title: Donor 2 Left Ventricle snRNA

city: La Jolla

first: Sebastian

last: Preissl

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: Libraries were sequenced on both Illumina NextSeq 500 and Illumina HiSeq 4000 instruments.

data_processing:
Raw sequencing data was demultiplexed and preprocessed using the Cell Ranger software package v3.0.2 (10x Genomics). Raw sequencing files were first converted from Illumina BCL files to FASTQ files using cellranger mkfastq. Demultiplexed FASTQs were aligned to the GRCh38 reference genome (10x Genomics), and reads for exonic and intronic reads mapping to protein coding genes, long non-coding RNA, antisense RNA, and pseudogenes were used to generate a counts matrix using cellranger count; expect-cells parameter was set to 5,000. A separate counts matrix for each sample was also generated using only reads mapped to intronic regions.  Next, exon + intron count matrices for individual datasets were processed using the Seurat v3.1.4 R package (https://satijalab.org/seurat/) to assess dataset quality. Features represented in at least 3 cells and barcodes with between 500 and 4,000 genes were used for downstream processing; additionally, barcodes with mitochondrial read percentages greater than 5% were removed. Counts were log-normalized and scaled by a factor of 10,000 using NormalizeData. To identify variable genes, FindVariableFeatures was run with default parameters except for nfeatures = 3000 to return the top 3,000 variable genes. All genes were then scaled using ScaleData, which transforms the expression values for downstream analysis. Next, principal component analysis was performed using RunPCA with default parameters and the top 3,000 variable features as input. The first 20 principal components were used to run clustering using FindNeighbors and FindClusters (parameter res = 0.4). To generate UMAP coordinates RunUMAP was run using the first 20 principal components and with parameters umap.method = “umap-learn”, and metric = “correlation”. Doublet scores (pANN) were generated for cell barcodes using DoubletFinder (https://github.com/chris-mcginnis-ucsf/DoubletFinder) using the parameters pN =0.15 and pK = 0.005; the anticipated collision rate was set by specifying 2% collisions per thousand nuclei for individual datasets.  Individual datasets were merged together using the merge function in Seurat to combine the count matrices and designate unique barcodes. Cell barcodes with pANN scores greater than 0 were removed from downstream analysis. Metadata was also encoded for each barcode, and the merged dataset was processed in a similar manner as described above; clusters were identified using FindNeighbors and FindClusters (res = 0.8). To generate the UMAP coordinates, the first 14 principal components were used in RunUMAP; the UMAP algorithm for Seurat v3.1.4 uses the uwot R-package, and that setting was used to generate the coordinates here. To regress out donor specific effects, the Harmony R package (https://github.com/immunogenomics/harmony)  was used, and the recomputed principal components were used to re-cluster the cells and rerun UMAP using the above parameters. For downstream analysis and comparison to snATAC-seq data we combined ventricular cardiomyocyte clusters, atrial cardiomyocyte clusters, fibroblast clusters, and endothelial cell clusters manually based on shared gene expression patterns. Cluster-specific genes in the all-transcripts dataset were identified in a global differential gene expression test using FindAllMarkers with parameters logFC = 0.25, min.pct = 0.25, and only.pos = FALSE.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file, Tab-delimited values and .mtx

source_name: adult human heart tissue

extract_protocol:
~40 mg of frozen heart tissue was suspended in 2 ml of MACS dissociation buffer (5 mM CaCl2 (G-Biosciences, R040), 2 mM EDTA (Invitrogen, 15575-038), 1X protease inhibitor (Roche, 05-892-970-001), 3 mM MgAc (Grow Cells, MRGF-B40), 10 mM Tris-HCl pH 8 (Invitrogen, 15568-075), 0.6 mM DTT (Sigma-Aldrich, D9779), and 0.2 U/µL of RNase inhibitor (Promega, N251B) in water (Corning, 46-000-CV)) and placed on wet ice. Next, samples were homogenized using gentleMACS dissociator (Miltenyi) with gentleMACS M tubes (Miltenyi, 130-096-335)) and the “Protein_01_01” protocol. Suspension was filtered through a 30 µM CellTrics filter (Sysmex, 04-0042-2316). M tube and filter were washed with 3 mL of MACS dissociation buffer and combined with the suspension. Suspension was centrifuged in a swinging bucket centrifuge (Eppendorf, 5920R) at 500 g for 5 minutes (4°C, ramp speed 3/3). Supernatant was carefully removed and pellet was resuspended in 500 µL of nuclei permeabilization buffer (0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X protease inhibitor (Roche, 05-892-970-001), 1 mM DTT (Sigma-Aldrich, D9779), 0.2 U/µL RNase inhibitor (Promega, N251B), and 2% BSA (Sigma-Aldrich, SRE0036) in PBS). Sample was incubated on a rotator for 5 minutes at 4°C and then centrifuged at 500 g for 5 minutes (Eppendorf, 5920R; 4°C, ramp speed 3/3). Supernatant was removed and pellet was resuspended in 600-1000 µl of sort buffer (1 mM EDTA and 0.2 U/µL RNase inhibitor in 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and stained with DRAQ7 (1:100, Cell Signaling, 7406). 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 µL of collection buffer (1 U/ µL RNase inhibitor, 5% BSA (Sigma-Aldrich, SRE0036) in PBS); Sorted nuclei were then centrifuged at 1000 g for 15 minutes (Eppendorf, 5920R; 4°C, ramp speed 3/3) and supernatant was removed.
Nuclei were resuspended in 18-25 ul of reaction buffer (0.2 U/µL RNase inhibitor, 1% BSA (Sigma-Aldrich, SRE0036) in PBS) and counted using a hemocytometer. 12,000 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Single Cell 3′ Library Construction Kit v3 (10x Genomics, 1000078) according to manufacturer specifications. cDNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp.
Single nucleus RNA-seq libraries were sequenced using a NextSeq500 and HiSeq4000 (Illumina) using these read lengths: Read 1: 28 cycles, Read 2: 91 cycles, Index 1: 8 cycles.

value: heart

value: 53 yr

value: M

tag: race

value: White


title: WT Cerebellum 19 months male mRNA rep2 [10_19_24_mo]

status: Public on Apr 01 2021

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description:
mRNA
C50118_7416_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to rat genome Rat.B6.0.
a) Trimmed low-quality bases from the reads, aligned reads to the rat reference genome (Ensembl R89) with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Rat.B6.0
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM and Count values for each Sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: Cerebellum

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Cerebellum

tag: genotype

value: Wild type

tag: age

value: 19 months

tag: Sex

value: male


title: Donor 1 Right Atrium snRNA

organism: Homo sapiens

value: 55 yr

value: F


title: HT-29_A_D2

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

country: China

institute: Chinese Academy of Science

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to human with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

molecule: polyA RNA

source_name: Colon tumor cell

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01)

value: Human Caucasian colon adenocarcinoma

tag: cell line

tag: treatment

value: vehicle


title: Donor 1 Right Ventricle snRNA


title: WT Cerebellum 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7448_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Donor 1 Left Atrium snRNA


title: Donor 2 Left Atrium snRNA


title: Donor 1 Left Ventricle snRNA


title: CARE_ATAC_4-RV

library_source: genomic

data_processing:
For each sequenced snATAC-Seq library, we obtained four FASTQ files, two for paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4). We selected all nuclei that had at least 1,000 unique fragments and a transcriptional start site enrichment of at least 7 for all data sets. For processing we adapted our previously published method, SnapATAC. We utilized two rounds of clustering analysis to identify clusters. The first round of clustering analysis was performed on individual samples using 5 kbp consecutive bins, generating a bin-by-cell binary matrix for each sample. We filtered out those bins that are generally accessible in all nuclei for each sample using z-score threshold 1.65. Based on the filtered matrix, we then carried out dimensionality reduction followed by graph-based clustering to identify cell clusters. We called peaks using MACS2 for each cluster using the aggregated profile of accessibility and then merged the peaks from all clusters to generate a union peak list. Based on the peak list, we generated a cell-by-peak count matrix and used Scrublet to remove potential doublets.  Next, to carry out the second round of clustering analysis, we merged peaks called from all samples to form a reference peak list. We generated a binary cell-by-peak matrix using nuclei from all samples and again performed the dimensionality reduction followed by graph-based clustering to obtain the final cell clusters across the entire dataset. To reduce the dimensionality of the peak by cell count matrix, SnapATAC utilizes spectral embedding for dimensionality reduction. To further increase the performance and scalability of spectral embedding, we applied the Nyström method to enable handling of large datasets. To correct for donor/batch specific effects, after dimensionality reduction we performed cell grouping on individual samples using k-mean clustering with k equal to 20. We then constructed k-NN graphs for each sample and used the MNN correction method to identify mutual nearest neighbors. These mutual nearest neighbors were used as the anchors to match the cells between different samples and correct for donor/batch effects as described previously.  We constructed the k-nearest neighbor graph (k-NNG) using low-dimensional embedding of the nuclei with k equal to 50. We then applied the Leiden algorithm with constant Potts model (CPM) to find communities in the k-NNG corresponding to the cell clusters. Nuclei from two small clusters (280 and 254 nuclei) with low reproducibility and stability were discarded from downstream analysis. 34 nuclei that formed clusters of 1 and 2 nuclei were discarded as well.   MACS2 (v2.1.2) was used to identify accessible chromatin sites for each cluster with the following parameters: -q 0.01 --nomodel --shift -100 --extsize 200 -g 2789775646 --call-summits --keepdup-all. Estimated genome size was determined to be 2789775646 bp and was indicated by the -g parameter. We next filtered out peaks overlapping with the ENCODE blacklist (hg38, https://github.com/Boyle-Lab/Blacklist/). To generate the union of heart cCREs, we merged the blacklist-filtered peaks obtained for each cluster using the BEDtools merge command with default settings (v2.25.0)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values, tab-separated text files and .mtx

molecule: genomic DNA

extract_protocol:
Nuclei were isolated in gentleMACS M tubes (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT). Nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and resuspended in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor). Nuclei were rotated at 4 ˚C for 5 minutes before being pelleted again with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer.
Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). During the sort, nuclei with 2-8 copies of DNA (2-8n) were included since cardiomyocyte nuclei in human hearts are often polyploid. Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent).
Single-nucleus ATAC-Seq libraries were sequenced on a NextSeq500 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: 67 yr


title: WT Cerebellum 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7388_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: female


title: WT Cerebellum 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7391_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cerebellum 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7373_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_4-LV


title: CARE_ATAC_3-RV

value: 48 yr

value: Hispanic


title: CARE_ATAC_3-RA


title: WT Cerebellum 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7413_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_3-LV


title: Q130 KI Cerebellum 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7429_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Q130 KI Het


title: CARE_ATAC_3-LA

value: heart


title: Q130 KI Cortex 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7470_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

source_name: Cortex

value: Cerebral Cortex


title: CARE_ATAC_2-RV

value: 53 yr

value: M


title: Q130 KI Cortex 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7399_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cerebellum 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7383_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Cerebellum


title: Q130 KI Cerebellum 19 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7372_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_2-LV_2

value: White


title: CARE_ATAC_2-LV


title: Q130 KI Cerebellum 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7381_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: 19 months


title: Q130 KI Cerebellum 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7472_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_2-LA


title: CARE_ATAC_1-RV


title: Q130 KI Cerebellum 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7455_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_1-LV


title: Q130 KI Cerebellum 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7442_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: CARE_ATAC_1-RA


title: WT Cerebellum 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7412_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Wild type


title: CARE_ATAC_1-LA

value: 55 yr


title: Q130 KI Cerebellum 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7470_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300130_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

source_name: Striatum

value: Corpus Striatum

value: 10 months

value: male


title: Q130 KI Cerebellum 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7378_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR12-5: CR12 IL-1 Ze14 10%

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

data_processing:
Filtering out reads mapping to rRNA, tRNA, mitochondrial RNA, and other contaminants (e.g., adapters, etc.) using bowtie2
Reads were aligned onto the human reference genome (UCSC hg19 annotation) and quantified with Star to give the Counts file
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: primary OA chondrocyte

growth_protocol: Primary OA chondrocytes were isolated from cartilage after enzymatic digestion and growth in monolayer in high glucose DMEM containing 10% FBS, 2mM glutamine, 50 µg/ml ascorbic acid and 20 µg/ml proline during 5-7 days

extract_protocol:
Three wells of 6-wells plate were pooled and scrapped in 600 µl RTL lysis buffer (Qiagen) then extract using Rneasy mini kit from Qiagen according to the manufacturer's instructions. Dnase step were performed during extraction. Samples were eluted in 30 µl RNase free H2O
One µg of RNA from each culture condition was used for this analysis. Libraries were prepared with the Illumina Truseq stranded mRNA sample prep kit according to the manufacturer's instructions

treatment_protocol: Chondrocytes are cultured in 1% FBS, glutamine, ascorbic acid and proline 24h than with or without IL-1b 10-11M or Ze14 (10 or 20%) in this media for 24h

tag: cell type

value: primary osteoarthritic chondrocyte

tag: patient

tag: il-1b treatment

tag: ze14 treatment


title: HEE-CR12-4: CR12 IL-1


title: HEE-CR12-6: CR12 IL-1 Ze14 20%


title: WT Striatum 10 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300127_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR12-3: CR12 Ze14 20%


title: HEE-CR12-2: CR12 Ze14 10%


title: HEE-CR12-1: CR12 control


title: WT Striatum 10 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300128_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300141_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: female


title: WT Striatum 10 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300131_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR11-6: CR11 IL-1 Ze14 20%


title: Q130 KI Cerebellum 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7399_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300139_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300137_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300140_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR11-5: CR11 IL-1 Ze14 10%


title: HEE-CR11-4: CR11 IL-1


title: HEE-CR11-3: CR11 Ze14 20%


title: Q130 KI Striatum 10 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300122_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300129_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR10-6: CR10 IL-1 Ze14 20%


title: Q130 KI Striatum 10 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300126_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR11-1: CR11 control


title: HEE-CR11-2: CR11 Ze14 10%


title: HEE-CR10-5: CR10 IL-1 Ze14 10%


title: HEE-CR10-4: CR10 IL-1


title: Q130 KI Striatum 10 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300123_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 10 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300125_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 10 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300124_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR10-3: CR10 Ze14 20%


title: Q130 KI Striatum 10 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300134_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 10 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300135_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR10-2: CR10 Ze14 10%


title: Q130 KI Striatum 10 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300132_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR09-6: CR09 IL-1 Ze14 20%


title: HEE-CR10-1: CR10 control


title: Q130 KI Striatum 10 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300136_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 10 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300133_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 10 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300138_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR09-4: CR09 IL-1


title: HEE-CR09-3: CR09 Ze14 20%


title: WT Cortex 10 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300127_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 10 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300129_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 10 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300128_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 10 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300131_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 10 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300130_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-6: CR08 IL-1 Ze14 20%


title: HEE-CR09-1: CR09 control


title: WT Cortex 10 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300141_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-5: CR08 IL-1 Ze14 10%


title: WT Cortex 10 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300138_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-3: CR08 Ze14 20%


title: WT Cortex 10 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300139_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 10 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300140_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-2: CR08 Ze14 10%


title: WT Cortex 10 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300137_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-4: CR08 IL-1


title: HEE-CR09-5: CR09 IL-1 Ze14 10%


title: Q130 KI Cortex 10 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300125_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 10 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300124_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR07-5: CR07 IL-1 Ze14 10%


title: HEE-CR07-6: CR07 IL-1 Ze14 20%


title: Q130 KI Cortex 10 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300122_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR07-4: CR07 IL-1


title: HEE-CR07-2: CR07 Ze14 10%


title: HEE-CR09-2: CR09 Ze14 10%


title: HEE-CR07-1: CR07 control


title: Q130 KI Cortex 10 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300136_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 10 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300123_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR06-6: CR06 IL-1 Ze14 20%


title: Q130 KI Cortex 10 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300133_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 10 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300134_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR06-4: CR06 IL-1


title: Q130 KI Cortex 10 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300135_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR08-1: CR08 control


title: HEE-CR06-3: CR06 Ze14 20%


title: Q130 KI Cortex 10 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300132_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 10 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
Q1300126_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HEE-CR06-2: CR06 Ze14 10%


title: HEE-CR04-6: CR04 IL-1 Ze14 20%


title: HEE-CR06-1: CR06 control


title: HEE-CR04-5: CR04 IL-1 Ze14 10%


title: HEE-CR07-3: CR07 Ze14 20%


title: Double+DC_node_CD11a.KO_R2

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

description:
mLN_DP_repB
mLN-B3_S89
Double+ DC isolated from node
read_counts_DC_CD11a_KO.txt

data_processing:
FastQ files underwent quality control check using FastQC (v0.11.7).
FastQ files were aligned to the reference genome using STAR (v2.6) with --quantMode GeneCounts --outFilterMultimapNmax 1 and --outFilterMatchNmin 35. For each dataset, we used a Star index with a --sjdbOverhang of the maximum read length -1.
Next, read counts were merged and genes with an average of < 1 read per sample were excluded.
Genome_build: Sequences were aligned to the genome and transcriptome GRCm38 (release 93).
Supplementary_files_format_and_content: read_counts_DC_CD11a_KO.txt: Table of per sample / gene read counts as generated by Star. Uses ENSEMBL gene IDs.

organism: Mus musculus

source_name: Double+ dendritic cells with CD11a KO

extract_protocol:
Cells were isolated from C57BL/6 mice that previously underwent complete mesenteric lymphadenectomy. ILCs were identified as live, single, CD45+ IL-7Rα+ lineage- (CD3, CD5, CD11b, CD11c, B220) cells and T cells as live, single, CD45+ CD11b- CD11c- B220- CD3+ CD5+ CD4+ CD44high CD25- cells. Cells for RNA seq were purified by flow cytometric sorting, collected into 350 μl RLT plus buffer (Qiagen) and stored at -80°C until further processing. Samples were sorted in quadruplicates and isolated cell types included migratory ILCs (n = 15) and T cells (n = 8) from afferent lymph of thoracic duct cannulated mice in steady state, ILCs (n = 4) and T cells (n = 4) from the colonic and small intestinal lamina propria at similar proportions, and migratory ILCs (n = 25) from afferent lymph of Salmonella infected mice that underwent thoracic duct cannulation. RNA was isolated according to the manufacturer’s protocol (RNeasy plus micro kit, Qiagen). CD11b+ CD103- and CD11b+ CD103+ DCs (live, single, CD45+, CD64- MHCIIhigh CD11c+) were isolated from the small intestinal lamina propria of C57BL/6 mice after removal of Peyer’s Patches. The migratory DC counterparts were isolated by thoracic duct cannulations of mice that previously underwent complete mesenteric lymphadenectomy. RNA was isolated according to the manufacturer’s protocol (RNeasy kit, Qiagen).
Libraries were prepared using the Smart-seq v4 ultra-low input kit (Takara Bio, Kusatsu, Japan).
Samples were sequenced to a mean depth of 37.5 million read pairs per sample using a HiSeq4000 (Illumina, San Diego, California, USA). The read length was 75bp.

treatment_protocol: C57BL/6 mice were either used at steady state or infected with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. For S. Typhimurium infections, mice received 20 mg streptomycin (Sigma) in 100 μl PBS via oral gavage 24h before infection with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. S. Typhimurium was grown in Luria broth (LB) at 37°C for 5h at 180 rpm. After incubation, the cultures were diluted 1:2 in LB and further kept in a static incubator overnight. The following day, bacterial cell density was adjusted to an OD600 of 0.75. Intact or lymphadenctomised mice received 5-8 x 10^7 colony forming units (CFU) bacteria in 100μl PBS via oral gavage.

value: Double+ dendritic cells

tag: strain

value: Intestinal lymph node

value: CD11a KO


title: HEE-CR04-2: CR04 Ze14 10%


title: Double+DC_node_CD11a.KO_R3

description:
mLN_DP_repC
mLN-C3_S84
Double+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: HEE-CR04-1: CR04 control


title: HEE-CR04-3: CR04 Ze14 20%


title: Double+DC_node_CD11a.KO_R1

description:
mLN_DP_repA
mLN-A3_S86
Double+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: CD103+DC_node_CD11a.KO_R3

description:
mLN_CD103_sp_repC
mLN-C2_S83
CD103+ DC isolated from node
read_counts_DC_CD11a_KO.txt

source_name: CD103+ dendritic cells with CD11a KO

value: CD103+ dendritic cells


title: HEE-CR03-6: CR03 IL-1 Ze14 20%


title: CD103+DC_node_CD11a.KO_R2

description:
mLN_CD103_sp_repB
mLN-B2_S88
CD103+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: HEE-CR03-5: CR03 IL-1 Ze14 10%


title: HEE-CR06-5: CR06 IL-1 Ze14 10%


title: CD103+DC_node_CD11a.KO_R1

description:
mLN_CD103_sp_repA
mLN-A2_S85
CD103+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: HEE-CR03-3: CR03 Ze14 20%


title: HEE-CR03-4: CR03 IL-1


title: SGC-7901/DDP cells_control_rep1

type: RNA

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

description: Gene expression in control group

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: SGC-7901/DDP cells_control

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Human GC cisplatin-resistant cell line SGC-7901/DDP was obtained from Transformation Research Center at People's Hospital of Gansu Province (Lanzhou, China). The cells were maintained in Roswell Park Memorial Institute 1640 (RPMI-1640) supplemented with 10% fetal bovine serum and cultured at 37 ℃ with 5% CO2.

tag: source

value: SGC-7901/DDP cells


title: HEE-CR03-2: CR03 Ze14 10%


title: CD11b+DC_node_CD11a.KO_R3

description:
mLN_CD11b_sp_repC
mLN-C1_S82
CD11b+ DC isolated from node
read_counts_DC_CD11a_KO.txt

source_name: CD11b+ dendritic cells with CD11a KO

value: CD11b+ dendritic cells


title: HEE-CR03-1: CR03 control


title: CD11b+DC_node_CD11a.KO_R2

description:
mLN_CD11b_sp_repB
mLN-B1_S87
CD11b+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: Double+DC_gut_CD11a.KO_R2

description:
LP_DP_repB
LP-B3_S90
Double+ DC isolated from gut
read_counts_DC_CD11a_KO.txt

value: Small intestinal lamina propria


title: HEE-CR02-6: CR02 IL-1 Ze14 20%


title: CD11b+DC_node_CD11a.KO_R1

description:
mLN_CD11b_sp_repA
mLN-A1_S94
CD11b+ DC isolated from node
read_counts_DC_CD11a_KO.txt


title: Double+DC_gut_CD11a.KO_R3

description:
LP_DP_repC
LP-C3_S93
Double+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: Double+DC_gut_CD11a.KO_R1

description:
LP_DP_repA
LP-A3_S97
Double+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: HEE-CR04-4: CR04 IL-1


title: HEE-CR02-5: CR02 IL-1 Ze14 10%


title: HEE-CR02-2: CR02 Ze14 10%


title: HEE-CR02-4: CR02 IL-1


title: CD103+DC_gut_CD11a.KO_R2

description:
LP_CD103_sp_repB
LP-B2_S99
CD103+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: CD103+DC_gut_CD11a.KO_R1

description:
LP_CD103_sp_repA
LP-A2_S96
CD103+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: HEE-CR02-3: CR02 Ze14 20%


title: CD103+DC_gut_CD11a.KO_R3

description:
LP_CD103_sp_repC
LP-C2_S92
CD103+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: CD11b+DC_gut_CD11a.KO_R3

description:
LP_CD11b_sp_repC
LP-C1_S91
CD11b+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: HEE-CR02-1: CR02 control


title: SGC-7901/DDP cells_2 μg/ml cisplatin_rep1

description: Gene expression in DDP group

source_name: SGC-7901/DDP cells_2 μg/ml cisplatin


title: SGC-7901/DDP cells_2 μg/ml cisplatin+47℃ hyperthermia for 24 h_rep1

description: Gene expression in DDP+HT group

source_name: SGC-7901/DDP cells_2 μg/ml cisplatin+47℃ hyperthermiafor 24 h


title: SGC-7901/DDP cells_47℃ hyperthermia for 24 h_rep1

description: Gene expression in HT group


title: CD11b+DC_gut_CD11a.KO_R2

description:
LP_CD11b_sp_repB
LP-B1_S98
CD11b+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: H9_SCRAM_6

city: Madison

first: Carissa

middle: L

last: Sirois

state: WI

address: 1500 Highland Ave T515

department: Waisman Center

institute: University of Wisconsin-Madison

data_processing:
Trimmomatic v0.36: Remove Illumina adapter contamination: java -jar /home/CAM/csirois/Trimmomatic-0.36/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 1 [Read1 file.fastq.gz] [Read2 file.fastq.gz] [Read1.Paired.output.fastqz.gz] [Read1.Unpaired.output.fastqz.gz] [Read2.Paired.output.fastq.gz] [Read2.Unpaired.output.fastq.gz] ILLUMINACLIP:/home/CAM/csirois/Trimmomatic-0.36/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10
STAR v2.5.3a: Align to genome and extract gene counts: STAR --runThreadN 8 --genomeDir /home/CAM/csirois/STARgenome_May2018/ --sjdbGTFfile /home/CAM/csirois/gencode.v24lift37.annotation.gtf --readFilesIn /home/CAM/csirois/Fastq_merge_May2018/H9_1_R1.fastq /home/CAM/csiirois/Fastq_merge_May2018/H9_1_R2.fastq --genomeLoad NoSharedMemory --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode GeneCounts --outFileNamePrefix H9_1new --outSAMtype BAM SortedByCoordinate
sva v3.28.0: Surrogate variable analysis on dds object and addition of surrogate variables to model
DEseq2 v1.20.0: Differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: tab file reports raw gene counts for each sample (generated using STAR --quantMode GeneCounts)

source_name: stem cell-derived neurons

growth_protocol: hESCs were grown and maintained as previously described (Chamberlain SJ, et al. (2010), Proc Natl Acad Sci U S A 107(41):17668-17673); hESC-derived neural progenitors and neurons were differentiated as previously described (Germain, ND, et al. (2014) Mol Autism 5:44)

extract_protocol:
RNA was harvested using RNA Bee reagent
RNA libraries were prepared using the Illumina TruSeq Stranded RNA Sample Prep Kit on 500 ng of total RNA

treatment_protocol: CORR iPSCs were obtained by editing AS iPSCs using CRISPR sgRNA and single-stranded oligonucleotide; UBE3Adel hESCs were obtained by editing H9 hESCs using CRISPR sgRNAs; ASO and SCRAM hESCs were obtained by treating H9 hESCs with a UBE3A-specific or scramble (non-specific) antisense oligonucleotide, respectively

tag: source of neurons

value: hESCs

value: H9 hESCs treated with scramble ASO

value: 10 weeks

value: Normal


title: CD11b+DC_gut_CD11a.KO_R1

description:
LP_CD11b_sp_repA
LP-A1_S95
CD11b+ DC isolated from gut
read_counts_DC_CD11a_KO.txt


title: B6CTRL4

city: New York

first: Daniel

middle: Fernando

last: Zegarra-Ruiz

state: NY

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

description: untreated mice

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
The expression count matrix from the mapped reads was computed using HTSeq (www-huber.embl.de/users/anders/HTSeq) and processed using DESeq (www-huber.embl.de/users/anders/DESeq) to normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: excel file includes a matrix table with normalized gene abundance for each sample

source_name: Thymus CD4 single positive cells

extract_protocol:
Tet+ and Tet- CD4 single positive thymic cells were sorted into Trizol LS.RNA was extracted using RNeasy mini kit (Qiagen) per manufacturer instructions. After ribogreen quantification and quality control by Agilent BioAnalyzer, total RNA was amplified using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing (12 cycles of amplification for 2–10 ng of total RNA).
10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 4000, in a 50-bp/50-bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Mice from the TET group were colonized with SFB at weaning. Two weeks later SFB-Tetramer+ CD4 thymic cells were sorted into Trizol LS and compared with age-matched CD4 thymic cells from CTRL mice for RNA-seq.

value: Thymus

value: 5 weeks of age


title: B6CTRL5

description: untreated mice


title: H9_SCRAM_1


title: H9_SCRAM_3


title: B6CTRL2

description: untreated mice


title: H9_SCRAM_4


title: B6CTRL3

description: untreated mice


title: H9_ASO_6

value: H9 hESCs treated with ASO targeting UBE3A


title: H9_ASO_5


title: B6CTRL1

description: untreated mice


title: H9_SCRAM_5


title: H9_SCRAM_2


title: ΔTE1+2 rep4

city: Evanston

first: Thomas

last: Bozza

address: 2200 Campus Drive

institute: Northwestern University

data_processing:
Reads were aligned to a modified GRCm38.p6 genome with extended TAAR annotation using STAR v2.6.0 with default parameters with the exception of --outFilterMultimapNmax 1
Reads were normalized using DESeq2 with default paramaters after filtering for nonexpressed genes
Differential expression was performed with DESeq2
Genome_build: Mus musculus Gencode build M21: GRCm38.p6
Supplementary_files_format_and_content: Excel file of DESeq2 output including normalized counts, p-value, error and significance

source_name: Olfactory mucosa

extract_protocol:
Olfactory mucosae were dissected and total RNA was isolated using Qiagen RNeasy Kit according to manufacturer's protocol.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit (ribodepleted) and 1 ug of total RNA according to standard Illumina protocols.

tag: genotype/variation

value: p30 T element deletion

value: post natal day 30

value: Male


title: H9_ASO_3


title: H9_ASO_4


title: H9_ASO_1


title: H9_ASO_2


title: H9_5

value: H9 hESC parent line

value: 12 weeks


title: H9_6


title: ΔTE1+2 WT rep2

value: control


title: ΔTE1+2 rep2


title: ΔTE1+2 WT rep4


title: H9_3


title: ΔTE1+2 rep3


title: ΔTE1+2 WT rep3


title: H9_4


title: H9_1


title: Mat_UBE3Adel_5

value: H9 hESCs with maternal copy of UBE3A deleted

value: Maternal UBE3A deletion (CRISPR-generated)


title: Mat_UBE3Adel_4


title: Prostate CD2 - F1

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 and bowtie2 v2.1.0 aligner.
Quantification of gene expression was performed using HTSeq v0.6.1 using gene annotations from Ensembl release 81.
Comparison between CD and control samples was performed using the method implemented in the DESeq2 Bioconductor library (DESeq2 v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: bam files and corresponding indexes, tsv files (F1 and F3) containing expressed genes

source_name: Prostate

extract_protocol:
Total RNA was extracted using the RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample Preparation Guide - PN 15031047, version Rev.E Oct 2013.

treatment_protocol: Pregnant mice (F0) were treated during development (E6.5-E15.5) at dose 100 µg/kg/day and the progeny of exposed mice (F1) were crossed for three generations. The prostate of the first (F1) and third generation males (F3) were used for RNA extraction.

value: chlordecone (kepone)-treated

value: Prostate

tag: generation


title: Prostate CD3 - F1


title: Prostate CD1 - F1


title: Prostate C3 - F1


title: Prostate C2 - F1


title: ΔTE1+2 rep1


title: Mat_UBE3Adel_3

value: hESCs


title: Prostate CD2 - F3


title: Mat_UBE3Adel_2


title: ΔTE1+2 WT rep1


title: Mat_UBE3Adel_1


title: Corrected_5

value: iPSCs

value: CRISPR-corrected version of AS patient-derived iPSCs

value: Normal (CRISPR-corrected)


title: Corrected_6


title: Prostate CD1 - F3


title: Corrected_4


title: H9_2

value: Normal


title: Prostate C3 - F3


title: Prostate C2 - F3


title: Corrected_3


title: Prostate C1 - F3


title: Corrected_2


title: Corrected_1


title: Mat_UBE3Adel_6


title: AS_Pt_Mut_6

value: AS patient-derived iPSCs

value: Maternal UBE3A point mutation


title: AS_Pt_Mut_5


title: Control 2 – F3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
For each condition, peaks were identified using MACS 2.1.1 using a shift-size window of 73 bp, no model, and a p-value threshold < 1e-05.
Identification of differential peaks was done using a in-house script: from all of the peaks called we retained only those peaks with average values above the 50th quintile. Then, we selected peaks with fold changes above 1.5 and FDR < 10%. Statistical significance was calculated using a Limma test.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files, bed file containing differential peaks.

extract_protocol:
We performed ChIP using 1µg of H3K4me3 (Merck Millipore, 07-473). Immunoprecipitated DNA was purified with Qiagen MinElute kit.
Diagenode MicroPlex Library Preparation kit v2.02.15

treatment_protocol: The exposure window was embryonic day E6.5 to E15.5. CD was suspended in olive oil and administered at a dose of 100 μg/kg/day in a volume of 150 μl for each mouse. The control mice were treated with the same volume of oil

tag: experimental condition

value: Control

tag: antibody


title: CD 1 – F3

tag: tissue

value: Chlordecone-derived


title: CD 2 – F1

value: Chlordecone-exposed


title: CD 2 – F3


title: Input

value: Control (Input)

value: input


title: Prostate CD3 - F3


title: AS_Pt_Mut_3

value: 12 weeks

tag: genotype


title: Control 1 – F3


title: CD 1 – F1


title: Control 2 – F1


title: AS_Pt_Mut_1

tag: age


title: AS_Pt_Mut_2


title: Single cell murine Adult SVF

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd.

institute: University of Pennsylvania

description:
10X Genomics Single Cell RNA-Seq
rawAdaorta.rds
anotatedAdaorta.rds

data_processing:
CellRanger v3
Seurat v3
Genome_build: mm10; GRCh38
Supplementary_files_format_and_content: CellRanger Outputs (Barcodes.tsv, genes.tsv, matrix.mtx) and Seuratv3 RDS Files,

source_name: Thoracic PVAT

extract_protocol:
For single cell, Aorta were isolated from mice, minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37oC with constant agitation at 200 rpm. To enrich for cell populations with differential sensitivity to digestion, we utilized the following procedures. For embryonic/newborn mice, 20% of the digestion was quenched at 15 minutes, 20% at 20 minutes and the remaining 60% at 25 minutes (embryos/perinatal). For adult aortas 50% of the digestion was quenched at 30 minutes, 50% at 60 minutes. Single cells were isolated from dissected aortas and flow sorted to isolate live (DAPI-) cells and remove debris. Cells were collected as either CD45+ (immune) and CD45- (non-immune) cells. For adult single cell RNA Sequencing, CD45+ cells were mixed with CD45- cells to achieve a proportion of ~20%. For single nuclei experiments, 40-80 mg of frozen human PVAT was dounce homogenized using a glass homogenizer (Sigma-Aldrich, 7 mL) on ice in 2.5 mL homogenization buffer (0.32 M sucrose (Sigma, RNase & DNase free ultra pure grade), 5 mM CaCl2 (Sigma), 3 mM MgAc2 (Sigma-Aldrich), 10 mM Tris-HCl pH 8.0 (FisherChem), 0.1% TritonX-100 (Amresco), 0.1 mM EDTA (Fischer), protease inhibitor cocktail (Roche)) and layered into ultracentrifuge tubes (Beckman Coulter) over 12 mL sucrose cushion (1.8 M sucrose, 10 mM Tris-HCl pH 8.0 (FisherChem), 3 mM MgAc2 (Sigma-Aldrich), protease inhibitor cocktail (Roche) and topped with 14.5mL homogenization buffer. Samples were ultracentrifuged (Beckman Coulter L-70K) using a swinging bucket rotor (Beckman Coulter SW28) at 25,000 rpm for 2 hrs at 4°C. The supernatant was aspirated to remove debris and the nuclear pellet was resuspended in 1 mL of DPBS (Corning) with RNase inhibitor (Lucigen). Samples were filtered and nuclei were counted before loading for snRNA-Seq
For single cell experiments, single cell transcriptomes were collected  previously using the 10X Genomics platform with v2 (perinatal) and v3 (adult) chemistry (10× Genomics, Pleasanton, CA) and sequenced on Illumina HiSeq 4000. For single nucleus experiments, single nucleus transcriptomes were collected  using the 10X Genomics platform  v3 (adult) chemistry (10× Genomics, Pleasanton, CA) and sequenced on Illumina NovaSeq 6000.

value: 13 weeks

tag: gender

value: Male

value: Thoracic PVAT


title: Single cell murine P3 aortic SVF

description:
10X Genomics Single Cell RNA-Seq
rawPVAT.Integrated.rds
annotatedPVAT.Integrated.rds
rawP3aorta.rds
anotatedP3aorta.rds

value: Postnatal Day 3

value: Mixed male and female


title: Control 1 – F1

value: Prostate


title: Single cell murine E18 aortic SVF

description:
10X Genomics Single Cell RNA-Seq
rawPVAT.Integrated.rds
annotatedPVAT.Integrated.rds

value: Embryonic Day 18


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) Progenitors [Prog3]

data_processing:
Samples were sequenced on an Illumina HiSeq with a 2x150 Paired End (PE) configuration to generate FASTQ files
FASTQ files were aligned to mm10 using STAR (2.5.2a) with quantMode = GeneCounts
The unstranded genecounts for each sample were analyzed for differential gene expression using the R (3.6.3) package DESeq2 (1.26.0).
DESeq2 model was built with the design (~CellType) where “CellType” refers to the different sorted populations, with all CellTypes included in the model, and Raw gene count data, DESeq2 normalized gene count data, and RLD (regularized log transformed data) were extracted from the resulting DeSeq2 object
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts, DESeq2 Normalized Gene Counts, DESeq2 RLD (Regularized log transformed) Gene Counts

source_name: Mouse pup thoracic aorta PVAT

extract_protocol:
The inguinal white adipose tissue and the aorta along with associated perivascular adipose tissue were isolated from P3 mice (Biological replicates represent tissues from the same pools of mice. I.e. PVAT_Rep1 and Inguinal_Rep1 contain tissue from the same individuals). Tissues were minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37C with constant agitation at 200 rpm. FACS was performed as decribed in the manuscript to isolate intermediate cells, progenitor cells, preadipocytes, and smooth muscle cells. Cells were sorted into FBS catch buffer. After sorting, cells were spun down and the cells were resuspended in 250uL of FACS buffer. Cells were then lysed with the addition of 750uL of Trizol LS (Invitrogen) and RNA was purified by phenol chloroform extraction.
Genewiz Ultra Low Input Library Protocol "RNA was quantified using Qubit and TapeStation. RNA sequencing libraries were made using the SMART-Seq v4 Ultra Low Input Kit. This library prep uses Poly(A) selection to target mRNA, with enrichment for full length transcripts."

value: 3 days old (p3)

value: Thoracic aorta perivascular fat


title: KO_h3k4me3.2

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis

description:
KO_h3k4me3
KO_h3k4me3_minus_KO_igg.pooled.fc.signal.bigwig
KO_h3k4me3.epic2.naive_overlap_peaks.txt.gz

data_processing:
Sequencing reads were demultiplexed and processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with the “histone” option (https://github.com/ENCODE-DCC/chip-seq-pipeline2, version v1.1.6-10-gd4f6442) (Roadmap Epigenomics et al., 2015), which aligns reads to human genome (hg19) by bowtie2, and generates signal strength relative to the control samples using MACS2
epic2 were used to call peaks for the histone markers.
The stables sets of peaks were determined using the "naive ovelap" strategy as used in the ENCODE-chipseq pipline, i.e.,  peaks were called with the pooled reads, and 2 partions of the pooled psuedoreplicates, separately, using relaxed threshold of p<0.05; stable peaks are subset of the peaks from the pooled reads, which overlap at least 50% with peaks from both pseudoreplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for signal strength, tab-delimited text files for called peaks

source_name: human induced pluripotent stem cells

extract_protocol:
Cells extracted after 70% confluency, sonicated by using COVARIS, Histone -DNA complex extracted by using antibdy.
ChIPmentation protocol bySchimdl et al.,2015


title: KO_h3k27me3.1

description:
KO_h3k27me3
KO_h3k27me3_minus_KO_igg.pooled.fc.signal.bigwig
KO_h3k27me3.epic2.naive_overlap_peaks.txt.gz


title: KO_h3k27ac.1

description:
KO_h3k27ac
KO_h3k27ac_minus_KO_igg.pooled.fc.signal.bigwig
KO_h3k27ac.epic2.naive_overlap_peaks.txt.gz


title: KO_h3k27me3.2


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) Progenitors [Prog2]


title: KO_h3k27ac.2


title: AS_Pt_Mut_4

value: iPSCs

value: AS patient-derived iPSCs


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) Progenitors [Prog1]


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) PreAdipocytes [PreAd3]


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) PreAdipocytes [PreAd2]


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) ICAM1+ PreAdipocytes [ICAM13]

source_name: Mouse pup IWAT

value: Inguinal white adipose tissue


title: KO_igg.1

value: igg


title: KO_h3k4me1.1

description:
KO_h3k4me1
KO_h3k4me1_minus_KO_igg.pooled.fc.signal.bigwig
KO_h3k4me1.epic2.naive_overlap_peaks.txt.gz


title: BJFF_h3k27me3.2

description:
BJFF_h3k27me3
BJFF_h3k27me3_minus_BJFF_igg.pooled.fc.signal.bigwig
BJFF_h3k27me3.epic2.naive_overlap_peaks.txt.gz

value: WT


title: KO_h3k4me1.2


title: BJFF_h3k27me3.1


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) ICAM1+ PreAdipocytes [ICAM11]


title: BJFF_h3k27ac.2

description:
BJFF_h3k27ac
BJFF_h3k27ac_minus_BJFF_igg.pooled.fc.signal.bigwig
BJFF_h3k27ac.epic2.naive_overlap_peaks.txt.gz


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) DPP4+ Progenitor Cells [DPP42]


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) DPP4+ Progenitor Cells [DPP41]


title: BJFF_h3k4me3.1

description:
BJFF_h3k4me3
BJFF_h3k4me3_minus_BJFF_igg.pooled.fc.signal.bigwig
BJFF_h3k4me3.epic2.naive_overlap_peaks.txt.gz


title: KO_h3k4me3.1


title: Bulk RNA Seq of FACS Sorted Pup Perivascular SMCs [SMC3]

source_name: Mouse Pup Aorta and Perivascular Adipose Tissue

extract_protocol:
Aortas along with associated perivascular adipose tissue were isolated from P3 mice, minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37C with constant agitation at 200 rpm. FACS was performed as decribed in the manuscript to isolate intermediate cells, progenitor cells, preadipocytes, and smooth muscle cells. Cells were sorted into FBS catch buffer. After sorting, cells were spun down and the cells were resuspended in 250uL of FACS buffer. Cells were then lysed with the addition of 750uL of Trizol LS (Invitrogen) and RNA was purified by phenol chloroform extraction.
Genewiz Ultra Low Input Library Protocol "RNA was quantified using Qubit and TapeStation. RNA sequencing libraries were made using the SMART-Seq v4 Ultra Low Input Kit. This library prep uses Poly(A) selection to target mRNA, with enrichment for full length transcripts."

value: 3 days old (P3)

value: Aorta and Perivascular Adipose Tissue


title: BJFF_h3k4me1.2

description:
BJFF_h3k4me1
BJFF_h3k4me1_minus_BJFF_igg.pooled.fc.signal.bigwig
BJFF_h3k4me1.epic2.naive_overlap_peaks.txt.gz


title: Bulk RNA Seq of FACS Sorted Pup Perivascular SMCs [SMC2]


title: Donor 2 Right Ventricle snRNA

description: Libraries were sequenced on both Illumina NextSeq 500 and Illumina HiSeq 4000 instruments.

source_name: adult human heart tissue

value: heart

value: 53 yr

tag: Sex

value: M

tag: race

value: White


title: BJFF_igg.1


title: KO_igg.2


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Progenitor Cells [Prog2]


title: BJFF_h3k27ac.1


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Progenitor Cells [Prog3]


title: Bulk RNA Seq of FACS Sorted Pup Perivascular SMCs [SMC1]


title: Bulk RNA Seq of FACS Sorted Pup Perivascular PreAdipocytes [PreAd3]


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Progenitor Cells [Prog1]


title: Bulk RNA Seq of FACS Sorted Pup Perivascular PreAdipocytes [PreAd2]


title: BJFF_igg.2


title: KMT2C KO Rep2

description:
undifferentiated cells, 70% confluency
KMT2CKO
KMT2CKO_atac.pooled.fc.signal.bigwig
KMT2CKO_atac.idr.optimal.narrowPeak.gz

data_processing:
Sequencing reads were demultiplexed and aligned to human genome (hg19) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, narrowPeak

extract_protocol:
N/A
we used the Assay for Transposase Accessible Chromatin (ATAC-seq) protocol optimized by Semenkovich (SEMENKOVICH et al., 2016).

tag: cell type

value: human induced pluripotent stem cells

value: KMT2C KO


title: KMT2C KO Rep1


title: WT Rep2

description:
undifferentiated cells, 70% confluency
BJFF
BJFF_atac.pooled.fc.signal.bigwig
BJFF_atac.idr.optimal.narrowPeak.gz


title: WT Rep1


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) ICAM1+ PreAdipocytes [ICAM12]

value: Mixed male and female


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Intermediate Cells [Int3]


title: BJFF_h3k4me1.1


title: Bulk RNA Seq of FACS Sorted Pup Perivascular PreAdipocytes [PreAd1]


title: ATACseq_K562_HSS_pC60_rep2

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

description: Normalized_ATACseq_K562_HSS_pC60_BRs.bigWig

data_processing:
The paired-end reads were aligned to hg19 using Bowtie2 (Langmead et al., 2009).
Sam files were converted to bam files using samtools (Li et al., 2011) and to bed files using bedtools (Quinaln and Hall., 2009)
ATAC-seq enriched 'peaks' were called with MACS2 using bam files from all the samples, and correlation between replicated verified by analysing the correlation of read counts at each peak.
The replicate combined bed files were processed to FPM-normalized bedgraph and bigwig files.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized and replicate-combined bigWig files, reporting the whole Tn5-released fragment.

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
After treatments, the cells were harvested by centrifugation, and washed twice with PBS. Chromatin was isolated as in Chu et al., 2018, Nature Genetics, 50: 1553–1564 and run-on reactions performed with biotinylated nucleotides as described by Kwak et al., 2013, Science, 339:950-953. The run-on reaction was conducted in the presence of chromatin from S2 cells, which provides an invariant whole-genome spike-in control between samples.
The libraries were generated using Nextera adaptors. Half of the libraries were amplified for 12 cycles, after which the libraries were purified and size-selected with Ampure XP beads. Distinct libraries were combined for NextSeq 500 (Illumina) sequencing.

treatment_protocol: Preconditioning of K562 cells was conducted by submerging the cells into a 42°C heat bath. For preconditioning with a single heat shock (s_) the cells were retained in the 42C water bath in a culture flask for 1-hour. Preconditioning with multiple heat shocks (HS serie, HSS_) was conducted by submerging the cells in culture flask in total of nine 1-hour heat treatments at 42C water bath. These nine 1-hour heat shock treatments were divided to three heat treatments per day for three consecutive days. Recovery from the stress (inbetween heat shocks of the HSS, as well as after the single or HSS preconditioning) was conducted by placing the cells into a 37°C incubator. After the preconditioning (s_ and HSS_), the cells were allowed to recover for 48h in a 37°C incubator, during which they underwent two mitotic divisions. After preconditioning with multiple heat shocks, an additional heat shock was conducted by submerging cells in 10 mL culture media into 42C water bath and the cells were harvested at 30-minute and 60-minute time points. Cells that were not subjected to an (additional) heat shock exposure were also condensed to 10 mL, culture media, but maintained at 37C. After preconditioning with the single heat shock exposure, chromatin accessibility was tracked during rapid kinetics of heat-induced changes in transcription by collecting the cells at 12.5-minute, 25-minute, and 40-minute heat shock time points. The additional after the single heat shock preconditioning was conducted by centrifuging the cells, removing the supernatant and adding preconditioned media (cell-free media isolated from the same culture right before the treatment) that was prewarmed to 42C. Once suspended into the prewarmed preconditioned media, the cell suspension was placed to 42C water bath for the indicated time point. Cells with no (additional) heat shock treatment (uC0 and p0) were subjected to the same conditions, but 37C preconditioned media was used and the cells maintained at 37C.

tag: cell line

tag: preconditioning

value: 9 x 1h heat shock at 42C (divided to 3 consecutive days), followed by 48 h recovery at 37 C

tag: heat shock (additional to preconditioning)

value: 60 min at 42C water bath


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC2 Cells [Ao3-SMC_2]

source_name: Adult Aorta and Perivascular Adipose Tissue

extract_protocol:
Aortas along with associated perivascular adipose tissue were isolated from adult mice, minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37oC with constant agitation at 200 rpm. FACS was performed as decribed in the manuscript to isolate intermediate cells, progenitor cells, and smooth muscle cell populations SMC1 and SMC2. Cells were sorted into FBS catch buffer. After sorting, cells were spun down and the cells were resuspended in 250uL of FACS buffer. Cells were then lysed with the addition of 750uL of Trizol LS (Invitrogen) and RNA was purified by phenol chloroform extraction.
Genewiz Ultra Low Input Library Protocol "RNA was quantified using Qubit and TapeStation. RNA sequencing libraries were made using the SMART-Seq v4 Ultra Low Input Kit. This library prep uses Poly(A) selection to target mRNA, with enrichment for full length transcripts."

value: 13 weeks

value: Male

tag: strain

value: Perivascular SMC2 Cells


title: ATACseq_K562_HSS_pC30_rep2

description: Normalized_ATACseq_K562_HSS_pC30_BRs.bigWig

value: 30 min at 42C water bath


title: ATACseq_K562_HSS_pC60_rep1


title: ATACseq_K562_HSS_pC0_rep2

description: Normalized_ATACseq_K562_HSS_pC0_BRs.bigWig

value: no additional heat stress applied


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC1 Cells [Ao3-SMC_1]

value: Perivascular SMC1 Cells


title: Bulk RNA Seq of FACS sorted P3 Inguinal White Adipose Tissue (IWAT) DPP4+ Progenitor Cells [DPP43]

value: 3 days old (p3)

value: Inguinal white adipose tissue


title: ATACseq_K562_HSS_pC0_rep1


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Progenitor Cells [Ao3-Prog]

value: Aorta and Perivascular Adipose Tissue

value: Perivascular Progenitor Cells


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Intermediate Cells [Ao3-Int]

value: Perivascular Intermediate Cells


title: ATACseq_K562_HSS_uC60_rep2

description: Normalized_ATACseq_K562_HSS_uC60_BRs.bigWig


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC2 Cells [Ao2-SMC_2]


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC1 Cells [Ao2-SMC_1]


title: ATACseq_K562_HSS_uC30_rep2

description: Normalized_ATACseq_K562_HSS_uC30_BRs.bigWig


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Progenitor Cells [Ao2-Prog]


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC2 Cells [Ao1-SMC_2]


title: ATACseq_K562_HSS_uC0_rep2

description: Normalized_ATACseq_K562_HSS_uC0_BRs.bigWig

value: no heat stress applied


title: ATACseq_K562_HSS_uC30_rep1


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Intermediate Cells [Int2]

value: 3 days old (P3)


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Intermediate Cells [Ao2-Int]


title: ATACseq_K562_HSS_uC0_rep1


title: Bulk RNA Seq of FACS Sorted Adult Perivascular SMC1 Cells [Ao1-SMC_1]


title: Bulk RNA Seq of FACS Sorted Pup Perivascular Intermediate Cells [Int1]


title: ATACseq_K562_s_pC40_rep2

description: Normalized_ATACseq_K562_s_pC40_BRs.bigWig

value: 1h heat shock at 42C water bath, followed by 48 h recovery at 37 C

value: 40 min at 42C water bath (initiated with prewarmed preconditioned media)


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Progenitor Cells [Ao1-Prog]


title: Bulk RNA Seq of FACS Sorted Adult Perivascular Intermediate Cells [Ao1-Int]


title: ATACseq_K562_s_pC40_rep1


title: ATACseq_K562_HSS_pC30_rep1

value: 9 x 1h heat shock at 42C (divided to 3 consecutive days), followed by 48 h recovery at 37 C


title: ATACseq_K562_s_pC25_rep1

description: Normalized_ATACseq_K562_s_pC25_BRs.bigWig

value: 25 min at 42C water bath (initiated with prewarmed preconditioned media)


title: ATACseq_K562_s_pC12p5_rep2

description: Normalized_ATACseq_K562_s_pC12p5_BRs.bigWig

value: 12.5 min at 42C water bath (initiated with prewarmed preconditioned media)


title: ATACseq_K562_s_pC25_rep2


title: Allongeneic recipient biological rep3 [A4]

city: Ann Arbor

first: Keisuke

last: Seike

state: MI

address: 1500 E. Medical Center Drive

department: Internal Medicine

institute: University of Michigan

data_processing:
Mapping was done with STAR against the Mouse genome (mm10) with the default options and --quantMode geneCounts
Differential gene expression analysis was done in R with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts for all six samples from STAR with --quantMode geneCounts with Ensemble mouse gene names

source_name: Colonic epithelia cells from allogeneic recipient mouse

growth_protocol: Mice were housed in sterilized microisolator cages and received filtered acid water and normal chow after BMT. All animals were cared for under regulations reviewed and approved by the University Committee on Use and Care of Animals of the University of Michigan, based on University Laboratory Animal Medicine guidelines.

extract_protocol:
The RNA was extracted from colonic epithelial cells with RNeasy Mini Kit (Qiagen) and the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Colonic epithelial cells were isolated from BMT recipient mice on BMT day7

tag: recipient strain

tag: age/time point

value: BMT day7

tag: donor strain

value: BALB/c

value: Colonic epithelial cells


title: ATACseq_K562_s_pC12p5_rep1


title: Allongeneic recipient biological rep1 [A1]


title: ATACseq_K562_s_pC0_rep2

description: Normalized_ATACseq_K562_s_pC0_BRs.bigWig

value: no additional heat shock  applied


title: ATACseq_K562_HSS_uC60_rep1

value: 60 min at 42C water bath


title: Syngeneic recipient biological rep3 [S4]

source_name: Colonic epithelia cells from syngneic recipient mouse


title: Bulk RNA Seq of FACS sorted P3 Perivascular Adipose Tissue (PVAT) PreAdipocytes [PreAd1]

value: 3 days old (p3)

value: Mixed male and female

value: Thoracic aorta perivascular fat


title: ATACseq_K562_s_pC0_rep1

value: no additional heat shock applied


title: Syngeneic recipient biological rep1 [S2]


title: Naïve biological rep1 [n4]

source_name: Colonic epithelia cells from naïve mouse

value: 9 weeks old


title: Naïve biological rep2 [n5]


title: ATACseq_K562_s_uC40_rep2

description: Normalized_ATACseq_K562_s_uC40_BRs.bigWig


title: ATACseq_K562_s_uC40_rep1


title: ATACseq_K562_s_uC12p5_rep1

description: Normalized_ATACseq_K562_s_uC12p5_BRs.bigWig


title: ATACseq_K562_s_uC25_rep2

description: Normalized_ATACseq_K562_s_uC25_BRs.bigWig


title: ATACseq_K562_s_uC12p5_rep2


title: ATACseq_K562_s_uC25_rep1


title: ATACseq_K562_s_uC0_rep2

description: Normalized_ATACseq_K562_s_uC0_BRs.bigWig

value: no heat stress applied


title: Allongeneic recipient biological rep2 [A2]


title: Yound_Sham_rep4

city: Pittsburgh

first: Sruthi

last: Sivakumar

address: 450 Technology drive

institute: University of Pittsburgh

data_processing:
FastQC was applied to check the quality of the sequences
STAR alignment was done with reference genome mm10 downloaded from UCSC browser, and gene ID type ENSEMBL transcriptome ID.
ENSEMBL IDs were converted to ENTREZ IDs using biomaRt for downstream analysis
deseq2 was used on raw read tables for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Gastroc skeletal muscle

extract_protocol:
Supplemetal methods-Cryopreservation and preparation of skeletal muscle tissue
RNA libraries were prepared for sequencing using standard Illumina protocols

value: young

tag: treatment

value: Sham

value: Gastroc skeletal muscle


title: Yound_Sham_rep3


title: Yound_Sham_rep2


title: Yound_Sham_rep1


title: Young_GFP_rep4

value: AAV-GFP


title: ATACseq_K562_s_uC0_rep1


title: Syngeneic recipient biological rep2 [S3]


title: PCX-OE_4

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

description:
PCX-overexpressing Ishikawa cells
8-GN-Hudson_S1_R1.fastq.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw 75bp single-end FASTQ reads were assessed for quality using FastQC (Andrews 2010) and results aggregated using R/Bioconductor package ngsReports (Ward et al. 2019). Reads were then trimmed for sequence adapters using AdapterRemoval (Schubert et al. 2016) and aligned to the human genome GRCh37 using the RNA-seq alignment algorithm STAR (Dobin et al. 2013).
After alignment, mapped sequence reads were summarised to the GRCh37.p13 (NCBI:GCA_000001405.14 2013-09) gene intervals using featureCounts (Liao et al. 2014), and count table transferred to the R statistical programming environment for expression analysis
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: epithelial cells

extract_protocol:
Ishikawa cells were cultured overnight at 5.6 x 105 cells/well in a 6-well plate in MEM medium supplemented with 10% FBS, 1% antibiotic-antimycotic and 1% L-glutamine. The following day, cells were washed with PBS and total RNA was isolated from control and PCX-overexpressing Ishikawa cells using the RNeasy Mini Kit (Qiagen), and treated with TURBO DNA-free kit (Invitrogen).
Total RNA was converted to strand specific Illumina compatible sequencing libraries using the NEXTflex Rapid Directional mRNA-Seq library kit from BIOO Scientific (Austin ,Texas) as per the manufacturers instructions (v14.10). 400ng of total RNA was polyA-selected and the mRNA fragmented prior to reverse transcription and second strand cDNA synthesis using dUTP. The resultant cDNA is poly adenylated before the ligation of Illumina-compatible barcoded sequencing adapters. The cDNA libraries were treated with UDG to degrade the second strand and PCR amplified for 14 cycles prior to assessment by Agilent Bioanalyzer for quality and Qubit fluorescence assay for amount.  Sequencing pools were generated by mixing equimolar amounts of compatible sample libraries based on the Qubit measurements.  Sequencing of the library pools was done with an Illumina Nextseq 500 using single read 75bp v2 sequencing chemistry

value: Ishikawa cells

tag: genotype/variation

value: PCX-overexpression


title: Young_GFP_rep3


title: Young_GFP_rep2


title: CONTROL_4

description:
Control Ishikawa cells
7-GN-Hudson_S2_R1.fastq.gz

value: control


title: Naïve biological rep3 [n6]


title: PCX-OE_2

description:
PCX-overexpressing Ishikawa cells
4-GN-Hudson_S3_R1.fastq.gz


title: CONTROL_3

description:
Control Ishikawa cells
5-GN-Hudson_S8_R1.fastq.gz


title: Young_GFP_rep1


title: CONTROL_2

description:
Control Ishikawa cells
3-GN-Hudson_S5_R1.fastq.gz


title: Old_KL_rep4

value: old

value: AAV-Kl


title: PCX-OE_1

description:
PCX-overexpressing Ishikawa cells
2-GN-Hudson_S6_R1.fastq.gz


title: Old_KL_rep3


title: Old_KL_rep2


title: IMSA075

first: Anuradha

last: Ray

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

description:
IMSA075_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

data_processing:
Quality Control - FASTQC
Low quality and 3' adapters trimmed -Trim Galore
Sequence Aligned to hg19 - STAR
Gene expression quantified counts per gene - featureCounts
Sequence normalized DESeq2
Batch correction - COMBAT
Differential gene expression - DESeq2
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: IMSA_BAL_RAW_Counts.txt
Supplementary_files_format_and_content: IMSA_BAL_DESeq2norm_COMBAT.txt

source_name: Bronchoalveolar Lavage (BAL) cells

growth_protocol: BAL cells were obtained from human subjects enrolled in the IMSA (Immune Mechanisms Severe Asthma) study.

extract_protocol:
Frozen RNA samples were purified removing DNA and rRNA with standard procedures.
cDNA libraries were prepared for sequencing using Illumina protocols. (Illumina Document #1000000040499v00 and Illumina Kit #20020596).

treatment_protocol: 5X 50ml sequential bronchial lavages were performed. Each lavage collection was placed on ice with all 5 being pooled and centrifuged. BAL cells were collected, suspended in D-PBS and centrifuged. RNA from cell pellet was stabilized by resuspending in RLT Buffer (Qiagen #1053393) with 1% 2-Mercaptoethanol and stored at -80C.

value: Bronchoalveolar lavage cells

tag: asthma degree

value: healthy

value: male

tag: steroid

value: no

tag: patient clustering

value: Group 1

tag: sequencing batch


title: Old_GFP_rep3

tag: age

tag: tissue


title: Old_GFP_rep4


title: IMSA078

description:
IMSA078_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: severe

tag: gender

value: yes

value: Group 2


title: IMSA071

description:
IMSA071_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

tag: cell type

value: female


title: Old_GFP_rep2


title: IMSA069

description:
IMSA069_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA068

description:
IMSA068_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: mild/moderate


title: Old_GFP_rep1

value: Gastroc skeletal muscle


title: Oldest-old_KL_rep3

value: oldest-old


title: IMSA067

description:
IMSA067_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: PCX-OE_3

description:
PCX-overexpressing Ishikawa cells
6-GN-Hudson_S4_R1.fastq.gz

tag: cell line

value: Ishikawa cells


title: Oldest-old_KL_rep2


title: Oldest-old_KL_rep4


title: IMSA065

description:
IMSA065_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA064

description:
IMSA064_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA062

description:
IMSA062_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Oldest-old_GFP_rep4

value: AAV-GFP


title: Oldest-old_GFP_rep3


title: Oldest-old_KL_rep1


title: IMSA061

description:
IMSA061_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: Group 3


title: Oldest-old_GFP_rep2


title: IMSA059

description:
IMSA059_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: CONTROL_1

description:
Control Ishikawa cells
1-GN-Hudson_S7_R1.fastq.gz

value: control


title: IMSA077

description:
IMSA077_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Old_KL_rep1

value: old

value: AAV-Kl


title: Oldest-old_GFP_rep1


title: IMSA058

description:
IMSA058_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: Bronchoalveolar lavage cells


title: IMSA052

description:
IMSA052_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: healthy


title: IMSA049

description:
IMSA049_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: no


title: Ikkβca+Stat3KO rep1

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include unnormalized read counts for each Sample ...

source_name: esophageal epithelium

growth_protocol: Mice were aged to 6 weeks prior to harvest.

extract_protocol:
Esophagi were removed and epithelium was mechanically separated from stroma. Epithelium was minced and flash frozen on dry ice. RNA was isolated using Qiagen RNeasy Mini Kit (#74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophageal epithelium

value: 6 weeks

tag: genotype


title: IMSA054

description:
IMSA054_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: severe

value: yes


title: Ikkβca+Stat3KO rep2


title: Stat3KO rep2

value: ED/L2-Cre+; Stat3L/L


title: Prostate C1 - F1

value: Prostate

tag: generation


title: Ikkβca+Stat3KO rep3

tag: strain


title: Stat3KO rep3


title: IMSA047

description:
IMSA047_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: mild/moderate

value: female

value: Group 2


title: Stat3KO rep1


title: IMSA048

description:
IMSA048_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA045

description:
IMSA045_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: male


title: IMSA046

description:
IMSA046_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Ikkβca rep3

value: ED/L2-Cre+; ROSA26-StopFL-Ikk2ca+/L


title: Ikkβca rep2


title: IMSA040

description:
IMSA040_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Ikkβca rep1


title: IMSA039

description:
IMSA039_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Control rep2

value: ROSA26-StopFL-Ikk2ca+/L; Stat3L/L


title: IMSA044

description:
IMSA044_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Control rep1


title: IMSA036

description:
IMSA036_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: Group 1


title: IMSA035

description:
IMSA035_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: Group 3


title: IMSA034

description:
IMSA034_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: Bronchoalveolar lavage cells


title: Wild-type ES cell population Hi-C

city: Cambridge

first: Ernest

last: Laue

address: 80 Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

data_processing:
ChIP-seq:ChIP-seq data was trimmed using trim_galore and then aligned using BWA standard parameters to the Mus Musculus reference genome (mm10)
ChIP-seq:ChIP-seq bigwig tracks were calculated from the bamCompare output with options --extendReads 200 --binSize 1 --ratio log2.
ChIP-seq:The coverage was calculated with computeMatrix reference-point with options --binSize 10.
ChIP-seq:Peaks were called using MACS2 to be at FDR 5% and above 5-fold enrichment.
HiC:Population Hi-C was mapped to the genome using NucProcess (https://github.com/tjs23/nuc_processing) and analysed further using NucTools (https://github.com/tjs23/nuc_tools).
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Bigwig files were generated for ChIP-seq datasets
Supplementary_files_format_and_content: Population Hi-C txt file (.txt.gz) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed)

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatin-coated plates in 2i/LIF conditions as described (Ying et al., 2008).

extract_protocol:
ChIP-seq: Chromatin immunoprecipitations were carried out as previously outlined (Reynolds et al., 2012) with DNA fragmentation in the presence of 0.6% SDS. .
Hi-C: Population Hi-Cs were carried out as previously outlined (Stevens et al., 2017).5-10 million Haploid mouse ES cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
ChIP-seq: ChIP-seq libraries were prepared using the NEXTflex Rapid DNA-seq kit (Illumina)
Hi-C: Hi-C libraries were prepared as previously outlined (Stevens et al, 2017). Briefly, sonicated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. Biotinylated junctions were captured on streptavidin M-280 dynabeads and the blunt, phosphorylated ends were treated with Klenow fragment  exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: culture conditions

tag: chip antibody


title: Mbd3-knockout ES population Hi-C rep A


title: Mbd3-knockout ES cell input


title: IMSA031

description:
IMSA031_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: Wild-type ES cell input


title: IMSA023

description:
IMSA023_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA022

description:
IMSA022_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: IMSA026

description:
IMSA026_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: RNAseq_Tex191ESC_KO1

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

institute: MRC Human Genetics Unit

data_processing:
Adapter sequenced removed with TrimGalore! v0.4.1 with the following settings: --stringency 5 --length 30 --paired.
Sequences aligned to the mouse mm10 reference genome with TopHat2 v2.1.0 using using an Ensembl known transcriptome model and settings: -g 1 --mate-inner-dist 77 --mate-std-dev 64 --no-coverage-search --no-novel-juncs --no-novel-indels --b2-sensitive.
Counts were calculated using HTSeq v0.11.2 to count reads in GENCODE Basic VM18 gene predictions.
Read counts were normalised to the number of mapped reads (CPM, counts per million mapped reads) by EdgeR and low coverage genes (CPM<5 is more than half the samples) were removed. Differential enrichment analysis of read counts was performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by EdgeR that include logCPMs for all samples, and logFCs, P values and FDR-adjusted P values for the Tex19.1-/- vs Tex19.1+/- comparison.

growth_protocol: Mouse embryonic stem cells derived from the parental E14Tg2a line were cultured in gelatinised flasks in Glasgow Modified Eagle’s Media (GMEM), 10% foetal calf serum, 1% non-essential amino acid, 1% sodium pyruvate, 1% penicillin-streptomycin, 1% L-glutamine, 0.001% β-mercaptoethanol, and 0.2% leukaemia inhibitory factor-conditioned media at 37°C in 5% CO2 and passaged using 0.05% trypsin, 0.02% EDTA in PBS.

extract_protocol:
Cells were lysed with TRIzol reagent, and RNA used to construct Illumina TruSeq Stranded mRNA library.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep kit and sequenced using an Illumina HiSeq 4000 150PE sequencing system.

tag: strain background

value: Embryonic stem cells

tag: passages


title: RNAseq_Tex191ESC_Het3

tag: genotype/variation


title: IMSA020

description:
IMSA020_BAL_H
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

tag: asthma degree

value: healthy

value: no


title: RNAseq_Tex191ESC_KO2


title: RNAseq_Tex191ESC_KO3


title: H3K9me3_ChIPseq_Tex191ESC_KO3IP

description: IP DNA

data_processing:
Sequences aligned to the mouse mm10 reference genome with Bowtie2 v2.2.6 using settings: -X 500 --sensitive.
The alignment maps were converted into tag directories using HOMER v4.8 makeTagDirectory using settings: -sspe -unique. Peaks were found from the 'IP' sample relative to its 'Input DNA' sample for each replicate using HOMER v4.8 findPeaks using settings: -style histone.
Peaks common to at least two replicates of the same genotype were identified and merged using BEDTools v2.25.0.
Read coverage for the peak intervals was determined using HOMER v4.8 annotatePeaks using settings: -size given.
Read counts were normalised to the number of mapped reads (CPM, counts per million mapped reads) and low coverage peaks (CPM<1 in more than half the IP samples) were removed. Differential enrichment analysis of read counts was performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by edgeR that include CPM values in each Sample, logCPMs for all samples, and logFCs, P values and FDR-adjusted P values for the Tex19.1-/- vs Tex19.1+/- comparison.

extract_protocol:
Embryonic stem cells were detached from 70% confluent T75 flasks by scraping and resuspended in ice-cold PBS. Cross-linked ChIP was then performed essentially as previously described (Mortazavi et al., 2006, Genome Res. 16, 1208–1221) by fixing cells with formaldehyde, collecting nuclei from lysates, sonicating then isolating histone-DNA complexes with anti-histone H3K9me3 antibody (Abcam ab8898). Samples of input DNA were removed prior to the addition of anti-histone H3K9me3 antibodies.
Libraries were prepared using an NEBNext Ultra ChIPseq kit and sequenced using an Illumina HiSeq 4000 75PE sequencing system.

value: H3K9me3 (Abcam, ab8898)


title: IMSA017

description:
IMSA017_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

tag: steroid


title: Control rep3

value: esophageal epithelium

value: 6 weeks


title: IMSA013

description:
IMSA013_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: severe

value: yes

tag: patient clustering


title: RNAseq_Tex191ESC_Het1


title: IMSA011

description:
IMSA011_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: mild/moderate

tag: sequencing batch


title: RNAseq_Tex191ESC_Het2


title: H3K9me3_ChIPseq_Tex191ESC_KO3Input

description: Input DNA

value: none (input)


title: H3K9me3_ChIPseq_Tex191ESC_KO2IP

description: IP DNA


title: H3K9me3_ChIPseq_Tex191ESC_KO2Input

description: Input DNA


title: IMSA008

description:
IMSA008_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

tag: age

value: Group 2


title: IMSA010

description:
IMSA010_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: male


title: H3K9me3_ChIPseq_Tex191ESC_KO1IP

description: IP DNA


title: IMSA028

description:
IMSA028_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

value: female


title: H3K9me3_ChIPseq_Tex191ESC_KO1Input

description: Input DNA


title: IMSA027

description:
IMSA027_BAL_S
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt


title: H3K9me3_ChIPseq_Tex191ESC_Het3IP

description: IP DNA


title: H3K9me3_ChIPseq_Tex191ESC_Het3Input

description: Input DNA


title: H3K9me3_ChIPseq_Tex191ESC_Het2Input

description: Input DNA


title: H3K9me3_ChIPseq_Tex191ESC_Het2IP

description: IP DNA


title: BJFF_h3k4me3.2

description:
BJFF_h3k4me3
BJFF_h3k4me3_minus_BJFF_igg.pooled.fc.signal.bigwig
BJFF_h3k4me3.epic2.naive_overlap_peaks.txt.gz

tag: antibody

value: WT


title: H3K9me3_ChIPseq_Tex191ESC_Het1Input

description: Input DNA


title: RNAseq_Lung_TA_3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Whole tissue, lung

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Tet-inducible Ccne1; rtTA (CCNE-TA) mice and rtTA control (TA) mice were treated with doxycyclin (dox) from weaning age (3wks) onwards. Mice were euthanized at 4 months of age and tissues were subjected to RNA-sequencing.

tag: tissue

value: lung

tag: background strain

tag: condition

value: TA

value: 4 months


title: IMSA038

description:
IMSA038_BAL_M
processed data file: IMSA_BAL_RAW_Counts.txt
processed data file: IMSA_BAL_DESeq2norm_COMBAT.txt

tag: cell type

value: Bronchoalveolar lavage cells

tag: gender


title: RNAseq_Lung_TA_2


title: RNAseq_Lung_CCNETA_3

value: CCNE-TA


title: 218_pos_3

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

description:
location of sense strand RNA: R2
070717_218_pos_3_S12
08081717_218_pos_3_S12

data_processing:
Paired-end 150nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to homo sapiens sequence GRCh38 with CLCGenomicsServer 8.5.3 with: Mismatchh cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 8.5.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v6.6
Genome_build: HIV-1 (K03455.1, downloaded 24 Sep 2017), Human GRCh38 transcriptome of April 2017
Supplementary_files_format_and_content: FPKMs

source_name: Resting CD4+ T cells following ex vivo PMA/ionomycin activation

growth_protocol: Resting CD4+ T cells were isolated from ART-treated, virally suppressed, HIV-1-infected individuals using magnetic negative selection.

extract_protocol:
Cells were sorted by HIV-1 RNA SortSeq into bulk (8-30 cells per sample) or single cells into RNA preserving buffer. RNA was reverse crosslinked with proteinase K and SDS under 50°C for 1 hour. RNA was extracted by Quick-RNA Microprep (Zymo Research) with a built-in on-column DNase treatment step.
Total RNA was extracted followed by a ribosomal RNA depletion step using the SMARTer Stranded Total RNA-Seq Kit v1 (individuals 21, 108, 159, 361) and v2 (individuals 154, 218, 256, 381) - Pico Input Mammalian (Pico v2).
Samples with different barcodes were pooled into one high-output NextSeq 400M 2x150 platform, targeting an estimated reads of 20-40 million per sample.

treatment_protocol: Cells were treated with PMA (1 µg/ml) and ionomycin (1 µM) for 16-18 hours in the presence of enfurvitide to induce HIV-1 RNA expression without causing new rounds of infection in vitro.

tag: disease state

value: Resting CD4+ T cells

tag: treatment

value: PMA/ionomycin for 16-18 hours under enfurvitide

tag: individual


title: 154_pos_21

description:
location of sense strand RNA: R2
070717_154_pos_21_S7
08081717_154_pos_21_S7


title: 348_pos_1

description:
location of sense strand RNA: R2
070717_348_pos_1_S14
08081717_348_pos_1_S14