaginella moellendorffii

extract_protocol:
ReliaPrep™ RNA Miniprep Systems
BGI RNA Library Prep Kit protocol

treatment_protocol: 0.2 cm of the root tip of the root. Rna extraction with ReliaPrep RNA Miniprep Systems kit (Z6112)

tag: tissue

value: Root

tag: genotype

tag: treatment

value: 10μM NAA


title: WT(Col-0)_Mock_Bio3

description: Library name: WT(Col-0)_Mock_3

value: Mock


title: WT(Col-0)_NAA_Bio1

description: Library name: WT(Col-0)_NAA_1


title: SD033/15_BA46

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

country: USA

institute: New York Genome Center

description: Library name: CGND-HRA-02761

data_processing:
Demultiplex with bcl2fastq
Align to hg38 with STAR
Count using ENSEMBL v98 annotations with htseq-count
Assembly: hg38
Supplementary files format and content: BA44_BA46_COUNT_DATA.tsv.gz Raw integer count data in compressed TSV
Supplementary files format and content: BA44_BA46_TPM_DATA.tsv.gz Standardized TPM count data in compressed TSV
Supplementary files format and content: BA44_BA46_RNASEQ_PROCESSED.h5ad Combined RNAseq analysis in h5ad

organism: Homo sapiens

extract_protocol:
Trizol
KAPA Stranded RNA-Seq Kit with RiboErase

tag: donor id

tag: Sex

value: Female

tag: age

tag: als phenotype

value: ALS

tag: pmi


title: d05A106, d05A107, mESC, Mouse

description:
Library name: d05A106_d05A107
d05


title: Pancreas, KPC ASC KO, mouse 377


title: SD008/13_BA46

description: Library name: CGND-HRA-02760

value: Male


title: d05A104, d05A105, mESC, Mouse

description:
Library name: d05A104_d05A105
d05


title: WT(Col-0)_Mock_Bio2

description: Library name: WT(Col-0)_Mock_2


title: SD028/12_BA46

description: Library name: CGND-HRA-02756


title: d05A100, d05A101, mESC, Mouse

description:
Library name: d05A100_d05A101
d05


title: WT(Col-0)_Mock_Bio1

description: Library name: WT(Col-0)_Mock_1


title: d05A102, d05A103, mESC, Mouse

description:
Library name: d05A102_d05A103
d05


title: Pancreas, KPC ASC KO, mouse 384


title: SD047/13_BA46

description: Library name: CGND-HRA-02757

value: ALSci


title: d05A118, d05A119, mESC, Mouse

description:
Library name: d05A118_d05A119
d05


title: SD030/18_BA44

description: Library name: CGND-HRA-02754

value: Control


title: SAB treated 18day root replicate 3

city: singapore

first: Hitesh

last: Tikariha

address: 5A Engineering Drive 1, #02-03 T-Lab Building

country: Singapore

institute: National university of singapore

description: Library name: SAB_18d_Root_3

data_processing:
The erroneous k-mers were removed from the paired reads using run_rcorrector perl script. Trim Galore was used for removing low-quality and short length reads. Kraken2 was used to remove bacterial and human contaminations. All the clean reads from 24 samples were passed for de novo assembly by Trinity v2.14.0. Bowtie2 was used to quantify read support for the assembly.
Genes abundances were estimated using Kallisto method implemented in Trinity
genes were annotated by using blast with arabidopsis protein database
Assembly: assembly.fasta
Supplementary files format and content: count.csv

molecule: polyA RNA

organism: Brassica rapa subsp. chinensis

growth_protocol: two-time points were selected for RNAseq analysis (Day8: True leaf stage and Day18: Mature stage with no onset of flowering)

extract_protocol:
RNA was isolated from three independent biological replicates of whole roots and leaves separately of both consortia SAB treated and controlled on day 8 and day 18. Samples were snap-freeze by dipping them in liquid nitrogen and stored in a -80 deep freezer. After that samples were powdered with a mortar pestle in liquid nitrogen for RNA extraction using Qiagen Plant RNeasy extraction kit.
RNA quantity was determined using Qubit fluorometer from Life Technologies with the "dsDNA BR Assay Kit" and RIN value (>8) by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). oligo dT purification of RNA was followed by library preparation and subsequent sequencing of 40 million paired end 100bp reads/sample by Illumina HiSeq2500 at the SCLESE sequencing facility, Singapore.

treatment_protocol: For seed dressing, microbial adhesion onto sterilized seeds is allowed by immersing the seeds in 5ml of bacterial suspensions (Streptomyces and Agromyces-Bacillus as combined culture in 1:1 ratio) containing 1.6 x 108 cells per ml for 30 to 60 minutes with shaking at 50-100 rpm at room temperature. Seeds soaked in 10mM MgSO4 were used as control

tag: Stage

value: adult stage

value: wild type

value: Consortia treated


title: Pancreas, KPC ASC KO, mouse 335


title: SAB treated 18day root replicate 1

description: Library name: SAB_18d_Root_1


title: d05A93, d05A94, mESC, Mouse

description:
Library name: d05A93_d05A94
d05


title: d05A91, d05A92, mESC, Mouse

description:
Library name: d05A91_d05A92
d05


title: SAB treated 18day root replicate 2

description: Library name: SAB_18d_Root_2


title: Pancreas, KPC ASC KO, mouse 318


title: Pancreas, KPC, mouse 210

value: KPC


title: d05A95, d05A96, mESC, Mouse

description:
Library name: d05A95_d05A96
d05


title: SD015/16_BA44

description: Library name: CGND-HRA-02752


title: SD012/13_BA44

description: Library name: CGND-HRA-02750


title: Pancreas, KPC, mouse 145


title: SD014/16_BA44

description: Library name: CGND-HRA-02751


title: SAB treated 8day root replicate 3

description: Library name: SAB_8d_Root_3

value: seedling stage


title: SD004/16_BA44

description: Library name: CGND-HRA-02749


title: SD032/16_BA44

description: Library name: CGND-HRA-02753


title: SAB treated 18day leaf replicate 3

description: Library name: SAB_18d_Leaf_3

source_name: Leaf

value: Leaf


title: SAB treated 18day leaf replicate 1

description: Library name: SAB_18d_Leaf_1


title: d05A86, d05A87, mESC, Mouse

description:
Library name: d05A86_d05A87
d05


title: Pancreas, KPC, mouse 48

value: Pancreas


title: d05A84, d05A85, mESC, Mouse

description:
Library name: d05A84_d05A85
d05

value: mESC


title: Pancreas, KPC, mouse 154


title: Pancreas, KPC, mouse 89


title: SAB treated 18day leaf replicate 2

description: Library name: SAB_18d_Leaf_2


title: SD033/15_BA44

description: Library name: CGND-HRA-02748


title: d05A9, d05A90, mESC, Mouse

description:
Library name: d05A9_d05A90
d05

value: C57BI6/J(female)x CAST/EiJ(male)


title: Pancreas, KPC, mouse 40


title: SD008/13_BA44

description: Library name: CGND-HRA-02747


title: d05A88, d05A89, mESC, Mouse

description:
Library name: d05A88_d05A89
d05


title: SAB treated 8day root replicate 2

description: Library name: SAB_8d_Root_2

value: Root


title: d05A80, d05A81, mESC, Mouse

description:
Library name: d05A80_d05A81
d05


title: Pancreas, KPC, mouse 43


title: SD032/12_BA44

description: Library name: CGND-HRA-02746


title: d05A82, d05A83, mESC, Mouse

description:
Library name: d05A82_d05A83
d05


title: SAB treated 8day root replicate 1

description: Library name: SAB_8d_Root_1


title: SAB treated 8day leaf replicate 3

description: Library name: SAB_8d_Leaf_3


title: SD049/15_BA44

description: Library name: CGND-HRA-02745


title: d05A77, d05A78, mESC, Mouse

description:
Library name: d05A77_d05A78
d05


title: d05A79, d05A8, mESC, Mouse

description:
Library name: d05A79_d05A8
d05


title: SAB treated 8day leaf replicate 2

description: Library name: SAB_8d_Leaf_2


title: SD026/12_BA44

description: Library name: CGND-HRA-02744


title: Untreated 18day root replicate 2

description: Library name: UT_18d_Root_2

value: Untreated


title: Multiome, Immune cells, Adult 2, GEX

first: Siddhi

last: Nargund

address: 3960 Broadway, Lasker 203A

department: Department of Systems Biology

institute: Columbia University

description: Library name: PDC149 Spleen RNA

library_source: transcriptomic single cell

data_processing:
Data was processed using Cell Ranger pipeline and fastqs were made using Cell Ranger(atac) mkfastq
Assembly: hg38
Supplementary files format and content: Cellranger output files:filtered_feature_bc_matrix.h5
Supplementary files format and content: Cellranger output files:atac_fragments.tsv.gz

molecule: nuclear RNA

source_name: Spleen

extract_protocol:
Nuclei were isolated from infant and adult spleen samples following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression sample preparation workflow (10x Genomics). Tissue was dissociated, lysed, filtered, and washed according to the manufacturer’s instructions to obtain clean, intact nuclei suitable for Multiome library preparation.
Single-nucleus Multiome ATAC and gene expression libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics). Library construction followed the standard workflow, including GEM generation and barcoding, post-GEM cleanup, amplification, and construction of separate indexed ATAC and gene expression libraries for sequencing on an Illumina platform.

value: Spleen


title: Pancreas, wild type, mouse 1213

value: WT


title: Untreated 18day root replicate 3

description: Library name: UT_18d_Root_3


title: d05A75, d05A76, mESC, Mouse

description:
Library name: d05A75_d05A76
d05


title: d05A73, d05A74, mESC, Mouse

description:
Library name: d05A73_d05A74
d05


title: Pancreas, wild type, mouse 1197


title: Pancreas, wild type, mouse 1237


title: Pancreas, wild type, mouse 69


title: Pancreas, wild type, mouse 1238


title: Multiome, Immune cells, Adult 2, ATAC

description: Library name: PDC149 Spleen ATAC

library_source: genomic single cell


title: SAB treated 8day leaf replicate 1

description: Library name: SAB_8d_Leaf_1


title: Untreated 18day root replicate 1

description: Library name: UT_18d_Root_1


title: Pancreas, wild type, mouse 1202


title: d05A7, d05A70, mESC, Mouse

description:
Library name: d05A7_d05A70
d05


title: d05A71, d05A72, mESC, Mouse

description:
Library name: d05A71_d05A72
d05


title: d05A68, d05A69, mESC, Mouse

description:
Library name: d05A68_d05A69
d05


title: Es-1T_MRV_2d_1

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: Es-1T_MRV_2d_1
TruSeq Stranded mRNA Kit

data_processing:
STAR aligner (version 2.7.11b)
RSEM (version 1.3.3)
Assembly: Greater horseshoe bat genome (R. ferrumequinum; GCF_004115265.2), Big brown bat (E. fuscus; GCF_027574615.1), MRV, Shaanvirus-like, IAV (human H1N1), MERS-CoV, and SeoV
Supplementary files format and content: tsv files

organism: Cnephaeus serotinus

source_name: Trachea organoid

extract_protocol:
Trizol LS reagent (Ambion)
TruSeq Stranded mRNA Kit (illumina)

value: Trachea organoid


title: Untreated 18day leaf replicate 3

description: Library name: UT_18d_Leaf_3


title: ckit_NoRh_2_Rloop

city: NY

first: Bin

last: Lu

address: 417 East 68th Street New York,

institute: mskcc

data_processing:
*library strategy: cut&tag
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Assembly: mm10/hg38

source_name: bone marrow

growth_protocol: leukemia cell lines were cultured at RPMI. All primary cells were enriched from mouse bone marrow, human cord blood, or human adult blood sample.

extract_protocol:
All the cells were first fixed by methanol, mobilized on Concanavalin A beads, folllowed by S9.6 anbibody incubation and nanobody Tn5 binding. Mg2+ was added to activate the cutting of Tn5
Recovered chromotain DNA was first end repaired using Bst 2.0, followed by in vitro transcription of T7 promoter. Transcribed RNA was first reverse converted to first cDNA and second DNA strand. Double strand DNA was cut by second Tn5. Library was amplified by DNA polymerase.

treatment_protocol: ckit+positive enrichment kit was used to enrich HSPCs cells, mature cells were flow through of HSPC enrichment process. CD34+ kit was used to enrich human HSPCs, mature cells were flow through of cd34+ enrichment process.

value: bone marrow

tag: cell line

value: ckit + cells

value: CD117 enrichment


title: ckit_Rh_1_Rloop


title: Es-1T_MRV_2d_3

description:
Library name: Es-1T_MRV_2d_3
TruSeq Stranded mRNA Kit


title: Es-1T_MRV_2d_2

description:
Library name: Es-1T_MRV_2d_2
TruSeq Stranded mRNA Kit


title: ckit_Rh_2_Rloop


title: Es-1T_MRV_1d_2

description:
Library name: Es-1T_MRV_1d_2
TruSeq Stranded mRNA Kit


title: Untreated 18day leaf replicate 2

description: Library name: UT_18d_Leaf_2

value: adult stage


title: Untreated 8day root replicate 2

description: Library name: UT_8d_Root_2

value: wild type


title: ckit_NoRh_1_Rloop


title: Untreated 18day leaf replicate 1

description: Library name: UT_18d_Leaf_1


title: d05A62, d05A63, mESC, Mouse

description:
Library name: d05A62_d05A63
d05


title: Es-1T_MRV_1d_3

description:
Library name: Es-1T_MRV_1d_3
TruSeq Stranded mRNA Kit


title: d05A64, d05A65, mESC, Mouse

description:
Library name: d05A64_d05A65
d05


title: single cell  mouse ckit rep1 R_loop

data_processing:
*library strategy: Cut&Tag
Raw fastq reader files were first mapped to hg38 or mm10 using bwa-mem2 with default setting. Generated bam files were indexed using samtools and then used to create fragment file using Sinto package with the parameter of - –barcode_regex ‘[^:]*’. Generated files were further coordinate sorted, compressed by bgzip, indexed by tabix, and used for all the downstream analysis.
To quantify the counts of genomic region of each single cell, the function of AggregateTiles in Signac was used with a binsize of 10,000, min_counts=1 using hg38 or mm10 genome. Cells with < 10,000 total counts and > 100 counts were retained for further analysis. Count matrix was first normalized by performing TF-IDF, followed by RunTFIDF and RunSVD function in package Signac with default setting. UMAP for visualization was generated by running RunUMAP, followed by clustering classification using function FindNeighbors and FindCluster with reduction and dims set as reduction=“lsi”, dim=”2:10”. DimPlot function was finally used to generate 2D UMAP.
To annotate each cluster of single cell data, cell barcodes x fragments matrix file was first obtained from Seurat project. This same fragment region was next used to quantify the reads of each purified hematopoietic cells and form a matrix file by using tool multicov from bedtools. Since no defined marker of R-loop within distinct hematopoietic cell types is available, we used Reference component analysis (RCA) package to compare the similarity of each cluster versus purified hematopoietic populations. HSC/MPP population was first annotated using the Pearson correlation matrix with sorted progenitor cells. When one cluster was predicted to resemble multiple sorted progenitor populations, manual annotation was then used to nominate it. The populations with less cell amounts were classified as mature cells, and Pearson correlation matrix was obtained by comparing with sorted mature cells. As done progenitor cells, manual annotation is used to separate similar groups in mature populations.
bamCoverage was used to generate bigwig file for genome browser visualization.
Supplementary files format and content: mm10/hg38

extract_protocol:
All the cells were fixed by methanol first, and co-icubate with S9.6 antibody for 1 hour, followed by binding of nano body -Tn5 and activated by addition of Mg2+
For human cells, 1 million umbilical cord blood CD34+ positive cells were used as input for single cell R-loop mapping was performed. For mouse cells, 1 million c-Kit+ positive cells were used. Primary cells were firstly subjected to nuclear extraction with lysis buffer. Extracted nuclei were centrifugates and incubated with S9.6 containing antibody buffe. Unbound S9.6 was washed away with the same buffer followed by incubating cells with Dig300 washing buffer containing 5 mM nanobody Tn5 . Library preparation protocol was following the procedure of single cell nano-tag Tn5


title: Es-1T_MERS_2d_2

description:
Library name: Es-1T_MERS_2d_2
TruSeq Stranded mRNA Kit


title: Untreated 8day leaf replicate 3

description: Library name: UT_8d_Leaf_3


title: d05A66, d05A67, mESC, Mouse

description:
Library name: d05A66_d05A67
d05


title: B220LPS_pos_IFN_2_Rloop

data_processing:
*library strategy: Cut&Tag
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Assembly: hg38 or mm10
Supplementary files format and content: bw

value: B cell

value: cell culture


title: B220PBS_1_Rloop


title: B220PBS_2_Rloop


title: single cell mouse ckit rep2 R_loop


title: d05A59, d05A6, mESC, Mouse

description:
Library name: d05A59_d05A6
d05


title: d05A53, d05A54, mESC, Mouse

description:
Library name: d05A53_d05A54
d05


title: Untreated 8day root replicate 1

description: Library name: UT_8d_Root_1

value: seedling stage


title: d05A60, d05A61, mESC, Mouse

description:
Library name: d05A60_d05A61
d05


title: Es-1T_MRV_1d_1

description:
Library name: Es-1T_MRV_1d_1
TruSeq Stranded mRNA Kit


title: Es-1T_MERS_2d_3

description:
Library name: Es-1T_MERS_2d_3
TruSeq Stranded mRNA Kit


title: Untreated 8day leaf replicate 2

description: Library name: UT_8d_Leaf_2

value: Leaf


title: RN2_2_Rloop


title: B220LPS_pos_IFN_1_Rloop


title: Untreated 8day leaf replicate 1

description: Library name: UT_8d_Leaf_1


title: d05A57, d05A58, mESC, Mouse

description:
Library name: d05A57_d05A58
d05


title: Es-1T_MERS_1d_3

description:
Library name: Es-1T_MERS_1d_3
TruSeq Stranded mRNA Kit


title: Es-1T_MERS_1d_2

description:
Library name: Es-1T_MERS_1d_2
TruSeq Stranded mRNA Kit


title: Es-1T_MERS_2d_1

description:
Library name: Es-1T_MERS_2d_1
TruSeq Stranded mRNA Kit


title: Es-1T_MERS_1d_1

description:
Library name: Es-1T_MERS_1d_1
TruSeq Stranded mRNA Kit


title: d05A55, d05A56, mESC, Mouse

description:
Library name: d05A55_d05A56
d05


title: RN2_1_Rloop


title: hnf4β-knockout mutants, dexamethasone treatment combined with GCRV-II infection, Day 6, rep2

city: Wuhan

first: siyao

last: Zheng

address: No.7, Donghu South Road, Wuchang

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description:
Library name: DG-4B-2
hnf4β-knockout mutants

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
Assembly: Danio_rerio.GCF_000002035.6_GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Danio rerio

source_name: bony fishes

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: bony fishes

value: hnf4beta-knockout mutants


title: d05A5, d05A50, mESC, Mouse

description:
Library name: d05A5_d05A50
d05

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: Es-1T_IAV_2d_3

description:
Library name: Es-1T_IAV_2d_3
TruSeq Stranded mRNA Kit


title: d05A51, d05A52, mESC, Mouse

description:
Library name: d05A51_d05A52
d05


title: Untreated 8day root replicate 3

description: Library name: UT_8d_Root_3

value: Root

value: Untreated


title: d05A48, d05A49, mESC, Mouse

description:
Library name: d05A48_d05A49
d05


title: hnf4β-knockout mutants, GCRV-II infection, Day 6, rep3

description:
Library name: G-4B-3
hnf4β-knockout mutants

value: GCRV-II infection


title: hnf4β-knockout mutants, dexamethasone treatment combined with GCRV-II infection, Day 6, rep3

description:
Library name: DG-4B-3
hnf4β-knockout mutants


title: C1498_2_Rloop


title: hnf4β-knockout mutants, dexamethasone treatment combined with GCRV-II infection, Day 6, rep1

description:
Library name: DG-4B-1
hnf4β-knockout mutants


title: Es-1T_IAV_2d_2

description:
Library name: Es-1T_IAV_2d_2
TruSeq Stranded mRNA Kit

value: Trachea organoid


title: d05A46, d05A47, mESC, Mouse

description:
Library name: d05A46_d05A47
d05


title: C1498_1_Rloop

value: bone marrow


title: d05A44, d05A45, mESC, Mouse

description:
Library name: d05A44_d05A45
d05


title: hnf4β-knockout mutants, GCRV-II infection, Day 6, rep2

description:
Library name: G-4B-2
hnf4β-knockout mutants


title: hnf4β-knockout mutants, dexamethasone treatment, Day 6, rep3

description:
Library name: D-4B-3
hnf4β-knockout mutants

value: dexamethasone treatment


title: Es-1T_IAV_1d_1

description:
Library name: Es-1T_IAV_1d_1
TruSeq Stranded mRNA Kit


title: Es-1T_IAV_1d_3

description:
Library name: Es-1T_IAV_1d_3
TruSeq Stranded mRNA Kit


title: hnf4β-knockout mutants, GCRV-II infection, Day 6, rep1

description:
Library name: G-4B-1
hnf4β-knockout mutants


title: d05A40, d05A41, mESC, Mouse

description:
Library name: d05A40_d05A41
d05


title: mNeutrophil_1_Rloop

value: ckit + cells

value: CD117 enrichment


title: Es-1T_IAV_2d_1

description:
Library name: Es-1T_IAV_2d_1
TruSeq Stranded mRNA Kit


title: d05A39, d05A4, mESC, Mouse

description:
Library name: d05A39_d05A4
d05


title: hnf4β-knockout mutants, dexamethasone treatment, Day 6, rep2

description:
Library name: D-4B-2
hnf4β-knockout mutants


title: Es-RNA_oh-3_TrO

description:
Library name: Es-RNA_oh-3_TrO
TruSeq Stranded mRNA Kit


title: mNeutrophil_2_Rloop


title: hnf4β-knockout mutants, dexamethasone treatment, Day 6, rep1

description:
Library name: D-4B-1
hnf4β-knockout mutants


title: d05A42, d05A43, mESC, Mouse

description:
Library name: d05A42_d05A43
d05


title: mST_HSC_2_Rloop


title: Es-1T_IAV_1d_2

description:
Library name: Es-1T_IAV_1d_2
TruSeq Stranded mRNA Kit


title: mST_HSC_1_Rloop


title: mMPP_2_Rloop


title: mMONO_2_Rloop


title: d05A35, d05A36, mESC, Mouse

description:
Library name: d05A35_d05A36
d05


title: Es-RNA_oh-1_TrO

description:
Library name: Es-RNA_oh-1_TrO
TruSeq Stranded mRNA Kit


title: mMPP_1_Rloop


title: d05A37, d05A38, mESC, Mouse

description:
Library name: d05A37_d05A38
d05


title: d05A31, d05A32, mESC, Mouse

description:
Library name: d05A31_d05A32
d05


title: hnf4β-knockout mutants, control, Day 6, rep1

description:
Library name: U-4B-1
hnf4β-knockout mutants

value: Day 6


title: Es-RNA_oh-2_TrO

description:
Library name: Es-RNA_oh-2_TrO
TruSeq Stranded mRNA Kit


title: hnf4β-knockout mutants, control, Day 6, rep3

description:
Library name: U-4B-3
hnf4β-knockout mutants


title: d05A33, d05A34, mESC, Mouse

description:
Library name: d05A33_d05A34
d05


title: hnf4β-knockout mutants, control, Day 6, rep2

description:
Library name: U-4B-2
hnf4β-knockout mutants


title: mMONO_1_Rloop


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep7

city: shanghai

first: xiaoyu

last: cheng

address: siping road

institute: tongji university

description: GGAGAACA

data_processing:
RNA-seq raw reads were trimmed with Cutadapt to remove poly A, TSO, low quality and adaptor-contaminated reads and quality control by using FastQC.
Then the clean reads were aligned to the GRCz11 reference zebrafish genome using STAR and  quantificated  by featureCounts.
Differential expressed genes were found using edgeR and the threshold was set at fold changes of >1.5-fold in either direction and P-value <0.05.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each groups (sibling or actl6a mutant)

source_name: pronephric duct

growth_protocol: Zebrafish (transgenic Na, K-ATPase alpha1A4:GFP line that GFP is highly expressed in pronephric epithelia) were maintained and bred according to the standard condition. Zebrafish embryos of  mutant line were obtained from natural mating(incross) and cultured at 28.5 °C.

extract_protocol:
RNA was harvested according to the following step. Prepared the lysis solution of the following system(0.1ul RRI; 0.19ul 10% triton x 100; 2.41ul nuclear free water; 1 ul dNTP(10mM) ), placed the pronephros ducts in it, and stored it frozen in liquid nitrogen . The extracted total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Hyper Prep Kits following manufacturer’s protocols.

treatment_protocol:
The CRISPR/Cas9 system was used to generate zebrafish mutants. In a nutshell, 1 nl of the mixture of guide RNAs (gRNAs) (100 ng/µl) and Cas9 mRNA (4 µm) was injected into the cell of a zebrafish embryo at the 1-cell stage. Injected embryos were raised to adulthood and then outcrossed to transgenic Na, K-ATPase alpha1A4:GFP fish. Positive founder fish (F0) were identified by genotyping the offspring embryos from the outcrosses, and there was green fluorescence in the pronephros ducts of the embryo . F1 fish, which were off-springs from positive F0 fish outcrossed with wild-type fish, were raised. Positive F1 fish were crossed to each other to collect homozygous mutant embryos.
For isolation of pronephros ducts, 72 hpf. Fifteen zebrafish embryos per group were incubated in 10 mmol/ml DTT in egg water for 1 hour at room temperature. They were then incubated at 37 °C in 5 mg/ml collagenase I in DMEM/F12 and triturated gently five times with a 1000 μl pipette tip every 10 minutes until the end of 30 minutes of incubation. The larvae were then put in DMEM/F12, so that the disintegrated, approximately 10 pronephric duct fragments were collected by visual identification according to the GFP fluorescence.

value: pronephric duct

value: actl6a knockout

value: Constructing mutants using CRISPR/Cas9


title: mMEP_1_Rloop


title: d05A28, d05A29, mESC, Mouse

description:
Library name: d05A28_d05A29
d05


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep8

description: GGTGCGAA


title: mMEP_2_Rloop


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep6

description: GCTCGGTA


title: d05A24, d05A25, mESC, Mouse

description:
Library name: d05A24_d05A25
d05


title: d05A3, d05A30, mESC, Mouse

description:
Library name: d05A3_d05A30
d05


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep5

description: GCTAACGA


title: d05A22, d05A23, mESC, Mouse

description:
Library name: d05A22_d05A23
d05


title: mLT_HSC_2_Rloop


title: mGMP_1_Rloop


title: mycelium - Vea_KO_MEA - rep3

type: RNA

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Fungi_Pexp_Afla_Afum GE 8x60K (design 084703)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 084703_D_F_20170227). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}. We firstly selected control probes and probes targeting Penicillium expansum transcripts (GeneNames begining by 'PEX1_') giving a dataset with 31803 entries. We next selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 28179 spots were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 9947 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Penicillium expansum

source_name: mycelium

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Strains were incubated for 5 days in the dark at 25°C in a incubator.

extract_protocol: Total RNA was isolated at the end of the growth period. The mycelium was transferred to lysing matrix D tubes (1.4 mm ceramic spheres), to which 760 µL of lysis buffer (10 μL of β-mercaptoethanol and 750 μL of RLT buffer) were added, and the tubes were placed in liquid nitrogen. The mycelium cells were broken down in a Precellys homogenizer with three grindings at a speed of 6,500 rpm for 15 s followed by 5 min incubation on ice, at 6,500 rpm for 25 s and 5 min on ice, and a final 6,500 rpm for 15 s. The samples were subsequently centrifuged at 16,000 g at 4 °C for 10 min. The supernatant was recovered in QIAshredder spin columns (QIAGEN) and the total RNA was purified using RNeasy spin minicolumns (QIAGEN).

treatment_protocol: Strains were centrally inoculated onto plates, either containing MEA medium alone or MEA medium supplemented with 400 μL (280 mM) DMSO covered with sterile cellophane sheets.

tag: medium

value: MEA


title: mycelium - WT_MEA - rep4

value: WT


title: mycelium - PatL_KO_MEA - rep5


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep3

description: GCCAAGAC


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep2

description: GATGAATC


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep1

description: GATAGACA


title: d05A17, d05A18, mESC, Mouse

description:
Library name: d05A17_d05A18
d05


title: mycelium - Vea_KO_MEA - rep5


title: d05A20, d05A21, mESC, Mouse

description:
Library name: d05A20_d05A21
d05


title: mGMP_2_Rloop


title: mLT_HSC_1_Rloop


title: mycelium - WT_MEA_DMSO - rep5


title: mycelium - WT_MEA_DMSO - rep4


title: d05A19, d05A2, mESC, Mouse

description:
Library name: d05A19_d05A2
d05


title: pronephric duct, mutant in CRISPR/Cas9 mutant lines, 72hpf, rep4

description: GCCACATA


title: mCMP_2_Rloop


title: mycelium - Vea_KO_MEA - rep6


title: d05A26, d05A27, mESC, Mouse

description:
Library name: d05A26_d05A27
d05


title: mCMP_1_Rloop


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep7

description: TTCACGCA


title: d05A15, d05A16, mESC, Mouse

description:
Library name: d05A15_d05A16
d05


title: mycelium - WT_MEA_DMSO - rep6


title: mycelium - WT_MEA - rep6


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep6

description: TGGCTTCA


title: mCD8_2_Rloop


title: mCD71_2_Rloop


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep4

description: TGAAGAGA


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep5

description: TGGAACAA


title: d05A13, d05A14, mESC, Mouse

description:
Library name: d05A13_d05A14
d05


title: mCD8_1_Rloop


title: mCD71_1_Rloop


title: d05A11, d05A12, mESC, Mouse

description:
Library name: d05A11_d05A12
d05


title: mycelium - PatL_KO_MEA - rep1


title: d05A1, d05A10, mESC, Mouse

description:
Library name: d05A1_d05A10
d05


title: mCD4_2_Rloop


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep1

description: AAGAGATC


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep3

description: TCTTCACA


title: pronephric duct, sibling in CRISPR/Cas9 mutant lines, 72hpf, rep2

description: AATCCGTC


title: mycelium - WT_MEA_DMSO - rep3


title: mycelium - WT_MEA_DMSO - rep2


title: mycelium - Vea_KO_MEA - rep2


title: mycelium - PatL_KO_MEA - rep2


title: mB220_2_Rloop


title: mCD4_1_Rloop


title: pronephric duct, actl6a morpholino injected, 30hpf, rep8

description: GTACGCAA

data_processing:
RNA-seq raw reads were trimmed with Cutadapt to remove poly A, TSO, low quality and adaptor-contaminated reads and quality control by using FastQC.
Then the clean reads were aligned to the GRCz11 reference zebrafish genome using STAR and  quantificated  by featureCounts.
Differential expressed genes were found using edgeR and the threshold was set at fold changes of >1.5-fold in either direction and P-value <0.05.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each groups (ctrl or actl6a morphants)

growth_protocol: Zebrafish (transgenic Na, K-ATPase alpha1A4:GFP line, the transgenic line has GFP fluorescence in the pronephros) were maintained and bred according to the standard condition. Zebrafish embryos for injection were obtained from natural mating and cultured at 28.5 °C.

treatment_protocol:
Antisense morpholinos (MOs) were used to block the translation of actl6a, and a standard control MO was used as the negative control. All MOs were injected into embryos at the 1-cell stage.
For isolation of pronephros ducts, 30 hpf. Fifteen zebrafish embryos were incubated in 10 mmol/ml DTT in egg water for 1 hour at room temperature. They were then incubated at 37 °C in 5 mg/ml collagenase I in DMEM/F12 and triturated gently five times with a 1000 μl pipette tip every 10 minutes until the end of 30 minutes of incubation. The larvae were then put in DMEM/F12, so that the disintegrated, approximately 10 pronephric duct fragments were collected by visual identification according to the GFP fluorescence.

value: actl6a knockdown

value: actl6a morpholino injected


title: ckit_400k_2 R loop


title: mycelium - WT_MEA_DMSO - rep1


title: mycelium - Vea_KO_MEA - rep1


title: ckit_400k_1 R loop


title: mB220_1_Rloop


title: pronephric duct, actl6a morpholino injected, 30hpf, rep4

description: GCTAACGA


title: RNaseH ckit 32k_1 Rloop

description: RNaseH ckit 32k_1


title: pronephric duct, actl6a morpholino injected, 30hpf, rep5

description: GCTCGGTA


title: ckit_64k_1 Rloop


title: pronephric duct, actl6a morpholino injected, 30hpf, rep6

description: GGAGAACA


title: mycelium - WT_MEA - rep5


title: RNaseH  ckit 32k_2 Rloop

description: RNaseH  ckit 32k_2


title: mycelium - PatL_KO_MEA - rep3


title: pronephric duct, actl6a morpholino injected, 30hpf, rep7

description: GGTGCGAA


title: pronephric duct, actl6a morpholino injected, 30hpf, rep2

description: GCCACATA


title: mycelium - WT_MEA - rep2


title: pronephric duct, actl6a morpholino injected, 30hpf, rep3

description: GCGAGTAA


title: pronephric duct, actl6a morpholino injected, 30hpf, rep1

description: GATAGACA


title: ckit_32k_1 Rloop


title: MockT_Day2_5

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

description: Library name: 24_Sample24_new

data_processing:
34 totalRNA-Seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing. The samples have 87 to 174 million pass filter reads with more than 95% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 91%. Unique alignment is above 72%. There are 6.46 to 15.04% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 1.75% ribosomal bases. Percent coding bases are between 30-42%. Percent UTR bases are 28-40%, and mRNA bases are between 61-80% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 54-73% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
344SQ tumors from saline-treated mice were harvested on day 0 post-treatment. 344SQ tumors from CAR-T- or mock-T-treated mice were harvested on day 2, 7 and 12 post-treatment. Tumors from 4-5 different mice were harvested per treatment group. Tumor tissue was stored in RNAlater Stabilization Solution (Invitrogen), homogenized and RNA was isolated using RNAeasy kit (Qiagen) according to the manufacturer’s instructions.
Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.

treatment_protocol: CAR-T cell treatment

value: lung

tag: tumor model_type

value: lung adenocarcinoma

tag: mouse strain

value: Female

value: 8-10 weeks old

tag: scan date


title: MockT_Day7_5

description: Library name: 29_Sample29_new


title: MockT_Day12_4

description: Library name: 33_Sample33_new


title: MockT_Day7_2

description: Library name: 26_Sample26_new


title: MockT_Day7_4

description: Library name: 28_Sample28_new


title: MockT_Day12_2

description: Library name: 31_Sample31_new


title: MockT_Day12_1

description: Library name: 30_Sample30_new


title: MockT_Day7_3

description: Library name: 27_Sample27_new


title: MockT_Day7_1

description: Library name: 25_Sample25_new


title: MockT_Day12_3

description: Library name: 32_Sample32_new


title: MockT_Day12_5

description: Library name: 34_Sample34_new


title: ckit_16k_2 Rloop


title: pronephric duct, ctrl morpholino injected, 30hpf, rep9

description: TGGTGGTA

value: ctrl morpholino injected


title: MockT_Day2_3

description: Library name: 22_Sample22_new


title: mycelium - WT_MEA - rep3


title: MockT_Day2_4

description: Library name: 23_Sample23_new


title: mycelium - PatL_KO_MEA - rep4


title: pronephric duct, ctrl morpholino injected, 30hpf, rep10

description: TTCACGCA


title: MockT_Day2_2

description: Library name: 21_Sample21_new


title: pronephric duct, ctrl morpholino injected, 30hpf, rep8

description: TGGCTTCA


title: ckit_16k_1 Rloop

value: bone marrow


title: ckit_32k_2 Rloop


title: CART_Day12_4

description: Library name: 18_Sample18_new


title: MockT_Day2_1

description: Library name: 20_Sample20_new


title: CART_Day12_5

description: Library name: 19_Sample19_new


title: CART_Day12_3

description: Library name: 17_Sample17_new


title: pronephric duct, ctrl morpholino injected, 30hpf, rep6

description: TGAAGAGA


title: ckit 8k Rloop

description: ckit 8k_1


title: 23P36 Injured scRNA-seq

city: Los Angeles

first: Dmitriy

last: Sheyn

address: 127 S San Vicente Blvd

institute: Cedars-Sinai Medical Center

description: Library name: 23P36 Injured

data_processing:
For scRNA-seq: Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20. Cell Ranger v7.1.0 (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the pig reference genome Sscrofa11 with intron mode used. For bulk RNA-seq (both sample types): Raw reads obtained from RNA-Seq 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) with default parameters, using a custom pig Sscrofa11 transcriptome reference downloaded from https://useast.ensembl.org/, containing all protein-coding and long non-coding RNA genes based on Sscrofa11.1.104 annotation.
Assembly: For scRNA-seq: Sscrofa11. For bulk RNA-seq: custom pig Sscrofa11 transcriptome reference downloaded from https://useast.ensembl.org/, containing all protein-coding and long non-coding RNA genes based on Sscrofa11.1.104 annotation.
Supplementary files format and content: tsv and mtx files

organism: Sus scrofa

source_name: Nucleus Pulposus

extract_protocol:
For scRNA-seq: The NP and surrounding transition zone (n = 3 injured and 3 non-injured discs) were isolated and manually morselized to ~1mm^3 pieces. The tissue was then enzymatically digested for 1 hour at 37°C in 2 mg/mL of Pronase Protease (Millipore, Temecula, CA) in growth media containing 1% antibiotic-antimycotic solution (Gibco, Carlsbad, CA) and 10% fetal bovine serum (FBS, Gemini Bioproducts, West Sacramento, CA) in Dulbecco’s modified eagle media-F12 media (DMEM/F12, GIBCO, Carlsbad, CA), followed by an ~18 hours digestion at 37°C in 0.25 mg/mL of Collagenase Type 1S (Sigma Aldrich) in growth media. The resulting sample was pushed through a 70μm cell strainer, and cells were isolated via centrifugation at 300G for ten minutes. The pellet was resuspended in phosphate-buffered saline at a concentration of 1,500 cells/uL. For bulk RNA-seq (both DRGs and IVD): Total RNA for the nucleus pulposus and dorsal root ganglia were collected using a RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol. The isolated RNA was transcribed into cDNA using a high-capacity reverse transcription kit (Applied Biosystems, Waltham, MA). Pig Taqman gene expression assays (Thermo Fisher Scientific) as detailed in Supplemental materials were used for analysis (Supplemental Table 2). All assays were normalized to 18S housekeeping gene.
Single cell suspensions were stained with ViaStain AOPI Staining Solution (Nexcelom Bioscience, Lawrence, MA) and imaged on an EVOS M7000 Imaging System (Thermo Fisher Scientific, Waltham, CA) to determine cell suspension quality and cell viability.  Cell suspensions with a minimum viability of 70% were partitioned (10,000 target capture) into Gel Beads-in-emulsion (GEMs) on the Chromium X (10x Genomics, Pleasanton, CA) per the Chromium NextGEM Single Cell 3’ v3.1 Gene Expression kit user guide.  Following reverse transcription and cDNA amplification, single cell libraries were prepared on the Chromium Connect (10x Genomics) using the Automated Gene Expression Library Construction kit (10x Genomics).  Barcoded libraries were quantified by quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific) and library size was measured via the 4200 TapeStation (Agilent Technologies, Santa Clara, CA).  Libraries were sequenced on a NovaSeq 6000 or X Plus (Illumina, San Diego, CA) with sequencing configuration 28x10x10x90bp, and a sequencing depth of 50,000 reads/cell. Bulk RNA seq for DRGs: RNA integrity was analyzed on the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) and RNA quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).  Four hundred ng RNA was ribodepleted using the Lexogen RiboCop Depletion Kit Human/Mouse/Rat v2 kit (Lexogen Inc., Greenland, NH).  Stranded RNA-Seq library construction was performed using the IDT xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA) with 11 cycles of PCR amplification.  Library concentration was measured via the Qubit 1X dsDNA HS Assay kit, and library size on the Agilent 4200 TapeStation (Agilent Technologies) with the Agilent HS D1000 ScreenTape.  Multiplexed libraries were pooled and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 1x75bp sequencing at 50M reads/sample. Bulk RNA-se2q for IVD: RNA integrity was analyzed on the 2100 Bioanalyzer using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) and RNA quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).  Library construction was performed using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit (Takara Bio USA, Inc., Mountain View, CA).  Three ng of total RNA was used for library construction with 13 cycles of PCR amplification.  Final libraries were quantified via the Qubit 1X dsDNA HS Assay kit and analyzed for size on the 4200 TapeStation (Agilent Technologies) with the Agilent HS D1000 ScreenTape.  Multiplexed libraries were pooled and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 1x75bp sequencing at 50M reads/sample.

value: Nucleus Pulposus

value: Needle injury


title: pronephric duct, ctrl morpholino injected, 30hpf, rep7

description: TGGAACAA


title: pronephric duct, ctrl morpholino injected, 30hpf, rep4

description: AATCCGTC


title: Lv_NC_2

city: Jinan

first: Kailiang

last: Zhang

state: Shandong

address: 25 Shifan Raod

institute: the 960th Hospital of Joint Logistic Support Force

description:
Library name: Sample 5
Column name in gene_count.csv: Lv_NC_2

data_processing:
Analysis workflow established on a local server v 1.1
Assembly: hg38
Supplementary files format and content: comma-delimited csv file includes raw countsfor each Sample
Supplementary files format and content: txt file includes FPKM values for each Sample

source_name: Osteosarcoma

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen)
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA;

value: Osteosarcoma

value: osteosarcoma cell line

value: NC


title: pronephric duct, ctrl morpholino injected, 30hpf, rep3

description: AAGGACAC

value: pronephric duct


title: Lv_NC_1

description:
Library name: Sample 4
Column name in gene_count.csv: Lv_NC_1


title: 23P35 Injured scRNA-seq

description: Library name: 23P35 Injured


title: 23P36 Healthy scRNA-seq

description: Library name: 23P36 Healthy

value: Non-injured


title: Lv_LINC00673_3

description:
Library name: Sample 3
Column name in gene_count.csv: Lv_LINC00673_3


title: pronephric duct, ctrl morpholino injected, 30hpf, rep5

description: TCTTCACA


title: pronephric duct, ctrl morpholino injected, 30hpf, rep2

description: AAGAGATC


title: ckit 8k_2 Rloop

description: ckit 8k_2

value: ckit + cells

value: CD117 enrichment


title: mycelium - PatL_KO_MEA - rep6

value: MEA


title: CART_Day12_2

description: Library name: 16_Sample16_new


title: 23P35 Healthy scRNA-seq

description: Library name: 23P35 Healthy


title: Lv_LINC00673_2

description:
Library name: Sample 2
Column name in gene_count.csv: Lv_LINC00673_2


title: CART_Day7_5

description: Library name: 14_Sample14_new


title: pronephric duct, ctrl morpholino injected, 30hpf, rep1

description: AACTCACC

value: WT


title: Lv_LINC00673_1

description:
Library name: Sample 1
Column name in gene_count.csv: Lv_LINC00673_1


title: Lv_NC_3

description:
Library name: Sample 6
Column name in gene_count.csv: Lv_NC_3


title: CART_Day7_4

description: Library name: 13_Sample13_new

value: lung


title: 22P70 Injured scRNA-seq

description: Library name: 22P70 Injured


title: CART_Day12_1

description: Library name: 15_Sample15_new

value: lung adenocarcinoma


title: Facial nerve tissue, Itrans_1

city: Kunming

first: Yu

last: Liu

address: No.295 Xichang Rd

institute: Affiliated Stomatology Hospital of Kunming Medical University

description:
Library name: Sample 4
Counts_Facial nerve tissue, Itrans_1

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomaticl1l. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
Assembly: OryCun2.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Oryctolagus cuniculus

source_name: facial nerve

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

value: facial nerve

value: Wild Type

value: Facial nerve transection injury and implantation of I-125 seed


title: Facial nerve tissue, ctrl_3

description:
Library name: Sample 3
Counts_Facial nerve tissue, ctrl_3

value: Facial nerve transection injury


title: CART_Day7_3

description: Library name: 12_Sample12_new

value: Female

value: 8-10 weeks old


title: Facial nerve tissue, Itrans_2

description:
Library name: Sample 5
Counts_Facial nerve tissue, Itrans_2


title: ETM E18 Whole Brain 3

first: Zixuan

last: Fan

address: No. 2 Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

description: Library name: ETM_E18_Whole Brain_3

data_processing:
Raw reads were quality checked using Fastp.
Adapter sequences and low-quality reads were trimmed usingFastp.
Clean reads were aligned to the Gallus gallus reference genome (GRCg7b)
Gene-level quantification was performed using featureCounts (Subread v2.0.6).
Differential gene expression analysis was conducted using DESeq2 v3.5.0 in R.
Assembly: Gallus gallus genome assembly GRCg7b (Ensembl release 110)
Supplementary files format and content: TXT (tab-delimited): raw gene counts; TXT: normalized expression values (FPKM/counts).

organism: Gallus gallus

source_name: Embryonic day 18, ETM treated

growth_protocol: Fresh fertilized eggs of White leghorn chicken were incubated at 37.8 °C with 60% relative humidity under standard conditions until embryonic day 18 (ED18).

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, Cat# 15596018CN) according to the manufacturer's instructions.
RNA libraries were prepared using the Fast RNA-seq Lib Prep Kit V2.

treatment_protocol: Control group (CT) embryos were incubated under standard conditions without intervention.ETM group embryos were exposed to elevated temperature (39.5 °C) from ED 13 to 18 and otherwise maintained under control conditions.

value: whole brain

value: ETM

tag: batch


title: Facial nerve tissue, Itrans_3

description:
Library name: Sample 6
Counts_Facial nerve tissue, Itrans_3


title: Facial nerve tissue, ctrl_1

description:
Library name: Sample 1
Counts_Facial nerve tissue, ctrl_1


title: Input_ctrl,TCDD

city: Stanford

first: Juyong

middle: Brian

last: Kim

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Quality control of ChIP-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ChIP-seq reads were aligned to the hg19 genome assembly using BWA mem version 0.7.17-r1188 with the default configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: BED6+4

source_name: human coronary arterysmooth muscle cell

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Libraries were prepared with KAPA Hyper Prep kit (KK8502) per standrad instruction.

treatment_protocol: cells were treated or not treated with 10nM TCDD for 24 hours.

tag: chip antibody

value: human coronary arterysmooth muscle cell

value: Dioxin


title: Facial nerve tissue, ctrl_2

description:
Library name: Sample 2
Counts_Facial nerve tissue, ctrl_2


title: CART_Day7_2

description: Library name: 11_Sample11_new


title: CART_Day7_1

description: Library name: 10_Sample10_new


data_processing:
all sequence data reads were aligned to the GRCz11 reference genome using Bowtie2 with the parameters “-N 0 -X 2000 --no-mixed --no-unal --no-discordant” after trimming with trim-galore with the parameters “--length 20 --paired -q 20 --trim-n” and quality control by using FastQC.
Signal tracks for each sample were generated using the deepTools bamCoverage function with normalization to RPKM (Reads Per Kilobase Million). The results (bigWig files) are shown in the track view generated with Integrative Genomics Viewer (IGV).
To check the reproducibility of the CUT&RUN and ATAC experiments, we calculated the Pearson correlation coefficients and Principle Components Analysis of the ctrl and actl6a morphants signals between biological replicates in the merged peaks.
The peaks of ctrl and morphants were called with MACS2 with the parameter “-g 1.35e9 –nomodel -q 1e-5”.
Assembly: GRCz11
Supplementary files format and content: bedGraph, bed

growth_protocol: Zebrafish (transgenic Na, K-ATPase alpha1A4:GFP line that GFP is highly expressed in pronephric epithelia) were maintained and bred according to the standard condition. Zebrafish embryos for injection were obtained from natural mating and cultured at 28.5 °C.

extract_protocol:
For isolation of pronephros ducts, 30 hpf. Fifteen zebrafish embryos were incubated in 10 mmol/ml DTT in egg water for 1 hour at room temperature. They were then incubated at 37 °C in 5 mg/ml collagenase I in DMEM/F12 and triturated gently five times with a 1000 μl pipette tip every 10 minutes until the end of 30 minutes of incubation. The larvae were then put in DMEM/F12, so that the disintegrated, approximately 10 pronephric duct fragments were collected by visual identification according to the GFP fluorescence and dissociated into single cells.
10000-20000 viable cells per sample was resuspended for library construction. The Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, China ) was used to prepare an ATAC-seq library following the manufacturer's suggested procedures.

treatment_protocol: Antisense morpholinos (MOs) were used to block the translation of actl6a, and a standard control MO was used as the negative control. All MOs were injected into embryos (transgenic Na, K-ATPase alpha1A4:GFP line) at the 1-cell stage.

value: pronephric duct

value: actl6a knockdown

value: actl6a morpholino injected


title: 22P70 Healthy scRNA-seq

description: Library name: 22P70 Healthy

value: Nucleus Pulposus

value: Non-injured


title: actl6a morphant, Smarca4a, FitCUT&RUN, rep5

source_name: Whole embryo

growth_protocol: Zebrafish were maintained and bred according to the standard condition. Zebrafish embryos for injection were obtained from natural mating and cultured at 28.5 °C.

extract_protocol:
To prepare samples for use with the FitCUT&RUN approach, the embryos at 30hpf were collected according to time after co-injection. For isolation of whole embryos cells, five zebrafish embryos were incubated in 10 mmol/ml DTT in egg water for 1 hour at room temperature. They were then incubated at 37 °C in lysis solution and triturated gently five times with a 1000 μl pipette tip every 10 minutes until the end of 30 minutes of incubation. Finaly,The larvae were dissociated into single cells and then put in stop solution. Approximately 200000 viable cells per sample was resuspended for library construction.
For FitCUT&RUN, the antibody incubation step was skipped, and the libraries were amplified from purified DNA using a Hyper Prep kits (KAPA Biosystems KK8504, USA). Finally, the libraries were sequenced by the Illumina Novaseq.
FitCUT&RUN

treatment_protocol: Antisense morpholinos (MOs) were used to block the translation of actl6a, and a standard control MO was used as the negative control. For mRNA injection, C-terminal rFc-tagged Smarca4a mRNA was transcribed in vitro. All MOs and mRNA were co-injected into embryos at the 1-cell stage.

value: Whole embryo

value: actl6a morpholino and Smarca4a-rFc mRNA injected


title: Input_ctrl,DMSO

value: DMSO


title: TCF21_ab,TCDD,ChIP

value: TCF21,HPA013189, Sigma


value: WT

value: ctrl morpholino injected


title: ETM E18 Whole Brain 2

description: Library name: ETM_E18_Whole Brain_2


title: CT E18 Whole Brain 3

description: Library name: CT_E18_Whole Brain_3

source_name: Embryonic day 18, control group

value: CT


title: actl6a morphant, Smarca4a, FitCUT&RUN, rep4


title: actl6a morphant, Smarca4a, FitCUT&RUN, rep3


title: ETM E18 Hypothalamus 3

description: Library name: ETM_E18_Hypothalamus_3

value: hypothalamus


title: AHR_ab,DMSO,ChIP

value: AHR,Santa Cruz, sc-5579


title: AHR_ab,TCDD,ChIP


title: TCF21_ab,DMSO,ChIP


title: TCDD treated, batch2, rep1,RNA

data_processing:
First, the fastqs were trimmed  by cutadapt to remove adaptor sequences. For unstranded samples, reads were aligned to GRCh38 reference genome with STAR and the alignments were assigned to  GENCODE reference annotation gencode.v25 by featureCounts,
DEseq2 were used for gene-level qutification and differential genes discovery.
Assembly: hg19
Supplementary files format and content: tab-delimiteed text files include raw counts for each sample

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kits (Qiagen, #74034).
RNA integrity was determined via bioanalyzer (Agilent) using standard RNA 6000 Pico chip. The libraries of samples for unstranded sequencing were constrcuted by TruSeq RNA Library Prep Kit and sequenced. Samples for stranded sequencing underwent ribosomal depletion, strand-specific library (dUTP method) synthesis followed by deep sequencing on NovaSeq 6000 platform.


title: CART_Day2_4

description: Library name: 9_Sample9_new

value: lung

value: lung adenocarcinoma

value: Female

value: 8-10 weeks old


title: CT E18 Whole Brain 1

description: Library name: CT_E18_Whole Brain_1

value: whole brain


title: TCDD treated, batch2, rep2,RNA

value: human coronary arterysmooth muscle cell

value: Dioxin


title: CT E18 Whole Brain 2

description: Library name: CT_E18_Whole Brain_2


title: CART_Day2_3

description: Library name: 8_Sample8_new


title: CART_Day2_1

description: Library name: 6_Sample6_new


title: CART_Day2_2

description: Library name: 7_Sample7_new


title: Untreated_Day0_4

description: Library name: 4_Sample4_new


title: Untreated_Day0_5

description: Library name: 5_Sample5_new


title: wildtype zebrafish, Smarca4a, FitCUT&RUN, rep5

value: ctrl morpholino and Smarca4a-rFc mRNA injected


title: TCDD treated, batch1, rep2,RNA


title: CT E18 Hypothalamus 3

description: Library name: CT_E18_Hypothalamus_3


title: Untreated_Day0_3

description: Library name: 3_Sample3_new


title: ETM E18 Hypothalamus 2

description: Library name: ETM_E18_Hypothalamus_2

value: ETM


title: ETM E18 Hypothalamus 1

description: Library name: ETM_E18_Hypothalamus_1


title: ETM E18 Whole Brain 1

description: Library name: ETM_E18_Whole Brain_1


title: actl6a morphant, Smarca4a, FitCUT&RUN, rep1

value: Whole embryo

value: actl6a knockdown

value: actl6a morpholino and Smarca4a-rFc mRNA injected


title: actl6a morphant, Smarca4a, FitCUT&RUN, rep2


title: TCDD treated, batch1, rep1,RNA


title: wildtype zebrafish, Smarca4a, FitCUT&RUN, rep4

value: WT


title: DMSO ctrl for TCDD, batch2, rep2,RNA

value: DMSO


title: DMSO ctrl for TCDD, batch2, rep1,RNA


title: Untreated_Day0_1

description: Library name: 1_Sample1_new


title: CT E18 Hypothalamus 1

description: Library name: CT_E18_Hypothalamus_1

value: CT


title: Wild type round spermatids_rep3

first: Yuling

last: Cai

address: Qianfoshan Street

department: CCenter of reproductive medicine

institute: Shandong University

description: Library name: Sample 6

data_processing:
Adaptor sequences were removed from the reads using Trim Galore (https://github.com/FelixKrueger/TrimGalore/releases). The trimmed reads were then aligned to the reference genome with HISAT2 (http://github.com/infphilo/hisat2). with standard parameters. SAMtools 1.1671 was used to convert the comparison files into bam format, and Picard (http://broadinstitute.github.io/picard/) was used to delete the duplicates generated by PCR of the above file to obtain clean reads. All peak calling was performed using model-based analysis of chip-seq (MACS2). To identify enriched regions from biologically replicated samples in SKO ATAC-seq, we used the Irreproducible Discovery Rate (IDR) method (https://github.com/nboley/idr), where the parameter setting of MACS2 should not be too strict to identify more peaks. Following this method, peak calling was performed using MACS2 with relaxed conditions (--shift −100 --extsize 200 --nomodel -B --SPMR -g mm) on each of the two replicates of the pooled dataset. IDR analysis was then performed, and reproducibility was checked. To obtain the final peak sets, the data were sorted by -log10 (p value). The threshold recommended by the authors was used. The peaks were annotated and visualized using the R package ChIPseeker. R package DiffBind was used to find the difference in peaks between the SKO and control groups, false discovery rate (FDR) ≤ 0.01. Motif calling was performed using the Homer command annotate Peaks and Homer command find Motifs Genome (http://homer.ucsd.edu/homer/motif/) with parameter “-size 200 and -len 8, 10, and 12”.
Assembly: mm10
Supplementary files format and content: Genome-wide signal tracks representing normalized ATAC-seq read coverage, typically used for visualization in genome browsers such as IGV or UCSC. The values reflect chromatin accessibility across the genome, processed from aligned BAM files using deepTools or a similar tool.

source_name: testis

extract_protocol:
Round spermatids were sorted by FCAS from three mice in each of the control and SKO groups. ATAC-seq was performed following the manufacturer's instructions (Vazyme, TD711). The library preparations were sequenced on an Illumina HiSeq platform and 150 bp paired-end reads were generated.
Round spermatids were sorted by FCAS from three mice in each of the control and SKO groups. ATAC-seq was performed following the manufacturer's instructions (Vazyme, TD711). The library preparations were sequenced on an Illumina HiSeq platform and 150 bp paired-end reads were generated.

value: testis

tag: cell type

value: Round spermatids

value: Wild type


title: Wild type  round spermatids_rep2

description: Library name: Sample 5

tag: tissue


title: CT E18 Hypothalamus 2

description: Library name: CT_E18_Hypothalamus_2

value: hypothalamus


title: ralp1-S-knockdown-rep1

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

description: Library name: sample7

data_processing:
RNA-seq reads were trimmed by trim-galore.
The resulting data was aligned to genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Using Picard, PCR duplicates were removed from the sequencing data.
Read counts  were obtained using FeatureCounts. The BAM alignment files were processed with bamCoverage to generate BigWig coverage files.
Assembly: Pf 3D7 v64
Supplementary files format and content: FPKM values for all Plasmodium falciparum samples were compiled in an Excel file.

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
The RNA was extracted with the TransZol Up Plus RNA kit. 500ng of  total RNA was used  for the construction of sequencing libraries.
Libraries were constructed ollowing the manufacturer's protocols.

treatment_protocol: Parasites were tightly synchronized by percoll or sorbitol.

tag: developmental stage

value: schizont

value: protozoa

tag: genotype

value: knockdown


title: wildtype zebrafish, Smarca4a, FitCUT&RUN, rep3

tag: treatment


title: 7001_liver_sham_Male_52-U1

type: other

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

description: Xenium panels used: MMTPS + custom Q6VTXC

hyb_protocol: After RNase treatment to release the RNA strand, a polishing step was performed, followed by overnight probe hybridization utilizing Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10x Genomics, 1000725) of probes for 5001 genes and an additional custom panel of probes for 100 genes (design ID: Q6VTXC). Probes were subsequently ligated and underwent rolling circle amplification, generating multiple copies of the gene-specific barcode for each RNA target.

scan_protocol: Cell segmentation reagents were applied during a staining workflow to label nuclei, membranes, and cytoplasmic regions for automated morphology-based segmentation. The background was quenched using an auto-fluorescence mixture, and nuclei were counterstained with DAPI to aid in sample tracking and cell boundary segmentation (10x Genomics, CG000760, Rev C). Xenium slides were then loaded onto the 10X Xenium Analyzer instrument (10x Genomics, 1000481) for imaging and initial data processing following manufacturer’s instructions (10x Genomics, CG000584, Rev F). Fluorescently labeled oligos bind to the amplified DNA probes, and iterative rounds of probe hybridization, imaging, and stripping generated optical signatures for each barcode, which were decoded to gene identities.

data_processing:
Nuclear segmentation and transcript assignment was performed on the Xenium instrument using Xenium's proprietary DAPI-based algorithm. In mouse samples Xenium's multimodal segmentation was used, in which three different markers were tested to determine the optimal method for cell segmentation. The best approach, as determined by a proprietary algorithm, combined markers for cell boundaries (epithelial markers : ATP1A1, E-Cadherin and pan-lymphocyte marker: CD45), cell interiors (18S rRNA), and nuclear expansion (DAPI). Segmentation quality was assessed using Xenium Q-Scores. Output files generated by the Xenium instrument were subsequently converted into HDF5, MEX, parquet, and CSV formats using Cell Ranger for downstream off-instrument analysis
Raw matrices represent individual transcript counts per gene per cell

molecule: other

source_name: Liver from Sham cohort at 52 wks

extract_protocol: Formalin-fixed paraffin-embedded (FFPE) blocks of interest were identified and screened by performing hematoxylin and eosin (H&E) staining. FFPE passed screening were sectioned at 5 µm and mounted onto Xenium slides following a modified version of the FFPE Tissue Preparation Guide (10x Genomics, CG000578, Rev D). Slides were deparaffinized with sequential xylene and ethanol washes, followed by decrosslinking using the FFPE Tissue Enhancer and diluted Perm Enzyme B (10x Genomics, CG000580, Rev E).

treatment_protocol: All animal studies were approved by Washington University in St. Louis Institutional Animal Care and Use Committee protocol  #(23-0421). All experiments were performed in accordance with relevant guidelines and regulations, including the ARRIVE guidelines (https://arriveguidelines.org/). 8-week-old male C57BL/6J mice (purchased from The Jackson Laboratory; Bar Harbor, ME) received sham or 75% proximal small bowel resection (SBR). Mice were randomized into 2-, 5-, 10-, 26-, and 52-week cohorts. The sham operation involves a transection of the small bowel 6 cm proximal to the cecum with primary end-to-end anastomosis with 9-0 nylon sutures placed in an interrupted fashion. For the 75% SBR operations, the small bowel is transected at two points: 1-2cm distal to the ligament of Treitz and 6cm proximal to the cecum. The intervening mesentery is tied off and the small bowel is resected. An end-to-end primary anastomosis is completed with 9-0 nylon sutures placed in an interrupted fashion. Postoperative care included no food for 24 hours and 1 week of incubator housing. All mice were fed a liquid enteral diet (LD101 #0007551, Test Diet; Richmond, IN) ad lib.

value: Liver

tag: Sex

value: Male

tag: cohort

value: sham

tag: timepoint (weeks)


title: wildtype zebrafish, Smarca4a, FitCUT&RUN, rep2

value: ctrl morpholino and Smarca4a-rFc mRNA injected


title: DMSO ctrl for TCDD, batch1, rep1,RNA

value: human coronary arterysmooth muscle cell


title: ralp1-S-knockdown-rep2

description: Library name: sample8


title: wildtype zebrafish, Smarca4a, FitCUT&RUN, rep1

value: Whole embryo


title: 7239_liver_sbr_Male_52-U1

source_name: Liver from SBR cohort at 52 wks

value: sbr


title: Wild type round spermatids_rep1

description: Library name: Sample 4


title: ralp1-S-control-rep1

description: Library name: sample5

value: normal


title: 7248_liver_sham_Male_26-U1

source_name: Liver from Sham cohort at 26 wks


title: TCDD,ATAC

data_processing:
Quality control of ATAC-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ATAC-seq reads were aligned to the hg19 genome assembly using BOWTIE2  version 2.2.6 with the --local configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: BED6+4

extract_protocol:
Approximately 5e4 fresh cells were collected and nuclei-enriched fractions were extracted with cold resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin). Nuclei pellets were collected by centrifugation and resuspended with transposition reaction buffer containing Tn5 transposases (Illumina Nextera). Transposition reactions were incubated at 37 °C for 30 min, followed by DNA purification using the DNA Clean-up and Concentration kit (Zymo D4013).
Libraries were amplified using Nextera barcodes and High-Fidelity polymerase (NEB M0541S) and purified using Agencourt Ampure XP beads (Beckman Coulter A63880) double-side selection (0.5X:0.9X).

value: Dioxin


title: ralp1-R-knockdown-rep1

description: Library name: sample3

value: ring


title: Untreated_Day0_2

description: Library name: 2_Sample2_new

value: lung

value: lung adenocarcinoma

value: Female

tag: age

value: 8-10 weeks old


title: Patient4

city: Ningbo

first: Shibo

last: Wu

address: Ningbo Medical Center

institute: Department of Respiratory Medicine, Lihuili Hospital

description: 10x Genomics

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cancer tumor tissues

extract_protocol:
Surgically resected fresh tumor tissues from six patients were cut into pieces of approximately 1-3 mm³ . Then, the pieces were transferred to the gentle MACS C Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) for 60 min on a rotor at 37℃ according to the manufacturer’s instructions. After removing of red blood cells using erythrocyte lysis solution (Miltenyi Biotec, Bergisch Gladbach, Germany), the cells were filtered using a 40 µm strainer (BD Falcon, New York, USA). CD45+ cells were sorted by using the Human CD45 Microbeads Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
Cell suspensions (700-1200 living cells/μL determined by trypan blue staining) were loaded on a 10x Genomics ChromiumTM Single Cell Controller Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs) by using Chromium Single Cell 5' Library & Gel Bead Kit v1.0 (10x Genomics, Cat# 1000006) and Single Cell A Chip Kit (10x Genomics, Cat# 1000152). Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEM. Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Thermo Fisher, Cat# 37002D), and then amplified and cleanup for further next generation library construction.

value: cancer tumor tissues

tag: group

value: treatment-naive

value: All cells

tag: pathology

value: LUAD


title: OvSvK Day2 CUT&Tag-seq of Sox2 rep2

city: Guangzhou

first: Hui

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

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

description:
Library name: S3vFd2B2
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

data_processing:
Raw CUT&Tag reads were trimmed and ﬁltered for quality control using Trim Galore v0.6.7.
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2(v2.4.5)  with parameters  '--very-sensitive'.
PCR duplicates were removed with picard(v2.26.10).
For histone marks enriched in Narrow domains, the NarrowPeak  representation was used applying following settings : -f BAM --keepdup all -q 0.05 --bdg. For histone marks enriched in broad domains, the broadPeak representation was used applying following settings: -f BAM --keepdup all  -q 0.05 --broad --broad-cutoff 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: GSE222746
Library strategy: CUT&Tag

source_name: Mouse embryonic fibroblasts

growth_protocol: Cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were collected by trypsin digestion.
Libraries for CUT&Tag were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with different TF combinations or siRNA combinations.

tag: cell line

value: Mouse embryonic fibroblasts

value: reprgramming cells

value: OvSvK CUT&Tag seq of Sox2


title: 7239_tumor_sbr_Male_52-U1

source_name: benign tumor in liver from SBR cohort at 52 wks

value: Liver

value: Male


title: 7250_liver_sham_Male_26-U1

value: sham


title: 7260_liver_sbr_Male_26-U1

source_name: Liver from SBR cohort at 26 wks

value: sbr


title: ralp1-S-control-rep2

description: Library name: sample6

value: schizont

value: protozoa

value: normal


title: DMSO ctrl for TCDD, batch1, rep2,RNA

value: human coronary arterysmooth muscle cell

value: DMSO


title: Patient6

description: 10x Genomics


title: ralp1-R-knockdown-rep2

description: Library name: sample4

value: ring

value: knockdown


title: Patient2

description: 10x Genomics

value: cancer tumor tissues

value: EGFR-TKI resistance


title: DMSO,ATAC


title: Eif5a SKO round spermatids_rep2

description: Library name: Sample 2

value: testis

value: Round spermatids

value: Eif5a SKO


title: Rf-1_sIO_ShVl_2d_3

description:
Library name: Rf-1_sIO_ShVl_2d_3
TruSeq Stranded mRNA Kit

data_processing:
STAR aligner (version 2.7.11b)
RSEM (version 1.3.3)
Assembly: Greater horseshoe bat genome (R. ferrumequinum; GCF_004115265.2), Big brown bat (E. fuscus; GCF_027574615.1), MRV, Shaanvirus-like, IAV (human H1N1), MERS-CoV, and SeoV
Supplementary files format and content: tsv files

organism: Rhinolophus ferrumequinum

source_name: Small intestine organoid

extract_protocol:
Trizol LS reagent (Ambion)
TruSeq Stranded mRNA Kit (illumina)

value: Small intestine organoid


title: 7259_liver_sbr_Male_26-U1

value: Liver


title: Eif5a SKO round spermatids_rep1

description: Library name: Sample 1


title: OSK Day3 CUT&Tag-seq of Sox2 rep2

description:
Library name: S3Fd3B2
MEF infected with Oct4, Sox2, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: Mouse embryonic fibroblasts

value: reprgramming cells

value: OSK CUT&Tag seq of Sox2


title: Eif5a SKO round spermatids_rep3

description: Library name: Sample 3


title: 7435_liver_sham_Male_10-U1

source_name: Liver from Sham cohort at 10 wks

value: Male

value: sham


title: ralp1-R-control-rep1

description: Library name: sample1

value: protozoa

value: normal


title: Patient5

description: 10x Genomics

value: treatment-naive

value: All cells

value: LUAD


title: ralp1-R-control-rep2

description: Library name: sample2

value: ring


title: mycelium - WT_MEA - rep1

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 084703_D_F_20170227). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}. We firstly selected control probes and probes targeting Penicillium expansum transcripts (GeneNames begining by 'PEX1_') giving a dataset with 31803 entries. We next selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 28179 spots were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 9947 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: mycelium

extract_protocol: Total RNA was isolated at the end of the growth period. The mycelium was transferred to lysing matrix D tubes (1.4 mm ceramic spheres), to which 760 µL of lysis buffer (10 μL of β-mercaptoethanol and 750 μL of RLT buffer) were added, and the tubes were placed in liquid nitrogen. The mycelium cells were broken down in a Precellys homogenizer with three grindings at a speed of 6,500 rpm for 15 s followed by 5 min incubation on ice, at 6,500 rpm for 25 s and 5 min on ice, and a final 6,500 rpm for 15 s. The samples were subsequently centrifuged at 16,000 g at 4 °C for 10 min. The supernatant was recovered in QIAshredder spin columns (QIAGEN) and the total RNA was purified using RNeasy spin minicolumns (QIAGEN).

value: WT

tag: medium

value: MEA


title: hepG2-S4-rep3-rna

city: Minneapolis

first: Quinn

last: Dickinson

state: MN

address: 100 Church Street SE

institute: University of Minnesota

description: Library name: S4-3-rna

data_processing:
For repliseq data reads were trimmed with cutadapt and aligned with bwa
Alignments were filtered and duplicates removed with samtools
reads were counted within genomic bins of 50kb to create final bedgraphs
For RNA data reads were trimmed with trimmomatic and aligned with HISAT2
alignments were filtered and counts calculated with SAMtools.
TPM was calculated from raw counts in python
Assembly: hg38
Supplementary files format and content: G1-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G1-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G1-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: bulk-r1-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: bulk-r2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: bulk-r3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G1-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G1-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G2-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G2-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S1-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S1-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S2-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S2-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S3-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S3-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S4-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S4-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id

extract_protocol:
DNA samples were processed using the optimized Repli-seq protocol as previously described (Rivera-Mulia et al., 2022). Briefly, purified DNA from sorted cells was directly processed using the KAPA HyperPlus library preparation kit (Roche Cat. No. 07958978001) according to the manufacturer instructions. PARTAGE RNA-seq: RNA samples were processed using the SMARTer Stranded Total RNA-Seq ultra-low inputs (Takara Cat. No. 634411) according to the manufacturer instructions. Bulk RNA samples were isolated from 0.5 million HepG2 cells using the RNeasy Plus Kit (Qiagen 74004)
Libraries were purified using the Zymo DNA Clean & Concentrator-5 kit and processed for BrdU-IP. Immunoprecipitated libraries were amplified using the KAPA HiFi HotStart from the KAPA HyperPlus kit according to the manufacturer instructions. Repli-seq libraries were sequenced on the Illumina NextSeq P2 platform at ~ 8 M reads per library and 100 bp of single-end sequencing. PARTAGE RNA-seq libraries were sequenced on the Illumina NovaSeqX platform at  ~ 40 M reads per library and 150 bp of pair-end sequencing. Bulk rna libraries were prepared with the TruSeq Stranded mRNA Library Prep (Illumina) according to the manufacturer instructions. Standard RNA-seq libraries were sequenced on the Illumina NovaSeq platform at  ~ 20 M reads per library and 150 bp of pair-end sequencing”


title: OvSvK Day2 CUT&Tag-seq of Oct4 rep2

description:
Library name: O3vFd2B2
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: OvSvK CUT&Tag seq of Oct4


title: 7352_liver_sham_Male_2-U1

source_name: Liver from SBR cohort at 2 wks


title: OvSvK Day2 CUT&Tag-seq of Oct4 rep1

description:
Library name: O3vFd2
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming


title: Patient3

description: 10x Genomics

value: cancer tumor tissues

value: EGFR-TKI resistance


title: Rf-1_sIO_ShVl_1d_2

first: Dongbin

address: 55, Expo-ro

institute: Institute for Basic Science

description:
Library name: Rf-1_sIO_ShVl_1d_2
TruSeq Stranded mRNA Kit

value: Small intestine organoid


title: OSK Day3 CUT&Tag-seq of Sox2 rep1

description:
Library name: S3Fd3
MEF infected with Oct4, Sox2, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: Mouse embryonic fibroblasts


title: Rf-1_sIO_ShVl_2d_2

description:
Library name: Rf-1_sIO_ShVl_2d_2
TruSeq Stranded mRNA Kit


title: hepG2-S3-rep2-rna

description: Library name: S3-2-rna


title: Rf-1_sIO_ShVl_1d_1

description:
Library name: Rf-1_sIO_ShVl_1d_1
TruSeq Stranded mRNA Kit


title: 7450_liver_sbr_Male_10-U1

source_name: Liver from SBR cohort at 10 wks

value: Liver

value: sbr


title: 7448_liver_sbr_Male_10-U1

value: Male


title: OvSvK Day2 CUT&Tag-seq of H3K27ac rep2

description:
Library name: B3vFAcB2
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: reprgramming cells

value: OvSvK CUT&Tag seq of H3K27ac