title: BMSC, 21%O2, control 2

first: Ximeng

last: Cao

address: No.371 Yanqiao Rd.

institute: Shanghai Jiaotong University

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged rat pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: BMSC cell

growth_protocol: BMSCs were harvested from the tibias and femurs of 4-week-old male SD rats by flushing the bone marrow cavity and cultured in Dulbecco’s modification of Eagle’s medium containing 10% fetal bovine serum and 1% penicillin-streptomycin at 37℃ with 5% CO2.

extract_protocol:
total RNA was extracted from extracellular vesicles derived from BMSCs
miRNA was isolated from the exosomal total RNA using the TaqMan ABC miRNA Purification Kit
The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were successively ligated to RNA samples. Then, the adaptor-ligated RNA was reversely transcribed into cDNA, followed by PCR amplification. After amplification, the cDNA libraries were size-selected for miRNA fractions before sequencing and then sequenced in a HiSeq platform (Illumina).

treatment_protocol: hypoxia group:1%O2, 5%CO2; control: 21%O2.5%CO2

value: BMSC cell

tag: cell type

value: messenchymal stem cells

value: normoxia control


title: kidney biopsy [GSM3524295 re-analysis]

status: Public on Sep 04 2024

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rej7aaclust (nr, minor, tcmr1, tcmr2, eabmr, fabmr, labmr)

tag: tissue

value: kidney biopsy


title: Donor5, Skin

type: SRA

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

description:
single cell transcriptomics sequencing
PWH26D0
cell_metadata.txt

library_source: transcriptomic single cell

data_processing:
The single-cell sequence data were mapped with CellRanger (version 5.0.1) to a manually built human reference genome GRCh38 with annotation file GENCODE version 38. The low-quality cells expressing <500 genes, >20% mitochondrial genes, and <1000 gene counts were filtered out. We excluded mitochondrial and hemoglobin genes, as well as genes expressed in fewer than 10 cells. The Scrublet (v0.2.3) and DoubletFinder (v2.0.3) were further performed on each sample to detect potential doublets. Cell doublets identified by overlaps of two tools or in the same cluster with well-known markers of distinct cell types were also excluded from the analysis.
Data normalization and scaling were performed using the SCTransform package with regressing out the mitochondrial percentage and cell cycle effects. Top 4000 variable genes were used for principal component analysis (PCA). The batch effect of sample-to-sample variation was corrected using top 40 PCs as input of the RunHarmony function when integrating data. Uniform Manifold Approximation and Projection (UMAP) and k-nearest neighbors graph were generated using the RunUMAP and FindNeighbors functions inside Seurat (v4), respectively. The major cell clusters were identified using the Louvain graph-based algorithm with a resolution of 0.8, which resulted in 27 clusters. The differentially expressed genes among clusters were calculated using the FindAllMarkers functions with the MAST method. Genes with adjusted Pvalue<0.05, log fold change>0.25, and detected in at least 25 percent of cells were considered significantly high in the cluster. The clusters were annotated according to the top 20 marker genes of each cluster and documented signature genes of different cell types.
Assembly: GRCh38
Supplementary files format and content: zip files: contain the raw counts of gene expression, cell barcodes, and gene IDs.
Supplementary files format and content: txt file: cell and cluster annotation information

molecule: polyA RNA

source_name: Skin

extract_protocol:
The healthy volunteers were enrolled at the Karolinska University Hospital, Stockholm, Sweden. To study the gene expression patten of human acute wound, 2-3 full-thickness skin wounds were made by using 3-mm biopsy punch at the upper buttock area of each donor. On day1, day7 or day30, the wound edge tissues were collected by using a 6-mm biopsy punch and snap-frozen for the following studies. Written informed consent was obtained from all donors for the collection and use of tissues for research. This study was approved by the Stockholm Regional Ethics Committee and conducted according to the Declaration of Helsinki’s principles.
Wound skin tissues were incubated with 5U/ml Dispase II at 4°C overnight. The epidermis was separated from dermis by tweezers gently and incubated in 0.025% Trypsin/ EDTA (Thermo Fisher) for 10-15 minutes at 37 ℃. The dermal cell suspension was prepared using the whole skin dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions. To capture as many cell types as possible, equal amounts of epidermal and dermal cells were mixed. The red blood cells and dead cells were depleted by Red Blood Cell Removal Solution (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec), respectively. After cleaning, viable cells were loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics). The libraries were subsequently sequenced on an Illumina Novaseq6000 platform to achieve an average of approximately 50K read-pairs per cell.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

tag: individual

value: Skin

tag: treatment

value: intact skin


title: Donor4-Wound30

description: Fresh frozen spatial transcriptomics sequencing

library_source: transcriptomic

data_processing:
The raw spatial sequence data were processed using the standard Space Ranger pipeline (version 1.2) with the GRCh38 human reference genome and GENCODE v38 gene annotations and visualized by BBrowser (BioTuring) and Seurat R package.
Assembly: GRCh38
Supplementary files format and content: Skin/Wound1/Wound7/Wound30_filtered_feature_bc_matrix.h5: contain spatial barcodes, genes IDs, and gene expression count data in matrix
Supplementary files format and content: Skin/Wound1/Wound7/Wound30_spatial_images.zip: contain aligned fiducials of image, image of tissue and spots, scalefactors in jsonformat, hi-res and low-res images, and list of spatial barcodes and the coordinates specifying spots
Library strategy: spatial transcriptomics

extract_protocol:
Fresh frozen tissues were embedded in the OCT, and were cryosectioned in 10 µm with cryostat.
The spatial transcriptomics libraries sequencing was prepared with 10X Genomics Visium Spatial Gene Expression Slide & Reagents Kit according to manufacturers' construction.

tag: time point

value: day 30

tag: donor

tag: Sex

value: Female

tag: age


title: BMSC, 21%O2, control 1

city: Shanghai

country: China

organism: Rattus norvegicus

tag: cell line


title: kidney biopsy [GSM3525631 re-analysis]

value: NR


title: Donor4-Wound7

value: day 7


title: BMSC, 1%O2, hypoxia 3

value: hypoxia preconditioning


title: kidney biopsy [GSM3524531 re-analysis]

value: EABMR


title: Donor5, Wound30

description:
single cell transcriptomics sequencing
PWH26D30
cell_metadata.txt

value: skin wound day 30


title: Donor4-Wound1

value: day 1


title: BMSC, 1%O2, hypoxia 1


title: shCon_TGFb_2

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
The fastq data were cleaned with the Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the default protocol by the manufacturer. The Blastn (http://blast.ncbi.nlm.nih.gov/) was used to annotated the mRNA. The Bowtie ( http://bowtie-bio.sourceforge.net/index.shtml ) was used to mapped the sequences to reference gennome.
Assembly: hg38
Supplementary files format and content: Raw counts

source_name: human embryonic stem cells -derived retinal pigment epithelium cells

extract_protocol:
The  total RNA  of the cells was isolated by TRIzol® Reagent (Invitrogen)
then the construction of cDNA library was performed by Illumina TruSeq Small RNA sample prep kit. The target PCR products were purified through 6% Novex TBE PAGE gel and the quality was checked by TBS380 (Picogreen). Then PCR amplification was performed and the generated clusters were sequenced by Illumina HiSeq platform.

tag: genotype

value: shCon


title: Sample_6,Control,SP

status: Public on Sep 03 2024

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

country: USA

institute: Memorial Sloan Kettering

data_processing:
Single cell RNA data were processed using Cellranger v7.0.0 count workflow to generate gene expression count matrices.
Assembly: Mouse reference,GRCm39 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz

organism: Mus musculus

source_name: Spleen

extract_protocol:
Sorted live cells were harvested from frozen/thawn bone marrow and spleen samples from Mx1-cre-Map2k1-E102_I103del mutant (n=3) and control mice (n=3) mice for 3' scRNA sequencing.
Sequencing libraries were prepared from polyA-selected RNA with 10x 3' protocol according to manufacturer-recommended instructions.

value: Spleen

tag: library type

value: mRNA


title: BMSC, 21%O2, control 3

value: BMSC cell


title: Sample_5,Mx1-cre-Map2k1-E102_I103del Mutant,SP


title: BMSC, 1%O2, hypoxia 2

value: messenchymal stem cells


title: Sample_4,Control,BM

source_name: Bone Marrow

value: Bone Marrow


title: Sample_4,Control,SP


title: Sample_5,Mx1-cre-Map2k1-E102_I103del Mutant,BM


title: Sample_3,Control,SP


title: Sample_3,Control,BM


title: Sample_2,Mx1-cre-Map2k1-E102_I103del Mutant,SP


title: Sample_2,Mx1-cre-Map2k1-E102_I103del Mutant,BM


title: Sample_1,Mx1-cre-Map2k1-E102_I103del Mutant,SP


title: SPNK02_3

city: Jinan

first: Deyan

last: Jiao

address: wenhuaxi road

institute: shandong university

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes Differential expressed genes.

source_name: spleen

extract_protocol:
Cell pellets were resuspended with TRIzol and total RNA was extracted using a RNeasy Mini Kit
The libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI  according to the manufacturer's instructions.

treatment_protocol: Purified mouse splenic NK cells were treated with or without OA (0.2mM oleic acid (OA) for 36h. The treatment processed only once.)

value: spleen

value: NK cell

value: OA treated


title: Sample_1,Mx1-cre-Map2k1-E102_I103del Mutant,BM


title: SPNK00_3

value: control


title: kidney biopsy [GSM3523919 re-analysis]

value: kidney biopsy


title: SPNK00_2


title: SPNK02_2


title: SPNK00_1


title: Donor4-Skin

value: Female

value: Skin


title: SPNK02_1


title: Patient 4 Sample_NE1

city: Ube

first: Takanori

last: Tokunaga

address: 1-1-1 Minami-kogushi

country: Japan

institute: Yamaguchi University

description: Renal cancer tissue samples were collected from patients treated with immune checkpoint inhibitors (ICI). A total of 4 samples, including FFPE renal cancer tissues from both treated and untreated patients, were analyzed for lncRNA and mRNA expression profiling. The Human LncRNA Array v5.3 (Arraystar) was used, and data from control spots were excluded from the final analysis.

hyb_protocol: Labeled cRNA was hybridized to the Human LncRNA Array v5.0.

scan_protocol: Arrays were scanned using an Agilent Scanner G2505C.

data_processing: Raw data was normalized using quantile normalization with GeneSpring GX v12.1.

source_name: Renal cancer tissue

label_protocol: cRNA was labeled using the Arraystar Flash RNA Labeling Kit.

extract_protocol: Total RNA was extracted using the Maxwell RSC RNA Tissue Kit.

treatment_protocol: Samples were treated with immune checkpoint inhibitors.

value: Renal cancer tissue


title: Patient 2 Sample_E2

description: Renal cancer tissue samples were collected from patients treated with immune checkpoint inhibitors (ICI). A total of 4 samples, including FFPE renal cancer tissues from both treated and untreated patients, were analyzed for lncRNA and mRNA expression profiling. The Human LncRNA Array v5.1 (Arraystar) was used, and data from control spots were excluded from the final analysis.


title: Patient 3 Sample_NE1

description: Renal cancer tissue samples were collected from patients treated with immune checkpoint inhibitors (ICI). A total of 4 samples, including FFPE renal cancer tissues from both treated and untreated patients, were analyzed for lncRNA and mRNA expression profiling. The Human LncRNA Array v5.2 (Arraystar) was used, and data from control spots were excluded from the final analysis.


title: Sample_6,Control,BM


title: P10-C1

first: Rao

last: hanyu

address: Huashan Road NO.1954

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <50 bp) and low quality reads using Cutadapt (v1.9.1)(Anthony M et al., Bioinformatics 2014) and Trimmomatic (v0.35) (Martin M et al., EMBnet.J 2011).
Then FastQC (Andrews S et. al., FastQC 2010) is used to ensure high reads quality.
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 (Kim, D et al., Nat. Methods 2015) software.
Peak detection was performed using the MACS (v2.1.1) (Zhang et al., Genome Biol 2008) peak finding algorithm with 0.01 set as the p-value cutoff.
Assembly: hg18
Supplementary files format and content: processed data file includes raw counts for each sample.

source_name: umbilical cord

growth_protocol: MSCs were isolated from three umbilical cord tissues obtained from three donors. Cells were cultured with Xeno-Free Human Mesenchymal Stromal Cell Medium (Transgene, MM102-01) at 37°C in humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

treatment_protocol: MSCs from each donor were cultured and harvested at passage 2, 6 and 10 to represent different stages of cell proliferation.

value: umbilical cord

value: primary cell

value: Mesenchymal stem cells

value: Wild-type

value: Passage 10


title: P6-C2

value: Passage 6


title: P6-C3


title: P2-C2

value: Passage 2


title: P10-C2


title: P6-C1


title: P2-C3


title: P2-C1


title: P10-C3


title: Patient 1 Sample_E1

description: Renal cancer tissue samples were collected from patients treated with immune checkpoint inhibitors (ICI). A total of 4 samples, including FFPE renal cancer tissues from both treated and untreated patients, were analyzed for lncRNA and mRNA expression profiling. The Human LncRNA Array v5.0 (Arraystar) was used, and data from control spots were excluded from the final analysis.


title: Control 2

city: Hangzhou,

first: Guangyue

last: Li

state: Zhejiang

address: No.600 Dunyu Rd., Xihu District

institute: westlake university

data_processing:
Samples concentration were detected using Agilent 2100, Frgment Analyzer, Qsep-400Agilent 4200
HISAT (v2.2.1) was used to align the clean reads to the reference genome
Alignment of the clean reads to the reference genes was carried out using Bowtie2 (v2.4.5)
Gene expression levels were calculated by RSEM (v1.3.1)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: commas-delimited text file includes raw counts for each Sample

source_name: Liver

growth_protocol: HepG2 was cultured in MEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in an atmosphere with 5% CO2.

extract_protocol:
RNA extraction using the TRIzol reagent (Thermo Fisher Scientific, cat#15596026).
The sequence library for each sample was prepared using the BGISEQ-500 platform with a 50-bp single-end (SE50) format

treatment_protocol: HepG2 cells were treated by 150 µM β-caryophyllene or ethanol for 24 h.

value: Liver

value: Hepatocellular carcinoma cells

value: WT

value: 151 uM ethanol


title: Treatment 3

value: 152 uM Beta-caryophyllene


title: Treatment 2

value: 151 uM Beta-caryophyllene


title: Control 3

value: 152 uM ethanol


title: Control 1

value: 150 uM ethanol


title: E15_FT_Polr2a_Lhx2cKO_2

first: XIAOSU

last: LI

state: Shanghai

address: 131 Dongan Road

institute: Fudan University

description: Polr2a CUT&Tag-seq of E15 Lhx2cKO cortex

library_source: genomic

data_processing:
Trim Galore was used to remove low-quality bases and adapter sequences from the FastQ files.
The cleaned reads were alignment using Subread
BAM files were then converted into RPKM-normalized bigWig files using deepTools
Peak calling was performed on the bigWig files using LanceOtron
scRNA-seq and snATAC-seq was processed using CellRanger piplines
Assembly: mm39
Supplementary files format and content: bigwig
Supplementary files format and content: hd5; expression matrix
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: cerebral cortex

extract_protocol:
fresh brain
scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1, following the manufacturer’s instructions (manual document part number: CG000205 Rev C, 10x Genomics).The DNA fragments were purified using 2X VAHTS DNA Clean Beads (Vazyme, N411-01). PCR (12–15 cycles) was used to amplify the Tn5-fragmented DNA and incorporate i5/i7 adapters, sequencing primers, and sample indices for Illumina sequencing.  For bulk ATAC-seq, 20,000 to 50,000 cells were pelleted at 500 × g for 3 minutes. We added 20 μL of the Tn5 tagmentation mixture to simultaneously facilitate cell/nuclear membrane penetration and Tn5 tagmentation.  snATAC-seq libraries were constructed using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1, following the manufacturer’s instructions (manual document part number: CG000209 Rev F, 10x Genomics).

value: cerebral cortex


title: E15_FT_Polr2a_WT_2

description: Polr2a CUT&Tag-seq of E15 control cortex

value: wild type


title: E15_FT_H3K27me3_Lhx2cKO_1

description: H3K27me3 CUT&TAg-seq of E15 Lhx2cKO cortex


title: E15_FT_H3K27me3_Lhx2cKO_2


title: E15_FT_Polr2a_WT_1


title: E15_FT_H3K27me3_WT_2

description: H3K27me3 CUT&TAg-seq of E15 control cortex


title: E15_H3K4me3_Lhx2cKO_2

description: H3K4me3 CUT&TAg-seq of E15 Lhx2cKO cortex


title: E15_H3K4me3_Lhx2cKO_1


title: E15_H3K4me3_WT_2

description: H3K4me3 CUT&TAg-seq of E15 control cortex


title: E15_FT_H3K27me3_WT_1


title: E15_FT_ATAC_WT_2

description: ATAC-seq of E15 FlashTag/FACS sorted control cortical progenitors

data_processing:
Trim Galore was used to remove low-quality bases and adapter sequences from the FastQ files.
The cleaned reads were alignment using Subread
BAM files were then converted into RPKM-normalized bigWig files using deepTools
Peak calling was performed on the bigWig files using LanceOtron
scRNA-seq and snATAC-seq was processed using CellRanger piplines
Assembly: mm39
Supplementary files format and content: bigwig
Supplementary files format and content: hd5; expression matrix


title: E15_ATAC_Lhx2cKO_1

description: ATAC-seq of E15 Lhx2cKO cortex


title: E15_ATAC_WT_2

description: ATAC-seq of E15 control cortex


title: E15_ATAC_Lhx2cKO_2

description: ATAC-seq of E15 Lhx2cKO cortex


title: E18_FT_Lhx2_2

description: Lhx2 CUT&Tag-seq of E18 FlashTag/FACS sorted cortical progenitors


title: E15_ATAC_WT_1

description: ATAC-seq of E15 control cortex


title: E15_Lhx2_2

description: Lhx2 CUT&Tag-seq of E15 cortex


title: E15_FT_ATAC_Lhx2cKO_1

description: ATAC-seq of E15 FlashTag/FACS sorted Lhx2 cKO cortical progenitors


title: E15_FT_ATAC_Lhx2cKO_2


title: E15_FT_ATAC_WT_1


title: E15_Lhx2_1

description: Lhx2 CUT&Tag-seq of E15 cortex


title: E18_FT_Lhx2_1


title: E15_FT_Lhx2cKO

description: scRNA-seq of E15 FlashTag/FACS sorted Lhx2 cKO cortical progenitors


title: E15_FT_Polr2a_Lhx2cKO_1


title: E13_Lhx2_1

description: Lhx2 CUT&Tag-seq of E13 cortex


title: E13_snATAC

description: snATAC-seq of E13 cortex

data_processing:
Trim Galore was used to remove low-quality bases and adapter sequences from the FastQ files.
The cleaned reads were alignment using Subread
BAM files were then converted into RPKM-normalized bigWig files using deepTools
Peak calling was performed on the bigWig files using LanceOtron
scRNA-seq and snATAC-seq was processed using CellRanger piplines
Assembly: mm39
Supplementary files format and content: bigwig
Supplementary files format and content: hd5; expression matrix
Library strategy: snATAC-seq


title: E18_hGFAP_a

description: scRNA-seq of E18 hGFAP-GFP/FACS sorted cortical progenitors

value: hGFAP-GFP


title: Back skin, WT, noUV, Sample 45

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

data_processing:
Reads were mapped using STAR using the mouse reference genome (mm10), and genes were quantified with HTSeq.
We utilized only genes with an average of at least one read/sample.
Expression normalization was by DEseq2.
Assembly: Reads were mapped using STAR using the mouse reference genome (mm10).
Supplementary files format and content: Tab-delimited text file includes the normalized counts for each sample

source_name: Back skin

extract_protocol:
RNA was isolated per manufacturer protocol using the RNeasy plus mini kit (Qiagen). Poly-A libraries were generated, and RNA-sequencing was completed with the assistance of the University of Michigan Advanced Genomics Core using the Illumina NovaSeq 6000 platform.
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: 10–13-week-old female mice of each strain were treated with acute (300mJ/cm2 x1), chronic (100mJ/cm2 daily x5 days), or no UVB followed by biopsy of skin 24 hours after the final dose of UVB.

value: Back skin

value: noUV


title: P1_hGFAP_a

description: scRNA-seq of P1 hGFAP-GFP/FACS sorted cortical progenitors


title: P1_hGFAP_b


title: E15_FT

description: scRNA-seq of E15 FlashTag/FACS sorted cortical progenitors


title: E13

description: scRNA-seq of E13 cortex


title: Wild type, scRNA-seq

first: Shuai

last: Xu

address: Wujin Road 85, Shanghai, China

institute: Shanghai General Hospital, Shanghai Jiaotong university of  Medicine

description: 10X Genomics

data_processing:
Cell Ranger software (version 2.2.0), provided by 10× Genomics, was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: mm10
Supplementary files format and content: Cell Ranger outputs

source_name: Testis

extract_protocol:
Testicular tissues were washed three times and then cut the testicular tissues into 0.2 cm × 0.2 cm pieces and incubated with Enzyme I (10 mL of DMEM containing 2 mg/mL type IV collagenase and 10 mg/mL DNase I) at 34 °C for 15 min. After that, seminiferous tubules were washed again and incubated with Enzyme II (4 mg/mL collagenase IV, 2.5 mg/mL hyaluronidase, 2 mg/mL trypsin, and 10 mg/mL DNase I) at 34 °C for 10–15 min. Tissue block were ﬁltered by a 40-mm cell strainer.
Individual mouse testicular cells were obtained through enzymatic digestion and loaded on a 10×Genomics chip to form gel beads in emulsion, which were subjected to reverse transcription and PCR amplification, and then sequenced on a Nove-seq 6000 platform (Illumina). A cell-gene expression matrix was obtained with Cell Ranger software (10×Genomics).

value: Testis

value: Wild type


title: Igf2bp1 KO, scRNA-seq

description: 10X Genomics

value: Igf2bp1 KO


title: E15_H3K4me3_WT_1


title: Back skin, WT, noUV, Sample 44


title: Back skin, WT, noUV, Sample 41


title: E13_Lhx2_2

description: Lhx2 CUT&Tag-seq of E13 cortex


title: Back skin, iNZM, noUV, Sample 37

value: iNZM


title: Back skin, iNZM, noUV, Sample 38


title: Back skin, NZM, noUV, Sample 35

value: NZM


title: Back skin, WT, noUV, Sample 43


title: Back skin, iNZM, noUV, Sample 40


title: Back skin, NZM, noUV, Sample 31


title: Back skin, WT, chronicUV, Sample 28

value: chronicUV


title: Back skin, NZM, noUV, Sample 32


title: Back skin, NZM, noUV, Sample 34


title: Back skin, WT, chronicUV, Sample 59

value: WT


title: Back skin, WT, chronicUV, Sample 27


title: Back skin, WT, chronicUV, Sample 29


title: Back skin, NZM, noUV, Sample 33


title: Back skin, iNZM, chronicUV, Sample 25


title: Back skin, iNZM, chronicUV, Sample 24


title: Back skin, WT, chronicUV, Sample 58


title: Back skin, iNZM, chronicUV, Sample 23


title: Back skin, NZM, chronicUV, Sample 55


title: Back skin, NZM, chronicUV, Sample 56


title: Back skin, iNZM, chronicUV, Sample 57


title: Back skin, NZM, chronicUV, Sample 18


title: Back skin, iNZM, chronicUV, Sample 22


title: Back skin, iNZM, noUV, Sample 39


title: Back skin, NZM, chronicUV, Sample 17


title: Back skin, WT, acuteUV, Sample 15

value: acuteUV


title: Back skin, WT, acuteUV, Sample 50


title: Back skin, WT, acuteUV, Sample 51


title: Back skin, WT, acuteUV, Sample 52


title: Back skin, iNZM, acuteUV, Sample 10


title: Back skin, NZM, chronicUV, Sample 54


title: Back skin, iNZM, acuteUV, Sample 49


title: Back skin, iNZM, acuteUV, Sample 48


title: Back skin, iNZM, acuteUV, Sample 6


title: Back skin, NZM, acuteUV, Sample 47


title: Back skin, NZM, acuteUV, Sample 3


title: Back skin, NZM, acuteUV, Sample 1


title: Back skin, NZM, acuteUV, Sample 5


title: Back skin, NZM, acuteUV, Sample 46


title: F9.1

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
Nearly 85% of reads were uniquely mapped to the mouse genome reference mm10 using STAR (Spliced Transcripts Alignment to a Reference). To evaluate the quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes was determined using bamUtils. Low-quality mapped reads (including reads mapped to multiple positions) were excluded, and featureCounts was used to quantify gene expression. The data were filtered using a read count >10 in at least two of the samples, normalized using TMM (trimmed mean of M values) method, and subjected to differential expression analysis using edgeR.
Assembly: mm10
Supplementary files format and content: tab delimited txt files; data show DEGs

source_name: Liver tissue

extract_protocol:
Qiagen midiprep
KAPA mRNA Hyperprep kit

value: Liver tissue

tag: strain

value: female


title: F7.4


title: F9.2


title: F7.2


title: F8.2


title: F8.1


title: F6.1


title: F3.4


title: Back skin, WT, acuteUV, Sample 13


title: F5.1


title: F3.3


title: F4.2


title: F4.1


title: Back skin, iNZM, acuteUV, Sample 9


title: F2.3


title: M7.1

value: male


title: M8.2


title: M9.2


title: M7.2


title: F2.2


title: M6.1


title: M6.3(2)


title: M4.2


title: M5.2


title: M5.1


title: M2.2


title: M2.1


title: M3.2


title: M3.1


title: F6.4


title: F5.2


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep5

city: Urbana

first: Natalia

middle: Julianna

last: Krawczynska

state: illinois

address: 407 South Goodwin Ave

department: MIP

institute: UIUC

data_processing:
FASTQ read data were processed using the nf-core smrnaseq workflow v1.1.0, using miRBase 22.1 and Gencode M25.
The mature counts were read into R (v4.1.2) and normalized using TMM. miRNA genes without at least one count in four samples were removed.
The workflow was run using Nextflow v. 21.10.6 with the command line call ‘nextflow run nf-core/smrnaseq -r 1.1.0 -c smrna.conf’, with the workflow configuration file settings including the miRNA protocol to ‘qiaseq’ and the species to ‘mmu’.
Final normalized expression values were made by re-running TMM and then converting to log2-based counts per million (logCPM) using edgeR’s cpm Function.
Differential gene expression (DE) analysis was performed using the limma-trend method using a model of ~Treatment + Group to control for batch effects of the sample processing group. Multiple testing correction was done using the False Discovery Rate method.
Assembly: GRCm39/mm39
Supplementary files format and content: mature_counts - raw microRNA counts for all samples in ne file

source_name: bone marrow of WT BALB/c mice

extract_protocol:
Total RNA from small extracellular vesicles was isolated using miRNeasy Micro kit (Qiagen) according to the manufacturer’s protocol with supported modification for small RNA quantities.
Total RNA was used for miRNA libraries preparation with the QIAseq miRNA library preparation kit (Qiagen), according to the manufacturer's protocols.

value: bone marrow of WT BALB/c mice

value: sEVs from Ly6G positive cells

tag: time


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep3


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep7


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep6


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep4


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep1


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep7

value: DMSO


title: M9.1


title: Evs_PMNs, from 27HC treated neutrophils, 48h, rep2


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep6


title: M8.1 (2)


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep5


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep3


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep4


title: 4T1, non-adherent, 27HC sEVs treated, 72h, rep4

description:
HC_NA_72_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx

data_processing:
The trimming step was skipped - The average per-base read quality scores are over 30 in all samples and no adapter sequences were found indicating those reads are high in quality.
Raw reads were mapped to indexed GRCm39/mm39 using Salmon version 1.10.0 for quasi-mapping.
Gene-level counts were estimated based on transcript-level counts using the “lengthScaledTPM” method from thetximportpackage.
Assembly: GRCm39/mm39
Supplementary files format and content: GeneLevel_counts - raw gene counts for all samples in one file (does not include outlier sample HC_NA_72_5)
Supplementary files format and content: TMMnormalized_logCPM for all samples in one file (does not include outlier sample HC_NA_72_5)

extract_protocol:
Total RNA was extracted using Rneasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocols.
The total RNAs were converted into individually barcoded polyadenylated mRNAseq libraries with the Kapa HyperPrep mRNA kit (Roche). Libraries were barcoded with Unique Dual Indexes (UDI’s) which have been developed to prevent index switching. The adaptor-ligated double-stranded cDNAs were amplified by PCR for 10 cycles with the Kapa HiFi polymerase (Roche).

value: mammary breast cancer

value: 27HC_sEVs from primary neutrophils

tag: subpopulation


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep2


title: M4.1


title: 4T1, non-adherent, 27HC sEVs treated, 72h, rep5

description: HC_NA_72_5 (outlier for the group, which is why it was removed from the analysis)


title: Evs_PMNs, from DMSO treated neutrophils, 48h, rep1


title: 4T1, non-adherent, 27HC sEVs treated, 72h, rep3

description:
HC_NA_72_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 72h, rep1

description:
HC_NA_72_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 48h, rep4

description:
HC_NA_48_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 48h, rep5

description:
HC_NA_48_5
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 48h, rep3

description:
HC_NA_48_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 48h, rep1

description:
HC_NA_48_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 72h, rep3

description:
HC_A_72_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx

value: adherent


title: 4T1, adherent, 27HC sEVs treated, 72h, rep1

description:
HC_A_72_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 72h, rep2

description:
HC_A_72_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 48h, rep4

description:
HC_A_48_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 72h, rep4

description:
HC_A_72_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 72h, rep5

description:
HC_A_72_5
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 48h, rep1

description:
HC_A_48_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 48h, rep5

description:
HC_A_48_5
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 72h, rep3

description:
D_A_72_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx

value: DMSO_sEVs from primary neutrophils


title: 4T1, adherent, 27HC sEVs treated, 48h, rep3

description:
HC_A_48_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, 27HC sEVs treated, 48h, rep2

description:
HC_A_48_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 72h, rep5

description:
D_A_72_5
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 72h, rep4

description:
D_A_72_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 72h, rep2

description:
D_A_72_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 48h, rep1

description:
D_A_48_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 48h, rep2

description:
HC_NA_48_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 48h, rep3

description:
D_A_48_3
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, adherent, DMSO sEVs treated, 48h, rep4

description:
D_A_48_4
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1, non-adherent, 27HC sEVs treated, 72h, rep2

description:
HC_NA_72_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1_NTC_2

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

data_processing:
Base calling - Illumina real-time analysis v. 3.4.4
Demultiplex/fastq conversion - Illumina Bcl2fastq v. 2.20.0
Quality Check - FastQC v. 0.11.7
Read Mapping - Bowtie2 v. 2.4.1
Read Counting - FeatureCounts/Subread v. 2.0.0
Assembly: Mouse - GRCm39/mm39; Human - GRCh38
Supplementary files format and content: 4T1-coldata.csv: DESeq2 experimental design for 4T1 data
Supplementary files format and content: 4T1-rawcounts.csv: raw transcript counts from FeatureCounts for 4T1 data
Supplementary files format and content: 231-coldata.csv DESeq2 experimental deisng for MDA-MB_231 data
Supplementary files format and content: 231-rawcounts.csv raw transcript counts from FeatureCounts for MDA-MB-231 data
Supplementary files format and content: 231and4T1-coldata.csv: DESeq2 experimental design for combined 4T1 and MDA-MB-231 data
Supplementary files format and content: 231and4T1-normalizedcounts.csv: Normalized transcript counts for all samples in this study calculated in DESeq2

source_name: Cell Line

extract_protocol:
RNA was extracted and purified using only the Zymo Quick-RNA 96 kit.
RNA sequencing was performed by the Michigan State University Genomics Core. Sequencing libraries were prepared using the Illumina stranded mRNA library prep kit (Illumina, catalog no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters following the manufacturer’s recommendations, except that half-volume reactions were performed. Libraries were assessed for quantity and quality using a combination of Qubit dsDNA HS (Thermo Fisher Scientific, catalog no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, catalog no. 5067-5584). Libraries were pooled in equimolar amounts, and the pool was quantified using an Invitrogen Collibri quantification quantitative PCR kit (Invitrogen, catalog no. A38524100). The pooled library was loaded onto two lanes of a NovaSeq S1 flow cell, and sequencing was performed in a 1 × 100-bp single-read format using a NovaSeq 6,000 v1.5 100-cycle reagent kit (Illumina, catalog no. 20028316). Base calling was performed with Illumina real-time analysis (version 3.4.4), and the output of real-time analysis was demultiplexed and converted to the fastq format with Illumina Bcl2fastq (version 2.20.0).

value: Cell Line

value: Mouse Breast Cancer

value: Red-Fluc


title: 4T1_NTC_3


title: 4T1, adherent, DMSO sEVs treated, 48h, rep2

description:
D_A_48_2
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: 4T1_MN_Anti10b_2


title: 4T1_NTC_1


title: 4T1_MN_Anti10b_3


title: 4T1_MN_Anti10b_1


title: 4T1_MN_3


title: 4T1_MN_2


title: 4T1_MN_1


title: BM_Lin_neg_CD117_posctrl-rep2

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

description: cellranger demultiplexed

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: bone marrow

extract_protocol:
Tissues were minced and homogenized in 24-well plates using scalpels and pestles, with 0.5 ml of DMEM. Subsequently, 1 ml of tissue dissociation buffer was added, and the mixture was incubated at 37°C for 45 minutes. The dissociation solution was prepared by dissolving collagenase A (Sigma, 11088793001) in a mixture of 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to achieve a working concentration of 1 mg ml⁻¹. The resulting tissue suspension was filtered through a 70-μm strainer to ensure complete homogenization, and the strainer was rinsed with DMEM to recover any remaining single cells. The flow-through was then centrifuged at 500g for 5 minutes, and the supernatant was carefully decanted. In cases where red blood cells (RBCs) were present, a 1×RBC lysis buffer (1:10 dilution of 10× RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied and incubated at room temperature for 10 minutes. To halt and remove RBC lysis, 20 ml of DMEM was added, and the mixture was centrifuged at 450g for 5 minutes. The supernatant was discarded, and the cell pellet was washed with 10 ml of cold DMEM at 4°C. After another centrifugation at 500g for 5 minutes, the supernatant was removed, and the cells were resuspended in cold PBS (Sigma, D8537) containing 0.04% BSA. Finally, the cell suspension was passed through a 40-μm flowmi cell strainer to ensure uniformity.
Library construction follows CellPlex and TotalSeqC sample multiplexing protocal, for CellPlex multiplexed sample, we used 3' end sequencing protical, while we used 5' end sequencing for TotalSeqC multiplexed samples.

value: bone marrow

tag: group

value: immune

value: ctrl


title: BM_Lin_neg_CD117_pos-vehicle-rep1

description: cellranger demultiplexed

value: vehicle


title: BM_Lin_neg_CD117_pos-IACS_70654-rep1

description: cellranger demultiplexed


title: BM_Lin_neg_CD117_pos-vehicle-rep2

description: cellranger demultiplexed


title: BM_Ter119_neg-IACS_70654-rep2

description: cellranger demultiplexed


title: BM_Ter119_neg-vehicle-rep2

description: cellranger demultiplexed


title: 4T1, adherent, DMSO sEVs treated, 48h, rep5

description:
D_A_48_5
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx


title: Treatment 1

value: Liver

value: Hepatocellular carcinoma cells

value: WT

value: 150 uM Beta-caryophyllene


title: BM_Lin_neg_CD117_pos-IACS_70654-rep2

description: cellranger demultiplexed


title: BM_Ter119_neg-IACS_70654-rep1

description: cellranger demultiplexed


title: 2208L-combination

description: cellranger demultiplexed

value: cancer

value: IACS-70654 and anti-PD1


title: BM_Ter119_neg-ctrl-rep2

description: cellranger demultiplexed


title: BM_Ter119_neg-ctrl-rep1

description: cellranger demultiplexed


title: BM_Ter119_neg-vehicle-rep1

description: cellranger demultiplexed


title: 2208L-vehicle

description: cellranger demultiplexed


title: PCRC, TNFα, 6 hours, replicate #1

city: New Haven

first: Leyuan

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

data_processing:
Raw reads from RNA sequencing were aligned to mouse genome mm10 with STAR.
Gene expression levels were measured by FeatureCounts.
Differential expression analysis between different groups was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PCRC treated with TNFα

growth_protocol: Primary culture of renal cells (PCRCs) were isolated from Wild-type mice. Briefly, donor mouse kidneys were minced in 2 mm3 cubes with a razor blade, and incubated with Liberase (5 mL per kidney, 0.5 mg/mL, Roche), supplemented with DNaseI (100 µg/mL, Roche) and MgCl2 (0.1%) in PBS for 30 min with gentle pipetting every 10 min. The digested mixture was passed through a 70 µm cell strainer (Falcon) mounted on a 50 mL tube, rinsed with 45 mL ice-cold PBS, and spun down at 1,000 rpm for 5 min at 4 °C. The pellets containing single cells/tubule segments were resuspended with 3 mL red blood cell lysis buffer (Alfa Aesar) and incubated at room temperature for 3 min to lyse red blood cells. Primary culture was established in a complete medium: DMEM supplied with 10% FBS and Antibiotic-Antimycotic. After one medium change 48 hrs after seeding, the culture was continued for 3 more days

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) suppled with RNase-free DNase I treatment (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by the Yale Center for Genome Analysis (YCGA) core facility.

treatment_protocol:
PCRC were trypsinized and plated in 6-well plates in the complete media for 24 hrs and then treated with 20 ng/mL TNFα in the presence or absence of 1 µM ACHP for 6 hrs.
After treatment, cell lysates were prepared with RLT buffer (Qiagen) supplied with freshly added β-mercaptoethanol for RNA extraction.

value: PCRC

value: Primary cultured renal cells

value: Wild-type

value: TNFα

value: 6 hours


title: PCRC, TNFα, 6 hours, replicate #2


title: 2208L-Anti_PD1

description: cellranger demultiplexed


title: PCRC, TNFα, 6 hours, replicate #3


title: PCRC, TNFα+ACHP, 6 hours, replicate #1

source_name: PCRC co-treated with TNFα and ACHP

value: TNFα+ACHP


title: PCRC, TNFα+ACHP, 6 hours, replicate #2


title: PCRC, TNFα+ACHP, 6 hours, replicate #3


title: PCRC, PBS control, 6 hours, replicate #2

source_name: PCRC treated with PBS control

value: PBS


title: BM_Lin_neg_CD117_pos-ctrl-rep1

description: cellranger demultiplexed

value: bone marrow


title: PCRC, PBS control, 6 hours, replicate #1


title: 2208L-IACS_70654

description: cellranger demultiplexed


title: KLF4_IL4_rep1

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
Samples were processed using an in-house nextflow-based pipeline available at https://github.com/michaelbale/jlabflow
reads were trimmed using the Cutadapt wrapper trim-galore and mapped to mm10 with bowtie2 using --very-sensitive-local with a maximum insert size of 1000 bp. The initial bam file was then filtered for a minimum MAPQ of 30. Subsequently, PCR duplicates and reads mapping to the mitochondrial chromosome or within regions from a unified forbidden list from ENCODE and .Finally, only correctly mated mapped reads were retained. Peak calls were made using MACS2 on each individual sample and merged using the IDR framework within sample conditions in an iterative manner then merged across sample conditions for GRIP1 or retaining peaks that reciprocally overlapped each other’s lengths by at least 30% for KLF4. Finally, TMM-normalized signal tracks were visualized using deeptools bamCoverage with a calculated scaleFactor derived from the edgeR package calcNormFactors function.
Assembly: mm10
Supplementary files format and content: bw - TMM-normalized signal tracks in bigWig format
Library strategy: CUT&RUN

source_name: Bone marrow

growth_protocol: Bone Marrow derived macrophages were prepared from 8- to 10-week-old male mice.Bbone marrow was flushed from the femurs and tibiae of mice and differentiated for 5 days in the DMEM (1 g/l glucose) supplemented with 20% bovine serum and 10% L-cell conditioned media. Adherent cells were scraped, seeded into 150 mm or 6-well plates.

extract_protocol:
CUT&RUN assay was performed using the EpiCypher CUTANATM ChIC/CUT&RUN kit v2.1 according to manufacturer’s protocol. In brief, 106 cells were harvested for each condition, washed with 1X PBS, and resuspended in wash buffer, followed by incubation at RT for 10 min with activated Concanavalin A (ConA) beads. Cells were then permeabilized and incubated overnight on a nutator at 4°C with 1 μg of normal rabbit IgG (EpiCypher), KLF4 (proteintech, 1180-1-AP), or GRIP1 (Novus Biologicals, NB100-1756) antibody. Cell-bead antibody complex was then washed with cell permeabilization buffer and incubated with pAG-MNase (EpiCypher), followed by addition of 2 mM CaCl2 and incubation for 2 h at 4°C. Stop buffer was added to the reaction mixture and DNA fragments were released and purified with a CUTANA DNA purification kit (EpiCypher).
DNA library construction was performed using the NEBNext Ultra II DNA Library Prep Kit from NEB (E7645L). The libraries were sequenced on Illumina NovaSeq 6000 system (50 bp paired-end) at the Genomics Resources Core Facility at Weill Cornell Medicine

treatment_protocol: Adherent macrophages were  polarized for 24 h with 10 ng/ml IL4 or 100 nM Dex

value: Bone marrow

value: primary cells

value: Bone Marrow derived macrophages


title: GRIP1_IL4_rep3


title: GRIP1_IL4_rep2


title: GRIP1_Control_rep3

value: untreated


title: GRIP1_Dex_rep3

value: Dexamethasone, 100nm, 24h


title: KLF4_Dex_rep2


title: GRIP1_Control_rep2


title: GRIP1_IL4_rep1


title: GRIP1_Dex_rep2


title: KLF4_Dex_rep1


title: PCRC, PBS control, 6 hours, replicate #3


title: PG9VN brain, mouse ID 93, 7.5-month-old

city: Cincinnati

first: Yi

last: Lin

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital

data_processing:
Reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic (Version 0.33). A quality control check on the fastq files was performed using FastQC.
The trimmed reads were then mapped to a reference genome using default parameters with strandness option in Hisat2 (Version 2.0.5)
Transcript or gene abundance was determined using kallisto (Version 0.43.1)
A transcriptome index in kallisto was created using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and transcript per million (TPM)
Assembly: mm39
Supplementary files format and content: Excel file includes raw counts for all samples for each transcript and gene ID

source_name: Brain tissues containing thalamus, hypothalamus and midbrain

growth_protocol: WT, PG9V and PG9VN mice were maintained within the animal housing facilities at Cincinnati Children’s Hospital Medical Center (CCHMC).

extract_protocol:
Total RNAs were extracted from brain tissues using RNeasy Mini Kit (Qiagen, Tokyo, Japan).
Total RNA (150 to 300 ng) determined by Invitrogen Qubit high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit (Illumina, San Diego, CA, USA).

treatment_protocol: No treatment.


title: GRIP1_Control_rep1


title: PG9VN brain, mouse ID 76, 7.5-month-old

value: Brain tissues containing thalamus, hypothalamus and midbrain


title: PG9VN brain, mouse ID 75, 7.5-month-old


title: PG9V brain, mouse ID 146, 7.5-month-old


title: WT brain, mouse ID 113, 7.5-month-old

value: WT


title: WT brain, mouse ID 105, 7.5-month-old


title: PG9V brain, mouse ID 141, 7.5-month-old


title: KLF4_IL4_rep2


title: F36

city: San Francisco

first: Muriel

middle: Elisabeth

last: Babey

state: CA

address: 1550 4th Street

department: Department of Medicine, Division of Endocrinology

institute: University of California, San Francisco

data_processing:
For all tissue samples, sequencing-generated reads were aligned to the mouse transcriptome (mm10) using Kallisto in gene mode.
Differential gene expression was evaluated using the likelihood-ratio test by Sleuth (qval <0.05).
All heatmaps were generated with the top 50 female/male-biased genes obtained from 27-week-old mice and were generated in R.
Assembly: mm10
Supplementary files format and content: gene_quants

source_name: ARC

extract_protocol:
For ARC, total RNA was purified using the RNA Mini Kit (Invitrogen, Waltham MA).
For bulk-RNA-Seq analyses, barcoded sequencing libraries were prepared via NEBNext® Ultra™II RNA Library Prep Kit for Illumina® from RNA samples after a quality check (QC), and sequencing was performed on Illumina's NovaSeq 6000, S4 flow cell. These steps were carried out by Novogene (Davis, CA).

value: ARC

value: Ctrl

value: HFD


title: F13

value: NkxCre


title: F15


title: F19


title: F56

value: chow


title: F14


title: GRIP1_Dex_rep1


title: F60


title: F10


title: F9


title: P388

data_processing:
For all tissue samples, sequencing-generated reads were aligned to the mouse transcriptome (mm10) using Kallisto in gene mode.
Differential gene expression was evaluated using the likelihood-ratio test by Sleuth (qval <0.05).
All heatmaps were generated with the top 50 female/male-biased genes obtained from 27-week-old mice and were generated in R.
Supplementary files format and content: mm10
Supplementary files format and content: gene_quants

source_name: pituitary gland

extract_protocol:
For pituitary, total RNA was purified using the RNA Mini Kit (Invitrogen, Waltham MA).
For bulk-RNA-Seq analyses, barcoded sequencing libraries were prepared via NEBNext® Ultra™II RNA Library Prep Kit for Illumina® from RNA samples after a quality check (QC), and sequencing was performed on Illumina's NovaSeq 6000, S4 flow cell. These steps were carried out by Novogene (Davis, CA).

value: pituitary gland

value: Esr1Nkx2-1Cre mutant


title: F46


title: F5


title: F3


title: P391


title: P385


title: P390


title: P392


title: P387


title: WT brain, mouse ID 79, 7.5-month-old


title: PG9V brain, mouse ID 145, 7.5-month-old


title: P384

value: CHOW


title: P383


title: P359


title: P381


title: P382


title: P341


title: L339

data_processing:
For all tissue samples, sequencing-generated reads were aligned to the mouse transcriptome (mm10) using Kallisto in gene mode.
Differential gene expression was evaluated using the likelihood-ratio test by Sleuth (qval <0.05).
All heatmaps were generated with the top 50 female/male-biased genes obtained from 27-week-old mice and were generated in R.
Supplementary files format and content: ene_quants

source_name: liver

extract_protocol:
For liver, total RNA was purified using the Isolate II RNA Mini Kit (Bioline, Meridian Bioscience).
For bulk-RNA-Seq analyses, barcoded sequencing libraries were prepared via NEBNext® Ultra™II RNA Library Prep Kit for Illumina® from RNA samples after a quality check (QC), and sequencing was performed on Illumina's NovaSeq 6000, S4 flow cell. These steps were carried out by Novogene (Davis, CA).

value: liver

value: Mutant


title: P339


title: L328

value: Chow


title: P358


title: P356


title: L342


title: L325


title: L341


title: L316


title: L338


title: L326


title: L233


title: Wild type, Dexamethasone , 24h, rep4

description:
Chinenov_Deochand_submission_ATACseq_peak_count_matrix.csv
Chinenov_Deochand_submission_ATACseq_differential_peak_analysis_.csv

data_processing:
Paired-end reads are pre-processed using fastp which supports adapter trimming, low quality base trimming, and calculation of additional quality control metrics. Trimmed reads were aligned to the mm10 genome using bowtie2  with --very-sensitive-local -q -p options set. Low quality, improper, multimapping alignments, and PCR duplicates are filtered using SAMtools
Peaks are called on each sample (replicas are not pooled) with MACS2  using macs2 callpeak --nomodel --shift -100 --extsize 200 -q 0.05 options. After peak calling, all peaks from all samples called separately were combined and adjacent peaks (within 10bp) were merged. Reads from each sample within the combined set of peaks are then counted using featureCounts to produce an initial reads-per-peak count matrix. The ATACseq/CHIPseq pipeline is publicly available at https://gitlab.com/hssgenomics/pipelines/ATACseq.
The reads-per-peak counts were analyzed for differential peaks using the edgeR quasi-likelihood framework which allows for building complex modeling solutions not attainable by peak calling algorithms at the peak calling step (e.g., with MACS2 directly). Before the analysis, we removed poorly reproducible peaks containing zero reads in more than 3 samples within a group and peaks with the length of more >1000 base pairs. Modeling the replicated ATACseq data using the counts-per-peak framework allows us to calculate logFC, p-values, and FDR for each peak. All peaks were annotated to the nearest gene and TSS, if the peak overlaps an annotated Fantom5  enhancer, that enhancer is reported. Peaks with FDR<0.05 were considered differential.
Assembly: mm10
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: csv peak count matrices, differential peak analysis

source_name: Bone Marrow

growth_protocol: BMDM were prepared from 8- to 10-week-old male mice as previously describe . Briefly, bone marrow was flushed from the femurs and tibiae of mice and differentiated for 5 days in the DMEM (1 g/l glucose) supplemented with 20% bovine serum and 10% L-cell conditioned media

extract_protocol:
Briefly, 105 cells were lysed in ATAC lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and IGPAL CA-630] to isolate nuclei. The resultant nuclei were resuspended in the transposase reaction mix (25 μL x TD buffer (Nextera DNA Sample Preparation Kit), 5 μL Illumina Tn5 transposase, and 22.5 μL nuclease-free water and incubated at 37 °C on a thermomixer at 1000 rpm for 30 min. The transposed DNA was purified using a QIAGEN MinElute Purification Kit, then amplified using NEBNext High-Fidelity 2X PCR Master Mix and unique ATAC indexing primer for 10 cycles.
Post-amplification, libraries were double size-selected for removal of primer dimers and DNA fragments (>1000 bp). The amplified libraries were quality-controlled by Agilent BioAnalyzer and pooled. 50-bp paired-end sequencing was performed on an Illumina NovaSeq 6000 system

treatment_protocol: Adherent cells were scraped, seeded into 150 mm or 6-well plates and polarized for 24 h with 10 ng/ml IL4 or 100 nM Dex

value: Bone Marrow

value: primary cells

value: C57BL/6, LysM-Cre+/+ ; GRIP1wt/wt

value: Dexamethasone, 24 hours


title: Wild type, IL4, 24h, rep4

value: Bone Marrow derived macrophages

value: IL,4 24 hours


title: P357


title: Wild type, vehicle , 24h, rep4

value: Vehicle, 25 hours


title: Wild type, IL4, 24h, rep3


title: L324

value: Ctrl


title: L314


title: L315


title: L327


title: Wild type, Dexamethasone , 24h, rep2


title: L231

value: HFD


title: L234


title: L232


title: Wild type, vehicle ,24h, rep3


title: PTU exposed replicate 4 [M0718-15_serum]

city: Research Triangle Park

first: Katherine

last: O'Shaughnessy

state: North Carolina

address: 919 TW Alexander Drive

department: Public Health and Integrated Toxicology Division

institute: US Environmental Protection Ageny

description: Cell free total RNA

data_processing:
Adapters from the resulting reads were trimmed and aligned to the Rattus norvegicus reference genome (RGSC3.4) from the MirBase 20 annotation.
Differentially expressed miRNAs were identified by using EdgeR on data normalized using Trimmed Mean of M-values (TMM) in Bioconductor (http://www.bioconductor.org/).
Assembly: Rattus norvegicus reference genome (RGSC3.4) from the MirBase 20 annotation.
Supplementary files format and content: file resulting from the described analyses.

source_name: Long Evans

extract_protocol:
RNA was isolated using Qiagen’s miRNeasy Serum/Plasma kit.
Libraries were prepared using QIAseq miRNA Library Kit (Qiagen 331502) utilizing 22 cycles of PCR for cDNA amplification. Library quality was evaluated using Bioanalyzer 2100 (Agilent) and quantity by Qubit. All library samples were normalized to 4 nM, pooled.

treatment_protocol: Pregnant rats were exposed to 0 (control) or 3 ppm PTU through their drinking water through pregnancy or lactation. This exposure induced mild hypothyroidism in the mothers, and hypothyroidism in the offspring. On postnatal day 8 (PN8), serum was collected from 1 female pup/litter for miRNA-Seq.

value: Long Evans

value: Female

tag: cell population

value: Serum

tag: developmental stage

value: postnatal day 8 (PN8)

value: maternal PTU exposure (PTU)

tag: physiological stage

value: Hypothyroid


title: PTU exposed replicate 6 [M0718-4_serum]

description: Cell free total RNA


title: Wild type, IL4, 24h, rep1

tag: tissue

tag: cell type


title: Wild type, vehicle, 24h, rep2

tag: treatment


title: PTU exposed replicate 3 [M0718-13_serum]

description: Cell free total RNA


title: Wild type, Dexamethasone, 24h,  rep1


title: PTU exposed replicate 1 [M0718-10_serum]

description: Cell free total RNA


title: PTU exposed replicate 2 [M0718-11_serum]

description: Cell free total RNA


title: Control replicate 8 [M0718-9_serum]

description: Cell free total RNA

value: vehicle control (Control)

value: Euthyroid


title: GRIP1 KO, Dexamethasone, 24h, rep4

value: Bone Marrow

value: C57BL/6, LysM-Cre+/+; GRIP1fl/fl


title: GRIP1 KO, vehicle, 24h, rep4

value: primary cells


title: GRIP1 KO, IL4, 24h, rep4


title: Control replicate 7 [M0718-7_serum]

description: Cell free total RNA


title: Control replicate 6 [M0718-5_serum]

description: Cell free total RNA


title: Wild type, IL4, 24h,  rep2

value: C57BL/6, LysM-Cre+/+ ; GRIP1wt/wt


title: GRIP1 KO, IL4, 24h, rep3

value: Bone Marrow derived macrophages


title: Wild type, Dexamethasone , 24h, rep3

value: Dexamethasone, 24 hours


title: GRIP1 KO, Dexamethasone, 24h, rep3


title: GRIP1 KO, vehicle, 24h, rep3

value: Vehicle, 25 hours


title: Control replicate 4 [M0718-16_serum]

description: Cell free total RNA


title: Control replicate 5 [M0718-3_serum]

description: Cell free total RNA


title: PTU exposed replicate 5 [M0718-2_serum]

description: Cell free total RNA


title: GRIP1 KO, IL4, 24h, rep2

value: IL,4 24 hours


title: Control replicate 1 [M0718-1_serum]

description: Cell free total RNA


title: Wild type, vehicle, 24h, rep1


title: GRIP1 KO, IL4, 24h, rep1


title: GRIP1 KO, vehicle, 24h, rep2


title: Control replicate 2 [M0718-12_serum]

description: Cell free total RNA


title: Control replicate 3 [M0718-14_serum]

description: Cell free total RNA


title: GRIP1 KO, Dexamethasone, 24h, rep1


title: 4T1, adherent, DMSO sEVs treated, 72h, rep1

description:
D_A_72_1
GeneLevel_counts.xlsx
TMMnormalized_logCPM.xlsx

value: mammary breast cancer

value: DMSO_sEVs from primary neutrophils

value: adherent


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep4

data_processing:
Read quality filtering and adapter trimming were performed with fastp (0.23.2, ). Filtered reads were mapped to the mouse genome (mm10) with the STAR aligner (2.7.0) and exonic reads were counted against GENCODE release 27 annotation with featureCount  sing a customised pipeline available at https://gitlab.com/hssgenomics/pipelines/RNAseq.
Differential gene expression analysis was performed with edgeR(3.38.4, ) using quasi-likelihood framework. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. P values were adjusted to correct for multiple testing using the Benhamini-Hochberg FDR procedure. Genes with adjusted P values < 0.05 and log2 fold change >1 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes raw counts for  each sample
Supplementary files format and content: xlsx file with the results of differential analysis and datanormalization/transformation

extract_protocol:
Total RNA from macrophages treated as described in Figure legends was isolated using Qiagen RNAeasy Plus Mini kit
The Quality of total RNA was assessed using Agilent BioAnalyzer 2100 for RNA integrity. Samples with RIN>8 were used for library preparations. Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer’s instructions. Libraries quality was evaluated using Agilent BioAnalyzer 2100 and the libraries were sequenced by a NovaSeq 6000 system (50 bp, paired-end)

treatment_protocol: Adherent cells were scraped, seeded into 150 mm or 6-well plates and polarized for 24 h with 10 ng/ml IL4, 500 nM Cort or 100 nM Dex

value: Bone marrow derived macrophages


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep3


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep2


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Corticosterone – treated bone marrow derived macrophages, rep4

value: Corticosterone, 24 hours


title: GRIP1 KO, Dexamethasone, 24h, rep2


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Corticosterone – treated bone marrow derived macrophages, rep1


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Corticosterone – treated bone marrow derived macrophages, rep2


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Corticosterone – treated bone marrow derived macrophages, rep3


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours IL4 – treated bone marrow derived macrophages, rep4

value: IL4, 24hours


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours IL4 – treated bone marrow derived macrophages, rep1


title: GRIP1 KO, vehicle, 24h, rep1


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours IL4 – treated bone marrow derived macrophages, rep2


title: Prefrontal Cortex Female VPA Biological Rep 2

city: Guelph

first: Olivia

middle: Olga Fraser

last: Williams

state: ON

address: 50 Stone Road West

department: Biomedical Sciences

institute: Unviersity of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Porcine Gene 1.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

source_name: Female, VPA Autism

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: Prefrontal cortex tissue was dissected on postnatal day 0 (birth) from male or female rodents exposed to either saline (control) or valproic acid (VPA) (autism group) in utero

extract_protocol: not provided

treatment_protocol: Saline group: administered same volume saline by weight (0.9% saline) on gestation day 12.5 VPA group: concentration: 250mg/mL dose: 500mg/kg valproic acid dissolved in 0.9% saline injected on gestation day 12.5 in utero.

value: Sprague-Dawley

value: Female

tag: condition

value: Autism

tag: in utero exposure

value: VPA

value: Prefrontal cortex


title: Prefrontal Cortex Female VPA Biological Rep 3

tag: Sex


title: Prefrontal Cortex Male VPA Biological Rep 3

source_name: Male, VPA Autism

value: Male


title: Prefrontal Cortex Male VPA Biological Rep 2


title: Prefrontal Cortex Female VPA Biological Rep 4


title: Prefrontal Cortex Female VPA Biological Rep 1


title: Prefrontal Cortex Female VPA Biological Rep 5


title: Prefrontal Cortex Male VPA Biological Rep 5


title: LysM-Cre+/+; GRIP1fl/fl, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep1

value: Bone Marrow

value: primary cells

value: C57BL/6, LysM-Cre+/+; GRIP1fl/fl


title: Prefrontal Cortex Male VPA Biological Rep 4


title: Prefrontal Cortex Male VPA Biological Rep 1


title: Prefrontal Cortex Female Saline Control Biological Rep 5

source_name: Female, Saline Control

value: Control

value: SAL


title: Prefrontal Cortex Female Saline Control Biological Rep 2


title: LysM-Cre+/+; GRIP1fl/fl  , vehicle treated bone marrow derived macrophages, rep2

value: vehicle


title: Prefrontal Cortex Female Saline Control Biological Rep 4


title: LysM-Cre+/+; GRIP1fl/fl  , vehicle treated bone marrow derived macrophages, rep1


title: BL6, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep3

value: C57BL/6, LysM-Cre+/+ ; GRIP1wt/wt

value: Dexamethasone, 24 hours


title: Prefrontal Cortex Female Saline Control Biological Rep 1


title: Prefrontal Cortex Female Saline Control Biological Rep 3


title: Prefrontal Cortex Male Saline Control Biological Rep 4

source_name: Male, Saline Control


title: Prefrontal Cortex Male Saline Control Biological Rep 3


title: Prefrontal Cortex Male Saline Control Biological Rep 5


title: LysM-Cre+/+; GRIP1fl/fl  , vehicle treated bone marrow derived macrophages, rep3

value: Bone marrow derived macrophages


title: BL6, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep1


title: BL6, 24 hours Dexamethasone – treated bone marrow derived macrophages, rep2


title: LysM-Cre+/+; GRIP1fl/fl  , vehicle treated bone marrow derived macrophages, rep4


title: Prefrontal Cortex Male Saline Control Biological Rep 1


title: Prefrontal Cortex Male Saline Control Biological Rep 2


title: BL6, 24 hours Corticosterone – treated bone marrow derived macrophages, rep2

value: Corticosterone, 24 hours


title: BL6, 24 hours Corticosterone – treated bone marrow derived macrophages, rep1


title: BL6, 24 hours Corticosterone – treated bone marrow derived macrophages, rep3


title: BL6, 24 hours IL4 – treated bone marrow derived macrophages, rep3

value: IL4, 24hours


title: BL6, vehicle treated bone marrow derived macrophages, rep2


title: BL6, 24 hours IL4 – treated bone marrow derived macrophages, rep1


title: BL6, 24 hours IL4 – treated bone marrow derived macrophages, rep2


title: BL6, vehicle treated bone marrow derived macrophages, rep3


title: BL6, vehicle treated bone marrow derived macrophages, rep1


title: RNA-seq.LS10.Setd1bKO.rep2

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
Raw RNA-seq reads were firstly preprocessed to remove adapter contamination and low-qualified  sequences using trim_galore (version: 0.6.6) under paired-end mode, trimmed paired-end reads pairs shorter than 30bp were discarded.
Trimmed RNA-seq data were aligned to the mouse genome build mm10 using hisat2 (version: 2.2.1) with default parameters (--add-chrname), mapped RNA-seq reads in sam files were converted to bam files using ‘samtools sort’.
Mapped reads on transcripts of mm10 Refseq annotation were counted using htseq-count under the parameters: ‘-f bam -r pos -s no --nonunique all’ with bam files.
Differential expressed genes were identified using DEseq2 packages with the RNA-seq mapped reads counts on mm10 Refseq transcripts, under the parameters: Log2(Fold change)>=0.5 or <= -0.5, adjusted pvalue <= 0.05. Gene expression level (FPKM value) of each transcripts was calculated using FPKM_count.py in RSeQC package.
For the mm10 RefSeq genes, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values smaller than 0.5 were considered as indicative of unexpressed genes. Volcano plots for the visualization of differential expressed genes between adjacent stages were generated with "EnhancedVolcano" R package.
Assembly: mm10
Supplementary files format and content: FPKM, gene expression levels.
Supplementary files format and content: txt, reads counts on gene transcripts

source_name: Homogenous synchronous spermatogenic cells

growth_protocol: Briefly, 2-dpp mice were pipette fed 100 μg/g body weight WIN 18,446 (MP), suspended in 1% gum tragacanth, for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an i.p. injection of RA (Sigma; 30 μg/g body weight) in dimethyl sulfoxide (DMSO), and were then left to recover for sample collections. The undifferentiated spermatogonia was isolated from Lin28-YFP knockin mice. Testes from 3-week-old Lin28-YFP knockin mice were collected and digested by type I collagenase and 0.25% Trypsin as described previously1. After centrifugation, the pellet was resuspended in DMEM containing 2% BSA at a concentration of 1×106 cells/40 μL, followed by incubating with PE-conjugated anti-CD117 antibody (0.1 μg/106 cells; Molecular probes) for 30 min on ice. The undifferentiated spermatogonia (YFP-positive, PE-negative population) was collected using FACS (BD). The type A1 spermatogonia was isolated from synchronous Stra8-GFPCre mice. Testes were collected and digested. The type A1 spermatogonia (GFP-positive population) was collected using FACS. The type B spermatogonia and different stages of spermatocytes were isolated from synchronous Lin28-YFP and Vasa-tdTomato double positive mice. To isolate the type B spermatogonia, testes were digested and the synchronous advanced spermatogenic cells (tdTomato positive population) were collected using FACS. To isolate different stages of spermatocytes, testes were digested and the cell suspensions were stained with Hoechst 33342. The tdTomato positive 4N population were collected using FACS. The identity of sorted spermatocytes were validated using surface spreading and immunofluorescence.

extract_protocol:
ribo-minus total RNA
Total RNA were extracted from cells by using Trizol reagent (Thermo, 15596026). Total RNA were subjected to polyA selection by using Dynabeads mRNA purification kit (Thermo, 61006). 20 ng polyA RNA were used for library construction by using SMARTer Stranded RNA-seq kit (Takara, 634839).

treatment_protocol: Spermatogenesis was synchronized and validated as previously described.

value: Setd1b KO


title: RNA-seq.LS10.Setd1bKO.rep1

value: Homogenous synchronous spermatogenic cells


title: RNA-seq.LS10.WT.rep1

value: Wild type


title: RNA-seq.RS8.Setd1bKO.rep2


title: RNA-seq.LS10.WT.rep2


title: RNA-seq.RS8.Setd1bKO.rep1


title: RNA-seq.RS8.WT.rep2


title: RNA-seq.RS8.WT.rep1


title: RNA-seq.RS4.Setd1bKO.rep2


title: RNA-seq.RS4.WT.rep2


title: RNA-seq.RS4.WT.rep1


title: RNA-seq.Unsynchronized_RS.Setd1bKO.rep2

source_name: Unsynchronous spermatogenic cells

value: RS

value: Unsynchronous spermatogenic cells


title: RNA-seq.RS4.Setd1bKO.rep1


title: RNA-seq.Unsynchronized_RS.WT.rep1


title: RNA-seq.Unsynchronized_RS.WT.rep2


title: Renal cortex (GR KO, healthy), replicate 3

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

country: Germany

institute: German Cancer Research Center

description: Gene expression data from mouse renal cortex under homeostatic conditions (GR KO)

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data (CEL files) were background corrected, normalized and summarized using the rma function in the affy Bioconductor package and annotated on a transcript level using the getNetAffx function from the oligo package. Additional annotation was derived with the mogene10sttranscriptcluster.db package.

source_name: Mouse renal cortex (healthy mouse, genotype GR KO)

label_protocol: cDNA was fragmented and biotin-labeled using Nugen Encore Biotin Module (Nugen Technologies Inc.).

growth_protocol: Renal cortices for microarray analysis were freshly isolated from mouse kidneys and directly subjected to RNA isolation.

extract_protocol: Total RNA was isolated from renal cortices using RNeasy Micro Kit (Qiagen) and amplified using Nugen Ovation One-Direct System (Nugen Technologies Inc.).

treatment_protocol: Control and GR-deficient mice were intramuscularly injected with glycerol. A second cohort of mice was not injected (healthy mice). After 24 hours, the renal cortices were dissected from the kidneys.

value: tubular epithelial-specific glucocorticoid receptor deficient mice (Pax8-Cre;nr3c1 flox/flox)

tag: acute kidney injury

value: no


title: RNA-seq.Unsynchronized_RS.Setd1bKO.rep1

city: Shanghai


title: RNA-seq.RS8.rep1


title: iCD_hMES_5 (array)

type: genomic

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
CAT68_hMES
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 5

hyb_protocol: DNA samples were processed and hybridized to the Illumina EPIC array or the 850k Infinium Human-Methylation EPIC Bead Chip (Illumina Inc., San Diego, CA), developed to quantitatively assay more than 850,000 methylation sites across the genome at single-nucleotide resolution, following the Infinium HD Methylation Automated Assay Protocol with Illumina specified equipment and with hybridization setup and whasing and staining steps performed on a TECAN Evo 150 liquid handling instrument with Illumina control software.

scan_protocol: Hybridized Bead Chips were imaged on an Illumina HiScan system (Illumina Inc., San Diego, CA), following the manufacturer’s recommendations.

data_processing: Initial quality assessment was performed with Illumina Genome Studio (Illumina Inc., San Diego, CA),. Data were processed and analyzed with RnBeads, Minfi and BumpHunter softwares.

label: Cy3, Cy5

label_protocol: DNA (cytosine) methylation profiles were generated by combining bisulfite conversion of genomic DNA and whole-genome amplification with direct, array-based capture and scoring of the CpG (cyotosine-guanine) loci using the HD Infinium procedure following manufacturers specifications.

growth_protocol: Patients with CD, active and inactive, and controls were recruited at Joan XXIII Hospital (Tarragona, Spain) and Vall d’Hebron University Hospital (Barcelona, Spain) according to Helsinki’s statements. All participants gave their informed consent, and the study was reviewed and approved by the ethics and research committees of the respective hospitals (references CEIM 177/2018; CEIM 41p/2015; PR(CS)383/2021). Donors were classified as those in relapse (active) or in remission (inactive) following the Crohn’s Disease Activity Index (CDAI) criteria and also based on biological and clinical parameters such as high-sensitivity C-reactive protein (hsCRP) and fecal calprotectin levels. Endoscopic evaluation was performed in 80% of the patients, with complete correspondence with the clinical classification obtained by CDAI.2. Samples of visceral (VAT, mesenteric origin) AT and subcutaneous tissue (SAT) were obtained from patients with inactive CD (n=7) and from patients without CD (control group) (n=7) undergoing non-acute surgical interventions such as hernia or cholecystectomy, in a scheduled routine surgery. Samples of mesenteric perilesional (81% ileum, 5% colon and 14% ileocolon) “wrapping” VAT (creeping fat origin) (n=7) were obtained from patients with active CD scheduled for surgery for symptomatic complications or failure of medical therapy. All tissue samples were aseptically collected. Clinical data, anthropometric, demographic, and biochemical variables of the cohort are shown in Table 1. Groups were matched by body mass index (BMI), gender and age.

extract_protocol: Genomic DNA was extracted from cells using the NucleoSpin® Tissue Kit (Macherery-Nagel GmbH, Dueren, Germany).

treatment_protocol: Tissue samples were first washed with PBS to remove any traces of blood, and when needed, the parts damaged by the extraction were removed with a scalpel. The tissue was then treated with 0.1% collagenase with PBS and 1% BSA for 90 minutes at 37°C under gentle agitation. The digested samples were centrifuged at 300G at 24°C for 5 minutes to obtain a phase separation, with the mature adipocytes at the top, and the vascular stroma in the pellet, consisting of stem cells, macrophage cells, endothelial cells, blood cells, etc. Mature adipocytes were stored, and another wash and centrifugation was performed to isolate the stem cells (ASCs). The pellet resulting from this last centrifugation step was resuspended with DG maintenance medium (DMEM / F12 in 10% fetal bovine serum (FBS)), seeded in a T75 flask and left to grow for seven days in an incubator at 37°C. (Dubois et al. 2008).DNA for methylation assays was extracted from cells at passage 3 whereas RNA for transcriptomic profiling was estracted from cells at passage 4. Adipose tissue (VAT)-derived macrophages (ATMs) were also isolated from the stromal vascular fraction of AT biopsies as described.

tag: tissue type

value: Mesenteric fat, associated to healthy intestine

value: visceral adipose tissue

value: Adipose tissue derived stem cells

tag: individual

tag: gender

value: Female

tag: disease status

value: Inactive Crohn’s Disease

tag: bmi

tag: hospital

value: VH

tag: age

tag: tnf treated

value: Untreated


title: Renal cortex (GR KO, healthy), replicate 1

tag: genotype


title: aCD_hMES_7 (array)

description:
CAT78_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 7

value: Active Crohn’s Disease

value: Treated


title: iCD_hMES_3 (array)

description:
CAT73_hMES
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 3


title: aCD_hMES_4 (array)

description:
CAT75_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 4

value: Male


title: aCD_hMES_6 (array)

description:
CAT77_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 6


title: RNA-seq.RS8.rep2

tag: strain

tag: developmental stage


title: RNA-seq.RS4.rep2

tag: cell type


title: iCD_hMES_4 (array)

description:
CAT82_hMES
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 4

tag: tissue


title: aCD_hMES_3 (array)

description:
CAT74_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 3


title: RNA-seq.RS4.rep1


title: iCD_hMES_1 (array)

description:
CAT71_hMES
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 1


title: aCD_hMES_5 (array)

description:
CAT76_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 5


title: RNA-seq.RS2.rep2


title: aCD_hMES_2 (array)

description:
CAT17_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 2


title: RNA-seq.RS2.rep1


title: aCD_CF_6 (array)

description:
CAT86_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 6

value: Creeping fat, associated to inflamed intestine


title: RNA-seq.D.rep2

value: D

value: Homogenous synchronous spermatogenic cells


title: RNA-seq.D.rep1

value: Wild type


title: iCD_hMES_2 (array)

description:
CAT64_hMES
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 2


title: aCD_CF_4 (array)

description:
CAT69_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 4


title: aCD_CF_1 (array)

description:
CAT76_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 1


title: RNA-seq.mP.rep2

value: mP


title: RNA-seq.Z.rep2

value: Z


title: aCD_hMES_1 (array)

description:
CAT53_hMES
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 1


title: RNA-seq.mP.rep1


title: C_hMES_2 (array)

description:
AT205_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 2

value: Healthy


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep3 (BS-seq)

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
FastQC was used to check sequencing quality and clean reads were mapped to the Phaseolus vulgaris genome
Clean reads were mapped to the Phaseolus vulgaris genome version 2.1 using Bismark software (Krueger and Andrews, 2011). After mapping, deduplication of sequences and quantification of cytosine methylation was performed using Bismark_deduplicate and Bismark_methylation_extractor.
Each context of methylation was considered independently: CG, CHG, or CHH and corresponding bigwig files were generated using bismark_to_bigwig python script
Assembly: Phaseolus vulgaris genome version 2.1 (https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1)
Supplementary files format and content: Processed data are bw files for the whole genome at the three methylation context (cg, chg, chh)

organism: Phaseolus vulgaris

source_name: Mature seed (42DAP)

growth_protocol: Experiments were performed with a variety of common bean (Phaseolus vulgaris L. cv. Flavert) susceptible to common bacterial blight. Seeds were sown in pots containing one liter of soil substrate (Tray substrat, NF U 44–551, Klasmann- Deilmann GmbL, Rippert France). Plants were grown in a controlled growth chamber with 16 h of light at 23 °C and 8 h of darkness at 20 °C and a relative humidity (RH) of 70%. Plants were watered twice a week during the first three weeks and then with a nutrient solution (N/P/K=15/10/30).

extract_protocol:
we performed DNA extraction, on the three biological replicates of Xcf- and H2O-inoculated seeds at 42 DAP  (i.e. mature stage), using the NucleoSpin® DNA Food Kit (Macherey‐Nagel, Düren, Germany), according to the manufacturer’s instructions, then quantified DNA using a NanoDrop ND‐1000 (NanoDrop Technologies, Wilmington, DE, USA).
DNA samples were sent to the BGI for bisulfite treatment using a ZYMO EZ DNA Methylation‐Gold kit, library construction and paired‐end sequencing using DNBseq sequencing technology (PE100 45M).

treatment_protocol: Plants were spray-inoculated with water or bacterial suspension(106 CFU/ml) at the flower bud stage (R5 stage, Michael 1994). The day prior to inoculation, temperature (day 25°C/night 23°C) and relative humidity (RH, 95%) were increased. Inoculation was performed in a two-step protocol. First, small green flower buds were sprayed. Three days later, flower buds at the pollination stage were tagged. Then, a second inoculation was performed at one DAP (day after pollination) when tagged organs became open flowers. RH was reduced to 70% the day after to limit symptom development and seed abortion. Three independent replicates of 15 plants per treatment were inoculated. Pods of five plants per repeat were harvested at 42 DAP. Seeds were collected aseptically from pods to avoid contamination by contact with external bacterial populations on pods (Darsonval et al., 2008).

tag: cultivar

value: Flavert

value: Mature seed (42DAP)

tag: treatment

value: Xcf CFBP7767R

value: 47 DAP seed (mature)

value: Phaseolus vulgaris Flavert

value: Inoculated with Xcf 10power6 CFU ml-1 by spray-inoculation


title: C_hMES_7 (array)

description:
AT99_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 7

value: Mesenteric fat, associated to healthy intestine

value: visceral adipose tissue

value: Adipose tissue derived stem cells

value: Untreated


title: aCD_CF_3 (array)

description:
CAT84_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 3

value: Creeping fat, associated to inflamed intestine

value: Female

value: Active Crohn’s Disease

value: VH


title: RNA-seq.Z.rep1

value: Homogenous synchronous spermatogenic cells

value: Wild type


title: aCD_CF_2 (array)

description:
CAT77_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 2


title: C_hMES_4 (array)

description:
AT180_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 4

value: Male

value: Healthy


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep2 (BS-seq)

value: Flavert

value: Mature seed (42DAP)

value: 46 DAP seed (mature)


title: RNA-seq.L.rep1

value: L


title: C_hMES_3 (array)

description:
AT193_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 3


title: aCD_CF_5 (array)

description:
CAT80_CF
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 5


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep1 (BS-seq)

value: Xcf CFBP7767R

value: 45 DAP seed (mature)

value: Phaseolus vulgaris Flavert

value: Inoculated with Xcf 10power6 CFU ml-1 by spray-inoculation


title: RNA-seq.mPL.rep2

value: mPL


title: RNA-seq.L.rep2


title: Renal cortex (GR KO, AKI), replicate 2

description: Gene expression data from mouse renal cortex 24h after AKI (GR KO)

source_name: Mouse renal cortex (mouse with AKI, genotype GR KO)

value: tubular epithelial-specific glucocorticoid receptor deficient mice (Pax8-Cre;nr3c1 flox/flox)

value: yes


title: C_hMES_6 (array)

description:
AT261_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 6

value: Mesenteric fat, associated to healthy intestine

value: visceral adipose tissue

value: Adipose tissue derived stem cells

value: Untreated


title: Renal cortex (control, healthy), replicate 1

description: Gene expression data from mouse renal cortex under homeostatic conditions (control genotype)

source_name: Mouse renal cortex (healthy mouse, genotype control)

value: control (nr3c1 flox/flox)

value: no


title: Renal cortex (GR KO, healthy), replicate 2

description: Gene expression data from mouse renal cortex under homeostatic conditions (GR KO)


title: RNA-seq.mPL.rep1

value: Homogenous synchronous spermatogenic cells

value: Wild type


title: RNA-seq.TypeB.rep2

value: TypeB


title: 231_NTC_3

source_name: Cell Line

value: Cell Line

tag: cell line

value: Human Breast Cancer


title: RNA-seq.A1.rep2


title: RNA-seq.TypeB.rep1


title: 231_NTC_2


title: Renal cortex (control, healthy), replicate 3

tag: acute kidney injury


title: C_hMES_5 (array)

description:
AT211_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 5

tag: tissue type

value: Male

value: Healthy


title: Renal cortex (GR KO, AKI), replicate 1


title: Renal cortex (control, AKI), replicate 3

description: Gene expression data from mouse renal cortex 24h after AKI (control genotype)

source_name: Mouse renal cortex (mouse with AKI, genotype control)


title: C_hMES_1 (array)

description:
AT102_VAT
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 1

tag: individual

value: Female


title: Renal cortex (control, AKI), replicate 2


title: 42 DAP seed inoculated by water rep3 (BS-seq)

value: Flavert

value: Mature seed (42DAP)

value: no strain

value: 44 DAP seed (mature)

value: Phaseolus vulgaris Flavert

value: Inoculated by water


title: RNA-seq.A1.rep1


title: 231_NTC_1


title: Renal cortex (GR KO, AKI), replicate 3

value: tubular epithelial-specific glucocorticoid receptor deficient mice (Pax8-Cre;nr3c1 flox/flox)

value: yes


title: RNA-seq.Undiff.rep1

value: Undiff


title: RNA-seq.Undiff.rep2

value: Homogenous synchronous spermatogenic cells


title: 231_MN_Anti10b_3


title: Renal cortex (control, healthy), replicate 2

value: control (nr3c1 flox/flox)

value: no


title: 42 DAP seed inoculated by water rep2 (BS-seq)

value: 43 DAP seed (mature)


title: Renal cortex (control, AKI), replicate 1


title: 42 DAP seed inoculated by water rep1 (BS-seq)

value: 42 DAP seed (mature)


title: 231_MN_Anti10b_1

value: Cell Line

value: Human Breast Cancer


title: TAF3.Unsynchronized_RS.Setd1bKO.rep2

description:
TAF3.Unsynchronized_RS.Setd1bKO.merged.ext150.bigWig
TAF3_Unsynchronized_RS_Setd1bKO_peaks.bed

data_processing:
Raw ChIP-seq data were firstly preprocessed to eliminate adapter contamination and low-quality sequences using trim_galore (version: 0.6.6). Trimmed reads shorter than 30 bases were discarded.After trimming, the ChIP-seq data was aligned to the mouse genome build mm10 using bowtie2 (version: 2.4.1) with default parameters. The aligned reads were stored in sam files and then converted to bam files using 'samtools sort'. Duplicates were subsequently removed from the bam files using 'samtools rmdup'.
Uniquely mapped reads were extended to 150 bp using awk command, based on the average length of sonicated chromatin DNA fragments.
The uniquely mapped reads with 150bp extension were converted into base-resolution coverage data in bedGraph format using 'bedtools genomecov'. The resulting bedGraph files were then used to normalize the data based on spike-in reads. After normalization, the bedGraph files were converted to bigWig files using a public UCSC script. These bigWig files are suitable for use in downstream analysis and visualization.
These normalized bedGraph files were uploaded to UCSC genome browser for visualization.
Uniquely mapped reads with 150bp extension in bed format were also used to call peaks by comparing to Input using macs14 (version: 1.4.2) or macs2 (version: 2.2.7.1) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig, genome coverage signals.
Supplementary files format and content: bed, peaks

extract_protocol:
genomic DNA
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

value: RS

value: Unsynchronous spermatogenic cells

value: Setd1b KO

tag: chip antibody


title: 231_MN_Anti10b_2

data_processing:
Base calling - Illumina real-time analysis v. 3.4.4
Demultiplex/fastq conversion - Illumina Bcl2fastq v. 2.20.0
Quality Check - FastQC v. 0.11.7
Read Mapping - Bowtie2 v. 2.4.1
Read Counting - FeatureCounts/Subread v. 2.0.0
Assembly: Mouse - GRCm39/mm39; Human - GRCh38
Supplementary files format and content: 4T1-coldata.csv: DESeq2 experimental design for 4T1 data
Supplementary files format and content: 4T1-rawcounts.csv: raw transcript counts from FeatureCounts for 4T1 data
Supplementary files format and content: 231-coldata.csv DESeq2 experimental deisng for MDA-MB_231 data
Supplementary files format and content: 231-rawcounts.csv raw transcript counts from FeatureCounts for MDA-MB-231 data
Supplementary files format and content: 231and4T1-coldata.csv: DESeq2 experimental design for combined 4T1 and MDA-MB-231 data
Supplementary files format and content: 231and4T1-normalizedcounts.csv: Normalized transcript counts for all samples in this study calculated in DESeq2

extract_protocol:
RNA was extracted and purified using only the Zymo Quick-RNA 96 kit.
RNA sequencing was performed by the Michigan State University Genomics Core. Sequencing libraries were prepared using the Illumina stranded mRNA library prep kit (Illumina, catalog no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters following the manufacturer’s recommendations, except that half-volume reactions were performed. Libraries were assessed for quantity and quality using a combination of Qubit dsDNA HS (Thermo Fisher Scientific, catalog no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, catalog no. 5067-5584). Libraries were pooled in equimolar amounts, and the pool was quantified using an Invitrogen Collibri quantification quantitative PCR kit (Invitrogen, catalog no. A38524100). The pooled library was loaded onto two lanes of a NovaSeq S1 flow cell, and sequencing was performed in a 1 × 100-bp single-read format using a NovaSeq 6,000 v1.5 100-cycle reagent kit (Illumina, catalog no. 20028316). Base calling was performed with Illumina real-time analysis (version 3.4.4), and the output of real-time analysis was demultiplexed and converted to the fastq format with Illumina Bcl2fastq (version 2.20.0).


title: TAF3.Unsynchronized_RS.Setd1bKO.rep1


title: 231_MN_3


title: 231_MN_2


title: TAF3.Unsynchronized_RS.WT.rep2

description:
TAF3.Unsynchronized_RS.WT.merged.ext150.bigWig
TAF3_Unsynchronized_RS_WT_peaks.bed

value: Wild type


title: TAF3.Unsynchronized_RS.WT.rep1


title: Pol2-NTD.LS10.Setd1bKO.rep2

description:
Pol2-NTD.LS10.Setd1bKO.ext150.bigWig
Pol2-NTD_LS10_Setd1bKO_peaks.bed

value: Rpb1 NTD (D8L4Y) Rabbit mAb#14958


title: Pol2-NTD.LS10.WT.rep2

description:
Pol2-NTD.LS10.WT.ext150.bigWig
Pol2-NTD_LS10_WT_peaks.bed


title: Pol2-NTD.LS10.Setd1bKO.rep1


title: 231_MN_1


title: Pol2-NTD.RS8.Setd1bKO.rep1

description:
Pol2-NTD.RS8.Setd1bKO.ext150.bigWig
Pol2-NTD_RS8_Setd1bKO_peaks.bed


title: Pol2-NTD.RS8.Setd1bKO.rep2