title: bulk_RNA-seq_PT2_day_14_replicate_2

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

country: Sweden

institute: Lund University

description:
hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt
pantro6.s2.multi.Gencode27.Exon.sjdb.v2.txt

data_processing:
bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the genome (GRCh38 and PanTro6) using STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
The Subread package FeatureCounts was used to quantify the reads overlapping Gencode v27 gene annotations. The human Gencode annotation was lifted over to PanTro6 using UCSC LiftOver tool.
single cell fastqs:
I1 Technical: Index read
R1 Technical: 16 bp Barcode and 10bp UMI
R2 Biological
Genome_build: GRCh38 and PanTro6
Supplementary_files_format_and_content: matrix.mat: raw read counts
Supplementary_files_format_and_content: Exon.sjdb.txt: featureCounts

organism: Pan troglodytes

source_name: forebrain neural progenitors

growth_protocol: iPS cells were differentiated into forebrain neural progenitor cells using the following protocol: The iPSCs were plated at 10.000 cells/cm2 in N2 medium (1:1 DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), 0.2% penicillin/streptomycin (Gibco)) with dual SMAD-inhibition (10 µM SB431542 (Axon), 100 ng/ml noggin (Miltenyi)) as well as ROCK inhibitor (10 µM Y27632) on LN111 coated Nunc delta surface multidishes (1.14 µg/cm2; Biolamina). The media was changed every 2-3 days to N2 medium with SMAD-inhibitors up until day 9 of differentiation when only N2 medium was used. On day 11 the cells were dissociated using StemPro accutase (75  µl/cm2; Gibco) and replated at 800,000 cells/cm2 on LN111-coated Nunc plates in B27 medium (Neurobasal supplemented with 1% B28 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) supplemented with 10 µM ROCK inhibitor, BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2mM; Sigma-Aldrich). The cells were then harvested at day 13, 14, 15, or 16.

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen) for bulk RNA-seq
Libraries for bulk RNA-seq were prepared withTruSeq RNA Library prep kit v2 (Illumina). Single cell libraries were prepared with Chromium Single Cell 3' Library & Gel Bead kit v2 (10x Genomics)

tag: cell type

value: iPSC-derived forebrain neural progenitors


title: RNA-seq of A11-120-15

status: Public on Dec 31 2021

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1017 Post-treatment
A11-120-15

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

molecule: total RNA

organism: Homo sapiens

source_name: prostate

extract_protocol:
RNA was extracted from FFPE prostate tissues using the Qiagen RNeasy FFPE kit
Libraries were prepared with the NEBNext Globin and rRNA depletiion library construction kit and the Illumina TruSeq stranded total RNA with ribo-zero globin kit.

treatment_protocol: Patients with prostate cancer received systemic intense neoadjuvant androgen deprivation therapy for six months and then underwent radical prostatectomy. Biopsies acquired prior to treatment , or post-treatment surgical prostatectomy specimens were grossed, accessioned, fixed in formalin, and embedded in paraffin.

tag: treatment status

value: Post-treatment

tag: gender

value: male

tag: subjectid


title: D16_H6

city: Pittsburgh

first: Neil

last: Hukriede

state: PA

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Genes were mapped using STAR and counted using featureCounts
Differential expression analysis was carried out using edgeR (67) and limma (68) with a threshold of log fold change = 1 and adjusted P value of <0.05
Gene set enrichment analysis was performed for the hallmark gene sets and Gene Ontology (GO) classification from the MSigDB collections using the clusterProlifer package
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: count matrix txt file

source_name: Kidney organoids

growth_protocol: kidney organoids were grown according to the Przepiorski et al. 2021 protocol.

extract_protocol:
Trizol with phase separation reagent and Ambion PureLink RNA Mini Kit.
TruSeq Stranded mRNA (PolyA+) kit
Bulk RNA-seq

treatment_protocol: Day 14 kidney organoids were treated with or without 25 µM Hemin in protein free medium (F12: DMEM low glucose, 1% Pen-Strep, 1% Hepes) for 48 hrs.

value: induced pluripotent stem cells

tag: cell line

tag: tissue

value: Kidney organoids

tag: treatment

value: Hemin

tag: time

value: Day 16 of assay


title: sc_RNA-seq_PT1_day_14

molecule: polyA RNA

tag: time point


title: Hippocampus_db/db_vehicle_rep3

type: RNA

city: Nanning

first: Lihui

last: Wang

address: No. 22 Shuangyong Road

country: China

institute: Guangxi Medical University

description: gene expression in 14 weeks db/db_vehicle mice hippocampus

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Mus musculus

source_name: hippocampus, db/db mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and Rnase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: After behavioral tests, microarray analysis was performed on the hippocampal tissues of 3 db/db_vehicle and 3 db/db_DMDD mice at the age of  14 weeks.

value: hippocampus

tag: age

value: 14 weeks

tag: mice

value: db/db


title: D16_H3


title: C1_diff_day5_1_SPOND19

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

description: Replicate 1

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the hg38UCSC genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene in the hg38UCSC gene annotation

source_name: H1 ESC

growth_protocol: H1 human embryonic stem cell (hESC) lines were grown under feeder-free conditions on Matrigel (Corning) in Essential 8™ Flex Medium (A2858501, ThermoFisher Scientific) and regularly passaged as aggregates with ReLeSR (STEMCELL Technologies, Cat# 05872). PSC colonies (especially the H3K27M mutant colonies) showing increased differentiation were carefully cleaned up manually scratching the colonies with a pipette tip under the microscope and maintained over time.  Experiments adhered to protocols approved by the Washington University hESC Research Oversight Committee (#12-002). As this work was designated “nonhuman subjects research” by Washington University’s Institutional Review Board, informed consent was not required. Cells were regularly checked for Mycoplasma contamination (Mycoalert Mycoplasma Detection Kit, Lonza, Cat# LT07-118). The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC), Washington University in St. Louis. Prior to transfection the cells were treated with 10 µmol Rock (Y-27632) inhibitor for at least 1 hr. Approximately 1.5 × 106 H1ESC cells were resuspended in P3 primary buffer and electroporated using a 4D-Nucleofector (Lonza) with 1 μg of H3F3a-K28M-KI-Puromyocin donor plasmid (GeneArt), 1 μg gRNA SM928.H3F3a.g37 targets 5’- atgctggtaggtaagtaagg agg-3’  and 1.2 μg Cas9 vectors. Nucleofected cells were plated in media containing Rock inhibitor for 24hrs post nucleofection and then returned to regular E8-Flex media. Following nucleofection, cells were screened with PCR using primer sets specific to the 5' and 3' junctions of the donor plasmid and the target gene. After confirmation of donor plasmid KI in the nucleofected pool the cells were treated with 0.2 µg/ml of Puromycin for 72 hrs. Surviving cells were then passaged and treated with 0.5 µg/ml of Puromycin for 72 hrs and Sanger sequencing was used to confirm the homozygous KI of the K28M mutation in the 5' junction PCR product of the subclones. Karyotyping of H3F3a-K28M line was performed by Cell Line Genetics.

extract_protocol:
High quality RNA from H1 hESC and their differentiated derivatives was isolated with RNeasy Plus Mini kit (Qiagen, cat # 74134) using QIAshredder (Qiagen, cat # 79654) and on-column digestion of genomic DNA following manufacturer’s recommendations. The kit captures RNA molecules higher than 200 nucleotide length effectively removing smaller RNAs such as 5.8S rRNA, 5S rRNA and tRNAs. For RNA-Seq, RNA was initially quantified by NanoDropND-1000 spectrophotometer (Thermo Scientific) and the concentration/quality of total RNA was further confirmed on Agilent Bioanalyzer2100. Only samples that had RNA integrity number (RIN) > 8 were used for RNA-Seq studies.
RNA-seq library preparation and Illumina sequencing were performed by the Genome Technology Access Center (GTAC) at Washington University School of Medicine. Total RNA was enriched for polyA-tailed mRNA and mRNA fragmentation, first- and second-strand cDNA synthesis, and addition of indexed adapters was carried out as previously described [S. J. Matkovich, G. W. Dorn, 2nd, Deep sequencing of cardiac microRNA-mRNA interactomes in clinical and experimental cardiomyopathy. Methods Mol. Biol. 1299, 27-49 (2015)].
non-strand-specific, single-end RNA-SeqSingle-end, 50 nt reads were obtained on an Illumina HiSeq 3000 instrument and the sequencing reads were mapped to the human genome (hg19 UCSC) using HISAT2 [M. Pertea, D. Kim, G. M. Pertea, J. T. Leek, S. L. Salzberg, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650-1667 (2016)]. The mean number of transcriptome-aligned reads per heart was 17.2 million.  Read quantitation on a per-gene basis was performed with HTSeq [S. Anders, P. T. Pyl, W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015)]. Detectable RNAs were assessed as those present at or above 1 read per million (18 reads) in at least 2 of 4 samples from any treatment group, resulting in 16,083 RNAs for downstream analyses.  Calculation of fold-change and FDR for differentially expressed RNAs used the R/Bioconductor packages limma and edgeR/voom [C. W. Law, M. Alhamdoosh, S. Su, G. K. Smyth, M. E. Ritchie, RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res 5, 1408 (2016)]. Partek Genomics Suite v6.6 (Partek, St. Louis, MO) was used for inter-sample quality control by principal components analysis and for heat map construction. To visualize differentially expressed mRNAs, normalized read counts from edgeR were subjected to unsupervised hierarchical clustering with Euclidean distance and average linkage using Partek Genomics Suite v6.6. Unless otherwise specified, standardized heatmaps are shown in which map colors represent the extent of deviation from the row average. For clarity of presentation and to enable comparison with other studies, individual gene expression levels in column graphs are rendered as FPKM (Fragments Per Kilobase of exon per Million reads mapped to the transcriptome), calculated from Tophat-aligned read counts using Cufflinks 2.1.1 [C. Trapnell et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012)].

treatment_protocol: For hESC Differentiation into Early Cortical Neural Progenitor Cells (NPCs), hESCs were dissociated with Accutase to single cells, counted and 1.5-3.5 (mostly it was 3.5 million )million cells per well were seeded into each well (with 300 microwells each) of anti-adherent AggreWell™800 Plates ((Stem Cell Technologies, Cat# 34815) the cell number is within the manufacturer’s recommended range for each well of the AggreWell 800 plate)) to produce uniform size embryoid bodies (EBs) (~11,666 cells/EB). AggreWell plates were prerinsed with warm neural induction medium (NIM) before plating the single cell suspension of H1 hESCs (WT and H3K27M mutant) and the plates were spun at 100 × g for 3 min to capture the cells into the microwells and were incubated at 37 °C with 5% CO2 in NIM medium for 2 days for the EB formation. The NIM medium was based on published protocols (Chambers et al., Nat. Biotech., 2009, Surmacz et al., Stem Cells, 2013, Mark Tomishima, Stem Book, 2012) and consisted of Neurobasal-A (Life Technologies), 1x B27 supplement without vitamin A (LifeTechnologies, 12587010), 10 μM SB-431542 (Tocris Biosciences), 100 nM LDN-193189 (Stemgent), and 10 μM Y-27632 (Tocris Biosciences). On day 2, EBs were removed from the AggreWell 800 plates and seeded onto poly-L-ornithine (20μg/mL) and laminin (10μg/mL)-coated plates to grow them into neural rossettes. Medium was replenished every other day and the NPCs of telencephalic character were isolated on day 5 using Accutase (Gibco, A1110501).

tag: genotype

value: Mutant C1

tag: group

value: differentiated

value: Day 5


title: bulk_RNA-seq_PT2_day_14_replicate_1


title: bulk_RNA-seq_PT1_day_16_replicate_2


title: N2

city: Shanghai

first: Han

last: Zhou

address: No.639 Zhizaoju Road

department: Neurosurgery

institute: Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Barcode data quality analysis. Cellbarcodes with lower sequencing qualitywere filtered out to ensure the accuracy of subsequent analysis.
FastQC for quality evaluation, fastp for trimming, STAR aligner (2.5.3a) for alignment, featureCounts (1.6.2) for transcript counting.
The cells with genes ＞2500 or ＜200 and the cells that have >5% mitochondrial genes were filtered out. Gene expressions of each cell were normalized by total expression, multiplied by a scale factor of 10,000, and log-transformed.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every single cell in the specific samples

organism: Rattus norvegicus

source_name: Dorsal root ganglion

extract_protocol:
The single-cell suspensions of DRG tissue were loaded onto microfluidic devices. Then, millions of beads with unique cell-barcodes and unique molecular identifiers (UMIs) were loaded similar to cells. Only one bead was loaded in each microwell. Following lysis, mRNA were captured onto the beads for the construction of sequencing libraries.
single-cell RNA libraries were prepared for sequencing using standard Illumina protocols accompanying the GEXSCOPE Single-Cell RNA Library Kit (Singleron, China)
single-cell RNA seq

treatment_protocol: Diabetic rats were induced by injected streptozotocin (STZ) on Day 0. We grouped diabetic rats according to the 50% paw withdrawal threshold (PWT) on Day 28. Rats with PWT ≤ 8 g were selected into the PDPN group and rats with PWT ≥ 15g were selected into the DM group. Rats in normal group (N group) were injected vehicle on Day 0.

tag: strain

value: Sprague Dawley

value: Dorsal root ganglion

value: vehicle

tag: disease state

value: normal


title: RNA-seq of A11-120-13

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1015 Post-treatment
A11-120-13


title: RNA-seq of A11-120-14

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1016 Post-treatment
A11-120-14


title: N1


title: RNA-seq of A11-120-12

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1013 Post-treatment
A11-120-12


title: D16_H2


title: D16_H1


title: RNA-seq of A11-120-11

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1012 Post-treatment
A11-120-11


title: HHDST_2366 [26625]

city: Boston

first: Alice

middle: H

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

description: 24359 genes with unique exon read data

data_processing:
After sequencing, raw data in FASTQ format was processed for quality using CLC Bio Genomic Workbench (Qiagen, Valencia, CA).
The transcriptome was assembled using the annotated Sus scrofa 11.1  as a reference genome
Differential expression analysis was performed on using a two-factor model design matrix in edge R, a Bioconductor package based on a negative binomial distribution
To assess consistency of jejunal mucosa sampling, the RNA sequencing data (reads per kilobase million [RPKM]) was analyzed using principal component analysis and hierarchical clustering (Spearman ranking method; RStudio, Version 1.0.153, Boston, MA), following xCell analysis, a tool that utilizes transcriptome signals to predict enrichment of different cell types. On the basis of these analysis, one sample in the WD+S group was identified as an outlier and showed a high enrichment of preadipocytes and T-helper 1 cells relative to the other samples in the group and among all four groups, suggesting an error during sample collection. Hence, this sample was not included in subsequent analysis, resulting in a final sample size of 29 pigs. Count data on annotated genes was filtered based on a minimum of at least one count per million across six samples in all groups and normalized using the trimmed mean of M values (TMM) method. The edge R two-factor model was designed to determine differential gene expression attributable to diet, statin, or a diet x statin interaction. Differentially expressed genes were identified using the Cox-Reid profile-adjusted likelihood method and likelihood ratio test. A Benjamini-Hochberg false discovery rate (FDR) method was used to adjust p-values for multiple comparisons
Thus, given the ancillary nature of this study genes were considered differentially expressed based on an FDR adjusted p <0.2 and absolute fold change ≥1.5. Fold change for genes identified by the edge R two-factor model were interpreted as diet effect: fold change of WD relative to HHD and statin effect: fold change of atorvastatin relative to no atorvastatin. Differentially expressed genes were only attributed to main effects (diet and statin).
Genome_build: The transcriptome was assembled using the annotated Sus scrofa11.1 as a reference genome
Supplementary_files_format_and_content: comma-separated value files with Unique Exon Read counts for gene

organism: Sus scrofa

source_name: Jejunal mucosa

growth_protocol: After one month of acclimatization to a “grower diet” and another month of a gradual shift to the experimental diets, the pigs were fed their respective diets in isocaloric amounts, with a gradual increase in total energy to meet growth requirements, for six months.

extract_protocol:
Jejunal mucosa was homogenized and RNA was isolated using TRI reagent. Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Only samples with an RNA Quality Indicator (RQI) greater than 8 were sequenced.
Prior to RNA sequencing (RNA-seq) samples were processed (mRNA purification and fragmentation, cDNA synthesis, end repair, 3’ adenylation, adaptor ligation, and DNA enrichment) using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) and AMPure XP beads (Beckman Coulter, Brea, CA) per the manufacturer’s instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was completed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA). Raw data in FASTQ format was processed for quality using CLC Bio Genomic Workbench (Qiagen, Valencia, CA). The transcriptome was assembled using the annotated Sus scrofa 11.1 as a reference genome
Samples were sequenced on an Illumina NextSeq 500 sequencer (Illumina, San Diego, CA) with 150 base pair single end reads.

treatment_protocol: Isocaloric diets were designed to represent typical Western and heart healthy dietary patterns consumed by humans. Detailed diet composition and ingredient sources have been reported previously. Briefly, both diets contained 38% of energy (E) as fat, 47% E as carbohydrate and 15% E as protein. The major differences between the WD and HHD were the types of carbohydrate and fat, and amount of fiber, cholesterol, fruits, vegetables, and fish oil. The WD was rich in saturated fat (butter fat), cholesterol, and refined carbohydrate (sugar, white flour), and low in fiber, whereas the HHD was rich in unsaturated fat (canola, soybean and corn oils), unrefined carbohydrate (whole wheat flour, oats), fruits/vegetables (freeze dried mix, Futureceuticals, Momence, IL) and fiber, and low in cholesterol. Pigs fed the HHD were administered fish oil capsules (Epanova 1000 mg [550 mg EPA + 200 mg DHA as free fatty acids], AstraZeneca, Cambridge, MA) three times per week. Pigs in the atorvastatin (Lipitor, Pfizer, New York, NY) groups were given 20 mg/day during the first three months and 40 mg/day during the latter three months of the intervention period.

tag: diet

value: Heart Healthy + Statin

value: Jejunal mucosa

tag: rna id

tag: breed

value: Ossabaw


title: bulk_RNA-seq_PT1_day_15_replicate_1

tag: cell type

value: iPSC-derived forebrain neural progenitors


title: RNA-seq of A11-120-10

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1011 Post-treatment
A11-120-10

tag: treatment status

value: Post-treatment

tag: gender

value: male


title: HHDST_2346 [26615]

description: 24359 genes with unique exon read data


title: D16-C7

value: induced pluripotent stem cells

tag: cell line

value: Kidney organoids

value: Control

value: Day 16 of assay


title: bulk_RNA-seq_PT1_day_14_replicate_2


title: D16-C5

tag: tissue


title: HHDST_2339 [26609]

description: 24359 genes with unique exon read data


title: RNA-seq of A11-120-1

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1001 Post-treatment
A11-120-1

tag: subjectid


title: bulk_RNA-seq_PT1_day_16_replicate_1


title: D15-H7

tag: treatment

value: Hemin

tag: time

value: Day 15 of assay


title: bulk_RNA-seq_PT1_day_14_replicate_1

tag: time point


title: HHDST_2358 [26622]

description: 24359 genes with unique exon read data


title: HHDST_2334 [26605]

description: 24359 genes with unique exon read data


title: HHDST_2329 [26600]

description: 24359 genes with unique exon read data


title: D15-H4


title: HHDST_2328 [26599]

description: 24359 genes with unique exon read data


title: D15-H3


title: bulk_RNA-seq_PT1_day_13_replicate_2


title: bulk_RNA-seq_PT1_day_15_replicate_2


title: D16-C6


title: D15-H2


title: SUM190 - BC Cell Line - scRNAseq

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
To generate a counts matrix, the sequenced files from each independent sample were processed through 10X Genomics Cell Ranger software v3.0.2 or v3.1.0. Here, the raw base call (BCL) files were demultiplexed using Cellranger mkfastq pipeline to generate FASTQ files. Cellranger count pipeline was applied to the FASTQs to perform alignment against GRCh38 human reference build, filtering, barcode counting and UMI counting. The feature-barcode matrices were analyzed through a series of open-source R platforms, including Seurat (Satija Lab) and ClusterProfiler (He Lab). The counts matrix is a fundamental unit of scRNAseq where column barcodes correspond to cell identities and rows are filled by gene names. The matrix values represent detected gene expression with the representative individual cell barcode. The counts matrix is a fundamental unit of scRNAseq where column barcodes correspond to cell identities and rows are filled by gene names. The matrix values represent detected gene expression with the representative individual cell barcode.
Counts matrix generated through Cell Ranger v3.0.2 or v3.1.0
Raw base call files demultiiplexed with Cell Ranger mfastq pipeline
Cell Range count pipeline used for alignment to GRCh38 reference (GRCh38-3.0.0)
Feature filtering using Seurate for genes detected in less than 0.3% of the individual sample cells.
Filter cell barcodes with low Unique Molecular Identifier, sample dependent filtering
Filter cell barcodes with high total feature count, sample dependent filtering
Filter cell barcodes with high percentage mitochondrial genes, sample dependent filteirng
Supplementary_files_format_and_content: tsv files are generated by Cellranger. Each contain either detected cellular barcodes or features for expression matrices.
Supplementary_files_format_and_content: mtx files are the expression matrices generated by Cellranger.
Supplementary_files_format_and_content: rds files contain Seurat R objects

source_name: SUM190 - BC Cell Line

growth_protocol: Breast cancer cell lines were thawed from frozen aliquots and cultured in CytoOne T25 flasks (USA Scientific) with culture media composition dependent on ATCC guidelines. Typical media recipes included DMEM/DMEM/F-12 media (Thermo Fisher), 5% FBS (Sigma-Aldrich), 1% Pen-Strep (Gibco), supplemented with 10 µg/ml Insulin (Sigma-Aldrich), and 5ng/ml Endothelial Growth Factor (Thermo Fisher) depending on cell line. Upon 80% confluency, the sample was passaged following the recommended sub-culturing protocol for adherent cells. All cell lines were cultured for a maximum of five passages from original ATCC sample collection to limit divergence from original reference strain.

extract_protocol: For single-cell RNA sequencing, cells were collected before passage 5 and suspended in 1X PBS (calcium and magnesium-free) containing 0.04% weight/volume BSA (400 µg/ml) at 1 x 106 cells/mL. Cells were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics) using manufacturer’s guidelines followed by sequencing on a S1 NovaSeq chip (Illumina Inc.). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent) were used for quality check of cDNA. The output BAM file from sequencing was processed through 10X Genomics Cell Ranger software v3.1.0. This outputs a read counts matrix that we used for downstream analyses using Seurat, a customizable R-Studio Package for scSEQ analysis. We successfully generated scRNASeq data at least ~20,000 2x150bp reads per cell with 36,195 total cells sequenced, generating over 2B reads with an average 97% mapping rate.


title: T47D - BC Cell Line - scRNAseq

source_name: T47D - BC Cell Line


title: SUM149 - BC Cell Line - scRNAseq

source_name: SUM149 - BC Cell Line


title: HHDST_2327 [26598]

description: 24359 genes with unique exon read data


title: HH4_10X_data

city: Oxford

first: Tatjana

last: Sauka-spengler

address: Headley Way, Headington

department: Radcliffe Dept of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequenced files were demultiplexed and features counted using CellRanger (v3.0.0)
Seurat (v3.0.1) R package was used for data processing for scRNA samples
Genome_build: galGal6. Custom genomes were build using CellRanger to allow proper mapping of reads/fragments.
Supplementary_files_format_and_content: .tsv.gz containing barcodes, feature counts, and matrix data

organism: Gallus gallus

source_name: HH4 whole epiblast

growth_protocol: ferilized eggs were grown at 37C to the desired stage according Hamburger and Hamilton (1951)

extract_protocol:
embryonic material was dissected and disssociated for FACS using dispase/tyrpsin
As manufacturers protocol, 10X Genomics single-cell RNA-seq Cat. #1000075
3’ Library and Gel Bead Kit v3

treatment_protocol: untreated

value: chick embryonic epiblast

value: untreated


title: w1118_3

city: Arlington

first: Diwash

last: Jangam

state: TX

address: 701 S. Nedderman Drive

department: Biology

institute: University of Texas at Arlington

data_processing:
FastQC program was used to determine that all raw data passed quality control test to be used for downstream analyses.
STAR aligner (version 2.5) was used to map the RNA-Seq reads to the D. melanogaster reference genome (genome assembly BDGP6.88).
HTseq was used for counting reads.
DESeq2 was used for differential expression analyses with a FDR of 5%.
For analyzing differential transposable (TE) element expression, STAR aligner was used to map the RNA-Seq reads to the D. melanogaster reference genome with an additional flag --outFilterMultimapNmax 100 and TEtranscripts followed by DESeq2 was used for differential expression of TEs with FDR of 5%.
Genome_build: GRCh37
Supplementary_files_format_and_content: Files with raw gene counts for every gene

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: All flies were maintained at 25 degree centigrade in standard Drophila melanogaster media.

extract_protocol:
RNA was extracted using Direct-zol kit (Zymo Research) and stored at -70°C.
RNA was sent to Genomics Core Facility at Cornell University for library preparation.

value: control

value: ovary


title: SKBr3 - BC Cell Line - scRNAseq

source_name: SKBr3 - BC Cell Line


title: D16-C4


title: D15-C4


title: w1118_2


title: MDAMB468 - BC Cell Line - scRNAseq

source_name: MDAMB468 - BC Cell Line


title: w1118_1


title: D15-C3


title: MDAMB453-Treated - BC Cell Line - scRNAseq

source_name: MDAMB453-Treated - BC Cell Line


title: HHD_2356 [26620]

description: 24359 genes with unique exon read data

value: Heart Healthy


title: D15-C2


title: bulk_RNA-seq_PT1_day_13_replicate_1


title: DPLG4KO7

value: mutant for the gene DPLG4


title: HHD_2343 [26613]

description: 24359 genes with unique exon read data

value: Jejunal mucosa


title: MDAMB436-Treated - BC Cell Line - scRNAseq

source_name: MDAMB436-Treated - BC Cell Line


title: HHD_2341 [26611]

description: 24359 genes with unique exon read data

value: Ossabaw


title: MDAMB453 - BC Cell Line - scRNAseq

source_name: MDAMB453 - BC Cell Line


title: D15-C1


title: DPLG4KO3


title: HHD_2336 [26606]

description: 24359 genes with unique exon read data


title: DPLG4KO15


title: D14-C5

value: Day 14 of assay


title: MDAMB436 - BC Cell Line - scRNAseq

source_name: MDAMB436 - BC Cell Line


title: HHD_2357 [26621]

description: 24359 genes with unique exon read data


title: HHD_2330 [26601]

description: 24359 genes with unique exon read data


title: DPLG1KO7

value: mutant for the gene DPLG1


title: MDAMB361 - BC Cell Line - scRNAseq

source_name: MDAMB361 - BC Cell Line


title: DPLG1KO5


title: D14-C4

source_name: Kidney organoids


title: ARST_2362 [26623]

description: 24359 genes with unique exon read data

value: Atherogenic + Statin


title: HHD_2325 [26596]

description: 24359 genes with unique exon read data


title: MDAMB231 - BC Cell Line - scRNAseq

source_name: MDAMB231 - BC Cell Line


title: MCF7s2 - BC Cell Line - scRNAseq

source_name: MCF7s2 - BC Cell Line


title: D14-C2

value: induced pluripotent stem cells


title: MCF7s1r2 - BC Cell Line - scRNAseq

source_name: MCF7s1r2 - BC Cell Line


title: ARST_2349 [26617]

description: 24359 genes with unique exon read data

source_name: Jejunal mucosa


title: DPLG1KO22


title: ARST_2345 [26614]

description: 24359 genes with unique exon read data


title: MCF7s1r1 - BC Cell Line - scRNAseq

source_name: MCF7s1r1 - BC Cell Line


title: H2AX HepG2 R2

city: Chicago

first: Julian

last: Lutze

state: IL

institute: University of Chicago

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Sequenced reads were aligned to hg19 using bwa version 0.7.12.
Reads were filtered using a q10 cutoff in samtools.
BAM files were generated using samtools
peaks were called using MACS2 with an FDR of 0.1 and a --broad flag
Genome_build: hg19
Supplementary_files_format_and_content: peak files are bed files indicating locations of called peaks. .bw files can be viewed in IGV

molecule: genomic DNA

growth_protocol: Cells were cultured in DMEM media supplimented with 10% FBS, l-Glut and Pen/Strep at 37C. In general cells were grown in t75 or t125 flasks

extract_protocol: CUT&RUN was carried out according to published protocols.

treatment_protocol: Irridiated cells were exposed to 6 Gy of IR from a 60Co source and allowed to recover for the indicated length of time

value: Hepatocellular Carcinoma cells

tag: chip antibody

value: Histone H4 (Rabbit pAb, ProteinTech),


title: H3K27me3 1 hour PIR K562 R1

value: AML erythroleukemic cells

value: 6 Gy IR

value: 1 hour PIR

value: Rabbit mAb, C36B11, CST


title: ARST_2340 [26610]

description: 24359 genes with unique exon read data


title: 20Z-pXyl-methane-Rep2

city: Yongin

first: Anh

middle: Duc

last: Nguyen

address: Kyung Hee University

country: South Korea

institute: Kyung Hee University

data_processing:
RNA-seq reads were aligned to reference sequence using Bowtie 1.2.1.1
The sequence alignment/map (SAM) files were post-processed using SAMTools 0.1.19
Differentially Expressed Genes (DEG) were analyzed by Cuffdiff to calculate fragments per kilobase of exon per million fragments (FPKM) and differential expression, respectively, with default options and library type of dUTP RNA-seq
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Methylotuvimicrobium alcaliphilum 20Z

source_name: cell culture

growth_protocol: M. alcaliphilum 20Z was grown in 50 mL NMS medium33 at 30 oC with 230 rpm agitation in a 500 mL baffled flask sealed with a screw cap, and ethane was supplied to a final concentration of 50% (v/v) by gas substitution using a gas-tight syringe. For mixed substrates, engineered M. alcaliphilum 20Z was cultured in the same medium with the addition of 10 g/L xylose as a co-substrate. The initial OD600 of each culture was 0.1 for growth rate experiments. For RNA-seq experiments, all cultures were grown in biological duplicates for subsequent RNA extraction and sequencing steps.

extract_protocol:
Total RNA was stabilized with the bacterial reagent RNAprotect (Qiagen, Hilden, Germany) and then extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany) along with On-Column DNase Digestion using RNAse-Free DNase Set (Qiagen, Hilden, Germany) following the manufacturer’s protocols.
Total RNA quality and quantity were measured using an RNA 6000 Nano kit with the Agilent Bioanalyzer (Agilent Technologies, CA, USA). Then rRNA was removed using Ribo-Zero rRNA removal kits (Gram-negative bacteria; Epicentre, Madison, WI, USA) and then RNA was used for sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Briefly, transcriptome sequencing was conducted using Illumina/Hiseq-2000 RNA sequencing (Macrogen, Korea).

treatment_protocol: Diffirent substrates (methane and methane plus xylose)


title: H2AX HepG2 R1

value: untreated


title: H2AX K562 R2


title: D14-C3

value: Kidney organoids

value: Control


title: H2AX K562 R1


title: 20Z-pXyl-methane-Rep1


title: ARST_2333 [26604]

description: 24359 genes with unique exon read data


title: BT474 - BC Cell Line - scRNAseq

source_name: BT474 - BC Cell Line


title: ARST_2332 [26603]

description: 24359 genes with unique exon read data


title: PLC_shDOCK1+M_rep2

city: Hefei

first: junru

last: feng

address: huangshan road #443

institute: USTC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR
Transcripts were assembled by StringTie v1.3.4d
Gene expression analysis was performed using DESeq2 v1.28.1
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

growth_protocol: PLC/PRF/5 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin–streptomycin (Hyclone)

extract_protocol:
Total RNA was extracted using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Metformin

tag: genotype


title: ARST_2326 [26597]

description: 24359 genes with unique exon read data


title: PLC_shDOCK1+M_rep1


title: 20Z-pXyl-methane+xylose-Rep2


title: gH2AX 1 hour PIR HepG2 R1

value: Mouse mAb, clone JBW301, Millipore Sigma


title: PLC_shDOCK1_rep2


title: 20Z-pXyl-methane+xylose-Rep1


title: AR_2363 [26624]

description: 24359 genes with unique exon read data

value: Atherogenic

value: Jejunal mucosa


title: BT549 - BC Cell Line - scRNAseq

source_name: BT549 - BC Cell Line


title: Reb1-AA-2h-rep2

city: Albuquerque

first: Peng

last: Mao

state: NM

address: 915 Camino de Salud. NE

institute: The University of New Mexico Comprehensive Cancer Center

description: Reb11 anchor-away 2 h

data_processing:
library strategy: N-methylpurine-sequencing (NMP-seq)
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using barcodes. The barcode sequences and the last nucleotide of  the read were trimmed, using a custom Python script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS bamtoBed
Damage coordinates and dinucleotide sequences were obtained using the flank and getfasta functions of BEDTOOLS. The reverse complementary sequence of the dinucleotide on the opposite strand was obtained using a custum Python script
Only reads mapping to G and A nucleotides, corresponding to MMS-induced 7meG and 3meA lesions were retained in BED file using a custom python script
BED files were split to plus and minus strands, sorted, and converted to 1-based WIG files using COUNT function of IGVTools
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of MMS damage reads filtered for G or A nucleotides. Note, rep1 and rep2 represent two biological repeats.

organism: Saccharomyces cerevisiae

source_name: Reb1 anchor-away strain

growth_protocol: Yeast strains were grown in YPD (yeast extract, peptone, dextrose) to OD600=0.8 in a yeast shaker at 30 0C.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 12 μg of DNA was used for each sequencing library preparation.
NMP-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, genomic DNA was sonicated to ~400 bp. Sonicated DNA fragments were purified, end-repaired, dA-tailed and ligated to a double-stranded adaptor DNA trP1. Free 3'-OHs were blocked by terminal transferase and dideoxy-ATP. MMS-induced lesions were cleaved with alkyladenine-DNA glycosylase (AAG) and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor A. Five different barcoded A adaptors (A1: AAGAGGAT, A2: TTCGTGAT, A3: CCTGAGAT, A4: ATCGCGAT, and A5: TACTGGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for 5-6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing using an Ion Torrent sequencer.

treatment_protocol: Yeast cells were treated with 0.4% MMS (v/v) for 10 min in the growth media in an incubator. After treatment, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before MMS  (No MMS), immediately after MMS treatment (0hr), and at different repair time points as indicated. Cells were spun down and kept at -80˚C until genomic DNA isolation.

value: WT-AA REB1-FRB-KanMX6

value: 1 μg/ml rapamycin for 1 h, followed by 0.4% MMS for 10 min

tag: repair time

value: 2 h


title: Abf1-AA-2h-rep2

description: Abf1 anchor-away 2 h

source_name: Abf1 anchor-away strain

tag: strain

value: WT-AA ABF1-FRB-KanMX6


title: Reb1-AA-0h-rep2

description: Reb11 anchor-away 0 h

value: 0 h


title: gH2AX 24 hour PIR K562 R1

value: 24 hour PIR


title: AR_2348 [26616]

description: 24359 genes with unique exon read data

value: Ossabaw


title: AR_2351 [26618]

description: 24359 genes with unique exon read data


title: PLC_shDOCK1_rep1


title: PLC_NTC+M_rep2

value: NTC


title: gH2AX 1 hour PIR K562 R1

value: AML erythroleukemic cells

value: 6 Gy IR

value: 1 hour PIR


title: Reb1-AA-0h-rep1

description: Reb11 anchor-away 0 h


title: Reb1-AA-2h-rep1

description: Reb11 anchor-away 2 h


title: Abf1-AA-2h-rep1

description: Abf1 anchor-away 2 h


title: AR_2342 [26612]

description: 24359 genes with unique exon read data


title: AR_2337 [26607]

description: 24359 genes with unique exon read data


title: pt7001031_adjNORM_CD45+_cells_scATACseq

city: Tarrytown

first: Qingqing

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: scATAC-seq data

data_processing:
Cell Ranger ATAC version 3.0.2 (10x Genomics) was used to perform demultiplexing and read alignment.
scATAC-seq data from 8 patients and three tissue types (PBMC, tumor, and adjacent normal) underwent quality control analysis and filtering based on enrichment of ATAC-seq accessibility at transcription start sites (TSSs) and the number of unique fragments per cell
A two-round feature selection, dimension reduction and cell clustering was performed, as previously described (Cusanovich et al., 2018; Satpathy et al, 2019). For immune cells clustering, first, a tiling window-by-cell counting matrix was constructed by counting the Tn5 insertion overlaps per window for each cell, using tiling window size of 2.5kb across the human genome (hg38). The matrix was then binarized and dimension reduction was conducted by computing the term frequency-inverse document frequency (TF-IDF) transformation. The resulted TF-IDF matrix then underwent irlba singular value decomposition (SVD) and the 2nd to 25th dimensions were retained; cells were then clustered using Seurat’s SNN graph clustering (v3.0) with a resolution of 0.8 and minimum size of a cluster 200. For the second round, Peaks were called in each crude cell cluster resulted from the first round using MACS2 (Zhang et al. 2008) and a union peak set was collected by combining peaks from all the cell clusters. A peak-by-cell counting matrix was then constructed by counting the Tn5 insertion overlaps per peak for each cell, and dimension reduction and cell clustering were performed as in round one. For the sub-clustering on the T cells, all the other parameters stay the same except that the minimum size of a cluster is set to be 250 for the first round of clustering.
The gene activity score is calculated based on the model described in Granja et al, 2021. ATAC-seq signal from the whole gene body is considered, and signal with bi-directional exponential decays from the gene TSS (extended 5kb upstream) and the gene transcription termination site is scaled after filtering signal from overlapping neighbor gene boundaries.
Genome_build: hg38
Supplementary_files_format_and_content: MetaData.txt file, phenotypic metadata for cells in dataset
Supplementary_files_format_and_content: peakSet.txt file, peaks called from the datasets
Supplementary_files_format_and_content: fragments.tsv.gz files; ATAC-seq fragments captured by the assay, analyzed by Cell ranger

source_name: Donor

extract_protocol:
Isolation of nuclei suspensions was performed according to (Satpathy et al, 2019) and the Demonstrated Protocol: Nuclei Isolation for Single Cell ATAC Sequencing (10x Genomics). Due to the limited numbers of immune cells from patient samples, we followed a low cell input nuclei isolation protocol. Briefly, cells were resuspended in 50 ul PBS + 0.04% BSA and transferred to a 0.2 ml tube and centrifuged (300g for 5 min at 4oC). The supernatant was removed and 45 ul of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% digitonin and 1% BSA) and gently pipette mixed. The tube was then incubated on ice for 3 min. After lysis, 50 ul of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA) was added without mixing. Nuclei were centrifuged (500g for 5 min at 4oC) and the supernatant was carefully removed. Next, 45 ul of Diluted Nuclei Buffer (10x genomics) was added without mixing, nuclei were centrifuged (500g for 5 min at 4oC) and the supernatant was carefully removed. Isolated nuclei were resuspended in 7 ul chilled Diluted Nuclei Buffer (10x Genomics). Nuclei were immediately used to generate scATAC-seq libraries as described in the methods.
Nuclei were suspended at a 1:20 dilution in 20X Nuclei Buffer provided by the Chromium NextGEM Single Cell ATAC Library & Gel Bead Kit. Nuclei were aliquoted for the transposition reaction to target 2000 recovered nuclei. Transposed nuclei were partitioned using the Chromium Single Cell Instrument (10x Genomics) and libraries were generated. Sequencing was performed on Illumina NextSeq® 500 (Illumina) by multiplexed paired-read run with 2X50 cycles. Cell Ranger ATAC version 1.2.0 (10x Genomics) was used to perform demultiplexing and read alignment.

treatment_protocol: Renal tumor and adjacent normal tissue samples were dissociated into single cells by a semi-automated mechanical and enzymatic process. Tumor tissue was cut into pieces of (~2-3 mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was performed on gentleMACS dissociator (program 37C_h_TDK_1). To allow for enzymatic digestion, the tube was incubated for 30 min at 37oC, with rotation, after the first and second mechanical dissociation step. Mononuclear cells (MNCs) from whole peripheral blood of paired subjects were isolated by density gradient centrifugation using SepMate Tubes (Stem Cell Technologies). Cells were then cryopreserved in Recovery Cell Culture Freezing Medium (ThermoFisher). Prior to single-cell sequencing cells were rapidly thawed in warm DMEM (Gibco) supplemented with 10% FBS and pelleted. Cell sorting. Tumor, adjacent normal tissue cells, and PBMCs were resuspended in FACS staining buffer (1% BSA and 1mM EDTA in DPBS; Gibco) and incubated with Human TruStain FcX (BioLegend) for 10 min on ice to block non-specific binding to Fc receptors. Cells were then washed and stained with CD45-PE-Dazzle594 (BioLegend) for 20 min on ice. Next, cells were filtered and resuspended in FACS staining buffer with addition of DNase for FACS sorting. DAPI was added to the cell suspension immediately before FACS sorting for dead cell exclusion. Live, CD45+ single cells were sorted for downstream single-cell analysis.

value: Adjacent normal kidney tissue

value: baseline

value: adjacent normal kidney immune cells

tag: disease state

value: Early Stage ccRCC

tag: library strategy

value: ATAC-seq


title: PLC_NTC+M_rep1

value: Metformin


title: AR_2331 [26602]

description: 24359 genes with unique exon read data

tag: diet

value: Atherogenic

value: Jejunal mucosa

tag: rna id


title: AR_2338 [26608]

description: 24359 genes with unique exon read data

tag: breed


title: gH2AX 24 hour PIR K562 R2

tag: cell type

value: Mouse mAb, clone JBW301, Millipore Sigma


title: WT-AA-2h

description:
Anchor-away control 2 h
W303 MATα tor1-1Δfpr1::NATI RPL13A-2×FKBP12-TRP1

source_name: Yeast anchor away control strain

value: W303 MAT{alpha} tor1-1{delta}fpr1::NATI RPL13A-2xFKBP12-TRP1

value: 1 μg/ml rapamycin for 1 h, followed by 0.4% MMS for 10 min

value: 2 h


title: pt7001031_tumor_CD45+_cells_scATACseq

description: scATAC-seq data

value: RCC tumor

value: tumor immune cells


title: Abf1-AA-0h-rep1

description: Abf1 anchor-away 0 h

value: WT-AA ABF1-FRB-KanMX6

value: 0 h


title: Abf1-AA-0h-rep2

description: Abf1 anchor-away 0 h


title: PLC_NTC_rep1

value: Control

value: NTC


title: gH2AX 1 hour PIR K562 R2

value: AML erythroleukemic cells

value: 6 Gy IR

value: 1 hour PIR


title: ChIP-seq_C65_Smc1a

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Clonal mESC line expressing endogenously tagged CTCF and Rad21, further modified to visualize CTCF looping in living cells (CTCF loop on chromosome 18  surrounding the Fbn2 gene marked with a TetO and an Anchor 3 array and visualized by expressing fluorescent TetR-mScarlet and EGFP-OR3 array binding proteins) and homozygously deleted of the L1, L2, and R1 CTCF binding sites.
C65_Smc1a_coverage.bw
ChIP-seq

data_processing:
Micro-C allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C mcool files were converted from allValidPairs by Cooler package
ChIP-seq raw reads were aligned onto the mouse genome using Bowtie, allowing for two mismatches (-n 2) and no multiple alignments (-m 1)
ChIP-seq bigWig files were computed with deepTools (version 2.4.1). We ran bamCoverage (--binSize 50 --normalizeTo1x 2150570000 --extendReads 250 --ignoreDuplicates -of bigwig) and normalized read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome.
Genome_build: mm10
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: ChIP-seq bigWig files: normalized read coverage per 50-bp bins across the whole genome

source_name: Embryonic stem cells

growth_protocol: JM8.N4 mESCs were grown on gelatin-coated plates in knock-out DMEM supplemented with 15% FBS, non-essential amino acids, glutamax, Penicillin-streptomycin, 2-mercapoethanol and LIF. mES cells were fed daily and passaged every 2-3 days by trypsinization.

extract_protocol:
Cells were cross-linked for 5 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. During the incubation, the lysates were repeatedly pipetted up and down every 5 minutes. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 40 cycles of 20" on and 40" off). Sonicated lysates were cleared by centrifugation and 800 g of chromatin were diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 ug/ul, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 8 ug of normal rabbit IgGs (ChromPure rabbit normal IgG; Jackson ImmunoResearch), anti-Smc1a (A300-055A; Bethyl Laboratories Inc.), or 1.6 ug of anti-CTCF antibodies (ab128873; Abcam). About 8% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit and eluted in 60 ul of water.
ChIP-seq libraries were prepared using the Solexa rapid library protocol. Immunoprecipitated DNA or 50 ng input DNA was end-repaired, phosphorylated and adenylated in a single 50 μl reaction containing 31.5 μl DNA, 5 μl spike-in yeast DNA from MNase treated nucleosomes (10 ng/ml) and 13.5 μl end-repair/3' A mix (1X T4 DNA ligase buffer, 0.5 mM dNTPs, 0.25 mM ATP  2.5% PEG 4000, 0.0025 U/μl T4 PNK, 0.0025 U/μL T4 DNA polymerase, 0.0025 U/μL Taq DNA polymerase). The reaction was incubated in a thermal cycler for 15' at 12'C, 15' at 37'C, 20' at 72'C, and held at 4'C. Reactions were added of 4 μl water, 1 μl Illumina TruSeq adapters, 55 μl 2x Rapid DNA ligase buffer (Enzymatics #B101L) and 5 µl DNA ligase (Enzymatics #L6030-HC-L), and incubated for 15' at 20'C. Ligations were cleaned up twice with AMPure XP beads (Agencourt #A63880) diluted 1:2 with 20% PEG, 1.25M NaCl (first cleanup: 38 μl; beads eluted with 53 μl 10 mM Tris-HCl pH 8.0, 50 μl transferred to a new tube and added of 55 μl beads:PEG solution). Final elution volume was in 22 μl 10 mM Tris-HCl pH 8.0, 20 μl of which were transferred to a new tube and amplified by PCR (45" at 98'C; 14 cycles of 15" at 98'C and 10" at 60'C; 1' at 72'C; hold at 4'C) with KAPA HS HIFI polymerase (1X KAPA buffer, 0.3 mM dNTPs, 0.5 μM TruSeq PCR primers, 1U KAPA polymerase). PCR reactions were cleaned up once with 38 μl AMPure XP beads diluted 1:2 with 20% PEG, 1.25M NaCl and eluted with 33 μl 10 mM Tris-HCl pH 8.0, 30 μl of which were transferred to a new tube.

value: FLAG-Halo-mCTCF / mRad21-SNAPf-V5 knock-in; chr18:58.131 224x TetO; chr18:58.646 Anchor3; pL30 TetR-NLS-3x-mScarlet-  NLS-DEx4; pL30 EGFP-OR3-DEx4; homozygous Delta_L1; homozygous Delta_L2; homozygous Delta_R1

value: anti-Smc1a (Bethyl Laboratories Inc A300-055A)


title: ChIP-seq_C65_CTCF

description:
Clonal mESC line expressing endogenously tagged CTCF and Rad21, further modified to visualize CTCF looping in living cells (CTCF loop on chromosome 18  surrounding the Fbn2 gene marked with a TetO and an Anchor 3 array and visualized by expressing fluorescent TetR-mScarlet and EGFP-OR3 array binding proteins) and homozygously deleted of the L1, L2, and R1 CTCF binding sites.
C65_CTCF_coverage.bw
ChIP-seq

value: anti-CTCF (Abcam ab128873)


title: WT-AA-0h

description:
Anchor-away control 0 h
W303 MATα tor1-1Δfpr1::NATI RPL13A-2×FKBP12-TRP1


title: DMSO_4_Days_TT_32b

city: South San Francisco

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl homosapiens annotations (GRCh38, Apr 2020) release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: hg38 v.13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: iPSC-CM

growth_protocol: iPSC culture, iPSC-CM differentiation, and blasticidin selection:   WTC iPSCs and derivative lines were fed daily with E8 medium (STEMCELL Technologies) and cultured under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences). iPSCs were dissociated non-enzymatically using 0.5 μM ethylenediaminetetraacetic acid (EDTA) (Thermo Fisher Scientific) and passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10 μM; Selleckchem). iPSCs were frozen in BamBanker human iPSC Freeze Media (Thermo Fisher Scientific). Differentiation of iPSCs was induced through the Wnt modulation method with 7 μM of glycogen synthase kinase 3 b (GSK3b) inhibitor CHIR99021 (Selleckchem) and 5 μM of inhibitor of WNT production 2 (IWP2) (Sigma). Basal Media was composed of RPMI media supplemented with B27 (Thermo Fisher Scientific). As previously described, we generated a blasticidin-selectable iPSC line to purify our iPSC-CMs using 1 μM blasticidin (Thermo Fisher Scientific). Eighteen days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum with 10% dimethyl sulfoxide (DMSO).

extract_protocol:
RNA extraction: Left ventricular cardiac tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq stranded library preparation Illumina protocols.

treatment_protocol: TYA-018 (highly selective HDAC6 inhibitor) was administered daily by oral gavage at 15 mg/kg starting when mice were 2 months old.

tag: timepoint

value: DMSO

tag: dose

value: iPSC cardiomyocytes


title: DMSO_4_Days_TT_32a


title: pt7001025_tumor_CD45+_cells_scATACseq

description: scATAC-seq data

tag: tissue

value: baseline

value: Early Stage ccRCC

value: ATAC-seq


title: Naked-DNA-0.2MMS

description: naked DNA control

source_name: Yeast naked genomic DNA

value: wild type

value: 0.2% MMS for 10 min

value: no


title: PLC_NTC_rep2

tag: cell line


title: pt7001025_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data

value: PBMC

tag: treatment

value: blood immune cells


title: ChIP-seq_C65_rIgG

description:
Clonal mESC line expressing endogenously tagged CTCF and Rad21, further modified to visualize CTCF looping in living cells (CTCF loop on chromosome 18  surrounding the Fbn2 gene marked with a TetO and an Anchor 3 array and visualized by expressing fluorescent TetR-mScarlet and EGFP-OR3 array binding proteins) and homozygously deleted of the L1, L2, and R1 CTCF binding sites.
C65_IgG_coverage.bw
ChIP-seq

value: Mouse normal IgG (Jackson ImmunoResearch 015-000-003)


title: Naked-DNA-0.4MMS

description: naked DNA control

value: 0.4% MMS for 10 min


title: ChIP-seq_C65_input

description:
Clonal mESC line expressing endogenously tagged CTCF and Rad21, further modified to visualize CTCF looping in living cells (CTCF loop on chromosome 18  surrounding the Fbn2 gene marked with a TetO and an Anchor 3 array and visualized by expressing fluorescent TetR-mScarlet and EGFP-OR3 array binding proteins) and homozygously deleted of the L1, L2, and R1 CTCF binding sites.
C65_input_coverage.bw
ChIP-seq


title: TYA-11018 (0.3uM)_4_Days_TT_31a


title: TYA-11018 (0.3uM)_4_Days_TT_31b


title: Micro-C_C36_rep5

description:
Clonal mESC line expressing endogenously tagged CTCF and Rad21, further modified to visualize CTCF looping in living cells (CTCF loop on chromosome 18  surrounding the Fbn2 gene marked with a TetO and an Anchor 3 array and visualized by expressing fluorescent TetR-mScarlet and EGFP-OR3 array binding proteins).
C36.mcool
Micro-C

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

value: FLAG-Halo-mCTCF / mRad21-SNAPf-V5 knock-in; chr18:58.131 224x TetO;  chr18:58.646 Anchor3; pL30 TetR-NLS-3x-mScarlet-NLS-DEx4; pL30 EGFP-OR3-DEx4


title: pt2001221_tumor_CD45+_cells_scATACseq

description: scATAC-seq data

value: RCC tumor

value: tumor immune cells


title: pt7001031_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data


title: pt7001025_adjNORM_CD45+_cells_scATACseq

description: scATAC-seq data

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: TYA-11018 (1uM)_4_Days_TT_30a


title: pt2001221_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data


title: TYA-11018 (1uM)_4_Days_TT_30b


title: Micro-C_C36_rep4


title: Micro-C_C36_rep3


title: pt2001215_tumor_CD45+_cells_scATACseq

description: scATAC-seq data


title: TYA-11018 (3uM)_4_Days_TT_29b


title: pt2001215_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data


title: Micro-C_C36_rep2


title: TYA-11018 (3uM)_4_Days_TT_29a


title: pt2001077_tumor_CD45+_cells_scATACseq

description: scATAC-seq data


title: Micro-C_C36_rep1


title: DMSO_4_Days_TT_28b

value: DMSO


title: DMSO_4_Days_TT_28a

value: iPSC cardiomyocytes


title: pt2001077_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data

value: baseline


title: pt2001055_tumor_CD45+_cells_scATACseq

description: scATAC-seq data

value: Early Stage ccRCC


title: pt2001055_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data

value: ATAC-seq


title: pt1002310_adjNORM_CD45+_cells_scATACseq

description: scATAC-seq data


title: pt1002310_tumor_CD45+_cells_scATACseq

description: scATAC-seq data


title: pt1002310_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data


title: pt1002300_adjNORM_CD45+_cells_scATACseq

description: scATAC-seq data


title: Tubastatin A (1uM)_4_Days_TT_26b

value: Tubastatin A


title: Tubastatin A (0.3uM)_4_Days_TT_27b


title: Tubastatin A (0.3uM)_4_Days_TT_27a


title: Mouse Reprogrammed Mammary epithelial cells rep 1

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent).

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent)

label_protocol: mRNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE).

growth_protocol: To prepare embryonic lung epithelium, noon of the day when a vaginal plug was detected was considered approximately E0.5. Embryos were collected in cold 1 X phosphate buffered saline (PBS). Lungs were dissected out from embryos at the E13.5 stages. Epithelium and mesenchyme were separated as reported previously86.  For adult donor cell preparation, female mice of 10-weeks of age were sacrificed and perfused with PBS. Lungs and mammary glands were harvested, minced and dissociated in buffer [5% fetal bovine serum (FBS), insulin 5 µg/ml, Penicillin-Streptomycin 100 U/ml in DMEM/F12] containing trypsin (2 mg/ml) and collagenase A (2 mg/ml) for 45 minutes and 30 minutes, respectively, at 37ºC. Primary epithelia were purified by differential centrifugation: specifically, lung and mammary epithelia were washed in dissociation buffer without collagenase and collected using a swing-bucket centrifuge at 400 X g. The process was repeated for seven and five times for lung and mammary tissues, respectively. To prepare single cells, primary epithelia from embryonic lung and adult lung and mammary gland were washed in Hank’s (Ca2+ Mg2+ free) buffer and dissociated in 0.05% Trypsin/EDTA buffer. Cells were counted using a Hausser Scientific Hemocytometer and prepared in 50% Matrigel™ (growth factor reduced, BD Biosciences) for transplantation.

extract_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: Reprogrammed Mammary

value: epithelial cells


title: Tubastatin A (1uM)_4_Days_TT_26a


title: Tubastatin A (3uM)_4_Days_TT_25a


title: PD_DDLS8817p10_slide986

type: genomic

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: array-based comparative genomic hybridization (CGH)

scan_protocol: Standard vendor (agilent) scanning

data_processing: Custom GC-Normalization full methods are here: http://cbio.mskcc.org/CGCC/; Copy number segmentation using Circular Binary Segmentation CBS in (https://bioconductor.org/packages/release/bioc/html/DNAcopy.html)

source_name: Cell Line

label_protocol: DNA libraries were prepared as per Agilent protocols

growth_protocol: Cell lines were grown in a 1:1 mixture of DMEM high glucose and F12 media with 10% fetal bovine serum, 100 units/mL penicillin plus 100 µg/mL streptomycin (complete medium) and maintained at 37 °C in 5% CO2

extract_protocol: Cryomolds were generated from human patient tumor tissue. Cryomolds containing > 75% cellularity were macrodissected to remove normal, fibrotic, inflammatory, and necrotic tissue. Genomic DNA was then prepared using a Dneasy Blood and Tissue kit (QIAGEN)

treatment_protocol: not treated

tag: histology

value: DDLS

source_name: Promega Ref DNA

tag: reference

value: Promega Ref DNA


title: Tubastatin A (3uM)_4_Days_TT_25b


title: Mouse Reprogrammed Lung epithelial cells rep 4

value: Reprogrammed Lung


title: Mouse Reprogrammed Mammary epithelial cells rep 3


title: Mouse Reprogrammed Mammary epithelial cells rep 2


title: Mouse Reprogrammed Lung epithelial cells rep 3


title: Mouse Mammary epithelial cells rep4

source_name: Mouse Mammary epithelial cells rep4

value: mammary


title: DMSO_4_Days_TT_24b


title: Mouse Reprogrammed Lung epithelial cells rep 1


title: Mouse Lung epithelial cells rep3

source_name: Mouse Lung epithelial cells rep3

value: lung


title: PD_DD172_slide704


title: Mouse Mammary epithelial cells rep1

source_name: Mouse Mammary epithelial cells rep1


title: DMSO_4_Days_TT_24a


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (TCR-Seq) 3

description:
TCR-seq (included in the 5' RNA sequencing)
7001031_1249087_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics, v3.0.2) was used to perform sample demultiplexing, alignment, filtering, and UMI counting.
scRNA-seq profiles were filtered using Seurat (v3.0) as instructed, with the following criteria: nFeature_RNA > 500 & nFeature_RNA < 5000 & percent.mito < 0.25 & nCount_RNA < 50000. Cells with multiple TCR alpha or beta chains were filtered as well.
Filtered data from 4 RCC patients were integrated, clustered, analyzed and visualized following the standard dataset integration and analysis workflow in Seurat 3.0
TCR-seq data were analyzed by Cell Ranger v3.0.2 and contig sequence as well as the combination of V,D,J genes extracted
Genome_build: hg38
Supplementary_files_format_and_content: genes.tsv file, 10X gene file for raw UMI counts
Supplementary_files_format_and_content: matrix.mtx file, 10X format, raw UMI counts
Supplementary_files_format_and_content: barcodes.tsv file, 10X barcodes file for raw UMI counts
Supplementary_files_format_and_content: Metadata.txt file, phenotypic metadata for cells in dataset
Supplementary_files_format_and_content: UMAP_coor_cell_embedding.txt file, UMAP coordinates of cells in dataset, from unsupervised clustering based on gene expression profiles
Supplementary_files_format_and_content: NormalizedCounts.txt file, normalized UMI counts (data integration, library-size normalization and log-transformation with Seurat)
Supplementary_files_format_and_content: cell barcode_TCR.txt file, TCR cloneType information for Tcells in the dataset
Supplementary_files_format_and_content: filtered_contig_annoatations.csv file, filtered VDJ contig information analyzed by Cell ranger v.3.0.2

extract_protocol:
Single cells suspended in PBS with 0.04% BSA were loaded on a Chromium Single Cell Instrument (10x Genomics).
RNA-seq and V(D)J libraries were prepared using Chromium Single Cell 5’ Library, Gel Beads & Multiplex Kit (10X Genomics). After amplification, cDNA was split into RNA-seq and V(D)J library aliquots. To enrich the V(D)J library aliquot for TCR a/b, the cDNA was split into two 20 ng aliquots and amplified in two rounds using primers designed in-house. Specifically, for first round amplification the primers used were MP147 (ACACTCTTTCCCTACACGACGC) for short R1, MP120 (GCAGACAGACTTGTCACTGGA) for human TRAC, and MP121(CTCTGCTTCTGATGGCTCAAACA) for human TRBC. For second round amplification, 20 ng aliquots from the first round were amplified using MP147, MP128 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRAC, and MP129 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRABC. V(D)J libraries were prepared from 25 ng each hTRAC and hTRBC amplified cDNA. Paired-end sequencing was performed on Illumina NextSeq500 for RNA-seq libraries (Read 1 26-bp for UMI and cell barcode, 8-bp i7 sample index, and Read 2 55-bp transcript read) and V(D)J libraries (Read 1 150-bp, 8-bp i7 sample index, and Read 2 150-bp read). For RNA-seq libraries, Cell Ranger Single-Cell Software Suite (10X Genomics, v2.2.0) was used to perform sample demultiplexing, alignment, filtering, and UMI counting. The human GRCh38 genome assembly and RefSeq gene model for human were used for the alignment. For V(D)J libraries, Cell Ranger Single-Cell Software Suite (10x Genomics, v2.2.0) was used to perform sample de-multiplexing, de novo assembly of read pairs into contigs, align and annotate contigs against the germline segment V(D)J reference sequences from IMGT, label and locate CDR3 regions, group clonotypes.

value: RCC tumor

value: RNA-seq


title: Mouse Lung epithelial cells rep1

source_name: Mouse Lung epithelial cells rep1


title: pt1002300_tumor_CD45+_cells_scATACseq

description: scATAC-seq data

value: tumor immune cells


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (RNA-Seq) 3

description:
single cell 5' RNA expression sequencing
ccRCC_4pt_scRNAseq_CD45plus_matrix.mtx
ccRCC_4pt_scRNAseq_CD45plus_barcodes.tsv
ccRCC_4pt_scRNAseq_CD45plus_genes.tsv
ccRCC_4pt_scRNAseq_CD45plus_NormalizedCounts.txt
ccRCC_4pt_scRNAseq_CD45plus_final_UMAP_coor_cell_embedding.txt
ccRCC_4pt_scRNAseq_CD45plus_final_Metadata.txt


title: IP of porcine alveolar macrophages infected with T. gondii RH, repeat 3

city: Wuhan

first: Jing

last: Yang

state: Hubei

address: Shizishan street 1

institute: Huazhong Agricultural University

data_processing:
ChIP-seq data were filtrated using FastQC (version: 0.11.5) and mapped to the reference genome by BWA (version: 0.7.15-r1140).
MACS was used to analyze peak information in the genome, and the threshold for screening the significant Peak was a value of q < 0.05. Peaks with FDR value < 0.05 and Fold > or < 0 in both replications were considered as differentially expressed peaks
Genome_build: https://www.ncbi.nlm.nih.gov/genome/84
Supplementary_files_format_and_content: annotated peaks

source_name: IP

growth_protocol: Porcine alveolar macrophages (3D4/21 cells) were cultured in DMEM with 10%, and T. gondii type Ⅰ strain RHΔhxgprt propagated in human foreskin fibroblast cells in DMEM supplemented with 2% FBS at 37℃ with 5% CO2

extract_protocol:
cells were cross-linked with 1% formaldehyde for ran chromatin extraction. After sonication, fragmented DNA was obtained and then incubated with antibody (anti-H2BK12cr)-coated beads for 12h at 4℃. After extensive washing, 20 μL 5M Nacl was added into immunoprecipitated chromatin to de-cross-linked overnight
Enriched DNA fragments were subjected to library preparation and constructing sequencing on Illumina HiSeq 2000 with PE 150 method.

treatment_protocol: Porcine alveolar macrophages (3D4/21 cells) were infected with tachyzoites of T. gondii type Ⅰ strain RHΔhxgprt (MOI=5) propagated in human foreskin fibroblast cells (obtained from ATCC, USA) in DMEM supplemented with 2% FBS at 37℃ with 5% CO2 or mock infected with an equal amount of phosphate-buffered saline (PBS, pH 7.4)

value: porcine alveolar macrophage

tag: chip antibody

value: infected with RH


title: Ricolinostat (0.3uM)_4_Days_TT_23b

value: Ricolinostat

value: iPSC cardiomyocytes


title: IP of porcine alveolar macrophages infected with T. gondii RH, repeat 2


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (TCR-Seq) 3

description:
TCR-seq (included in the 5' RNA sequencing)
7001031_1249087_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: baseline

value: Early Stage ccRCC


title: Ricolinostat (0.3uM)_4_Days_TT_23a


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (RNA-Seq) 3


title: Ricolinostat (1uM)_4_Days_TT_22b


title: pt1002300_PBMC_CD45+_cells_scATACseq

description: scATAC-seq data

value: PBMC

value: blood immune cells

value: ATAC-seq


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (TCR-Seq) 3

description:
TCR-seq (included in the 5' RNA sequencing)
7001031_1249085_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: Input of porcine alveolar macrophages infected with T. gondii RH, repeat 3

source_name: input


title: Input of porcine alveolar macrophages infected with T. gondii RH, repeat 2


title: Ricolinostat (3uM)_4_Days_TT_21b


title: Input of porcine alveolar macrophages infected with T. gondii RH, repeat 1


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (RNA-Seq) 3


title: Ricolinostat (3uM)_4_Days_TT_21a


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (TCR-Seq) 3

description:
TCR-seq (included in the 5' RNA sequencing)
7001031_1249083_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: IP of porcine alveolar macrophages infected with T. gondii RH, repeat 1


title: IP of the control of porcine alveolar macrophages, repeat 3

value: treated with phosphate-buffered saline


title: ATAC-Seq EXT rep2

city: St Lucia

first: Qiongyi

last: Zhao

state: Queensland

address: Building 79, QBI, The University of Queensland

department: Queensland Brain Institute

country: Australia

institute: The University of Queensland

description: ATAC-seq

data_processing:
Cutadapt (v1.17) was used to trim off low-quality nucleotides (Phred quality lower than 20) and Illumina adaptor sequences at the 3’ end of each read for both lncRNA capture sequencing (Capture-Seq) and ATAC sequencing data.
Processed reads were aligned to the reference genome of mouse (mm10) using HISAT2 (v2.1.0) and BWA-MEM (0.7.17) for Capture-Seq and ATAC-seq data, respectively.
SAMtools (version 1.8) was then used to convert “SAM” files to “BAM” files, remove duplicate reads, sort and index the “BAM” files. To avoid the artefact signals potentially introduced by misalignments, we only kept properly PE aligned reads with mapping quality at least 20 for downstream analyses.
For Capture-Seq data, three rounds of StringTie (v2.1.4) was applied to i) perform reference-guided transcriptome assembly by supplying the GENCODE annotation file (V25) with the “-G” option for each sample, ii) generated a non-redundant set of transcripts using the StringTie merge mode, and iii) quantitate the transcript-level expression for each sample, with the option of “-e -G merged.gtf”. For the lncRNA analysis, known protein-coding transcripts (with the GENCODE transcript biotype as “protein-coding”) or transcripts with a length of less than 200nt were removed from the StringTie results. Ballgown (v2.22.0) was then used to conduct transcript-level differential expression analysis.
For ATAC-seq data, BEDtools (v2.27.1) was used to convert the BAM files to BED files. Reads aligned to the mitochondrial genome were discarded as the mitochondrial genome is more accessible due to the lack of chromatin packaging. To account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase, reads were shifted + 4 bp and − 5 bp for positive and negative strand, respectively. MACS2 (v2.2.4) was used for peak calling with the option of “--shift -75 --extsize 150 --nomodel -B --SPMR -g mm --keep-dup all”. One Arc+ EXT sample was removed from the analysis due to extremely low sequencing quality. BEDtools with the “multiIntersectBed” function was used to identify the consistent peaks among biological replicates. Only consistent ATAC peaks detected in all biological replicates in at least one condition were collected and used for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using the UCSC_binary_utilities: "bedGraphToBigWig"

source_name: ILPFC

growth_protocol: 10-12-week-old C57BL/6 male mice were housed four per cage, maintained on a 12hr light/dark time schedule, and allowed free access to food and water. All experiments took place during the light phase in red-light-illuminated testing rooms following protocols approved by the Institutional Animal Care and Use Committee of the University of Queensland.

extract_protocol:
lncRNAcapseq: ILPFC tissue was collected immediately after RC or EXT training (N=24). 2mg of total RNA isolated from ILPFC tissue (4 pooled per library, 3 libraries per group) was used to generate the RNA library. Total RNA was treated with NEBNext® rRNA Depletion Kit (NEB) to remove rRNA. ATAC-seq: Five ILPFCs per sample were pooled together for FACS. After FACS, Arc+NeuN+ populations from RC or EXT group (n=3 libraries per pooled group) were used for ATAC-seq in following procedure. 50,000 cells were resuspended in 50 μl 2x lysis buffer (20 mM Tris–Cl, pH 7.4; 20 mM NaCl; 6 mM MgCl2; 0.10% Igepal CA-630) and spun down immediately (500 g for 10 min at 4 °C).
RNA libraries were then generated by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB). A custom-designed probe panel (Roche), which targets 28,228 known and predicted mouse lncRNAs (Bussotti et al, 2016), was used to capture lncRNAs in accordance with the manual of SeqCap EZ Hybridization and Wash Kit and SeqCap EZ Accessory Kit (Roche). Captured lncRNA libraries were sequenced on an Illumina HiSeq 4000 platform with the read length of 150 bp x 2. For ATAC-seq, the transposase reaction was performed using the ATAC-seq kit (Active motif) following the manufacturers protocol. Paired-end (PE) libraries were sequenced using an Illumina HiSeq 4000 sequencing platform with the read length of 150 bp x 2.

treatment_protocol: Fear conditioning consisted of three pairing (120 sec inner-trial interval ITI) of a 120 sec, 80dB, 16kHZ pure tone conditioned stimulus (CS) Co-terminating with a 1 sec, 0.7 mA foot shock in context A. Mice were matched into equivalent treatment groups based on freezing during the third training CS. Context A exposure group spent an equivalent amount of time in context A without any CS and US. One day later, the fear-conditioned mice were brought to context B, where the extinction group (EXT) was presented with 60 CS presentations (5s ITI). The retention control (RC) group spent an equivalent amount of time in context B without any CS presentations. ILPFC was collected from both of these groups immediately after the end of either context B exposure (RC) or extinction training (EXT).

value: FACS sorted Arc+NeuN+ cells

tag: developmental stage

value: adult

tag: Sex

value: male

tag: molecule subtype

value: genomic DNA


title: ATAC-Seq EXT rep1

description: ATAC-seq

tag: strain


title: ATAC-Seq EXT rep3

description: ATAC-seq(dropped due to low sequencing yield)


title: ATAC-Seq RC rep2

description: ATAC-seq


title: Mouse Mammary epithelial cells rep2

source_name: Mouse Mammary epithelial cells rep2

value: mammary

value: epithelial cells


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (RNA-Seq) 3

last: Wang

tag: disease state

tag: library strategy

value: RNA-seq


title: DMSO_4_Days_TT_20b

value: DMSO


title: Mouse Lung epithelial cells rep2

source_name: Mouse Lung epithelial cells rep2

value: lung


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249081_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: RCC tumor

value: baseline

value: tumor immune cells


title: IP of the control of porcine alveolar macrophages, repeat 2

value: porcine alveolar macrophage


title: ATAC-Seq RC rep3

description: ATAC-seq


title: DMSO_4_Days_TT_20a

value: iPSC cardiomyocytes


title: ATAC-Seq RC rep1

description: ATAC-seq


title: Ricolinostat (1uM)_4_Days_TT_22a

value: Ricolinostat


title: lncRNA Capture-Seq EXT rep3

description: lncRNA capture sequencing

data_processing:
Library strategy: lncRNA Capture-Seq
Cutadapt (v1.17) was used to trim off low-quality nucleotides (Phred quality lower than 20) and Illumina adaptor sequences at the 3’ end of each read for both lncRNA capture sequencing (Capture-Seq) and ATAC sequencing data.
Processed reads were aligned to the reference genome of mouse (mm10) using HISAT2 (v2.1.0) and BWA-MEM (0.7.17) for Capture-Seq and ATAC-seq data, respectively.
SAMtools (version 1.8) was then used to convert “SAM” files to “BAM” files, remove duplicate reads, sort and index the “BAM” files. To avoid the artefact signals potentially introduced by misalignments, we only kept properly PE aligned reads with mapping quality at least 20 for downstream analyses.
For Capture-Seq data, three rounds of StringTie (v2.1.4) was applied to i) perform reference-guided transcriptome assembly by supplying the GENCODE annotation file (V25) with the “-G” option for each sample, ii) generated a non-redundant set of transcripts using the StringTie merge mode, and iii) quantitate the transcript-level expression for each sample, with the option of “-e -G merged.gtf”. For the lncRNA analysis, known protein-coding transcripts (with the GENCODE transcript biotype as “protein-coding”) or transcripts with a length of less than 200nt were removed from the StringTie results. Ballgown (v2.22.0) was then used to conduct transcript-level differential expression analysis.
For ATAC-seq data, BEDtools (v2.27.1) was used to convert the BAM files to BED files. Reads aligned to the mitochondrial genome were discarded as the mitochondrial genome is more accessible due to the lack of chromatin packaging. To account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase, reads were shifted + 4 bp and − 5 bp for positive and negative strand, respectively. MACS2 (v2.2.4) was used for peak calling with the option of “--shift -75 --extsize 150 --nomodel -B --SPMR -g mm --keep-dup all”. One Arc+ EXT sample was removed from the analysis due to extremely low sequencing quality. BEDtools with the “multiIntersectBed” function was used to identify the consistent peaks among biological replicates. Only consistent ATAC peaks detected in all biological replicates in at least one condition were collected and used for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using the UCSC_binary_utilities: "bedGraphToBigWig"

value: ILPFC

value: nuclear RNA


title: lncRNA Capture-Seq EXT rep2

description: lncRNA capture sequencing


title: lncRNA Capture-Seq EXT rep1

description: lncRNA capture sequencing


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (RNA-Seq) 2

value: Early Stage ccRCC


title: HCC1954 - BC Cell Line - scRNAseq

source_name: HCC1954 - BC Cell Line


title: Givinostat (0.3uM)_4_Days_TT_19b

value: Givinostat


title: lncRNA Capture-Seq RC rep3

description: lncRNA capture sequencing

value: adult

value: male


title: Givinostat (0.3uM)_4_Days_TT_19a


title: Input of the control of porcine alveolar macrophages, repeat 2

value: treated with phosphate-buffered saline


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249081_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

source_name: Donor


title: lncRNA Capture-Seq RC rep2

description: lncRNA capture sequencing


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (RNA-Seq) 2


title: Givinostat (1uM)_4_Days_TT_18a


title: Input of the control of porcine alveolar macrophages, repeat 1


title: pt1002310_PBMC_CD45+_cells_scRNAseq_2 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249079_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: PBMC

value: blood immune cells


title: lncRNA Capture-Seq RC rep1

description: lncRNA capture sequencing


title: Givinostat (3uM)_4_Days_TT_17b


title: pt1002310_PBMC_CD45+_cells_scRNAseq_2 (RNA-Seq) 2

value: RNA-seq


title: WT_SCI_3

city: San Francisco

first: Jonathan

last: Pan

address: 1001 Potrero Ave, Bldg 5, Room 3C38

department: Anesthesia and Perioperative Care

institute: University of California, San Francisco

description: RNASeq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to the mm10 whole genome (Ensembl gene build GRCm38.96) using aligner STAR_2.7.2b
Raw read counts were used as input to DESeq2 v1.24.0
Genome_build: mm10
Supplementary_files_format_and_content: Read counts matrix

source_name: Spinal cord tissue

extract_protocol:
Total RNA was prepared using TRIzol and Qiagen RNA miniprep kit. Sample quaity was checked using bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols with Lexogen Quantseq Forward library kit

treatment_protocol: Wildtype mice had spinal cord contusion injury or laminectomy only at C5 (unilateral) using inifinite horizon device (50 Kdyne)

value: Spinal cord injury

value: spinal cord

tag: genotype

value: wildtype


title: IP of the control of porcine alveolar macrophages, repeat 1


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249079_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: baseline


title: Givinostat (3uM)_4_Days_TT_17a


title: WT_SCI_1

description: RNASeq


title: Input of the control of porcine alveolar macrophages, repeat 3

value: porcine alveolar macrophage


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_2 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249077_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: DMSO_24_Hours_TT_16b

value: DMSO

value: iPSC cardiomyocytes


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (RNA-Seq) 2

value: Early Stage ccRCC


title: WT_Sham_3

description: RNASeq

value: Laminectomy


title: WT_Sham_2

description: RNASeq


title: DMSO_24_Hours_TT_16a


title: Givinostat (1uM)_4_Days_TT_18b

value: Givinostat


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_2 (RNA-Seq) 2


title: WT_Sham_1

description: RNASeq


title: TYA-11018 (0.3uM)_24_Hours_TT_15a


title: WT_SCI_2

description: RNASeq


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (TCR-Seq) 2

description:
TCR-seq (included in the 5' RNA sequencing)
7001025_1249077_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: TYA-11018 (0.3uM)_24_Hours_TT_15b


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (RNA-Seq) 2


title: TYA-11018 (1uM)_24_Hours_TT_14b


title: TYA-11018 (1uM)_24_Hours_TT_14a


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249075_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: RCC tumor

value: tumor immune cells


title: ED2334 p10 FIBRO

description: Female breast cancer patient

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with the BioConductor package, Lumi in R.

label: biotin

source_name: Cancer-associated fibroblasts

label_protocol: RNA was biotinylated using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Primary human fibroblasts were isolated from breast cancer tumours from patients with ILC or IDC.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: No treatment.

tag: diagnosis

value: Breast cancer

value: Female

value: Cancer-associated fibroblasts


title: ED2425 p10 FIBRO

description: Female breast cancer patient

tag: cell type


title: ED2263 p7 FIBRO

description: Female breast cancer patient


title: D3 WT FGF SOX2 IP ChIP-seq biological replicate 2 (EXP6)

city: London

first: James

last: Briscoe

address: 1 Midland Road

institute: The Francis Crick Institute

description: ChIP-seq

data_processing:
The nf-core/chipseq pipeline (version 1.1.0; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3529400) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --input design.csv --genome mm10 --gtf refseq_genes.gtf --single_end --narrow_peak --min_reps_consensus 2 -profile crick -r 1.1.0".
All data was processed relative to the human UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on December 11th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using from the nf-core/chipseq pipeline command defined above.

source_name: In vitro differentiated epiblast-like cells

growth_protocol: ES cell lines were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then either N2/B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021, or N2/B27 + 10ng/ml bFGF + 5uM LGK974 until day 3.

extract_protocol:
For each sample approximately 5*10^6 cells were resuspended in ice cold shearing buffer (1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6), 0.3% SDS + protease inhibitors) and transferred to three Diagenode TPX tubes. Chromatin was sheared using a Bioruptor plus: 25 cycles of 30s On/30s Off on high setting. Sheared lysates were diluted to 0.15% SDS  prior to immunoprecipitation.
The DNA library for sequencing was prepared from Qiagen column purified DNA. DNA fragmentation of IP and input samples was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: Adherent cells were fixed for 45min at room temperature with 2mM Di(N-succinimidyl) glutarate, then fixed for an additional 10min at room temperature with 1% PFA. Fixation was quenched by addition of 250mM glyceine for 5 minutes.

value: Sox2 (R&D AF2018 goat)

value: wild-type

tag: timepoint

value: FGF


title: ED14 p4 FIBRO

description: Female breast cancer patient


title: D3 WT FGF SOX2 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells


title: TYA-11018 (3uM)_24_Hours_TT_13b

source_name: iPSC-CM

tag: dose


title: D3 WT FGF SOX2 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: pt1002310_tumor_CD45+_cells_scRNAseq_2 (RNA-Seq)

tag: tissue

value: baseline

value: RNA-seq


title: ED26 p4 FIBRO

description: Female breast cancer patient


title: HMF SC p2 2

description: Female breast cancer patient

source_name: Normal fibroblasts

value: Normal fibroblasts


title: ED9B p8 FIBRO

description: Female breast cancer patient


title: D3 WT FGF INPUT ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: TYA-11018 (3uM)_24_Hours_TT_13a


title: ED28 p6 Fibro

description: Female breast cancer patient


title: HMF SC p2 1

description: Female breast cancer patient


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249075_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: DMSO_24_Hours_TT_12b

value: DMSO


title: pt1002310_PBMC_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249073_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: PBMC

value: blood immune cells


title: pt1002310_tumor_CD45+_cells_scRNAseq_1 (RNA-Seq)

value: Early Stage ccRCC


title: D3 WT FGF INPUT ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: D3 WT FGF INPUT ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: CHIR FGF


title: pt1002310_PBMC_CD45+_cells_scRNAseq_2 (RNA-Seq)


title: Tubastatin A (0.3uM)_24_Hours_TT_11b

value: Tubastatin A

value: iPSC cardiomyocytes


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249073_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: ED29 p3

description: Female breast cancer patient

value: Breast cancer


title: Tubastatin A (1uM)_24_Hours_TT_10b


title: DMSO_24_Hours_TT_12a


title: pt1002310_PBMC_CD45+_cells_scRNAseq_1 (RNA-Seq)


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249071_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: Tubastatin A (1uM)_24_Hours_TT_10a


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_2 (RNA-Seq)


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)


title: Tubastatin A (3uM)_24_Hours_TT_9b


title: Tubastatin A (3uM)_24_Hours_TT_9a


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002310_1249071_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: LEF1 (Millipore CS200635)

value: wild-type


title: HMF U19 1

description: Female breast cancer patient

value: Female


title: Tubastatin A (0.3uM)_24_Hours_TT_11a


title: DMSO_24_Hours_TT_8b


title: HMF U19 2

description: Female breast cancer patient


title: D3 WT CHIR FGF INPUT ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells


title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq