title: sc V(D)J-seq of BCR in mouse29_lung

description: Library name: mouse29_lung_BCR

source_name: white nodules in lung

value: white nodules in lung

value: 12 months


status: Public on May 01 2026

type: SRA

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 120 South Road

country: USA

institute: University of North Carolina

description:
Library name: B1+veh
Wild-type callus line B1 treated with vehicle control

library_source: transcriptomic

data_processing:
For transcript quantification, raw sequencing reads were pseudo-aligned to the Oryza sativa Japonica reference transcriptome (IRGSP-1.0, ENA Assembly GCA_001433935.1) using Kallisto v0.46.1. Transcript-level abundance estimates (TPM and estimated counts) were generated using default parameters.
Assembly: IRGSP-1.0 (GCA_001433935.1)
Supplementary files format and content: Each processed data file is a tab-delimited text file with five columns: target_id (transcript identifier), length (transcript length in nucleotides), eff_length (effective transcript length used in abundance estimation), est_counts (estimated number of reads assigned to each transcript), and tpm (transcripts per million, a normalized expression estimate).

molecule: total RNA

organism: Oryza sativa

source_name: callus

growth_protocol: Callus was cultured from seeds. Seeds were dehusked, rinsed in 70% ethanol for 1 minute, rinsed with sterile deionized water, and  sterilized for 30 minutes in 50% bleach. After five rinses with sterile deionized water, seeds were placed on plates containing Initiation medium and incubated at 29°C under a 16 h light / 8 h dark cycle. Callus was cut from the seeds and sub-cultured onto fresh Initiation medium every 2-3 weeks.

extract_protocol:
Tissue was flash frozen in liquid nitrogen and then ground with a mortar and pestle. RNA was extracted from the ground tissue with RNAzol (Sigma, R4533). RNA quantity and quality was assessed using the Agilent 4200 Tapestation System (Agilent, G2991BA).
RNA-seq library preparation was performed by Innomics (Sunnyvale, CA, USA). Total RNA was enriched for mRNA using oligo(dT) beads, followed by fragmentation and first and second strand cDNA synthesis. Second strand synthesis incorporated dUTP to enable strand specificity. After end-repair and 3′ adenylation, adaptors were ligated, and libraries were PCR-amplified. Libraries were quality checked, circularized, and amplified into DNA nanoballs (DNBs) for sequencing. Sequencing was performed on a DNBSEQ-T7 platform (MGI Technology).

treatment_protocol: Tissue was incubated in Kimura B nutrient solution supplemented with either 5 μM BA or vehicle control for 1 hour, shaking.

tag: cultivar

value: Kitaake

tag: tissue

value: callus

tag: genotype

value: wild-type

tag: treatment

value: vehicle control


title: snail1_36h_1

city: shanghai

first: jing

last: chen

state: shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai

country: China

institute: shanghaitech university

description: Library name: sample10

data_processing:
Raw sequencing data were processed using FastQC for quality control.
Adapters were trimmed and low-quality bases removed using Cutadapt (v1.9.1).
Reads were aligned to the mouse reference genome (GRCm39.107) using HISAT2 (v2.2.1).
Gene expression levels were quantified using HTSeq and normalized to TPM values.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm39.107 (Mus musculus).
Supplementary files format and content: Processed data files are in CSV format and contain TPM values for each gene across all samples.

organism: Mus musculus

source_name: mammary gland

growth_protocol: Control or  Snail1 KD HC11 cells were sorted by flow cytometry and then cultured overnight in  RPMI 1640 with 2% FBS, 10 ng/ml EGF, 5 μg/ml insulin,1% L-Ala-Gln, and 1% P/S to facilitate aggregation.

extract_protocol:
Total RNA was extracted using either the Micro RNA extraction kit(Magen, R4125).
RNA libraries for RNA-seq were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (San Diego, CA)  according to the manufacturer’s protocols

treatment_protocol: In vitro migration assays were conducted on HC11 aggregates with either control or Snail1 knockdown (KD). Samples were collected at 0 hours and 36 hours for RNA extraction.

value: mammary gland

tag: cell line

tag: cell type

value: mammary epithelial cells

value: Snail1 KD


title: snail1_36h_3

description: Library name: sample12


title: snail1_36h_2

description: Library name: sample11


title: snail1_0h_3

description: Library name: sample9

value: migration 0h


title: scRNA-seq of mouse29_lung

city: xiamen

first: Lianghua

last: Lin

state: Fujian

address: Xiang An Nan Lu 4221

institute: 生命科学学院

description: Library name: mouse29_lung

library_source: transcriptomic single cell

data_processing:
SeekSoul Tools was used to process raw sequencing data. Reads were aligned to the mouse reference genome (GRCm38/mm10) and gene expression matrices were generated. Cells were filtered using default cell calling algorithms to obtain the final filtered feature-barcode matrices.
Raw sequencing data were processed using the SeekSoul® Tools vdj (v1.2.1) to assemble full-length V(D)J sequences and identify CDR3 regions. Using barcode and raw clonotype ID information, productive clonotypes were filtered. Processed FASTA sequences were further annotated using IMGT database.
Assembly: mm10
Supplementary files format and content: Filtered gene-barcode matrix in MEX format, provided as three separate files per sample: barcodes.tsv.gz (cell barcodes passing filtering), features.tsv.gz (gene identifiers and names), and matrix.mtx.gz (sparse UMI count matrix). The matrix contains only cells that passed the default cell calling filters from the SeekSoul pipeline.
Supplementary files format and content: filtered_contig_annotations.csv contains high-confidence V(D)J contig annotations for each cell barcode. This file includes information such as chain type (IGH, IGK, IGL for BCR), V/D/J gene calls, CDR3 nucleotide and amino acid sequences, and productive status.

growth_protocol: Mice were euthanized for analysis upon observation of poor condition or obvious visible enlargement.

extract_protocol:
The harvested white nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation. The nodules were washed in ice-cold PBS, and dissociated using SeekMate Tissue Dissociation Reagent Kit A Pro or SeekMate Tissue Dissociation Kit C from SeekGene following the manufacturer’s instructions. Samples were treated with DNase I and analyzed by Fluorescence Cell Analyzer or SeekMate Tinitan Fluorescence Cell Counter with AO/PI reagent after lysis of erythrocytes to measure cell counts and viability. Dead cells and debris were removed using Dead Cell Removal Kit. Cells were then washed twice with RPMI1640 and resuspended in RPMI1640 with 2% FBS at 1×106 cells per mL for further sorting or single cell sequencing library construction.
Single-cell V(D)J-seq libraries were constructed using SeekOne® DD Single Cell 5’ library preparation kit and SeekOne® DD Single Cell V(D)J Enrichment Kit (human TCR&BCR, SeekGene, Catalog No. K00601&K00701) or (mouse TCR&BCR, SeekGene, Catalog No. K01101&K01201) following the manufacturer’s instructions. The indexed sequencing libraries were cleaned up with VAHTS DNA Clean Beads (Vazyme, N411-01) and analyzed by Qubit (Thermo Fisher Scientific, Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400).

value: total cells in white nodules

value: The nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation and then dead cell removal

tag: age


title: 24005

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

description: Library name: Sample 103

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

value: whole blood

value: SLE


description:
Library name: A1+veh
Wild-type callus line A1 treated with vehicle control


description:
Library name: A1+BA
Wild-type callus line A1 treated with BA

value: 5 μM BA


title: 23802

description: Library name: Sample 101


title: snail1_0h_1

description: Library name: sample7


description:
Library name: 54b+veh
hk3,4,5,6 callus line 54b treated with vehicle control


title: snail1_0h_2

description: Library name: sample8


title: 23701

description: Library name: Sample 100


title: mix_scr_36h_4

description: Library name: sample6

value: WT


title: 23903

description: Library name: Sample 102


title: scr_36h_3

description: Library name: sample5


description:
Library name: 54b+BA
hk3,4,5,6 callus line 54b treated with BA


description:
Library name: 54a+BA
hk3,4,5,6 callus line 54a treated with BA


description:
Library name: 54a+veh
hk3,4,5,6 callus line 54a treated with vehicle control


title: 23206

description: Library name: Sample 98


title: 23217

description: Library name: Sample 99


title: control repeat2,sorted iGCB day3 YFP+ cells

description: Library name: d3_cgWT2

data_processing:
The clean data, with adapter sequences trimmed and low-quality reads removed, was used for downstream analysis. The clean data was processed to read counts following the Hisat2-StringTie pipeline58. Using prepDE.py provided by StringTie, read count information was extracted for differential analysis conducted by DESeq259.
Assembly: mm10
Supplementary files format and content: iGCBD3_rna_gene_count_matrix.csv contains raw gene count matrix for all samples, with genes as rows and samples as columns. This file can be used for downstream differential expression analysis.The iGCBD3_transcript_count_matrix.csv which is transcript-level matrix has transcripts as rows and samples as columns, with values representing raw read counts per transcript.

source_name: spleen

growth_protocol: Naïve B cells were cultured in 6- or 12-well plates (Thermo Fisher Scientific) for 4 days with 40LB cells irradiated with 120 Gy in the presence of IL-4, in 1640 complete medium supplemented with 10% FBS, 5.5×10-5 M β-mercaptoethanol (2-ME), 10 mM HEPES, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin (GIBCO), 1× NEAA (Gibco) and 1 ng/mL IL-4 (Noveprotein, CK74)24.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) following the manufacturer’s instructions. RNA samples were sent to Novogene for sequencing.
RNA integrity and concentration were assessed using Agilent 2100 Bioanalyzer. mRNA was enriched using Oligo(dT) magnetic beads, then fragmented randomly in NEB Fragmentation Buffer. First-strand cDNA was synthesized using random hexamer primers and M-MuLV reverse transcriptase. Second-strand cDNA synthesis was performed with dNTPs (dTTP replaced by dUTP for strand-specific libraries) using DNA polymerase I and RNase H. The double-stranded cDNA was purified, end-repaired, A-tailed, and ligated to Illumina sequencing adapters. cDNA fragments of 250-300 bp were selected with AMPure XP beads, followed by USER enzyme digestion (for strand-specific libraries) and PCR amplification. Libraries were qualified using Qubit 2.0 Fluorometer, Agilent 2100 Bioanalyzer for insert size validation, and qRT-PCR for accurate quantification. Sequencing was performed on Illumina platform.翻译

treatment_protocol: YFP+ iGCB cells were sorted on BD Aria FUSION (BD Biosciences)

value: spleen

value: igcb cells

value: control

value: Naïve B cells were cultured for 3 days with 40LB cells irradiated with 120 Gy in 1640 complete medium with IL4

tag: time

value: 3 days


title: control repeat3,sorted iGCB day3 YFP+ cells

description: Library name: d3_cgWT3


title: cKO repeat2,sorted iGCB day3 YFP+ cells

description: Library name: d3_3eKO2

value: eif3e ko


title: control repeat1,sorted iGCB day3 YFP+ cells

description: Library name: d3_cgWT1


title: scr_36h_1

description: Library name: sample4


title: cKO repeat1,sorted iGCB day3 YFP+ cells

description: Library name: d3_3eKO1


title: 23203

description: Library name: Sample 97


title: scr_0h_3

description: Library name: sample3


title: cKO repeat3,sorted iGCB day3 YFP+ cells

description: Library name: d3_3eKO3


title: 23122

description: Library name: Sample 95


title: 23125

description: Library name: Sample 96


title: FGF10-36h-4

description: Library name: FGF10-36h-4.bam

growth_protocol: Mammary gland organoids were cultured in DMEM/F12 with1% L-Ala-Gln,1% ITS and 1% P/S.

treatment_protocol: In vitro migration experiments were performed on mammary gland epithelial organoids and beads soaked in FGF10 or BSA in advance.Collect the migrated samples at 0 hours, 36 hours, and 72 hours for subsequent RNA extraction.


title: NF_31, primary rat hepatocytes, RH220314

city: Bochum

first: Eike

last: Steinmann

address: Universitätsstraße 150

department: Molecular and Medical Virology

country: Germany

institute: Ruhr University

description:
Library name: Sample 1
NF_31_MKRN250055377-1A_233LCMLT4_L4

data_processing:
Raw FASTQ sequencing reads were assessed for quality using FastQC (version 0.12.1; Andrews, 2010; FastQC: a quality control tool for high-throughput sequence data, available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc), followed by quality trimming using Trimmomatic. Low-quality bases and overrepresented sequences were removed. The trimmed reads were mapped to the brown rat (Rattus norvegicus) reference genome (mRatBN7.2; GCF_015227675.2) obtained from National Center for Biotechnology Information (NCBI. Mapping was performed using STAR version 2.7.11b 58. Optical duplicates were removed using Picard (Picard Toolkit, 2019; Broad Institute, GitHub Repository: https://broadinstitute.github.io/picard/). Gene level read counts were generated using FeatureCounts version 2.0.6 59, and the number of reads mapped to each gene in the reference genome was determined.
Unmapped reads from STAR were aligned to viral genomes using Burrows–Wheeler Aligner (BWA) version 0.7.18. These reads were mapped to the HEV strain Kernow-C1 (GenBank accession no.: HQ709170.1) and strain 83-2-27 (GenBank accession no.: AB740232.1). Alignment files were sorted and indexed, and coverage was calculated using Samtools version 1.21. Viral coverage plots were visualized in R using ggplot2.
Assembly: mRatBN7.2; GCF_015227675.2; HQ709170.1; AB740232.1
Supplementary files format and content: count_data.csv; raw count data

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA extraction was done using the NucleoSpin RNA kit (Macherey-Nagel)
The RNA sequencing of primary rat hepatocytes was done on the Illumina NovaSeq X Plus platform using the commercial service of Novogene (poly-A enrichment, paired-end 150 base pair reads mode, 20 million reads/sample). For cell line-derived samples, the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs) and the recommended related reagents were applied for library preparation according to the manufacturer´s instructions. The library was sequenced with P2 reagents (Illumina) on the Illumina NextSeq 1000 sequencing platform.

treatment_protocol: NITD008 (MedChemExpress) 0.5 μM; Baricitinib (MedChemExpress) 2 µM; 100 µl inoculum

value: liver

value: hepatocytes

value: no treatment

tag: batch


description:
Library name: 13+BA
hk3,4,5,6 callus line 13 treated with BA

value: Kitaake

value: callus


title: FGF10-36h-1

description: Library name: FGF10-36h-1.bam

value: mammary gland

value: mammary epithelial cells


title: scr_0h_2

description: Library name: sample2

value: migration 0h


title: scbatch2,control mice,sorted total splenocytes,2 month old

description: Library name: scbatch2_WT_total

data_processing:
SeekSoul Tools was used to process raw sequencing data. Reads were aligned to the mouse reference genome (GRCm38/mm10) and gene expression matrices were generated. Cells were filtered using default cell calling algorithms to obtain the final filtered feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Filtered gene-barcode matrix in MEX format, provided as three separate files per sample: barcodes.tsv.gz (cell barcodes passing filtering), features.tsv.gz (gene identifiers and names), and matrix.mtx.gz (sparse UMI count matrix). The matrix contains only cells that passed the default cell calling filters from the SeekSoul pipeline.
Supplementary files format and content: Supplementary file: DEGs_Eif3e_KO_vs_WT.xlsx contains the differential expression analysis results for all detected genes in each subcluster of CD4+ T cells, total B cells, and YFP+ B cells between cKO and control groups

extract_protocol:
The spleen and lymph nodes of 2-month-old control and cKO mice were harvested, washed in ice-cold PBS, and dissociated using SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene, K01801301) or SeekMate Tissue Dissociation Kit C (SeekGene, K01501) from SeekGene following the manufacturer’s instructions. Samples were treated with DNase I (Sigma, 9003-98-9) and analyzed by Fluorescence Cell Analyzer (Countstar® Rigel, S2) or SeekMate Tinitan Fluorescence Cell Counter (SeekGene, M002C) with AO/PI reagent after lysis of erythrocytes (Solarbio, R1010) to measure cell counts and viability. Cells were then washed twice with RPMI1640 (Gibco, 11875119) and resuspended in RPMI1640 with 2% FBS (Gibco, 10100147C) at 1×106 cells per mL for further sorting. Cells were sorted for total live cells or YFP+ cells on BD Aria III or BD Aria FUSION (BD Biosciences).
Single-cell RNA-seq libraries were prepared using SeekOne® DD Single Cell 3' library preparation kit following manufacturer's protocols.

treatment_protocol: Eif3e cg1cre conditional knockout mice and littermate controls were used. Spleens were collected from 2-month-old mice.

value: immune cells

value: sorted

value: 2 months


title: 23101

description: Library name: Sample 94

value: whole blood

value: SLE


title: scbatch2,cKO mice,sorted YFP+ cells,2 month old

description: Library name: scbatch2_KO_YFP

value: spleen


title: scbatch2,cKO mice,sorted total splenocytes,2 month old

description: Library name: scbatch2_KO_total


title: scbatch1,control mice,sorted YFP+ cells,2 month old

description: Library name: scbatch1_WT_YFP


title: scr_0h_1

description: Library name: sample1

value: WT


description:
Library name: 13+veh
hk3,4,5,6 callus line 13 treated with vehicle control

value: vehicle control


title: scbatch1,control mice,sorted total splenocytes,2 month old

description: Library name: scbatch1_WT_total


title: NF_32, primrary rat hepatocytes, RH190813

description:
Library name: Sample 2
NF_32_MKRN250055378-1A_233LCMLT4_L3


title: 23001

description: Library name: Sample 93


title: 19104

description: Library name: Sample 91


title: scbatch2,control mice,sorted YFP+ cells,2 month old

description: Library name: scbatch2_WT_YFP


title: FGF10-36h-3

description: Library name: FGF10-36h-3.bam


title: NF_33, primary rat hepatocytes, RH210219

description:
Library name: Sample 3
NF_33_MKRN250055379-1A_233LCMLT4_L3


title: 19208

description: Library name: Sample 92


title: Met1-iRFP TME cells (iRFP-), Exercise, rep10

city: Burnaby

first: Graeme

middle: J.

last: Koelwyn

state: BC

address: 8888 University Drive

department: Faculty of Health Sciences

country: Canada

institute: Simon Fraser University

description: Library name: SR10

data_processing:
For all samples, paired-end reads were mapped to the mm10 genome assembly using STAR with default parameters, except that all best alignments were retained by using the –outSAMprimaryFlag AllBestScore flag. Following alignment, reads were counted per gene using the featureCounts tool and the gencode vM18 annotation.
Assembly: mm10
Supplementary files format and content: txt file contains raw gene counts for each sample.

source_name: Met1-iRFP Breast Cancer Tumor

extract_protocol:
Total RNA was extracted using the Trizol method, with RNA integrity assessed using an Agilent Bioanalyzer 2100.
cDNA library was constructed using the KAPA Standard mRNA-Seq Kit.

treatment_protocol: Met1-iRFP mice were either exercised or sendentary.

value: Met1-iRFP Breast Cancer Tumor

value: TME cells (iRFP-)

tag: strain

value: FVB

value: Exercise


title: Met1-iRFP TME cells (iRFP-), Exercise, rep9

description: Library name: SR9


title: FGF0-72h-4

description: Library name: FGF0-72h-4.bam

value: migration 72h;FGF10


title: 19103

description: Library name: Sample 90


title: scbatch1,cKO mice,sorted YFP+ cells,2 month old

description: Library name: scbatch1_KO_YFP


title: 19102

description: Library name: Sample 89


title: Met1-iRFP TME cells (iRFP-), Exercise, rep8

description: Library name: SR8


title: FGF0-72h-3

description: Library name: FGF0-72h-3.bam


title: 18101

description: Library name: Sample 86


title: 19003

description: Library name: Sample 88


title: scbatch1,cKO mice,sorted total splenocytes,2 month old

description: Library name: scbatch1_KO_total


title: 19002

description: Library name: Sample 87


title: FGF0-72h-2

description: Library name: FGF0-72h-2.bam


title: Met1-iRFP TME cells (iRFP-), Sendentary, rep9

description: Library name: SN9

value: Sedentary


title: P1_day28, rep2

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

country: Japan

institute: Kanazawa University

description: Library name: Subcutaneous adipose SVF_Time course_20

data_processing:
The libraries were sequenced to generate an average of 26.7 million paired-end 150-bp reads using the NovaSeq6000 System (Illumina, San Diego, CA, USA).
The RNA-Seq fragment count was normalized relative to the fragments per kilobase of exon per million fragments mapped (FPKM).
The FPKM values were log2-transformed, and the relative abundances of transcripts were analyzed using Subio Platform ver. 1.24 and Subio Basic Plug-in (Subio, Tokyo, Japan).
Assembly: GRCm39
Supplementary files format and content: The Excel file includes the processed signals, where the FPKM signals were log2-transformed and normalized to the mean expression level across all groups.

source_name: subcutaneous adipose tissue

extract_protocol:
Total RNA (15 ng) was extracted from Sa-SVF cells using an ISOSPIN Cell & Tissue RNA Kit (Nippon Gene, Tokyo, Japan) or NucleoSpin RNA XS (Macherey-Nagel, Düren, Germany) for small sample volumes. The quality of the RNA was verified (RNA integrity number > 8) using a Bioanalyzer (Agilent 6000 Nano Assay, Agilent Technologies, Santa Clara, CA, USA).
Total RNA was amplified to produce cDNA, and cDNA libraries for RNA-Seq were constructed using a SMART-Seq HT PLUS Kit (R400749; Takara Bio USA, CA, USA).

value: subcutaneous adipose tissue

value: stromal vascular fruction

value: passage 1_day 28


title: 18001

description: Library name: Sample 85


title: P1_day28, rep1

description: Library name: Subcutaneous adipose SVF_Time course_19


title: Met1-iRFP TME cells (iRFP-), Sendentary, rep6

description: Library name: SN6


title: Met1-iRFP TME cells (iRFP-), Exercise, rep7

description: Library name: SR7


title: P1_day28, rep3

description: Library name: Subcutaneous adipose SVF_Time course_21


title: 17801

description: Library name: Sample 84


title: BSA-72h-2_1

description: Library name: BSA-72h-2_1.bam

value: mammary gland

value: mammary epithelial cells

value: migration 72h;BSA


title: P0_day28, rep3

description: Library name: Subcutaneous adipose SVF_Time course_18

value: primary culture_day 28


title: Met1-iRFP TME cells (iRFP-), Sendentary, rep4

description: Library name: SN4


title: BSA-36h-3

description: Library name: BSA-36h-3.bam


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep10

description: Library name: CR10

value: Cancer cells (iRFP+)


title: BSA-72h-3

description: Library name: BSA-72h-3.bam


title: P0_day28, rep2

description: Library name: Subcutaneous adipose SVF_Time course_17


title: BSA-72h-2_2

description: Library name: BSA-72h-2_2.bam


title: Met1-iRFP TME cells (iRFP-), Sendentary, rep10

description: Library name: SN10


title: BSA-36h-2

description: Library name: BSA-36h-2.bam


title: BSA-36h-1

description: Library name: BSA-36h-1.bam


title: 17301

description: Library name: Sample 82

value: whole blood

value: SLE


title: P0_day28, rep1

description: Library name: Subcutaneous adipose SVF_Time course_16


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep7

description: Library name: CR7


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep8

description: Library name: CR8


title: 17501

description: Library name: Sample 83


title: 0h-4

description: Library name: 0h-4.bam

value: WT

value: migration 0h


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep4

description: Library name: CR4

value: Met1-iRFP Breast Cancer Tumor


title: P0_day21, rep3

description: Library name: Subcutaneous adipose SVF_Time course_15

value: primary culture_day 21


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep5

description: Library name: CR5

value: FVB

value: Exercise


title: 17300

description: Library name: Sample 81


title: 16701

description: Library name: Sample 79


title: 0h-1

description: Library name: 0h-1.bam


title: P0_day21, rep1

description: Library name: Subcutaneous adipose SVF_Time course_13


title: P0_day21, rep2

description: Library name: Subcutaneous adipose SVF_Time course_14


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep2

description: Library name: CR2


title: 16902

description: Library name: Sample 80


title: P0_day14, rep3

description: Library name: Subcutaneous adipose SVF_Time course_12

value: primary culture_day 14


title: Met1-iRFP cancer cells (iRFP+), Exercise, rep1

description: Library name: CR1


title: 0h-2

description: Library name: 0h-2.bam


title: P0_day14, rep2

description: Library name: Subcutaneous adipose SVF_Time course_11

value: subcutaneous adipose tissue


title: 16503

description: Library name: Sample 78


title: 16501

description: Library name: Sample 77


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep10

description: Library name: CN10

value: Sedentary


title: K562 cells, parental negative control (control IgG)

city: Augusta

first: Nahid

middle: F

last: Mivechi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: Library name: sample15

library_source: genomic

data_processing:
CUT&RUN FASTQ files were trimmed using Trimmomatic v0.39 and aligned to the human reference genome hg38 (Gencode: GRCh38_v43) using BWA-MEM v0.7.18. Samtools v1.20 was used for BAM file filtering and indexing. deepTools v3.5.5 was used to remove ENCODE hg38 blacklist regions from the BAM files and to generate heatmaps. Signal peak regions were called with MACS v2.2.9.1. Differential peak identification between genotypes was performed using DiffBind v3.16.0.   Three samples that failed quality control were excluded from sequencing.
Assembly: human reference genome hg38 (Gencode: GRCh38_v43)
Supplementary files format and content: bigwig file
Library strategy: CUT&Run

molecule: genomic DNA

source_name: human leukemia

extract_protocol:
CUT&RUN assay was performed using Assay Kit from Cell Signaling (#86652).
The DNA was purified using DNA spin column (Cell Signaling #14209).   End Repair, A-Tailing, and Adapter ligation was performed on 50ng of DNA or 50µl volume equivalents (Roche, KK8501). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and PCR amplified (Roche, KK2602) with dual indexing Illumina compatible primers to generate a sequencing library.  Final libraries were again purified and size selected using AMPureXP beads, quantitated by QuBit (Life Technologies, Q33231), size distributions determined by bioanalyzer (Agilent 2100), pooled at equimolar ratios,

treatment_protocol: 150,000 cells per replicate (triplicate each of parental and sgHSF2 cells) were untreated or treated with 5Gy of IR followed by 2 hours and 4 hours of recovery period.

value: human leukemia

value: Parental

tag: antibody

value: control IgG


title: K562 cells, sgHSF2-3 IR-4h

description: Library name: sample14

value: RNAPII


title: K562 cells, sgHSF2-2 IR-4h

description: Library name: sample13


title: P0_day14, rep1

description: Library name: Subcutaneous adipose SVF_Time course_10

value: stromal vascular fruction


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep9

description: Library name: CN9

value: Cancer cells (iRFP+)


title: K562 cells, sgHSF2-1 IR-4h

description: Library name: sample12


title: P0_day7, rep3

description: Library name: Subcutaneous adipose SVF_Time course_09

value: primary culture_day 7


title: 16401

description: Library name: Sample 75

value: whole blood

value: SLE


title: 16402

description: Library name: Sample 76


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep7

description: Library name: CN7


title: K562 cells, parental-3 IR-4h

description: Library name: sample11


title: P0_day7, rep2

description: Library name: Subcutaneous adipose SVF_Time course_08


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep5

description: Library name: CN5


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep6

description: Library name: CN6


title: P0_day7, rep1

description: Library name: Subcutaneous adipose SVF_Time course_07


title: K562 cells, parental-2 IR-4h

description: Library name: sample10


title: K562 cells, parental-1 IR-4h

description: Library name: sample9


title: P0_day3, rep3

description: Library name: Subcutaneous adipose SVF_Time course_06

value: primary culture_day 3


title: 16202

description: Library name: Sample 74


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep4

description: Library name: CN4

value: Met1-iRFP Breast Cancer Tumor


title: 16112

description: Library name: Sample 73


title: P0_day3, rep2

description: Library name: Subcutaneous adipose SVF_Time course_05


title: K562 cells, sgHSF2-2 IR-2h

description: Library name: sample8


title: 16110

description: Library name: Sample 71


title: Ad5-HA_3_D7

city: Wuhan

first: YUAN

last: ZHANG

state: Hubei

address: Shizishan Street, Hongshan District, Wuhan City, Hubei Province

institute: Huazhong Agricultural University

description:
Library name: Ad5-HA-3
10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Lung

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

treatment_protocol: Following intranasal immunization with Ad5-HAPR8 or Ad5-HAPR8-VLP, lungs were harvested at 7 dpi. Lung tissues were mechanically dissociated using the gentleMACS™ Octo Dissociator (Lung_01_02 program; Miltenyi Biotec), followed by enzymatic digestion with a Lung Dissociation Kit for mice (Cat. No. 130-095-927, Miltenyi Biotec) for 30 min at 37°C. Tissues were further dissociated (gentleMACS™ Lung_02_01 program), filtered through a 40-μm nylon strainer, and subjected to red blood cell (RBC) lysis using ACK lysis buffer (Cat. No. BL503B, Biosharp). Single-cell suspensions were resuspended in ice-cold MACS® buffer (PBS + 0.5% BSA + 2 mM EDTA) and incubated with CD45 MicroBeads (Cat. No. 130-110-618, Miltenyi Biotec) for 15 min at 4°C. After washing with 2 mL MACS® buffer and centrifugation (300 ×g, 5 min), cells were filtered through a 30-μm pre-separation filter and magnetically sorted using a pre-wetted MS column on a MACS® Separator (Miltenyi Biotec). Purified cells were resuspended in 1 mL RPMI 1640 medium (Cat. No. 10-040-CVR, Corning) supplemented with 0.04% (w/v) BSA. Single-cell concentration and viability (>85% viability threshold) were quantified using the LUNA-FL™ automated cell counter (Logos Biosystems, South Korea).

value: Lung

value: immune cell


title: 16111

description: Library name: Sample 72


title: P0_day3, rep1

description: Library name: Subcutaneous adipose SVF_Time course_04


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep3

description: Library name: CN3

value: FVB


title: Met1-iRFP cancer cells (iRFP+), Sendentary, rep2

description: Library name: CN2


title: 16109

description: Library name: Sample 70


title: K562 cells, sgHSF2-1 IR-2h

description: Library name: sample7


title: K562 cells, Parental-2 IR-2h

description: Library name: sample6


title: K562 cells, Parental-1 IR-2h

description: Library name: sample5


title: Ad5-HA-VLP_2_D7

description:
Library name: Ad5-HA-VLP-2
10× Genomics


title: 15901

description: Library name: Sample 68


title: P0_day0, rep2

description: Library name: Subcutaneous adipose SVF_Time course_02

value: primary culture_day 0


title: 15803

description: Library name: Sample 67


title: Yolk sac

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

description:
Library name: sample 15
10x Genomics

data_processing:
Basic quality control for raw sequencing reads were performed using FastQC(v0.11.9). Sequencing adaptors and low-quality reads/bases were further removed using TrimGalore (v0.6.5).
Clean reads were then aligned to the mouse reference genome (mm10) using STAR (v2.7.6a) and only uniquely mapped reads were retained.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse E12.5-13.0 yolk sac

extract_protocol:
Cells purfied by FACS were used for scRNA-seq library construction.
scRNA-seq libraries were constructed according to the standard protocol of Chromium Next GEM Chip G Single Cell Kit (1000121, 10x Genomics) .

value: mouse E12.5-13.0 yolk sac

value: Yolk sac

value: Yolk sac cells

value: CAG-tdTomato-MuERVL-EGFP


title: Placeta

description:
Library name: sample 14
10x Genomics

source_name: mouse E12.5-13.0 placenta

value: mouse E12.5-13.0 placenta

value: Placenta

value: Placenta cells


title: Fetus

description:
Library name: sample 13
10x Genomics

source_name: mouse E12.5-13.0 fetus

value: mouse E12.5-13.0 fetus

value: Fetus

value: Fetus cells


title: P0_day0, rep1

description: Library name: Subcutaneous adipose SVF_Time course_01

value: subcutaneous adipose tissue

value: stromal vascular fruction


title: 15404

description: Library name: Sample 66

value: whole blood

value: SLE


title: EplLCs induced 1 day cells

description:
Library name: sample 12
10x Genomics
Epi_matrix.mtx.gz
Epi_features.tsv.gz
Epi_barcodes.tsv.gz

source_name: from mouse E3.5-4.5 embryos

value: from mouse E3.5-4.5 embryos

value: EplLCs induced 1 day cells

value: Wild-type

value: induced with chemicals:sodium D-lactate, NaB, A366, LIF, BMP4


title: 16106

description: Library name: Sample 69


title: 15401

description: Library name: Sample 65


title: K562 cells, sgHSF2-3

description: Library name: sample4

value: human leukemia

value: RNAPII


title: 15101

description: Library name: Sample 64


title: mCMG induced 4-day cells

description:
Library name: sample 11
10x Genomics

value: mCMG induced 4-day cells


title: K562 cells, Parental

description: Library name: sample1

value: Parental


title: K562 cells, sgHSF2-2

description: Library name: sample3


title: 15010

description: Library name: Sample 63


title: K562 cells, sgHSF2-1

description: Library name: sample2


title: Lrmda KO rep2

city: wuhan

first: yang

last: liping

address: 115 East Lake Road, Wuchang District, Wuhan City, Hubei Province, Wuhan University School of Medicine

institute: Wuhan University

description: Library name: Sample 6

data_processing:
Assembly: mouse genome assembly GRCm39
The mRNA-seq data were subjected to quality control using FastQc (version 0.11.8), and adapter sequences located at the 3’ end were trimmed with Cutadapt (version 4.4.0).
The resulting RNA-Seq fastq files were aligned to the mouse genome assembly GRCm39 using HISAT2 (version 2.2.1), with a maximum of two mismatches permitted per read.
Gene expression levels were quantified by HT-seq (version 2.0.5) under default parameters and normalized using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method.
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: tumor

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen).
RNA-seq library was constructed by using Oligo(dT) magnetic beads and the polyA structure of mRNA.

treatment_protocol: 8-week-old mice were injected i.p. with azoxymethane (AOM; Sigma) at a dosage of 10 mg per kilogram of body weight. Following this injection, the mice were maintained on regular drinking water for 7 days, then switched to 1.5% DSS-supplemented drinking water for another 7 days, and finally returned to regular drinking water for an additional 7 days. This three-stage cycle was repeated three times in total.

value: tumor

value: AOM/DSS-induced CRC


title: Lrmda KO rep4

description: Library name: Sample 8


title: mCMG induced 2-day cells

description:
Library name: sample 10
10x Genomics

value: mCMG induced 2-day cells


title: mCMG induced 1 day cells

description:
Library name: sample 9
10x Genomics

value: mCMG induced 1 day cells


title: Lrmda KO rep1

description: Library name: Sample 5


title: PR1643-K562-sgHSF2-1_S16

description:
Library name: sample4
sgHSF2_combined.bw

data_processing:
The data processing  and heatmap generation were performed using deepTools v3.5.1. The bigwig Compare tool was used to calculate the log₂ ratio differences between conditions. Count matrices were generated using the computeMatrix tool, and heatmaps were produced with the plotHeatmap tool. Regulatory elements were predicted using the dREG software and annotated with the ChIPseeker package v1.42.1.
Assembly: human reference genome hg38 (Gencode: GRCh38_v43)
Supplementary files format and content: bigwig file
Library strategy: PRO-Seq

growth_protocol: Parental and sgHSF2 K562 cells (in duplicates) were cultured in PRMI1640 medium with 10% FBS

extract_protocol:
total RNA using QIAGEN miRNeasy Mini Kit.
generated libraries with new SMARTer Stranded Total RNA-Seq Kit

treatment_protocol: Parental and sgHSF2 K562 cells (in duplicates) were rinsed with ice-cold PBS and were permeabilized using buffer containing 10mM Tris-HCl pH 8.0, 10% glycerol, 250mM sucrose,5mM MgCl2, 1mM EGTA, 10mM KCl 0.1 % (v/v) Igepal CA-630, 0.05 % (v/v) Tween-20.0.5mM DTT and SUPERase IN (0.2ml/ml).


title: WT rep4

description: Library name: Sample 4


title: 15009

description: Library name: Sample 62


title: PR1643-K562-sgHSF2-1_S15

description:
Library name: sample3
sgHSF2_combined.bw


title: Lrmda KO rep3

description: Library name: Sample 7


title: WT rep3

description: Library name: Sample 3


title: 15005

description: Library name: Sample 61


title: PR1641-K562-parental-2_S14

description:
Library name: sample2
Parental_combined.bw


title: WT rep2

description: Library name: Sample 2


title: PR1641-K562-parental-1_S13

description:
Library name: sample1
Parental_combined.bw


title: WT rep1

description: Library name: Sample 1


title: human lung primary fibroblast,MDK stimulation-3

city: Wuxi

first: Hua

last: Wenjie

address: NO.1800 Lihu Avenue

institute: Jiangnan University

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization. Differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: HG38
Supplementary files format and content: Gene Expression Profiling.xlsx

source_name: lung

extract_protocol:
total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA)
the rRNA-depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China)

value: lung

value: fibroblasts

value: MDK stimulation


title: 15002

description: Library name: Sample 60

value: whole blood


title: 15001

description: Library name: Sample 59

value: SLE


title: Lrmda KO rep3

description: Library name: Sample 6

source_name: intestinal tissue

treatment_protocol: 8-week-old mice were provided with drinking water containing 2.5% DSS (MP Biomedicals) for consecutive 5 days followed by sterile normal drinking water for 3 days prior.

value: intestinal tissue

value: colitis


title: EpiLCs

description:
Library name: sample 4
10x Genomics

source_name: EpiLCs

value: EpiLCs


title: ESCs

description:
Library name: sample 1
10x Genomics

source_name: ESCs

value: ESCs


title: EplLCs induced 4 day cells

description:
Library name: sample 3
10x Genomics

source_name: EplLCs induced 4 day cells

value: EplLCs induced 4 day cells


title: human lung primary fibroblast,MDK stimulation-2


title: Lrmda KO rep2

description: Library name: Sample 5


title: 14607

description: Library name: Sample 57

source_name: whole blood


title: human lung primary fibroblast,MDK stimulation-1


title: 7 months, scRNAseq

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

description: 10x Genomics

data_processing:
The Illumina bcl2fastq (v2.20.0) was used to convert Illumina base call files (bcl) to FASTQ files. Alignment of FASTQs to the mm10/hg19 reference was done by Cell Ranger (v6.1.2, 10X Genomics). mm10/hg19 reference downloaded from 10x and a tdTomato sequence gene was added to mm10. Library constriction was performed according to standard 3’ 10x genomics kit and sequence using illumine Hi-Seq and Next-seq machine. Single-cell gene expression datasets were analyzed using the Scanpy library (v 1.10.0). Doublet detection was executed employing Scrublet (v 0.2.3) with default settings, and cells exceeding a doublet score of 0.5 were filtered out. Cells with counts mapped to fewer than 200 genes and those with mitochondrial gene content exceeding 10% were excluded. Additionally, genes detected in fewer than three cells were removed. Total gene UMI per cell were normalized to a target sum of 104 and subjected to a log1p transformation. Subsequently, highly variable features were identified based on a minimum and maximum mean expression of 0.0125 and 3, respectively, and a minimum dispersion of 0.5. Principal Component Analysis was utilized for dimensionality reduction, and 50 principal components were employed for constructing a neighborhood graph with default parameters. The Leiden algorithm was employed for clustering across resolutions ranging from 0.2 to 0.6. The dataset was visualized in two dimensions using Uniform Manifold Approximation and Projection (UMAP) with a minimum distance of 0.5 and a learning rate of 1.
Assembly: mm10 and added tdTomato gene
Supplementary files format and content: .h5 file containing the filtered feature matrix and processed .h5ad file containig dimensionality reduction results and cell annotations

source_name: Pancreas

extract_protocol:
The pancreas was removed and washed and the acinar cells were isolated using 10mg collagenase P and 0.2mg trypsin inhibitor live cells were isolated by using MACS dead cells removal kit (Miltenyi Biotech #130-090-101) with MACS MS columns. The stomach was removed and the cells isolated first with dissociation buffer containing 2mg collagenase P and then with dissociation buffer containing 5 mg Dispase II (Roche #D4693) at 37C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreas

value: Pancreas cells

value: PTI, Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato

tag: time post_tamoxifen_injection_(pti)

value: 7 months


title: EpiLCs induced 2 day cells

description:
Library name: sample 2
10x Genomics

source_name: EpiLCs induced 2 day cells

value: EpiLCs induced 2 day cells


title: human lung primary fibroblast,control-2

value: WT


title: WT rep3

description: Library name: Sample 3


title: 14606

description: Library name: Sample 56


title: Lrmda KO rep1

description: Library name: Sample 4


title: 14608

description: Library name: Sample 58


title: Lung, C1-KO-Rapa-2h

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Visium libraries from mouse samples were mapped to mm10 mouse references (mm10-2020-A) with Space Ranger (v1.3.0, 10x Genomics).
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expresion count data in H5 format
Library strategy: Visium Spatial Transcriptomics

growth_protocol: Uky IACUC protocol # 2020-3685

extract_protocol:
10x Genomics (CG000409)
10x Genomics (Visium FFPE Reagent Kit )

treatment_protocol: Uky IACUC protocol # 2020-3685, 5 mg/kg body weight rapamycin injection into mice

value: Lung

value: KO

value: Rapamycin, 2h


title: Lung, D1-KO-Vehicle

value: Vehicle


title: human lung primary fibroblast,control-1

value: lung

value: fibroblasts


title: human lung primary fibroblast,control-3


title: WT rep2

description: Library name: Sample 2

value: intestinal tissue


title: 14501

description: Library name: Sample 54

value: whole blood

value: SLE


title: WT rep1

description: Library name: Sample 1

value: colitis


title: 14602

description: Library name: Sample 55


title: Lung, B1-KO-Rapa-8h

value: Rapamycin, 8h


title: 14017

description: Library name: Sample 53


title: sirk1, USIC, rep 3

city: Beijing

first: Qiangsheng

last: Yu

address: Tsinghua university

department: School of life sciences

institute: Tsinghua university

description: Library name: sirk1-USIC-3

data_processing:
For RNA-seq data, reads were mapped to the tair10 genome using STAR (version 2.7.3a) with parameter "--outSAMmultNmax 1". Read mapped to CDS annotated in tair10 were counted using featureCounts (version 1.6.2). For ribo-seq data, reads without 3’ adapter, with 5’ adapter, or with low sequencing quality were discarded. Reads mapped to rRNA and tRNA by bowtie (version 1.0.1) were also excluded. Cleaned reads were mapped to tair10 genome using STAR (version 2.7.3a) with parameters "--outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd". The gene expression levels were determined by featureCounts (version 1.6.2)".
Assembly: tair10
Supplementary files format and content: count matrix of RNA-seq and Ribo-seq data

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: The Col-0 wild-type and transgenic Dex::AvrRps4 seedlings were cultured in liquid medium.

extract_protocol:
For RNA-seq, RNA is extracted using TRIZOL reagent. For Ribo-seq, plant samples are lysed using an appropriate method. After nucleic acid digestion, ribosome-bound RNA is separated from free mRNA. Ribosome-mRNA complexes are then enriched to obtain ribosome-protected fragments (RPFs).
For RNA-seq, the enriched mRNA is subjected to fragmentation, and the RNA fragments are reverse-transcribed into cDNA. Sequencing adapters are added to the cDNA. PCR amplification is carried out on the adapter-containing cDNA fragments to enrich for those with specific adapters, thereby forming the final sequencing library. For Ribo-seq, Lyse plant samples, nucleic acids undergo digestion to separate ribosome-bound RNA from free mRNA. Ribosome-mRNA complexes are then enriched to obtain ribosome-protected fragments (RPFs). Following the removal of rRNA and purification by PAGE gel electrophoresis, the target RNA fragments are acquired. The ends of these fragments are repaired, and 5' and 3' adapters are directly added. Reverse transcription is carried out to synthesize cDNA, which is subsequently purified using PAGE gel. Sequencing adapters are attached, and PCR amplification is performed to enrich the fragments, resulting in the initial library. Finally, PAGE gel is used to screen for the target fragments, yielding a library containing the desired fragments.

treatment_protocol: 4-day-old seedlings cultured in liquid Murashige and Skoog (MS) medium with 20 g/L sucrose under a 16 h-light (22°C)/8 h-dark (20°C) photoperiod with a rotation speed of 120 rpm were treated with mock or 1 μM flg22 plus 10 μM dexamethasone for 1.5 h.

value: Seedling

value: USIC


title: Lung, A1-WT


title: sirk1, USIC, rep 2

description: Library name: sirk1-USIC-2


title: 14012

description: Library name: Sample 52


title: 14008

description: Library name: Sample 51


title: Lung, KO, scRNAseq

data_processing:
scRNA-seq gene expression libraries were mapped to mm10 mouse reference (10X Genomics pre-built reference, mm10-2020-A) using Cell Ranger (v6.1.1, 10x Genomics).
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix.h5

extract_protocol:
Lung dissociation, Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, Pleasanton, CA).
cDNA libraries were generated following the manufacturer’s (10x Genomics) directions.

treatment_protocol: No treatment

value: immune cells

value: 6-8 weeks


title: Lung, WT, scRNAseq


title: Fourth passage MEFs, KO control

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low-quality reads. Reads were mapped to Ensembl GRCm38 transcripts annotation using RSEM.
Assembly: GRCm38
Supplementary files format and content: star.genes.results: genecount from RSEM

source_name: MEFs

growth_protocol: Normal cell culture

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Novogen standard protocol

tag: passage

value: Fourth passage

value: MEFs


title: Y-S21d-1

first: Ge

last: Li

address: No.106 Zhongshan Rd.2

institute: Guangdong Provincial People's Hospital(Guangdong Academy of Medical Sciences),  Southern Medical University

description:
Library name: Sample7
Y-S21d-1_FPKM

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Hisat2（version:2.0.4）to map the cleaned reads to the GRCh38 reference genome with two mismatches. After genome mapping, Stringtie（version:1.3.0）  was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Stringtie]. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM in each sample.
Assembly: NCBI
Supplementary files format and content: csv files includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: spinal cord

extract_protocol:
Total RNA was isolated using MJzol animal RNA Extraction Kit (MagBeads) #T02096  (MJzol, China). Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina Noveseq 6000 (Illumina, USA). The library construction and sequencing was performed at Shanghai Biotechnology Corporation.

value: spinal cord


title: sirk1, USIC, rep 1

description: Library name: sirk1-USIC-1


title: Y-S21d-2

description:
Library name: Sample8
Y-S21d-2_FPKM


title: Y-S21d-3

description:
Library name: Sample9
Y-S21d-3_FPKM


title: 14005

description: Library name: Sample 50

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.


title: Fourth passage MEFs, WT control

value: WT


title: 13403

description: Library name: Sample 49


title: Y-S3d-3

description:
Library name: Sample6
Y-S3d-3_FPKM


title: sirk1, Mock, rep 3

description: Library name: sirk1-Mock-3

value: Mock


title: sirk1, Mock, rep 2

description: Library name: sirk1-Mock-2


title: sirk1, Mock, rep 1

description: Library name: sirk1-Mock-1


title: P0_day0, rep3

description: Library name: Subcutaneous adipose SVF_Time course_03

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: stromal vascular fruction

value: primary culture_day 0


title: 12510

description: Library name: Sample 48


title: Y-S3d-2

description:
Library name: Sample5
Y-S3d-2_FPKM


title: kin7, USIC, rep 3

description: Library name: kin7-USIC-3


title: 12508

description: Library name: Sample 47


title: Third passage MEFs, WT control

value: Third passage


title: Y-S3d-1

description:
Library name: Sample4
Y-S3d-1_FPKM


title: kin7, USIC, rep 2

description: Library name: kin7-USIC-2


title: Y-N-3

description:
Library name: Sample3
Y-N-3_FPKM


title: Second passage MEFs, KO control

value: Second passage

value: KO


title: 12411

description: Library name: Sample 46

value: whole blood

value: SLE


title: kin7, USIC, rep 1

description: Library name: kin7-USIC-1

value: Seedling


title: 12207

description: Library name: Sample 45


title: Y-N-1

description:
Library name: Sample1
Y-N-1_FPKM


title: Second passage MEFs, WT control


title: kin7, Mock, rep 3

description: Library name: kin7-Mock-3


title: Y-N-2

description:
Library name: Sample2
Y-N-2_FPKM


title: kin7, Mock, rep 2

description: Library name: kin7-Mock-2


title: 12202

description: Library name: Sample 44


title: 11810

description: Library name: Sample 43


title: 11807

description: Library name: Sample 42


title: B16_Gpr65

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

description: BD Rhapsody

data_processing:
Raw fastq-sequencing reads were loaded into BD Targeted Rhapsody Analysis Pipeline hosted by SevenBridgesGenomics and analyzed using version 1.9 of the pipeline.
Data were filtered as follows using Partek Flow version 10.0.20.1231: Cells with more than 10% mitochondrial genes and doublets/multiplets were excluded; a noise reduction filter was used to filter out features with an expression value of <1 in 99% of cells;
Data were normalized by calculating counts per million (CPM), adding 1 and log transforming to the base of 2
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every cell, gene and sample

source_name: B16 tumors

extract_protocol:
At day 17 (B16), respectively at day 16 (MC38) single cell suspensions were prepared from excised whole tumors by tissue digestion using murine tumor dissociation kit and gentleMACS dissociator (Miltenyi Biotec). CD45+ cells were enriched by murine CD45 (TIL) MicroBeads (Miltenyi Biotec) using MACS technology. To enrich purity viable CD45+ cells were sorted using AriaII flow cytometer (BD Bioscience).
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). For multiplexing samples, tumorinfiltrating CD45+ cells from WT and Gpr65-KO mice were labeled by sample tags against CD45 conjugated with unique oligos (B16_Gpr65 experiment: WT1=Sample tag (ST) 5; WT2=ST6; WT3=ST7, WT4=ST8; KO1=ST9; KO2=ST10; KO3=ST11; KO4=ST12); MC_38_Gpr65 experiment: WT1=ST7; WT3=ST9; KO1=ST10; KO2=ST11; KO3=ST12; Sequences of sample tags can be found under Doc ID 210970) and were loaded on BD Rhapsody cartridge. Capture of single RNA molecules on barcoded magnetic Oligo-dT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). mRNA and Sample Tag Libraries were prepared following the manual (mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol; 23--21712-00). Upon purifyingWTA and Sample tag library, concentration of libraries was assessed by Qubit 2.0 using the DNA high sensitivity kit and average library size was determined on a bioanalyzer using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling of mRNA and Sample tag library following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on a HiSeq2500 (B16_Gpr65) using a HiSeq PE Rapid Cluster Kit v2 (PE-402-4002) and combining three HiSeq Rapid SBS Kits v2 (50 cycles). MC38_Gpr65 libraries were sequenced on Illumina's NovaSeq 6000 at Novogene (Cambridge, UK). For processing of the sequencing raw data BD targeted multiplex Rhapsody analysis pipeline version 1.5 was used. For visualization the software Partek Flow (Partek Inc.) has been used.

treatment_protocol: Gpr65-deficient and respective littermate control mice were injected s.c. either with 2x10^5 B16F10 melanoma or 1x10^6 MC38 colon adenocarcinoma cells. Tumor growth was measured using a caliper.

value: B16 tumors

value: tumor-infiltrating CD45+ cells

value: WT and Gpr65-KO


title: kin7, Mock, rep 1

description: Library name: kin7-Mock-1


title: Col0, USIC, rep 3

description: Library name: Col0-USIC-3

value: USIC


title: Third passage MEFs, KO control

value: MEFs


title: APC mutant sample 2

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
small RNA
APCvsWT_DESeq.csv
M2_MIN_1_S64_R1_001.fastq

data_processing:
For single cell, sequencing was demultiplexed, aligned to the genome, and quality checked using 10X Genomics Cell Ranger software.
For RNA-seq, sequencing was aligned using STAR and quantified using Salmon. Normalization was accomplished by DESeq2.
For small RNA-seq, sequencing was processed using miRquant2.0.
Genome_build: mm10
Supplementary_files_format_and_content: For single cell, processed data contains barcodes, gene list, and counts matrix. For RNA-seq, processed data is a DESeq2 normalized counts matrix. For small RNA-seq, processed data is in Reads Per Million MiRs Mapped (RPMMM) or as DESeq2 results.

source_name: APC mutant intestinal cells -sample 2

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: small intestine

value: intestinal cells

value: APC mutant


title: Control sample 2  for APC mutant

description:
small RNA
APCvsWT_DESeq.csv
M2_MIN_S57_R1_001.fastq

source_name: APC control intestinal cells -sample 2

value: control


title: APC mutant sample 1

description:
small RNA
APCvsWT_DESeq.csv
F2_MIN_S65_R1_001.fastq

source_name: APC mutant intestinal cells -sample 1


title: 11805

description: Library name: Sample 41


title: 11604

description: Library name: Sample 40


title: Control sample 1 for APC mutant

description:
small RNA
APCvsWT_DESeq.csv
F2_S49_R1_001.fastq

source_name: APC control intestinal cells -sample 1


title: rFGF4_Day7_rep1

city: Wenzhou

first: Zhiming

address: Chashan Campus of Wenzhou Medical University

institute: Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

description:
Library name: Sample4
FGF4_1

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: proceseed data.xlsx

source_name: Skin

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Skin

value: rFGF4(100ng/ml), 10μl/day


title: rFGF4_Day7_rep2

description:
Library name: Sample5
FGF4_2


title: rFGF4_Day7_rep3

description:
Library name: Sample6
FGF4_3


title: Col0, USIC, rep 2

description: Library name: Col0-USIC-2


title: LEM

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description:
Library name: lemborexant treated mice
10x Genomics

data_processing:
Basecalling and demultiplexing with Illumina BCLConvert
Sequencing data were processed using Cell Ranger (v8.0.0) for alignment, barcode assignment, and UMI counting, generating gene-expression count matrices mapped to the mm10-2020-A mouse transcriptome.
Assembly: mm10
Supplementary files format and content: Tab separated value files and FASTQ files

source_name: Brain

extract_protocol:
Following Fc block with anti-CD16/32, cells were stained with CD45-FITC and CD11b-PE for 20 minutes on ice. After washing, DAPI was added to discriminate viable cells, and live microglia (CD45loCD11b⁺DAPI⁻) were sorted using a FACSAria II (BD Bioscience) directly into 1% BSA in PBS.
Sequencing libraries were prepared using the 10X Genomics Chromium Single Cell 5’ PE Library & Gel Bead Kit V2

treatment_protocol: Ten PSAPP mice (five treated with VEH, five with LEM 30 mg/kg/day) received daily oral gavage for one month beginning at 9 months of age. At 10 months, mice were perfused; one hemisphere was fixed for immunofluorescence, and the cortex and hippocampus from the contralateral hemisphere were processed into single-cell suspensions.

value: Brain

value: Microglia

value: Lemborexant 30mg/kg daily for 30 days


title: Col0, USIC, rep 1

description: Library name: Col0-USIC-1


title: 11603

first: Helen

institute: Eli Lilly and Company

description: Library name: Sample 39

value: whole blood


title: villi sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
VIL_2_S46_L004_R1_001

source_name: Villi dissected intestinal cells - sample 2

value: Villi dissected intestinal cells


title: Col0, Mock, rep 3

description: Library name: Col0-Mock-3

value: Seedling

value: Mock


title: villi sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
VIL_3_S47_L004_R1_001

source_name: Villi dissected intestinal cells - sample 3


title: PBS_Day7_rep2

description:
Library name: Sample2
PBS_2

value: PBS, 10μl/day


title: 11601

description: Library name: Sample 38

value: SLE


title: VEH

description:
Library name: Vehicle treated mice
10x Genomics

value: Vehicle daily for 30 days


title: Col0, Mock, rep 2

description: Library name: Col0-Mock-2


title: villi sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
VIL_4_S48_L004_R1_001

source_name: Villi dissected intestinal cells - sample 4


title: 11514

description: Library name: Sample 37

source_name: whole blood


title: villi sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
VIL_1_S45_L004_R1_001

source_name: Villi dissected intestinal cells - sample 1


title: PBS_Day7_rep1

description:
Library name: Sample1
PBS_1


title: Col0, Mock, rep 1

description: Library name: Col0-Mock-1


title: crypt sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
CRP_4_S44_L004_R1_001

source_name: Crypt dissected intestinal cells - sample 4

value: Crypt dissected intestinal cells


title: 11508

description: Library name: Sample 36


title: Seedling, PTI and ETI, RNA-seq rep 2

description: Library name: RNA-PE-2

source_name: Seedling

value: flg22 + Dex


title: crypt sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
CRP_3_S43_L004_R1_001

source_name: Crypt dissected intestinal cells - sample 3

value: small intestine


title: 11502

description: Library name: Sample 34


title: crypt sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
CRP_2_S42_L004_R1_001

source_name: Crypt dissected intestinal cells - sample 2


title: PBS_Day7_rep3

description:
Library name: Sample3
PBS_3


title: Seedling, Mock, RNA-seq rep 2

description: Library name: RNA-Mock-2


title: 11506

description: Library name: Sample 35


title: 11501

description: Library name: Sample 33


title: crypt sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
CRP_1_S41_L004_R1_001

source_name: Crypt dissected intestinal cells - sample 1


title: Seedling, Mock, RNA-seq rep 1

description: Library name: RNA-Mock-1


title: Sox9-eGFP negative sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
BC243_chow_Neg_GCCAAT_L004_R1

source_name: Sox9-EGFP Negative sorted intestine crypt cells from chow diet sample 4


title: Sox9-eGFP negative sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
BC183_chow_Neg_GTCCGC_L005_R1

source_name: Sox9-EGFP Negative sorted intestine crypt cells from chow diet sample 2


title: Seedling, PTI and ETI, Ribo-seq rep 3

description: Library name: Ribo-PE-3

data_processing:
For RNA-seq data, reads were mapped to the tair10 genome using STAR (version 2.7.3a) with parameter "--outSAMmultNmax 1". Read mapped to CDS annotated in tair10 were counted using featureCounts (version 1.6.2). For ribo-seq data, reads without 3’ adapter, with 5’ adapter, or with low sequencing quality were discarded. Reads mapped to rRNA and tRNA by bowtie (version 1.0.1) were also excluded. Cleaned reads were mapped to tair10 genome using STAR (version 2.7.3a) with parameters "--outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd". The gene expression levels were determined by featureCounts (version 1.6.2)".
Assembly: tair10
Supplementary files format and content: count matrix of RNA-seq and Ribo-seq data
Library strategy: Ribo-Seq


title: A223 cells, PRDX6 KD, 100nM largazole, 18 hours, replicate 1

city: Boulder

first: Zeyu

address: 3415 Colorado Ave

institute: University of Colorado Boulder

description: Library name: LCS10266_XL7_Clean

data_processing:
Raw reads were aligned and quantified using the NF Core RNA-Seq pipeline v3.12.0 using the iGenomes mm10 genome.
Assembly: mm10
Supplementary files format and content: Processed data files are raw count files generated by the NF Core pipeline.

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (thermofisher). 1.5 ug of total RNA was used for library construction.
RNA-Seq libraries were prepared using the NEB Ultra II Directional RNA Kit with Poly(A) Selection per the manufacturer's protocol.

value: PRDX6 KD

value: 18hr largazole


title: 11209

city: Indianapolis

address: 893 S Delaware St.

description: Library name: Sample 32


title: A223 cells, parental, 100nM largazole, 18 hours, replicate 1

description: Library name: LCS10266_XL3_Clean

value: Parental


title: 11207

description: Library name: Sample 31


title: 11206

description: Library name: Sample 30


title: A223 cells, parental, DMSO, 0h replicate 2

description: Library name: LCS10266_XL2_Clean

value: DMSO


title: Sox9-eGFP negative sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
BC180_chow_Neg_CTTGTA_L005_R1

source_name: Sox9-EGFP Negative sorted intestine crypt cells from chow diet sample 1


title: Seedling, PTI and ETI, RNA-seq rep 1

description: Library name: RNA-PE-1


title: Sox9-eGFP negative sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
BC241_HFD_Neg_GTTTCG_L004_R1

source_name: Sox9-EGFP Negative sorted intestine crypt cells from chow diet sample 3


title: Seedling, PTI and ETI, Ribo-seq rep 1

description: Library name: Ribo-PE-1


title: A223 cells, PRDX6 KD, 100nM largazole, 18 hours, replicate 2

description: Library name: LCS10266_XL8_Clean


title: Seedling, Mock, Ribo-seq rep 3

description: Library name: Ribo-Mock-3


title: Seedling, PTI and ETI, Ribo-seq rep 2

description: Library name: Ribo-PE-2


title: A223 cells, PRDX6 KD, DMSO, 0h replicate 1

description: Library name: LCS10266_XL5_Clean


title: A223 cells, PRDX6 KD, DMSO, 0h replicate 2

description: Library name: LCS10266_XL6_Clean


title: 11204

description: Library name: Sample 29


title: A223 cells, parental, DMSO, 0h replicate 1

description: Library name: LCS10266_XL1_Clean


title: 11202

description: Library name: Sample 28


title: A223 cells, parental, 100nM largazole, 18 hours, replicate 2

description: Library name: LCS10266_XL4_Clean


title: Conventionalized sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
CD270_Low_GCCAAT_L003_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized sample 4


title: Seedling, Mock, Ribo-seq rep 2

description: Library name: Ribo-Mock-2


title: 11201

description: Library name: Sample 27


title: Conventionalized sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
CD246_Low_CTTGTA_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized sample 3


title: 10902

description: Library name: Sample 26


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ VCD-treated female mice replicate 2

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

description: Library name: F_VCD_2

data_processing:
10x Genomics Cell Ranger 7.1 mkfastq wrapper and was used to perform sample demultiplexing and generate fastq files. The reads were aligned with 10x Genomics CellRanger 3.1.0 to the University of California, Santa Cruz (UCSC) mm39 reference transcriptome using STAR and transcript counts were generated. Cells with unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less 200 unique features, total gene counts more than more the 75th percentile plus 1.5 times the IQR or less than 1000 counts, and/or mitochondrial feature percentage more the 75th percentile plus 1.5 times the IQR or less than the 25th percentile minus 1.5 times the IQR were filtered out of the data. Next, the 2000 highest variable features were selected. The data were then scaled by a linear transformation and variation associated with cell death and cell cycling where regressed out of the scaled data using mitochondrial feature percentage and cell cycle scoring values. Counts were normalized using the SCTransform and PCA was performed on the scaled data. A Uniform Manifold Approximation and Projection (UMAP) was used to visualize and explore the clustering results. Seurat’s FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections. Seurat FindAllMarkers function was used to identify gene markers that define cluster cell types. Differential expression analysis was performed using the FindMarkers to compare similar cell types across the genders. The MAST test, a GLM-framework that treats cellular detection rate as a covariate, was used to determine statistically different transcription.
Assembly: GRCm39 /mm39
Supplementary files format and content: Supplementary files format and content: Hierarchical Data Format (H5) containing the barcodes, gene annotation, and gene counts for each sample.

source_name: Pituitary

growth_protocol: The FVB hybrid strain of mice was FVB.129P2-Pde6b + Tyr c-ch/AntJ. We used 28 3-4-month-old female mice divided into two groups: VCD-treated and Vehicle-treated Control.

extract_protocol:
Individual pituitary cell suspensions were then pooled within treatment groups (3 pituitaries/pool) for counting. Cell concentration within each pool was adjusted to optimally target 10,000 cells according to 10X Genomics guidelines and samples were then submitted to the UAMS Cancer Institute Genomics Core facility. Visual examination under a microscope (EVOS M7000, Thermo Fisher Scientific) was used to detected cell debris or aggregates, which were removed by passing cell suspensions through a Flowmi™ _(SP BEL-ART, catalog # 136800040) cell strainer (40 microns). Following centrifugation at 250 g for 10 min, cells were re-suspended in 1X PBS (Ca2+/Mg2+-free) containing 0.04% (w/v) BSA. Cell concentration and viability were detected with ReadyProbes™ _Cell Viability Imaging Kit, Blue/Green (Thermo Fisher Scientific, catalog # R37609), and manually counted.
Single-cell 3′ library generation was performed using a 10x Genomics Chromium Controller and Chromium next GEM Single Cell 3’ Reagent Kits v 3.1 (Dual index). Libraries were sequenced on the Illumina NovaSeq 6000 platform with paired-end mode (read1: 28 cycles, read 2: 90 cycles, i7: 10 cycles, i5: 10 cycles) to generate a minimum of 20,000 read pairs per cell.

treatment_protocol: We used 28 3-4-month-old female mice divided into two groups: VCD-treated and Vehicle-treated Control. We induced ovarian failure by treating 14 of the mice with 4-vinylcyclohexene diepoxide (VCD) using a well-established protocol for rodents.  Mice were injected intraperitoneally (IP) daily with VCD in sesame oil for 20 days (160 mg/kg) to cause the selective loss of all primary and primordial follicles during the subsequent 15 days.  Vehicle-treated females were treated with sesame oil only.   At day 120 post-treatment initiation, we collected blood via tail snip for quantification of LH and FSH (see details below) and tested cyclicity of all the mice by vaginal smears to confirm that the VCD mice were acyclic.  On days 133-138 (with day 1 being the first day of VCD treatment), we collected pituitaries and dispersed the cells for single cell RNA-sequencing transcriptome analysis.      For each group, we used cells from a total of six (6) of pituitaries per group (vehicle control or VCD-treated) and created two sample pools per group (n= 3 animals per pool).

value: Pituitary

value: FVB.129P2-Pde6b + Tyr c-ch/AntJ


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control female mice replicate 2

description: Library name: F_Con_2

value: Control, vehicle-treated (sesame oil)


title: Germ-free sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
GF315_Low_CGATGT_L004_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - sample 4


title: Seedling, Mock, Ribo-seq rep 1

description: Library name: Ribo-Mock-1


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ VCD-treated female mice replicate 1

description: Library name: F_VCD_1


title: 10802

last: Masson

description: Library name: Sample 25

value: whole blood


title: PR, temperature 24 hours of recovery after treatment at 37°C，rep3

city: Kunming

first: ya

middle: qi

last: xiao

state: Yunnan Province

address: Chenggong Campus of Yunnan University

department: Faculty of Ecology and Environment

institute: Yunnan University

description: Library name: PR_R24_3

data_processing:
RSEM
Assembly: TAIR10.1
Supplementary files format and content: gene.tpm.matrix.annot.txt files are files in excel format that quantify the expression levels of genes

source_name: seedling

growth_protocol: Plants were grown on half-strength MS (½MS) medium with 1.2% (w/v) sucrose.

extract_protocol:
1. Extract total RNA
2. Oligo dT enrichment of mRNA
3. Fragmented mRNA
Illumina TruseqTM RNA sample prep Kit

treatment_protocol: Some of the materials are treated at a high temperature of 37°C

value: seedling

value: PRMT5 T-insert

value: 24 hours of recovery after 3 days of treatment at 37°C


title: 10801

description: Library name: Sample 24


title: PR, temperature 24 hours of recovery after treatment at 37°C，rep2

description: Library name: PR_R24_2


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control female mice replicate 1

description: Library name: F_Con_1


title: PR, temperature 24 hours of recovery after treatment at 37°C，rep1

description: Library name: PR_R24_1


title: Germ-free sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
GF305_Low_ATCACG_L004_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - sample 3


title: WT, temperature 24 hours of recovery after treatment at 37°C，rep2

description: Library name: WT_R24_2

value: WT


title: Germ-free sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
GF271_Low_TAGCTT_L002_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - sample 2


title: 10547

description: Library name: Sample 21

source_name: whole blood

value: SLE


title: 10618

description: Library name: Sample 22


title: Germ-free sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
GF244_Low_TTAGGC_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - sample 1


title: Conventionalized sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
CVGF314_Low_AGTTCC_L005_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized sample 2


title: WT, temperature 24 hours of recovery after treatment at 37°C，rep3

description: Library name: WT_R24_3


title: Brain stromal, GEX

city: Melbourne

first: Lucas

last: Tobar

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Brain_CD45-_mRNA
GEX (5' mRNA) library: read file contains cell barcode and UMI; read2 file contains transcript
brain_cd45_neg_GEX_raw_feature_bc_matrix.h5

data_processing:
Demultiplexed data was processed using the Celranger count pipeline
Assembly: mm10
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5
Supplementary files format and content: feature_reference.csv

source_name: Brain

extract_protocol:
CD45+ and CD45- cells sorted from brain, dura, and calvarium. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 5' GEM Library and Gel Bead kit (Peter MacCallum Cancer Centre - Molecular Genomics Core).
The hashing protocol described by Stockius et al was used to generate a hashtag/lipid-modified oligo (HTO/LMO) library and a 5' gene expression library.

value: Brain


title: 10544

description: Library name: Sample 20


title: WT, temperature 24 hours of recovery after treatment at 37°C，rep1

description: Library name: WT_R24_1


title: 10703

description: Library name: Sample 23


title: Sox9-eGFP low sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
BC243_chow_Low_GTTTCG_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet sample 4


title: Dura stromal, GEX

description:
Library name: Dura_CD45-_mRNA
GEX (5' mRNA) library: read file contains cell barcode and UMI; read2 file contains transcript
dura_cd45_neg_GEX_LMO_raw_feature_bc_matrix.h5

source_name: Dura

value: Dura


title: Dura immune, GEX

description:
Library name: Dura_CD45+_mRNA
GEX (5' mRNA) library: read file contains cell barcode and UMI; read2 file contains transcript
dura_cd45_pos_GEX_LMO_raw_feature_bc_matrix.h5


title: Conventionalized sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
CVGF304_Low_TAGCTT_L005_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized sample 1


title: Sox9-eGFP low sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
BC241_HFD_Low_GGTAGC_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet sample 3


title: PR, temperature, 37℃，rep3

description: Library name: PR_RH_3


title: Brain immune, GEX

description:
Library name: Brain_CD45+_mRNA
GEX (5' mRNA) library: read file contains cell barcode and UMI; read2 file contains transcript
brain_cd45_pos_GEX_BC_raw_feature_bc_matrix.h5


title: 10542

description: Library name: Sample 19


title: PR, temperature, 37℃，rep2

description: Library name: PR_RH_2


title: 10541

description: Library name: Sample 18


title: PR, temperature, 37℃，rep1

description: Library name: PR_RH_1


title: 10540

description: Library name: Sample 17


title: Lgr5-High sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
LH_2_S53_L008_R1_001

source_name: Lgr4-High sorted intestinal cells - sample 2

value: Lgr4-High sorted intestinal cells


title: Sox9-eGFP low sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
BC183_chow_Low_CAGATC_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet sample 2

value: small intestine


title: Sox9-eGFP low sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
BC180_chow_Low_GCCAAT_L001_R1

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet sample 1


title: 10535

description: Library name: Sample 16


title: 10533

description: Library name: Sample 15


title: PR, temperature, 22℃，rep3

description: Library name: PR_CO_3


title: PR, temperature, 22℃，rep2

description: Library name: PR_CO_2


title: 10532

description: Library name: Sample 14


title: CD24 Low sample 3

description:
small RNA
smallRNA_RPMMM_all.csv
CD_24low_3_S44

source_name: Cd24-Low sorted intestinal cells - sample 3

value: Cd24-Low sorted intestinal cells


title: H3K27ME3 WT sFEB 1 (Chip)

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

description: Library name: WT sFEB 1 (Chip)

data_processing:
Supplementary files format and content: bigWig,Broad
basecall were  performed by using bcl2fastq for Novaseq input
bigWig were generated by using the genomicRanges R package
Assembly: mm10

source_name: sFEB

extract_protocol:
The cells were crosslinked with 1% formaldehyde for 10' at room temperature and next quenched by addition of glycine (125 mM). The samples were sonicated with Bioruptor Plus (Diagenode).
libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB)

value: sFEB

value: Sereum free Embryoid bodies

value: LIN28A WT


title: H3K27ME3 WT sFEB 2 (Chip)

description: Library name: WT sFEB 2 (Chip)


title: H3K27ME3 WT sFEB 3 (Input)

description: Library name: WT sFEB 3 (Input)


title: Lgr5-High sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
LH_1_S52_L008_R1_001

source_name: Lgr4-High sorted intestinal cells - sample 1


title: H3K27ME3 WT sFEB 1 (Input)

description: Library name: WT sFEB 1 (Input)


title: 10531

description: Library name: Sample 13


title: H3K27ME3 WT sFEB 3 (Chip)

description: Library name: WT sFEB 3 (Chip)


title: PR, temperature, 22℃，rep1

description: Library name: PR_CO_1

source_name: seedling


title: 10527

description: Library name: Sample 12


title: WT, temperature, 37℃，rep3

description: Library name: WT_RH_3


title: H3K27ME3 KO sFEB 3 (Input)

description: Library name: KO sFEB 3 (Input)

value: LIN28A KO


title: H3K27ME3 WT sFEB 2 (Input)

description: Library name: WT sFEB 2 (Input)


title: Calvarium, GEX

description:
Library name: Calvarium_mRNA
GEX (5' mRNA) library: read file contains cell barcode and UMI; read2 file contains transcript
calvarium_GEX_LMO_raw_feature_bc_matrix.h5

source_name: Calvarium

value: Calvarium


title: WT, temperature, 37℃，rep2

description: Library name: WT_RH_2


title: CD24 Low sample 4

description:
small RNA
smallRNA_RPMMM_all.csv
CD_24low_4_S45

source_name: Cd24-Low sorted intestinal cells - sample 4


title: WT, temperature, 37℃，rep1

description: Library name: WT_RH_1


title: CD24 Low sample 2

description:
small RNA
smallRNA_RPMMM_all.csv
CD_24low_2_S39

source_name: Cd24-Low sorted intestinal cells - sample 2


title: 10526

description: Library name: Sample 11

source_name: whole blood


title: H3K27ME3 KO sFEB 3 (Chip)

description: Library name: KO sFEB 3 (Chip)


title: CD24 Low sample 1

description:
small RNA
smallRNA_RPMMM_all.csv
CD_24low_1_S38

source_name: Cd24-Low sorted intestinal cells - sample 1


title: WT, temperature, 22℃，rep3

description: Library name: WT_CO_3


title: 10524

description: Library name: Sample 10


title: H3K27ME3 KO sFEB 2 (Input)

description: Library name: KO sFEB 2 (Input)


title: H3K27ME3 KO sFEB 2 (Chip)

description: Library name: KO sFEB 2 (Chip)


title: 10517

description: Library name: Sample 8


title: WT, temperature, 22℃，rep2

description: Library name: WT_CO_2


title: H3K27ME3 KO sFEB 1(Chip)

description: Library name: KO sFEB 1(Chip)


title: 10522

description: Library name: Sample 9


title: H3K27ME3 KO sFEB 1 (Input)

description: Library name: KO sFEB 1 (Input)


title: Irx4KO3_RNASeq

city: Ottawa

first: Kyoung-Han

last: Kim

state: Ontario

address: 40 Ruskin Street

institute: University of Ottawa Heart Institute

data_processing:
fastq reads were aligned to the mm9 transcriptome using kallisto 0.42.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.42.2

source_name: E14.5 heart

extract_protocol:
E14.5 ventricles were dissected and frozen at -80°C prior to RNA extraction with PureLink RNA Mini kit (Life Technologies). The integrity of the samples was checked on Agilent Bioanalyzer, and the samples with a RIN>8.5 were used. 1 to 2µg of RNA were used to prepare the PolyA RNA library.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.

tag: developmental stage

value: heart (ventricles)


title: WT2_RNASeq


title: WT1_RNASeq


title: Col-0_WT_Cold 24hr_Rep1

city: Seoul

first: Nassem

last: AlBakri

address: Gwangjin-gu

department: Biomedical Science and Engineering

country: South Korea

institute: Konkuk University

description: High Output 75bp

data_processing:
Raw read QC using FASTQC tool followed by adapter trimming by Trim Galore
Trimmed reads were aligned using Burrows-Wheeler Aligner (BWA) and duplicated reads identied by suing Picard mark duplicate and merged alignments from multiple libraries of the same sample using Picard and re-marked duplicates.
Unmapped, chloropast, mitochondrial reads with >4 mismatches were filtered using SAMTools and BAMTools.
Normalized bigwig files were generated using BEDTools and bedGraphToBigWig and visualized using IGV. Genebody profile, heatmaps and genome-wide enrichment were generated using deeptools
Peak were called using MACS2 and annotated relative to gene feature using HOMER. Consensus peak peak sets isolated and filtered using BEDTools. Differential amentccessibility, PCA analysis and clustering were performed using DESeq2.
Assembly: TAIR10
Supplementary files format and content: BigWig, BroadPeak

source_name: Seedling

growth_protocol: Arabidopsis (Col-0) Wild type plants were used in this study. All plants were grown in MS media contain 1% Sucrose under the condition (16 hr light/8hr dark, 20°C)

extract_protocol:
Open chromatin DNA was labeld with labeling solution for 2hr and labeled genomic DNA was isolated using Dneasy Plant Pro Kit (QIAGEN) and 200 ng of labeled genomic DNA were fragmentated by Covaris, 150bp
Pull-dwoned DNAs by adding Streptavidin Bead with high salt buffer were used for the NGS DNA library preparation described in MiMB Book Chapter 3: Chromatin Accessibility: Methods and Protocols, Chin et al., 2023
NicE-seq library

treatment_protocol: 2-3 week-old seedings (8 buds) were incubated at 0℃ for 0hr, 3hr, 6hr, 12hr, 24hr in the dark condition to treat cold stress and the nuclei sample were isolated by the following protocol described in method section.

value: Seedling

value: Wild Type

value: Cold


title: WT3_RNASeq


title: H3K27ME3 WT ESC 3 (Chip)

description: Library name: WT ESC 3 (Chip)

source_name: ESC

value: ESC

value: Embrionic Stem cells


title: Col-0_WT_Cold 24hr_Rep2

description: High Output 75bp


title: H3K27ME3 WT ESC 3 (Input)

description: Library name: WT ESC 3 (Input)


title: 10514

description: Library name: Sample 7

value: whole blood

value: SLE


title: 10510

description: Library name: Sample 6


title: Col-0_WT_Cold 24hr_Rep3

description: High Output 75bp


title: 10505

description: Library name: Sample 5


title: Irx4KO4_RNASeq


title: Irx4KO2_RNASeq


title: Col-0_WT_Cold 12hr_Rep3

description: High Output 75bp


title: Irx3KO4_RNASeq


title: 10202

description: Library name: Sample 4


title: H3K27ME3 WT ESC2 (Chip)

description: Library name: WT ESC2 (Chip)


title: H3K27ME3 WT ESC 2 (Input)

description: Library name: WT ESC 2 (Input)


title: 10104

description: Library name: Sample 3


title: Col-0_WT_Cold 12hr_Rep2

description: High Output 75bp


title: Irx3KO2_RNASeq


title: H3K27ME3 WT ESC 1 (Input)

description: Library name: WT ESC 1 (Input)


title: H3K27ME3 WT ESC 1 (Chip)

description: Library name: WT ESC 1 (Chip)


title: 10103

description: Library name: Sample 2


title: Col-0_WT_Cold 12hr_Rep1

description: High Output 75bp


title: Irx3KO1_RNASeq


title: Irx3KO_Irx4KO10_RNASeq


title: Col-0_WT_Cold 6hr_Rep1

description: High Output 75bp


title: H3K27ME3 KO ESC 3 (IP)

description: Library name: KO ESC 3 (Input)


title: Col-0_WT_Cold 6hr_Rep3

description: High Output 75bp


title: Col-0_WT_Cold 6hr_Rep2

description: High Output 75bp


title: Irx3KO_Irx4KO7_RNASeq


title: Col-0_WT_Cold 3hr_Rep2

description: High Output 75bp


title: Irx3KO_Irx4KO5_RNASeq


title: 10102

description: Library name: Sample 1


title: H3K27ME3 KO ESC 2 (IP)

description: Library name: KO ESC 2 (Input)


title: Col-0_WT_Cold 3hr_Rep3

description: High Output 75bp


title: H3K27ME3 KO ESC 3 (Chip)

description: Library name: KO ESC 3 (Chip)


title: H3K27ME3 KO ESC 1 (IP)

description: Library name: KO ESC 1 (Input)


title: Irx3KO_Irx4KO3_RNASeq