title: WT_37deg_mRNAseq_replicate3

last: Gerashchenko

address: 77 Louis Pasteur Ave, NRB 435

institute: Brigham and Women's Hospital

description:
Wild Type N2
mRNAseq_Metl5_vs_WT_37deg.csv
Transcriptome
mRNAseq_Metl5_vs_WT.csv

data_processing:
Detailed data processing pipeline is availale here: https://github.com/germaximus/Liberman_2019
Genome_build: C. elegans. PRJNA13758 WS268
Supplementary_files_format_and_content: *.counts contains gene expression tables from STAR for each sample presented as sequencing reads count per gene. First column - gene name, second column - reads mapped to both strands, third column - reads mapped to forward strand, forth column - reads mapped to reverse strand.  *.csv files contain differential gene expression analysis results from DESeq2

organism: Caenorhabditis elegans

source_name: adult worm

extract_protocol: TBD

value: Wild Type N2

tag: temperature


title: Metl5_37deg_RiboSeq_replicate3

status: Public on Dec 31 2019

type: SRA

city: Boston

first: Maxim

state: Massachusetts

department: Medicine

country: USA

description:
DC38D4.9
RiboSeq_Metl5_vs_WT_37deg.csv
Ribosomal profiling
RiboSeq_Metl5_vs_WT.csv

library_source: transcriptomic

data_processing:
Library strategy: Ribo-Seq
Detailed data processing pipeline is availale here: https://github.com/germaximus/Liberman_2019
Genome_build: C. elegans. PRJNA13758 WS268
Supplementary_files_format_and_content: *.counts contains gene expression tables from STAR for each sample presented as sequencing reads count per gene. First column - gene name, second column - reads mapped to both strands, third column - reads mapped to forward strand, forth column - reads mapped to reverse strand.  *.csv files contain differential gene expression analysis results from DESeq2

molecule: total RNA

tag: strain


title: Metl5_37deg_RiboSeq_replicate2


title: Metl5_20deg_RiboSeq_replicate2

description:
DC38D4.9
RiboSeq_Metl5_vs_WT_20deg.csv
Ribosomal profiling
RiboSeq_Metl5_vs_WT.csv


title: WT_20deg_RiboSeq_replicate1

description:
Wild Type N2
RiboSeq_Metl5_vs_WT_20deg.csv
Ribosomal profiling
RiboSeq_Metl5_vs_WT.csv


title: WT_20deg_RiboSeq_replicate3


title: Metl5_20deg_RiboSeq_replicate1


title: Metl5_37deg_RiboSeq_replicate1


title: Metl5_20deg_RiboSeq_replicate3


title: WT_37deg_mRNAseq_replicate1


title: WT_37deg_mRNAseq_replicate2


title: WT(MG20)_MAFF_10dai

city: Tsukuba

first: Yoshikazu

last: Shimoda

state: Ibaraki

address: 3-1-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Obtained Fastq sequences were subjected to four steps of quality filtering and trimming by FastX-toolkit. Step1: select the reads with more than QV10 accounting for more than 10% (fastq_quality_filter). Step2: trim the sequence less than QV10 and select the reads of more than 30bp (fastq_quality_trimmer). Step3: remove the repetitive sequences (fastx_artifacts_filter). Step4: Remove the adaptor sequences if the read contains more than 5 characters of the adapter sequence from the 3’ end and select the reads of more than 30bp (fastx_clipper).
Selected reads were mapped to Lotus japonicus coding sequence (build 2.5) including 5' UTR and 3' UTR using Bowtie2 (ver. 2.0.2).
Normalization of mapped read counts was performed using DEseq with iDEGES/DESeq (Sun et al., BMC Bioinformatics, 2013).
Genome_build: build 2.5
Supplementary_files_format_and_content: tab-delimited text files include original mapped read count and DESeq normalized count.

organism: Lotus japonicus

source_name: nodule

growth_protocol: Lotus japonicus was planted in vermiculite soil supplemented with nitrogen-free B&D medium and was grown in a growth chamber under 16 h/8 h light/dark cycle at 25°C/23°C.

extract_protocol:
Nodule primordias and developing nodules were excised from roots. Total RNA was isolated using Cetyltrimethylammonium Bromide (CTAB) and LiCl. Total RNA was treated with DNase (Qiagen) and Ribo-Zero kit for plant seed/root and for gram-negative bacteria (Epicentre) to remove genomic and ribosomal DNA. 50 ng of RNA was used for library preparation.
RNA libraries were prepared using Scriptseq Ver2 library preparation kit (Epicentre) by following manufacture's instructions

treatment_protocol: Mesorhizobium loti was inoculated at 7 days after planting into vermiculite.

tag: plant genotype

value: wild type

tag: inoculation (rhizobial strain)

value: Mesorhizobium loti MAFF303099

tag: time

tag: tissue

value: nodule


title: WT_20deg_mRNAseq_replicate3

description:
Wild Type N2
mRNAseq_Metl5_vs_WT_20deg.csv
Transcriptome
mRNAseq_Metl5_vs_WT.csv


title: WT_20deg_mRNAseq_replicate1


title: Metl5_37deg_mRNAseq_replicate2

description:
DC38D4.9
mRNAseq_Metl5_vs_WT_37deg.csv
Transcriptome
mRNAseq_Metl5_vs_WT.csv


title: 1BsiRNA_drought_1

city: Montreal

first: Mario

last: Houde

state: Quebec

address: 2080, rue Saint-Urbain

department: Sciences Biologique

country: Canada

institute: Université du Québec à Montréal

description:
Samples 1BsiRNA_drought_1 and 1BsiRNA_drought_2 represent the same biological sample.
1BsiRNA drought-treated plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence or low-quality sequence using Trim sequences. First base to keep 10 and Last base to keep 140.
Sequence reads were aligned to the wheat transcriptome (release 37) using Salmon and Transcripts Per Million (TPM) was the unit used for downstream analysis.
Genome_build: T. aestivum Ensembl release 37 (Triticum_aestivum.TGACv1.cdna.all.fa.gz)
Supplementary_files_format_and_content: *.tabular.txt: Tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: Supplementary_Table 1.xlsx: Excel file
Supplementary_files_format_and_content: Supplementary_Table 2.xlsx: Excel file

organism: Triticum aestivum

source_name: Wheat leaf tissue

growth_protocol: Wheat plants were grown in growth chambers under controlled conditions at 22°C, a 14 h photoperiod, 100 μmol m−2 s−1 irradiance (fluorescent and incandescent lighting), and 70% relative humidity.

extract_protocol:
The tissue was flash-frozen in liquid nitrogen and total RNA was extracted with the RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Four different types of plants were used in this study: wild-type, plants transformed with BSMV empty vector (BSMV:00), plants overexpressing TaZFP1B (1B-OEX) and plants under expressing TaZFP1B (1B-siRNA). Wheat seeds were inoculated with viral extracts for three days during seed imbibition as previously described (Cheuk and Houde, 2017; Cheuk and Houde, 2018). Seeds were then sown (10 per pot) in a mixture of black earth, peat moss and perlite (2:1:1 ratio), and pots were watered every day for 14 days. Drought stress was then initiated by withholding water for 7 days.

tag: cultivar

tag: genotype/variation

value: Under-expressing TaZFP1B

value: Leaf

tag: age

value: 21 days

tag: treatment

value: 7 days of drought treatment


title: Metl5_37deg_mRNAseq_replicate3


title: 1BsiRNA_drought_2


title: 1BsiRNA_control_2

description:
Samples 1BsiRNA_control_1 and 1BsiRNA_control_2 represent the same biological sample.
1BsiRNA well-watered plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx

value: Watered every day


title: VSMCs - 3days after inducing calcification 2

type: RNA

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

country: South Korea

institute: Chonnam Univ. Med. Sch.

description: Gene expression in rat carotid artery 3 days after baloon injury

hyb_protocol: Agilent’s miRNA Hybridization Kit

scan_protocol: Agilent’s DNA microarray scanner and Feature Extraction Software was used for scaning and data acquisition.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction, and GeneSpringGX v7.3 Software was used for LOWESS normalization.

organism: Rattus norvegicus

source_name: Rat aorta

label_protocol: Agilent’s miRNA Labeling Reagent

growth_protocol: VSMCs were grown in 10% FBS in DMEM supplemented with antibiotics at 37C, 5 %CO2, >80 %humidity.

extract_protocol: Total RNA was extracted using Trizol reagent following manufacturer's protocol. Quality was monitored using Agilent 2100 Bioanalyzer.

treatment_protocol: Calcification was induced in VSMCs with inorganic phosphate (2mmole/L).

value: Sprague-Dawley

value: carotid artery

tag: gender

value: male

tag: weight


title: WT_37deg_RiboSeq_replicate1

description:
Wild Type N2
RiboSeq_Metl5_vs_WT_37deg.csv
Ribosomal profiling
RiboSeq_Metl5_vs_WT.csv


title: 1BsiRNA_control_1


title: Metl5_37deg_mRNAseq_replicate1


title: bPAC - Low (JPF62)

city: San Francisco

first: Joao Pedro

last: Fons

state: CA

address: 1700 4th Street, Room BH409C

department: Biochemistry and Biopysics

institute: UCSF

data_processing:
bases called by Illumina software
aligning and gene count using Integrated QuantSeq data analysis pipeline on Bluebee platform
Genome_build: canFam3.1
Supplementary_files_format_and_content: txt; counts per gene

organism: Canis lupus familiaris

source_name: bPAC - Low

growth_protocol: Cells were grown in 6 well plates, with DMEM supplemented with 0.5% FCS and 1X GlutaMAX and no phenol red

extract_protocol:
RNA was extracted using Lexogen's SPLIT RNA Extraction Kit
Lexogen's QUANTSEQ 3' FWD

treatment_protocol: Cell were illuminated for 2h with no, low or high dose of light, 16h after plating

tag: cell type

value: MDCKI + bPAC

value: Low dose of light


title: VSMCs - 6days after inducing calcification 1

description: Gene expression in rat carotid artery 6 days after baloon injury


title: bPAC - Low (JPF61)


title: WT_20deg_RiboSeq_replicate2


title: 1BOEX_drought_2

description:
Samples 1BOEX_drought_1 and 1BOEX_drought_2 represent the same biological sample.
1BOEX drought-treated plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx

value: Over-expressing TaZFP1B


title: VSMCs - Control 2

description: MicroRNA expression in rat aorta vascular smooth muscle cells

value: vascular smooth muscle


title: VSMCs - 3days after inducing calcification 1


title: WT_20deg_mRNAseq_replicate2


title: VSMCs - Control 1


title: Metl5_20deg_mRNAseq_replicate3

description:
DC38D4.9
mRNAseq_Metl5_vs_WT_20deg.csv
Transcriptome
mRNAseq_Metl5_vs_WT.csv


title: Metl5_20deg_mRNAseq_replicate1


title: 1BOEX_drought_1


title: Metl5_20deg_mRNAseq_replicate2


title: WT_37deg_RiboSeq_replicate3


title: VSMCs - 6days after inducing calcification 2


title: WT_37deg_RiboSeq_replicate2


title: BSMV00_drought_2

description:
Samples BSMV00_drought_1 and BSMV00_drought_2 represent the same biological sample.
BSMV00 drought-treated plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx

value: Vector control


title: 1BOEX_control_1

description:
Samples 1BOEX_control_1 and 1BOEX_control_2 represent the same biological sample.
1BOEX well-watered plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx


title: BSMV00_drought_1


title: B6J_input_ChIP

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 300 Cedar Street

institute: Yale University School of Medicine

library_source: genomic

data_processing:
RNA-seq of cellular genes:
Btrim to trim adapters and low-quality read
Tophat2 to map reads
DEseq2 to analyze differential gene expression
RNA-seq of ERV or VL30:
Btrim to trim adapters and low-quality read
BWA-mem to map reads
SAMtools processing of unmapped reads
BEDTools to read mapping counts to ERV
DEseq2 to analyze differential gene expression
RNA-seq RepEnrich:
Btrim to trim adapters and low-quality read
Bowtie to map reads
SAMtools processing of uniquely mapped reads
RepEnrich analysis of non-uniquely mapped reads
DEseq2 to analyze differential gene expression
ChIP-seq:
Bowtie2
Picard to remove duplicates
deepTools to count reads and generate bigWig files
Genome_build: mm10
Genome_build: ChIP-seq: Unique ERV and VL30 loci
Supplementary_files_format_and_content: RNA-seq of cellular genes: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq of ERV or VL30: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq RepEnrich: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: ChIP-seq: bigWig files of normalized reads mapped to unique ERV and VL30 loci

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow-derived macrophage

extract_protocol:
Lysates were clarified from sonicated nuclei from paraformaldehyde-fixed cells and histone-DNA complexes were isolated with antibody.
NEBNext® Ultra II DNA Library Prep Kit for Illumina (E7645) was used with 100ng of total DNA for the construction of sequencing libraries

value: bone marrow-derived macrophage


title: BSMV00_control_2

description:
Samples BSMV00_control_1 and BSMV00_control_2 represent the same biological sample.
BSMV00 well-watered plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx


title: BSMV00_control_1


title: WT_control_1

description:
Samples WT_control_1 and WT_control_2 represent the same biological sample.
Wild type well-watered plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx

value: WT


title: WT_control_2


title: WT_drought_2

description:
Samples WT_drought_1 and WT_drought_2 represent the same biological sample.
Wild type drought-treated plants.
mRNA
processed data file: Supplementary_Table 1.xlsx
processed data file: Supplementary_Table 2.xlsx


title: 1BOEX_control_2


title: Hap2-GFP1

city: Edinburgh

first: Marcel

last: Lafos

state: Scotland

address: Max Born Crescent

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Quality filtering was performed using trimmomatic v0.36. Read mapping was performed using bwa v0.7.17 to S. pombe genome GCF_000002945.1. Bigwigs were generated using bamCompare v3.1.3 from deeptools. Peak calling was performed using macs2 v2.1.2. Overlap of the peak files were called using bamtools v2.5.1.
Genome_build: GCF_000002945.1
Supplementary_files_format_and_content: Bigwigs were generated using bamCompare v3.1.3 from deeptools.

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: Schizosaccharomyces pombe cell were gwon in rich medium (1X YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-seq libraries were prepared essentially as described in Shukla et al., 2017.

value: Hap2-GFP Arp5-3HA

tag: chip antibody

value: anti-GFP


title: Arp5-3HA2

value: anti-HA


title: Arp5-3HA1


title: WT_drought_1

value: Leaf


title: Hap2-GFP2


title: FNO12 28C R3

city: Belo Horizonte

first: Henrique

middle: César Pereira

last: Figueiredo

state: Minas Gerais

address: Av. Antônio Carlos 6627, Caixa Postal 567, Pampulha

country: Brazil

institute: AQUACEN - National Reference Laboratory for Aquatic Animal Diseases

description: Gene expression of FNO after incubation at 28°C R3

hyb_protocol: The cRNA fragmentation and hybridization were performed using Agilent Gene Expression Hybridization kit according to the manufacturer’s instructions. For this, 600 ng of Cy3-labeled cRNA, with specific activity ? 16.2 pmol Cy3/ng was fragmented at 60 °C for 30 min in a mix composed by 5 mL of 10X Blocking agent, 1 mL of 25X Fragmentation Buffer and nuclease-free water to reach a final volume of 25 mL. After fragmentation, 25 mL of 2X GEx Hybridization Buffer were added in each replicate, which were centrifuged at 21,900 x g for 2 min. Next, 45 µL of hybridization solution were dispensed into a custom-made Agilent slide (8 x 60K) formulated based on the FNO12  non-redundant genes (Agilent.SingleColor.62611).

scan_protocol: The slide was scanned using Agilent DNA Microarray Scanner (Agilent Technologies) using default parameters.

data_processing:
The data obtained from array images were extracted using Agilent Features Extraction software version 11.5 (Agilent Technologies)
raw data were evaluated using the limma package of R statistical software. Background corrections were performed with the “normexp” method. Normalization between arrays was done using the “cyclicloess” method.

organism: Francisella orientalis

source_name: Bacterial 28°C

label_protocol: A total of 50 ng of RNA of each biological replicate was amplified and Cy3-labeled using the Agilent Quick Amp Labeling kit (Agilent Technologies) along with RNA Spike-in controls according to Agilent One-Color Microarray-Based Expression Analysis protocol (Agilent Technologies).

growth_protocol: This isolate was streaked onto an CHAH plate and incubated at 28°C for 96 h. Then, one colony was inoculated into quadruplicate cultures of MMH, and incubated at 28°C or 22°C for approximately 29 h and 120 h, respectively, under constant agitation (100 rpm). The bacterial suspension from each culture (n = 8) was collected for RNA extraction once reaching an OD600 of 0.150.

extract_protocol: The mixture was centrifuged at 10,000 rpm for 10 min at 4°C and the pellets were stored at -80°C until use. Total RNA was extracted using TRIzol RNA Isolation Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. The extracted RNA of each replicate was treated with Turbo DNA-free kit (Ambion, Carlsbad, USA) and 1 µL was submitted to FNO-specific qPCR [26] to determine the absence of genomic DNA. The extracted RNA was quantified using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, USA) and its quality and integrity was evaluated using TapeStation 2200 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: a culture volume of 5 mL of each biological quadruplicate was immediately mixed in 10 mL of RNAlater (Life Technologies, Carlsbad, USA) and incubated at room temperature for 5 min.


title: 23 Pa CSS rep3

city: COLUMBUS

first: Yixiao

last: Cui

state: OH

address: 1502 King Ave Unit D

institute: The Ohio State University

description:
Gene expression data of LN229 cells treated with no CSS
Human glioblastoma cell lines

hyb_protocol: 15 µg of labeled,  fragmented, and biotin-labe led ss-cDNA was hybridized at 45 °C for 16 hr at 60 rpm in an Affymetrix 645 Hybridization oven

scan_protocol: GeneChips were washed and stained using an Affymetrix 450 Fluidics Station, and scanned with an Affymetrix 3000 7G GeneChip Scanner.

data_processing: Gene expression analysis was performed using the Ebayes ANOVA method in the Transcriptome Analysis Console (TAC 4.01, ThermoFisher) with false discovery rate (FDR) adjusted p < 0.05.

label: biotin

organism: Homo sapiens

source_name: LN229 cells treated with no CSS for 18 hr

label_protocol: 100 ng RNA was used to generate ss-cDNA according to the manufacturer’s protocol in the GeneChip® WT PLUS Reagent Kit. Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: LN229 were cultured using standard procedures. Cells were fed 2-3 times per week with DMEM/F12 media (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Fisher Scientific, Hampton, NH, USA), 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA) and 1% MycoZap (Life Technologies, Carlsbad, CA, USA).Cells were passaged at ~80% confluency.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Extracted RNA was further purified with an RNA clean-up and concentration kit (Norgen 23600) and tested for quality by Nanodrop analysis and a TapeStation RNA Bioanalyzer.

treatment_protocol: Cells were cultured on the membrane of a Transwell© insert (VWR® tissue culture plate inserts, polyester membrane, 12 mm diameter, 0.4 µm pore size) in a 12-well tissue culture plate (VWR). Cell culture media was added to the inner well. This pore size was selected to allow nutrient and oxygen exchange and prevent transmigration across the membrane. An agar cushion was placed atop the cells to protect against edge effects and from contact with the rigid weight discs used to create CSS. Finally, weight discs made of stainless steel were placed on top of the agar cushion to apply a compression level of 23 Pa. No agar cushion or stainless steel discs were added to the control.

tag: cell line


title: FNO12 28C R1

description: Gene expression of FNO after incubation at 28°C R1


title: FNO12 22C R4

description: Gene expression of FNO after incubation at 22°C R4

source_name: Bacterial 22°C


title: HBE_control

city: chongqing

first: hongqiang

last: chen

address: Gaotanyan, Shapingba District, Chongqing

country: China

institute: Third Military Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: bronchial epithelium cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The HBE cell line was derived from normal bronchial epithelium taken from a man undergoing lobectomy for squamous cell carcinoma. Cells from the primary explant in their first passage were infected with the recombinant retrovirus LXSN16E6E7 containing the human papilloma virus (HPV) E6E7 gene. HBE cells were cultured in DMEM medium (high-glucose) containing 10% fetal bovine serum (Gibco, USA) in a cell culture incubator with 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The HBE cells were divided and assigned to either the dimethylsulfoxide (DMSO)-treated group or the 3-MCA-treated (purity ≥ 97.5%, Sigma, USA) group. The DMSO group was treated with 0.1% DMSO, and the 3-MCA group was continuously cultured with 10 μM 3-MCA for 45 generations.

tag: passages

value: control


title: FNO12 28C R4

description: Gene expression of FNO after incubation at 28°C R4


title: Control, no CSS rep3

description:
Gene expression data of LN229 cells treated with 23 Pa CSS
Human glioblastoma cell lines

source_name: LN229 cells treated under 23 Pa CSS for 18 hr


title: FNO12 22C R3

description: Gene expression of FNO after incubation at 22°C R3


title: BCPAP_siNS_rep2

city: Columbus

first: Albert

last: de la Chapelle

address: 460 W. 12th Avenue

institute: The Ohio State University Wexner Medical Center

hyb_protocol: Samples were hybridized using herring sperm DNA, acetylated BSA (50 mg/mL). Eukaryotic Hybridization Controls (Affymetrix) were heated at 65°C for 5 minutes, 99°C for 5 minutes, 45°C for 5 minutes, centrifuged at maximum speed for 5 minutes, then hybridized 16 hours at 45°C at 60 rpm. Fluidics washing is protocol FS450_0001.

scan_protocol: The arrays were scanned with the Affymetrix Genen Chip Scannner 3000 7G system using Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Signal intensities were processed by RMA method using Affymetrix Expression Console software

label: Biotin

source_name: BCPAP cells treated with NS siRNA for 72 hours

label_protocol: 5.5 ug of single-stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: BCPAP cells were seeded in 6-well plate and grown to 75% confluence at the time of transfection.

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 40 uM siLRRC34 or siNS were transfected into BCPAP cells using 7.5 ul Lipofectamine RNAiMAX (Thermo Fisher Scientific). Cells were harvest after 72 hours of treatment.

value: BCPAP


title: Control, no CSS rep4


title: Control, no CSS rep1


title: 23 Pa CSS rep2


title: Control, no CSS rep2


title: FNO12 22C R2

description: Gene expression of FNO after incubation at 22°C R2


title: BCPAP_siLRRC34_rep1

source_name: BCPAP cells treated with LRRC34 siRNA for 72 hours


title: BCPAP_siLRRC34_rep2


title: HBE_3MCA

value: normal bronchial epithelium taken from a man undergoing lobectomy for squamous cell carcinoma


title: EOBC-143

city: Valencia

first: Sara

last: OLTRA SANCHIS

state: Valencia

address: Avda Menéndez Pelayo, 4 accesorio

department: Medical Oncology

country: Spain

institute: INCLIVA

hyb_protocol: Hybridization and scanning were performed according to the Clariom D  standard protocol

data_processing: Data quality of *.CEL sample files was analyzed by affy package from R/Bioconductor and Transcriptome Analysis Console 4.0

source_name: FFPE

label_protocol: standard Affymetrix protocol

extract_protocol: The RNA for the Clariom™ D study was extracted from tissue fixed in formaldehyde and embedded in paraffin, preserved at room temperature. Four sections of 20 μm from breast cancer tumour paraffin embedded were used. The extraction of the RNA material was carried out using the commercial kit RecoverAll ™ Total Nucleic Acid Isolation Kit from ambion® (Applied Biosystems ™ by Life Technologies ™, Carlsbad, California, USA)

value: breast cancer


title: BCPAP_siNS_rep3


title: 23 Pa CSS rep4


title: BCPAP_siNS_rep1


title: BCPAP_siLRRC34_rep4


title: EOBC-177

scan_protocol: Hybridization and scanning were performed according to the Clariom D  standard protocol


title: BCPAP_siLRRC34_rep3


title: EOBC-156


title: BCPAP_siNS_rep4


title: THP-1_E_Mock-Control

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description:
THP-1 RNA
sample excluded from analysis. No processed data available.

hyb_protocol: GeneTitan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg array using the Affymetrix GeneTitan Hybridization, Wash, and Stain Kit for WT Arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average (RMA) method with a log base 2 (log2) transformation (Irizarry et al., 2003).  Principal component analysis (PCA) was used to evaluate the overall performance of the arrays and identify outliers. A filtering step was performed to remove low expression probe sets. Gene expression differences were identified using ANOVA models with linear contrasts.

source_name: THP-1 monocytes

label_protocol: Following purification, 5.5 µg of ss-cDNA were fragmented and end labeled with biotin before hybridizing to the array plate

growth_protocol: THP-1 human monocytes (TIB-202, ATCC) were cultured in suspension in RPMI-1640 (ATCC) supplemented with 10% (v/v) Exosome-Depleted FBS (Gibco), penicillin-streptomycin (Gibco), and 0.05 mM β-mercaptoethanol (Sigma).

extract_protocol: Cells were lysed in QIAzol (Qiagen) and isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Exposures were conducted in 96-well round-bottom plates (Corning) at a density of 1 x 10^5 cells per well. THP-1 monocytes were exposed to 200 µg/ml HDE or the matched volume of mock in separate experiments for each hepatocyte donor.

tag: hepatocyte donor id

value: E

value: Mock-Control


title: FNO12 22C R1

description: Gene expression of FNO after incubation at 22°C R1

tag: temperature


title: 23 Pa CSS rep1


title: EOBC-105


title: EOBC-103


title: EOBC-154


title: THP-1_E_Mock-APAP

description:
THP-1 RNA
This sample was duplicated in the analysis.

scan_protocol: GeneTitan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg array using the Affymetrix GeneTitan Hybridization, Wash, and Stain Kit for WT Arrays.

value: Mock-APAP


title: THP-1_E_APAP HDE

description: THP-1 RNA

value: APAP HDE


title: EOBC-082


title: EOBC-084


title: THP-1_D_Mock-APAP

description: THP-1 RNA

value: D


title: THP-1_D_Mock-Control

description: THP-1 RNA


title: EOBC145


title: EOBC141


title: EOBC-070


title: EOBC075


title: EOBC012


title: 16BC_022


title: EOBC-101


title: THP-1_D_APAP HDE

description: THP-1 RNA


title: 16BC_020


title: EOBC014


title: 16BC_021


title: THP-1_D_Control HDE

description: THP-1 RNA

value: Control HDE


title: 16BC_027


title: 16BC_024


title: 16BC_029


title: 16BC_031


title: THP-1_C_Mock-Control

description: THP-1 RNA

value: C


title: FNO12 28C R2

description: Gene expression of FNO after incubation at 28°C R2

tag: strain


title: THP-1_C_Mock-APAP

description: THP-1 RNA


title: THP-1_B_Media

description: THP-1 RNA

value: B

value: Media


title: THP-1_C_APAP HDE

description: THP-1 RNA


title: THP-1_B_Mock-Control

description: THP-1 RNA


title: THP-1_B_Mock-APAP

description: THP-1 RNA


title: 16BC_026


title: THP-1_B_Control HDE

description: THP-1 RNA


title: 16BC_030


title: 16BC_028


title: THP-1_E_Control HDE

description: THP-1 RNA


title: THP-1_A_Media

description: THP-1 RNA

value: A


title: EOBC-056


title: 16BC_011


title: THP-1_C_Media

description: THP-1 RNA


title: 16BC_023


title: EOBC-134


title: 16BC_017


title: THP-1_A_Mock-Control

description: THP-1 RNA


title: 16BC_003


title: 16BC_016


title: 16BC_015


title: 16BC_004


title: EOBC-178


title: THP-1_A_APAP HDE

description: THP-1 RNA


title: THP-1_A_Mock-APAP

description: THP-1 RNA


title: THP-1_C_Control HDE

description: THP-1 RNA


title: THP-1_B_APAP HDE

description: THP-1 RNA


title: THP-1_A_Control HDE

description: THP-1 RNA


title: 16BC_025


title: 16BC_008


title: 16BC_007


title: 16BC_005


title: h19delta_1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Human lymphoid progenitors expressing a non-functional CD19 CAR

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ (MTA-1_0) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

molecule: polyA RNA

source_name: lymphoid progenitor

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

growth_protocol: Purified CD34+ HSPCs were transduced with lentiviral supernatant and transferred onto OP9-DL1 stromal cells in the presence of human (h)IL-7, hSCF, hTPO and hFLT3L. Human engineered lymphoid progenitors were harvested every 3-4 days and put onto new OP9-DL1 monolayers supplemented with the respective cytokines. h1928z3-lymphoid progenitors were stimulated by adding irradiated Daudi cells from day 4 of culture.

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

value: CD34+ HSPC

value: expressing a non-functional CD19 CAR


title: h19delta_5


title: 16BC_009


title: THP-1_D_Media

description: THP-1 RNA


title: h19delta_4


title: h1928z_stim3

description: Human lymphoid progenitors expressing a functional CD19 CAR stimulated with CD19


title: h1928z_stim2

value: expressing a functional CD19 CAR stimulated with CD19


title: h19delta_2


title: h1928z_1

description: Human lymphoid progenitors expressing a functional CD19 CAR

value: expressing a functional CD19 CAR


title: h1928z_3


title: h19delta_3


title: 16BC_032


title: h1928z_2


title: 16BC_012


title: 13c 10 uM UT-34+R1881

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

hyb_protocol: Samples were hybridized accroding to Affymetrix protocols

scan_protocol: Samples were scanned using Affymetrix GCS3000 scanner

data_processing: Data was normalized using Affymetrix expression console software.

source_name: MR49F_10 uM of UT-34 in combination with 0.1 nM R1881

label_protocol: 200 ng's of sample were amplified and labeled using Affymetrix WT Assay kit (Life Technologies)

extract_protocol: Total RNA was extracted from MR49F cells using the qiagen RNA isolation kit and its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).  200 ng of total RNA was used for microarray

treatment_protocol: MR49F cells (n=3-4/group) were maintained in charcoal-stripped serum containing medium for 48 hours and treated with vehicle, 0.1 nM R1881, or 10 uM of UT-34 in combination with 0.1 nM R1881. Twenty four hours after treatment, the cells were harvested, RNA was isolated and expression of genes was measured using microarray (Affymetrix Clarion S)


title: 13a 10 uM UT-34+R1881

value: 10 uM of UT-34 in combination with 0.1 nM R1881


title: Sham_sample_4

status: Public on Dec 23 2019

city: New York

first: Hongyan

last: Zou

state: NY

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw RNA-seq reads were mapped against the mouse genome (GRCm38) and rRNA sequences using ContextMap (version 2.7.9).
Number of read fragments per gene (Ensembl version 87) were determined from the mapped RNA-seq reads using featureCounts (version 1.4.6-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using featureCounts (version 1.4.6-p3) against Ensembl v87 annotation; Tab delimited text file include gene level RPKM values for each sample against Ensembl v87 annotation; List of differential exons in each condition using DEXSeq

source_name: Sham_spinal cord

growth_protocol: Animals were sacrificed in CO2 chambers, and spinal cords (5mm both rostral and caudal to the injury site) were rapidly dissected on ice in 1x PBS, and pooled from three animals for each sample.  Nuclei were separated from cellular debris using an iodixanol gradient, wherein the nuclei separated out at the interphase between the 30-40% gradient. We obtained between 1.5-2 million nuclei per purification, which were then incubated with 10μl of 0.2 mg/ml rabbit monoclonal anti-GFP antibody (Life Technologies G10362). ProteinG Dynabeads (Invitrogen 10004D) were added to this mixture, incubated for 20 min for magnetic separation of GFP-positive nuclei, and the solution was then passed through a 20um filter (CellTrics, Sysmex, Partec GmbH 04-0042-2315). All steps were performed at 4°C.

extract_protocol:
GFP+ bead-bound nuclei were resuspended in buffer RLT for RNA extraction using the RNeasy Micro Kit, along with the recommended on-column DNAse digestion (Qiagen 74004).  RNA quality and concentrations were measured using an Agilent Bioanalyzer (Agilent RNA 6000 Pico, 5067-1513) and samples having RIN Scores higher than 7 were used. Total RNA was converted to cDNA and amplified using the Ovation RNA- Seq System V2 (Nugen 7102).
All samples underwent SPIA Amplification (single primer isothermal amplification) (Ovation RNA-Seq System V2, NuGen, 7102-08) prior to library preparation (NEBNext Ultra DNA Library Prep Kit for Illumina, NEB, 7370S)
Macrogen, Illumina HiSeq2500, Rapid run mode, 2 x 50 bp

tag: sample group

value: sham

tag: days post injury

value: Spinal cord tissue

tag: sample type

value: microglia-specific nuclei


title: Sham_sample_3

tag: tissue


title: Sham_sample_2


title: SCI_T_7dpi_sample_4

source_name: SCI_T_7dpi_spinal cord

value: mice with spinal cord injury


title: 11d 0.1 nM R1881


title: 13b 10 uM UT-34+R1881


title: SCI_T_7dpi_sample_1


title: 11a 0.1 nM R1881


title: SCI_T_3dpi_sample_2

source_name: SCI_T_3dpi_spinal cord


title: 10a vehicle

value: vehicle


title: SCI_T_14dpi_sample_3

source_name: SCI_T_14dpi_spinal cord


title: SCI_T_3dpi_sample_1


title: 10c vehicle


title: 11b 0.1 nM R1881


title: SCI_T_7dpi_sample_3


title: SCI_T_14dpi_sample_2


title: 11c 0.1 nM R1881


title: 10b vehicle


title: s_AO58_2

status: Public on Dec 20 2019

last: Parsa

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

description: yoda___Auto_user_YOD-84-04421_AO58_2_51_051___basecaller_results___IonXpressRNA_013

data_processing:
First the RAW output BAMs are converted back to FASTQ using PICARD (version 1.119) Sam2Fastq
Reads were then trimmed using fastq_quality_trimmer (version 0.0.13) on default settings.
The trimmed reads are first mapped to the mouse genome using rnaStar (version 2.3.0e)
The genome used was MM9 with junctions from ENSEMBL (Mus_musculus.NCBIM37.67) and a read overhang of 49
Then any unmapped reads were mapped to MM9 using BWA MEM (version 0.7.5a).
The two mapped BAMs are then merged and sorted and gene level counts are computed using htseq-count (options -s y -m intersection-strict) and the same gene models (Mus_musculus.NCBIM37.67).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: B220+ sorted cells from  VavPBcl2/Myc lymphoma

growth_protocol: Isolated primary cells were harvested directly from mouse. No growth culture.

extract_protocol:
After RiboGreen quantification and quality control by Agilent BioAnalyzer, poly-adenylated RNA was isolated using Dynabeads mRNA DIRECT Micro Purification Kit (ThermoFisher Scientific catalog # 61021) from 1-5µg of total RNA.
mRNA was then fragmentated using RNaseIII and purified. The fragmented samples’ quality and yield were evaluated using Agilent BioAnalyzer before library preparation with the Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific catalog # 4475936) with 16 cycles of PCR.
Samples were barcoded, and template-positive Ion Sphere Particles (ISPs) were prepared using the Ion OneTouch 2 system and Ion PI Template OT2 200 Kit v2 (ThermoFisher Scientific). Enriched particles were sequenced on an Ion Proton System using 200bp v2 chemistry. An average of 69 million reads per sample were generated.

treatment_protocol: B220+ cells were purified from mouse lymphoma tumors by immunomagnetic enrichment with CD45R(B220) microbeads (Miltenyi Biotech)

tag: strain background

value: VavPBcl2/Myc lymphoma

value: B220+ sorted cells


title: s_AO58_1

description: luke___Auto_user_LUK-77-04421_AO58_1_126_217___basecaller_results___IonXpressRNA_012

tag: genotype/variation


title: s_AO58_5

description: yoda___Auto_user_YOD-85-04421_AO58_5_52_053___basecaller_results___IonXpressRNA_015


title: SCI_T_14dpi_sample_1


title: s_AO57_1

description: luke___Auto_user_LUK-76-04421_AO57_1_125_215___basecaller_results___IonXpressRNA_008


title: s_E205_5

description: han___Auto_user_HAN-89-04421_E205_5_116_201___basecaller_results___IonXpressRNA_006

source_name: B220+ sorted cells from  VavPBcl2/vector lymphoma

value: VavPBcl2/vector lymphoma


title: s_E205_4

description: yoda___Auto_user_YOD-82-04421_E205_4_49_047___basecaller_results___IonXpressRNA_005


title: s_AO57_2

description: yoda___Auto_user_YOD-83-04421_AO57_2_50_049___basecaller_results___IonXpressRNA_009


title: s_AO57_3

description: han___Auto_user_HAN-90-04421_AO57_3_117_203___basecaller_results___IonXpressRNA_010


title: SCI_T_3dpi_sample_3


title: s_AO56_5

description: luke___Auto_user_LUK-86-04421_AO56_5_135_235___basecaller_results___IonXpressRNA_011


title: s_AO56_3

description: leia___Auto_user_LEI-90-04421_AO56_3_98_155___basecaller_results___IonXpressRNA_012


title: s_AO55_5

description: yoda___Auto_user_YOD-90-04421_AO55_5_57_063___basecaller_results___IonXpressRNA_014


title: s_AO55_2

description: luke___Auto_user_LUK-85-04421_AO55_2_134_233___basecaller_results___IonXpressRNA_015


title: s_AO74_3

description: han___HAN-88-04421_AO74_3_reanalysis_200___basecaller_results___IonXpressRNA_003

source_name: B220+ sorted cells from  normal spleen

value: normal spleen


title: s_AO55_1

description: leia___Auto_user_LEI-89-04421_AO55_1_97_153___basecaller_results___IonXpressRNA_016


title: h1928z_stim1


title: s_AO74_2

description: leia___Auto_user_LEI-81-04421_AO74_2_89_137___basecaller_results___IonXpressRNA_002


title: s_AO74_4

description: luke___Auto_user_LUK-75-04421_AO74_4_124_213___basecaller_results___IonXpressRNA_004


title: s_AO58_4

description: luke___Auto_user_LUK-78-04421_AO58_4_127_219___basecaller_results___IonXpressRNA_014


title: bovine in control group 3

status: Public on Dec 17 2019

city: Beijing

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description: 1_all_miRNA_counts.xls, 2_all_miRNA_TPM.xls, 3_diff_expressed_miRNA.xls

data_processing:
Cutadapt (version 1.14), fastx_toolkit (version 0.0.13) and NGSQCToolkit (version 2.3.3) were used to get clean reads.
Clean reads were matched with Rfam (version 10.0), and rRNA, snRNA, cis-reg, tRNA and other specific sequences were annotated.
The transcripts were filtered using bowtie.
MiRBase (version 22.0) was used for miRNA alignment to annotate known miRNAs.
Novel miRNA prediction of unannotated sequences was performed with miRDeep2. Novel miRNA secondary structure prediction was performed using RNAfold.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The TPM (transcript per million) metric represented the miRNA expression level.

organism: Bos taurus

source_name: milk  EV

growth_protocol: Six Holstein cows (n=3, 101±10 DIM, 574±36 kg BW, 32±2 kg milk/d) were utilized in the experimental period while housed in 6 environmentally control chambers and exposed to constant 20°C, 40% humidity.

extract_protocol:
Total Exosome Isolation kit (from other body fluids) (Invitrogen, Catalog Number: 4484453) was used for the isolation of milk EVs. The miRNeasy Mini Kit (QIAGEN, Catalog Number: 217004) was used to extract EV-miRNAs.
TruSeq Small RNA Sample Prep Kits (no. RS-200-0012, Illumina), Qubit dsDNA Assay Kit (no. Q328520, Life Technologies), Qubit RNA Assay Kit (no. Q32852, Life Technologies), SuperScript II Reverse Transcriptase (no.18064-014, Invitrogen) and DNA loading dye (no.LC6678, Invitrogen) were utilized in this step, following the manufacturer’s instructions. Briefly, 3' adapter and 5' adapter were ligated to the end of the RNA molecules. Then the libraries were reverse transcribed and PCR amplified subsequently. The cDNA constructs were purified and recovered, and the libraries was checked and normalized eventually.

treatment_protocol: Control cows were fed with TMR while treat cows were fed with feed that partly replaced alfalfa hay with whole cotton seed and soybean hull.

value: Holstein cow

value: milk

tag: developmental stage

value: female, mid lactation

tag: diet

value: TMR


title: s_AO57_4

description: leia___Auto_user_LEI-83-04421_AO57_4_91_141___basecaller_results___IonXpressRNA_011


title: s_AO74_1

description: han___Auto_user_HAN-96-04421_AO74_1_123_215___basecaller_results___IonXpressRNA_001


title: IL18f/f FlkCre+ Prox Colon 2

status: Public on Dec 12 2019

first: Richard

last: Flavell

address: 300 Cedar Street, TAC S-569

department: Department of Immunobiology

institute: Yale University

description:
Il18floxFlk1CreProxColon.xlsx
F8

data_processing:
For RNA-seq raw data processing, trimming was performed using cutadapt.
Alignment was performed using STAR (version 2.5.3) and raw read counts were generated using HTSeq.
Differential analysis was performed using DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file in which the first four columns including normalized gene expression values for corresponding samples

source_name: Proximal Colon

extract_protocol:
1 cm of colon proximal from the cecum was dissected and flushed of fecal material. Tissue was opened longitudinally and further washed. Tissue was snap frozen on dry ice. 1ml of Trizol was added and tissue mechanically homogenized. RNA was initially extracted using Trizol reagent and the extracted RNA was further purified using a RNAeasy Plus mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Proximal Colon

tag: genotype

value: IL-18 Immune cell KO


title: bovine in control group 1


title: IL18f/f FlkCre- Prox Colon 2

description:
Il18floxFlk1CreProxColon.xlsx
F6

value: IL-18 WT


title: bovine in control group 2


title: IL18f/f FlkCre- Prox Colon 1

description:
Il18floxFlk1CreProxColon.xlsx
F5


title: IL18f/f Vil1Cre- Prox Colon 1

description:
Il18floxVil1CreProxColon.xlsx
V1


title: IL18f/f Vil1Cre+ Prox Colon 2

description:
Il18floxVil1CreProxColon.xlsx
V4

value: IL-18 Intestinal Epithelial KO


title: IL18f/f Vil1Cre- Prox Colon 2

description:
Il18floxVil1CreProxColon.xlsx
V2


title: IL18f/f Vil1Cre+ Prox Colon 1

description:
Il18floxVil1CreProxColon.xlsx
V3


title: IL18f/f Hand2Cre+ Prox Colon 1

description:
Il18floxHand2CreProxColon.xlsx
KO_Prx_7

value: Hand2Cre C57BL/6 x SJL backcrossed to Il18f/f C57BL/6

value: IL-18 Neuron KO


title: IL18f/f Hand2Cre- Prox Colon 2

description:
Il18floxHand2CreProxColon.xlsx
WT_Prx_6


title: IL18f/f Hand2Cre+ Prox Colon 2

description:
Il18floxHand2CreProxColon.xlsx
K0_Prx_8


title: s_AO56_2

description: leia___Auto_user_LEI-91-04421_AO56_2_99_157___basecaller_results___IonXpressRNA_008


title: T-S2.3

status: Public on Dec 10 2019

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: Sphere cells from the secondary induced glioblatoma (TP53 KO, PDGFRA mut)

data_processing:
alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: XXX_summary.html: summary HTML file containing summary metrics and automated secondary analysis results
Supplementary_files_format_and_content: XXX_filtered_gene_bc_matrices_h5.h5: gene-barcode matrix in sparse h5 format

source_name: induced glioblastoma cells

growth_protocol: Sphere cells were cultured in DMEM/F12 with EGF and bFGF. Tumor cells were directly obtained from orthotopic in vivo tumors in mice.

extract_protocol: 10X chromium chemistry V2

treatment_protocol: Sphere cells were dissociated using accutase. Tumor cells were obtained through trypsin digestion and mechanical dissociation of the tumors.

tag: original cell line

value: CVB - iPSC (Coriell GM25430)

value: TP53 KO / PDGFRA mut

tag: passage


title: T-S2.2


title: IL18f/f Hand2Cre- Prox Colon 1

description:
Il18floxHand2CreProxColon.xlsx
WT_Prx_5


title: T-S2.1


title: T-T2.2

description: Tumor cells from the secondary induced glioblatoma (TP53 KO, PDGFRA mut)


title: T-T2.1


title: P-S2.2

description: Sphere cells from the secondary induced glioblatoma (PTEN KO, NF1 KO)

value: PTEN KO / NF1 KO


title: P-S2.1


title: P-T2.2

description: Tumor cells from the secondary induced glioblatoma (PTEN KO, NF1 KO)


title: P-T2.3


title: IL18f/f FlkCre+ Prox Colon 1

description:
Il18floxFlk1CreProxColon.xlsx
F7


title: T-S1

description: Sphere cells from the primary induced glioblastoma (TP53 KO, PDGFRA mut)


title: P-S1

description: Sphere cells from the induced glioblastoma (PTEN KO, NF1 KO)


title: P-T2.1


title: sciPlex1_HEK293T_NIH3T3

status: Public on Dec 05 2019

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

department: Biomedical Engineering

institute: Columbia University

description: Species mixing (barnyard) experiment that demonstrates the ability of our sci-Plex approach to report on the identity of specific conditions from within a pooled single-nucleus RNA seq experiment.

data_processing:
Expression matrices, cell annotations and gene annotations were generated accodring to the protocol described in our manuscript as well as in Cao et al. 2017 Science 357(6352) p. 661-667 (two level sci-RNA-seq) and Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).
Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only pertains to sciPlex3, associated metadata to deconvolve hash combinations can be found in sciPlex3_A549_MCF7_K562_hashTable_metadata.txt). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out files) for each nuclear transcriptome in the  experiment. Tab delimited columns of hashTable.out files correspond to a sample id, the cell  barcode identified for that hash, a "_" delimited string with treatment metadata, an  axis id for each hash (important for multiple hash per well experiments such as in sci-Plex3) and umi counts for each hash. The first tab delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. For sciPlex1, the first "_" delimited string corresponds to the cell type, for sciPlex2 the first "_" delimited string corresponds to treatment  and the second to dose, for sciPlex4 the first "_" delimited string corresponds to an identifier that, with the hash, is identified using the metedata in sciPlex3_A549_MCF7_K562_hashTable_metadata.txt and for sciPlex4 the first "_" delimited string corresponds to the dose of the compounds in the second  "_" delimited string and similarly the third corresponds to the dose of the compounds in the fourth  "_" delimited string. For all experiments the last "_" string corresponds to the treatment well from multiwell plates.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

organism:
Homo sapiens
Mus musculus

source_name: HEK293T and NIH3T3 cells

growth_protocol: All cell lines were cultured in DMEM supplemented with 10% FBS and 1% penn-strep.

extract_protocol:
24 hours after drug exposure, cells were harvested following the sci-Plex protocol as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
Nucle were subjected to two or three level sci-RNA-seq following the protocols described in Cao et al. 2017 Science 357(6352) p. 661-667 (two level sci-RNA-seq) and Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).

treatment_protocol: Cells were seeded at 25,000 cells per well in 96 well plates. 24 hours after seeding cells were exposed to increasing doeses of small molecules or dmso vehicle control.

tag: cell type

value: Human embryonic kidney (HEK293T) and mouse embryonic fibroblast (NIH3T3) cells

tag: treatment

value: Untreated


title: sciPlex4_A549_MCF7_HDACi

description: sci-Plex of pooled single-nucleus transcriptional profiling of A549 or MCF7 cells exposed to the HDACi abexinostat and pracinostat with or without supplementation of acetyl-CoA precursors or inibitors to enzymes that serve to generate acetyl-CoA.

source_name: A549 and MCF7 cells

value: A549 human lung adenocarcinoma and MCF7 breast adenocarcinoma cells

value: Cells were treated with increasing doses of the small molecule inhibitors abexinostat, pracinostat  or dmso vehicle control with or without supplementation of acetyl-CoA precursors or inibitors to enzymes that serve to generate acetyl-CoA.


title: P-S2.3


title: sciPlex2_A549_Transcription_Modulators

description: sci-Plex pooled single-nucleus transcriptional profiling of A549 cells exposed to small molecules that target regulators of transcription or dmso vehicle control. Specifically, cells were exposed to the NF-kB inhibitor BMS345541, the HDAC class I and II inhibitor SAHA, the p53 agonist nutlin-3A and the glucocorticoid receptor agonist dexamethasone.

source_name: A549 cells

value: A549 human lung adenocarcinoma cells

value: Cells were treated with increasing doses of the small molecules BMS345541, dexamethasone, nutlin-3A, SAHA or dmso vehicle control.


title: FFPE-RNA-Seq_ACC_ER_S06_Reseq

status: Public on Nov 26 2019

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
STAR version 2.5.2b was used to align reads to human reference genome GRCh38, release 84
GeneCounts module in STAR was used to quantify genes
read counts for each gene as determined by STAR alignment and quantification
reverse strand counts used for Access samples (files contain _ACC_)
forward strand counts used for Nugen-Ovation samples (files contain _OVA_)
Genome_build: h38
Supplementary_files_format_and_content: read counts for each gene as determined by STAR alignment and quantification

extract_protocol:
RNA was extracted from single 10um FFPE section utilizing miRNeasy FFPE kit (Qiagen, Valencia, CA)
75ng input of FFPE derived RNA was used for TruSeq RNA Access Library Prep Kit (Illumina, San Diego, CA)  (Illumina-Acc), an input of 150 ng of total FFPE RNA was used with the Ovation Human FFPE RNA-seq Library System (NuGEN Technologies, San Carlos, CA)

tag: source (fresh or ffpe)

value: FFPE

value: breast cancer - mammary gland

tag: year_of_diagnosis_year_of_ffpe block

value: negative


title: FFPE-RNA-Seq_ACC_ER_S06


title: FFPE-RNA-Seq_ACC_ER_S03

value: positive


title: FFPE-RNA-Seq_ACC_ER_S02_Reseq


title: FFPE-RNA-Seq_ACC_ER_S05


title: FFPE-RNA-Seq_ACC_ER_S02


title: FFPE-RNA-Seq_ACC_ER_S01_Reseq


title: FFPE-RNA-Seq_ACC_ER_S04


title: FFPE-RNA-Seq_ACC_S2_01


title: FFPE-RNA-Seq_ACC_S2_02


title: FFPE-RNA-Seq_ACC_ER_S01


title: FFPE-RNA-Seq_ACC_S1_02


title: T-T2.3


title: FFPE-RNA-Seq_ACC_S2_03


title: FFPE-RNA-Seq_ACC_S1_03


title: FFPE-RNA-Seq_OVA_S2_02


title: FFPE-RNA-Seq_OVA_S2_03


title: FFPE-RNA-Seq_ACC_S1_01


title: FFPE-RNA-Seq_OVA_S2_01


title: FFPE-RNA-Seq_OVA_S1_02


title: FFPE-RNA-Seq_OVA_S1_01


title: Non Tumor T_ff_029

status: Public on Nov 21 2019

city: Hangzhou

first: Hechen

last: Huang

state: Zhejiang

address: 79 Qingchun Road

department: Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery

institute: First Affiliated Hospital, School of Medicine, Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg/GRCh38.p12 whole genome using hisat2 v2.1.0.
featureCounts'' v1.6.4 was used for counting reads to genomic features mapped to GENCODE v30. Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using gfold v1.1.4. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the library.
Genome_build: hg/GRCh38.p12
Supplementary_files_format_and_content: Microsoft Excel files include RPKM and TPM values for each Sample.

source_name: liver

extract_protocol:
liver tissues were resected from patients, 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 standard Illumina protocols.

tag: isolate

tag: age

tag: Sex

value: male


title: Non Tumor T_ee_028


title: Non Tumor T_aa_015


title: Non Tumor T_cc_022

value: female


title: Non Tumor T_dd_024


title: Non Tumor T_YY_003


title: Non Tumor T_bb_016


title: Non Tumor T_ZZ_006


title: Non Tumor T_XX_001


title: Tumor T_e_028


title: Tumor T_f_029


title: Tumor T_Z_006


title: Tumor T_a_015


title: Tumor T_c_022


title: Tumor T_Y_003


title: Tumor T_b_016


title: shSafb_RNAseq_rep2

status: Public on Nov 19 2019

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads from RNA-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
For differential gene expression analysis, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union. Fold-change and p values were calculated by the R package DESeq2.
To quantify the expression level of genes, we acquired the transcripts per million (TPM) using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including TPM values for each replicate.

source_name: Safb KD (shSafb)

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

tag: cell line

value: AML12 cells

tag: shRNA

value: Safb KD (shSafb)


title: Tumor T_X_001


title: FFPE-RNA-Seq_OVA_S1_03

tag: tissue


title: shSafb_RNAseq_rep1


title: shCtrl_RNAseq_rep2

source_name: shCtrl

value: shCtrl


title: stateFate_inVivo

status: Public on Nov 22 2019

city: Boston

first: Caleb

middle: D

last: Weinreb

state: MA

address: 200 Longwood avenue

department: Systems Biology

institute: Harvard Medical School

description: In three separate in vivo experiments, sorted Lin-Kit+ (two experiments) or Lin-Kit+Sca1hi cells (one experiment) were virally barcoded and then plated in round-bottom 96-well plates. After 2 days in culture, 20% of the cells were analyzed by inDrops, and the rest were transplanted retro-orbitally into ten C57BL/6J sub-lethally irradiated host mice (500 cGy). After one and two weeks, the transplanted cells were harvested from total bone marrow and spleen (six mice on week 1, four mice on week 2). Gr1-biotin (biolegend) and anti-biotin (Miltenyi) magnetic MACS beads were used to partially deplete Neu/Mo lineage cells (~10-fold depletion) and all remaining cells were labeled with Gr1-eFluor450 and Streptavidin-eFluor450 (to label remaining Gr1 cells), Ter119-PE/Cy5, cKit-APC and CD19/B220-APC/Cy7. All GFP+ cells were collected in their entirety, with the exception of Ter119+ cells, which were only sampled at 1/2 of the total (~2-fold depletion). Thus in final cell sample profiled by indrops included ~10% of Gr+ cells and 50% of Ter119+ cells and 100% of all other subsets.

data_processing:
Raw sequencing data were processed using the previously described (Zilionis et al., Nature Protocols 2017) inDrops.py bioinformatics pipeline, available at https://github.com/indrops/indrops, using library version "v3".
The cDNA read was trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 200 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.90) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols 2017).
Genome_build: GRCm38
Supplementary_files_format_and_content: *_cell_barcodes.txt: A single-column list of cell barcodes corresponding to the rows of the normed_counts .mtx file    *_gene_names.txt: A single-column list of gene names corresponding to the columns of the normed_counts .mtx file    *_library_names.txt: A single-column list of library names corresponding to the rows of the normed_counts .mtx file    *_metadata.txt: A tsv file with rows corresponding to the rows of the normed_counts .mtx file. Each column contains a metadata field. The field vary between metadata files in accordance with the experimental design for each dataset.     *_normed_counts.txt: A sparse matrix file in matrix-market format. Each row represents a cell, each column represents a gene, and each entry represents the normalized mRNA counts detected for the gene within the cell.     *_clone_matrix.mtx: A sparse matrix file in matrix-market format. Each row represents a cell, each column represents a clone, and each binary entry specifies whether a cell belongs to a clone.
Raw sequencing data are available via SRA. All files are already demultiplexed. Read labels in the fastq files have format @[cell barcode]:[UMI]:[remainder]

source_name: Bone marrow

extract_protocol:
Using inDrops, cells were encapsulated into 4-nL droplets on ice and lysed using a final concentration of 0.4% NP-40. Single-cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 7 of Tusi et al., Nature 2018.

treatment_protocol: After euthanasia, bone marrow from femur, tibia, pelvis and sternum was isolated by crushing with pestle and mortar to obtain all cells. Collected bone marrow cells were filtered through a 40-μm strainer and washed in cold ‘Easy Sep’ buffer (PBS; 2% fetal bovine serum (FBS); 1 mM EDTA; Pen/Strep). Red blood cells were then lysed using ammonium chloride (STEMCELL) and mature lineage cells were depleted magnetically using the EasySep Lineage Depletion Kit (STEMCELL). The resulting Lin- fraction was stained for Kit (CD117-PE, clone 2B8, Biolegend), Sca-1 (Ly6a-FITC, clone D7, Biolegend) and lineage markers (antibody mix from the same EasySep kit), and Lin-Kit+Sca-1+ (LSK) or Lin-Kit+ (LK) cells were isolated by flow activated cell sorting (FACS) on a Sony SH800 with a 130uM nozzle. Cells were virally barcoded using spin infection (800g for 90 minutes) in virus concentrate with DAEA-dextran hydrochloride (Sigma) and then plated in round-bottom 96-well plates. Unless otherwise indicated, the media contained a mixture of cytokines designed to support pan-myeloid differentiation, consisting of StemSpan media (STEMCELL), Pen/Strep, IL-3 (20ng/mL), FLT3-L (50ng/mL), IL-11 (50ng/mL), IL-5 (10ng/mL), EPO (3U/mL), TPO (50ng/mL) (Peprotech), and mSCF (50ng/mL) and IL-6 (10ng/mL) (R&D Systems).

tag: strain

value: bone marrow

tag: purification

value: Lin-Kit+ and Lin-Kit+Sca1hi


title: stateFate_cytokinePerturbation

description: Lin-Kit+Sca1- and Lin-Kit+Sca1+ cells were harvested and combined in proportions 33% Lin-Kit+Sca1+, 66% Lin-Kit+Sca1- (the native proportions are 10%/90%) and then barcoded and plated (n=20,000 initially plated cells across 4 wells). On day 2, 25% of cells were profiled for inDrops and the remaining cells were split evenly into four groups and re-plated in the following conditions respectively: (i) continuation of the same cytokine mixture; (ii) M-CSF (20ng/mL) in StemSpan media; (iii) G-CSF (20ng/mL) in StemSpan; (iii) EPO (3U/mL) in StemSpan. Pen/strep was included in the media for all conditions. Cells from all conditions were harvested at day 4 and day 6 for profiling by indrops.

value: Lin-Kit+


title: stateFate_inVitro

description: In three separate in vitro experiments, sorted Lin-Kit+ (two experiments) or Lin-Kit+Sca1+ cells (one experiment) were virally barcoded and then plated in round-bottom 96-well plates. The number of cells plated varied from 5,000 – 10,000. After two days in culture, cells were split evenly, with one half being sequenced immediately and the other half re-plated in two separate culture wells. After two further days in culture, cells were again split, with 30% taken for inDrops and the remainder re-plated in 6 wells. After two further days in culture, GFP+ cells were sorted using FACS and profiled using inDrops. For the latter pair of inDrops experiments, cells were dissociated from the well by 5-minute treatment with 2.5% Trypsin.

value: Lin-Kit+ and Lin-Kit+Sca1+


title: shCtrl_RNAseq_rep1


title: GMP_MDP_culture

description: Whole bone marrow (excluding the cranium) and spleen were dissected and processed separately. Lineage depletion was performed using Magnetic Assisted Cell Separation (Miltenyi Biotec) with anti-cKit magnetic beads. Monocyte-dendritic progenitors (MDP; Lin-cKit+Sca1-CD34+CD115+FcgRII/IIIloFlt3+) and granulocyte-monocyte progenitors (GMP; Lin-cKit+Sca1-CD34+CD115loFcgRII/III+Flt3-) were isolated using FACS. A subset of each population was immediately profiled with inDrops and the remainder was plated in a broad multilineage cocktail for 2 days, then transferred to M-CSF (20ng/mL in StemSpan media) for 4 days until profiling with inDrops.

value: GMP (Lin-cKit+Sca1-CD34+CD115loFcgRII/III+Flt3-) and MDP (Lin-cKit+Sca1-CD34+CD115+FcgRII/IIIloFlt3+)


title: AT-15-VAT

status: Public on Nov 04 2019

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

data_processing:
Primary Analysis of demultiplexing, barcode correcting, alignment and generation of gene expression matrix was done using cellranger v.2.1.0 from 10X Genomics using GRCh38 as reference
Seurat v. 2.3.3 was then used for downstream analysis of filtering, Normalization, clustering and dimensionality reduction.
All Samples were merged together and we removed cells with low gene (<200), low unique molecular identifier (UMI, < 200) and high mitochondrial gene expression (> 20%). In order to exclude doublets, we also removed cells with high Gene (>2,500) and high UMI (>13,750).
Clusters obtained from Seurat was annotated using SingleR
genome build: GRCh38
processed data files format and content: SVF_Normalised_Data.txt: Tab delimited file containing normalised, log transformed expression matrix.
processed data files format and content: Discovery_Cohort_barcodes.tsv: Barcode file of filtered feature barcode matrix obtained from Cell Ranger aggregate results of discovery cohort.
processed data files format and content: Discovery_Cohort_CellAnnotation.txt: Cell Annotation for the discovery cohort.
processed data files format and content: Discovery_Cohort_genes.tsv: Genes file of filtered feature barcode matrix obtained from Cell Ranger aggregate results of discovery cohort.
processed data files format and content: Discovery_Cohort_matrix.mtx: Matrix file of filtered feature barcode matrix obtained from Cell Ranger aggregate results of discovery cohort.

source_name: adipose derived stromal vascular fraction (SVF)

extract_protocol:
Adipose tissue was digested with collagenase according to a modification of the Robdell method (Tchernof et al., 2006). Briefly, adipose tissue samples were digested with collagenase type 1 in Krebs-Ringer-Henseleit (KRH) buffer for 45 minutes at 37°C. Cell suspensions containing mature adipocytes and the stromal-vascular fraction (SVF) were then filtered with a nylon mesh and washed 3 times with KRH buffer. The nature of the buoyancy adipocytes allows them to float to the surface. Mature adipocytes were discarded and the remaining solution containing the SVF was centrifuged 1500 rpm for 5 minutes. The pellet was washed with pre-adipocyte growth medium (PGM) (DMEM-F12 supplemented with 10% calf serum, 1% penicillin-streptomycin, 17µM pantothenic acid, 33µM biotin, 100µM ascorbic acid and 2,5 µm/ml amphoB) followed by a second centrifugation. Cells were cryopreserved using freezing medium (PGM supplemented with 40% FBS and 10% DMSO). The medium was added to the pellet and was frozen with a temperature gradient (-1 °C/ minutes) and store at -80°C until analysis. The FACS sorted SVF samples were incubated with primary antibody (CD34) and sorted using FACSAria II
Cells from the SVF were thawed and serially diluted in DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 15ml conical tube to a volume of 14ml. They were centrifuged at 300 rcf for 10 minutes and the supernatant was removed and discarded. The pelleted cells were suspended in an adequate amount of DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin and transferred to a 1.5ml microfuge tube for counting. 10 µl of the suspension was used for a cell count and viability assay on a Countess II Automated Cell Counter (Invitrogen) to determine the volume of suspension to be used in the 10x Chromium Single Cell Library protocol. The desired number of viable cells to be loaded onto the Chromium Single Cell A Chip (10x Genomics) was 12,000 cells. After cell capture, the remaining cells were centrifuged at 300 rcf for 10 minutes and cryopreserved using freezing medium (Recovery Cell Culture Freezing Medium, Thermo Fisher Scientific). The cells were suspended in freezing medium and frozen with a temperature gradient of -1⁰C per minute. Cell capture, cDNA amplification, and library preparation were performed using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics), according to the manufacturer’s protocol. The final libraries were analyzed using a TapeStation to determine library size and a Qubit Broad Range dsDNA assay to determine library concentration and sequenced using Illumina HiSeq.
Chromium Single Cell 3’ Library

tag: subject status

value: obese individual

tag: diabetic status

value: Non Diabetic

value: Visceral adipose tissue

tag: cd34 sorting

value: Not FACS Sorted


title: AT-15-SAT

value: Subcutaneous adipose tissue


title: AT-14-VAT


title: AT-14-SAT


title: Tumor T_d_024


title: AT-13-VAT

value: Diabetic


title: AT-13-SAT


title: AT-12-VAT


title: AT-12-SAT


title: AT-11-VAT


title: AT-11-SAT


title: AT-10-SAT


title: AT-09-SAT


title: AT-09-VAT


title: AT-10-VAT


title: AT-08-VAT


title: AT-08-SAT


title: AT-06-SAT


title: AT-06-VAT


title: AT-05-SAT


title: AT-05-VAT


title: AT-E03-VAT


title: AT-E07-SAT


title: AT-04-VAT


title: AT-22-SAT-CD34+


title: AT-E02-SAT


title: AT-22-VAT-CD34-


title: AT-22-VAT-CD34+


title: AT-21-SAT-CD34+


title: AT-21-VAT-CD34+


title: AT-21-SAT-CD34-


title: AT-21-VAT-CD34-


title: ANTSi_scRNAseq

status: Public on Nov 01 2019

city: Seattle

first: Thomas

middle: A

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structures

institute: University of Washington

description: Ascl1 + NMDA + TSA + STATi treatment

data_processing:
Reads were aligned to the mm10 genome and the filtered output files from Cell Ranger were processed in R using tools in the Seurat package. For Seurat analyses, the newly generated single-cell RNA-seq dataset from ANTSi-treated mice were compared with our previously generated WT and ANT-treated datasets.
genome build: mm10

source_name: FACS purified MG-derived neurons

extract_protocol: After euthanasia of mice, eyes were removed and retina dissected out and isolated from vitreous and retinal pigmented epithelium. Retinas were then dissociated in a Papain and DNase I solution for 20 minutes at 37 ºC on a nutator. After incubation, retinas were gently triturated to generate a single-cell suspension, followed by the addition of Ovomucoid. Cells were then spun down at 300 g at 4 ºC then resuspended in Neurobasal medium, passed through a 35 mm filter, and transferred to a BSA coated tube prior to FACS-purification. FACS was performed on a BD FACSAria III Cell Sorter (BD Biosciences) and the GFP-positive fraction was collected for single-cell RNA-seq. 44,000 cells in total were captured for single-cell RNA-seq. Four ANTSi-treated mice (8 eyes) had their retinas pooled for FACS-purified cells and were spun down at 300 g at 4 ºC then resuspended at a concentration of 1000 cells per uL in a 0.04 % BSA in PBS solution. Cells were processed through the 10x Genomics Single Cell 3’ Chip and processed through the standard Chromium Single Cell 3’ Reagent Kits User Guide protocol with a target capture of 4,000 cells. Library QC was determined by Bioanalyzer (Agilent). Libraries were then sequenced on Illumina NextSeq 500/550 vs kit and reads were processed through 10x Genomics Cell Ranger pipeline.

value: Adult


title: Hi-C, Primary CD4+ T-cells, 1hr stimulated, replicate 2

status: Public on Oct 31 2019

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

institute: Univeristy of Manchester

description:
Sample name: T1H_HiC  pool2
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz

data_processing:
CHiC were mapped to GRCh38 using HICUP, CHiCAGO was applied to each aligned bam file. Interactions across time with CHiCAGO score over 5 were picked up and corresponding counts data were extracted from CHiCAGO results
Individual ATAC-seq reads were mapped to GRCh38 by Bowtie2. Reads less than 30bp were filtered out by SAMtools. Duplicates were removed by Picard. Bam files of the three replicates for each time point were merged and MACS2 were applied to call peaks on each merged bam file. Peaks were then combined across all the time points and counts data were extracted for each time point by Diffbind.
RNA-seq data were mapped to GRCh38 by STAR. Counts data for exons and introns were generated using DEXSeq and summed to get the counts data for each gene.
Hi-C reads were mapped to GRCh38 by HiCUP and then converted to HOMER format. HOMER command makeTagDirectory  (-tbp 1) and analyzeHiC (-res 40000 -balance) were used to generate normalized Hi-C interaction matrices..
findTADsAndLoops.pl command from HOMER were used to find TADs from the normalized interaction matrices generated from Hi-C data. TADs generated were merged across replicates and time by command merge2Dbed.pl from HOMER.
runHiCpca.pl and findHiCCompartments.pl commands from HOMER were used to find compartments A and B (with option -opp).
Genome_build: GRCh38
Supplementary_files_format_and_content: bait_fragments.bed.gz: HindIII fragments targeted (chromsosome, start, end, locus)
Supplementary_files_format_and_content: merged_TADs.bed.gz: TAD coordinates (chromosome, start, end)
Supplementary_files_format_and_content: compartments.bed.gz: Hi-C compartment coordinates (chromosome, start, end)
Supplementary_files_format_and_content: ATAC.narrowPeak: ATAC-seq narrow peaks (chromosome, start, end, id, score, strand, signalValue, pValue, qValue, peak point-source)
Supplementary_files_format_and_content: interactions.txt.gz: CHi-C interacting HindIII fragments (bait chromosome, bait start, bait end, other-end chromosome, other-end start, other-end end, CHiCAGO score)
Supplementary_files_format_and_content: combined_RNA-seq_counts.csv: Raw RNA-seq counts for all experimental samples
Supplementary_files_format_and_content: Hi-C.tar.gz: tar archive of raw Hi-C contact matrices (one per chromosome)

source_name: Primary CD4+ T-cells

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015).
Primary human CD4+ T-cells were isolated from PBMCs using an EasySep T-cell isolation kit (StemCell)

value: Primary CD4+ T-cells

tag: stimulation

value: 1hr CD3/CD28 Dynabeads

tag: restriction enzyme

value: HindIII


title: Hi-C, Primary CD4+ T-cells, 4hr stimulated, replicate 2

description:
Sample name: T4H_HiC  pool2
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz

tag: cell type

value: 4hr CD3/CD28 Dynabeads


title: Hi-C, Primary CD4+ T-cells, unstimulated, replicate 2

description:
Sample name: T0_HiC  pool2
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: Hi-C, Primary CD4+ T-cells, 20min stimulated, replicate 2

description:
Sample name: T20_HiC  pool2
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz

value: 20min CD3/CD28 Dynabeads


title: Hi-C, Primary CD4+ T-cells, 20min stimulated, replicate 1

description:
Sample name: T20_HiC  pool1
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: Hi-C, Primary CD4+ T-cells, 1hr stimulated, replicate 1

description:
Sample name: T1H_HiC  pool1
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: Hi-C, Primary CD4+ T-cells, 4hr stimulated, replicate 1

description:
Sample name: T4H_HiC  pool1
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: Capture Hi-C, Primary CD4+ T-cells, 20min stimulated, replicate 2

description:
Sample name: T20_CHiC pool2
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015). Genomic regions of interest were captured using biotinylated RNA baits (Agilent Technologies).
Primary human CD4+ T-cells were isolated from PBMCs using an EasySep T-cell isolation kit (StemCell)


title: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 2

description:
Sample name: T0_CHiC pool2
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: Capture Hi-C, Primary CD4+ T-cells, 4hr stimulated, replicate 2

description:
Sample name: T4H_CHiC pool2
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: Capture Hi-C, Primary CD4+ T-cells, 1hr stimulated, replicate 2

description:
Sample name: T1H_CHiC pool2
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: Capture Hi-C, Primary CD4+ T-cells, 4hr stimulated, replicate 1

description:
Sample name: T4H_CHiC pool1
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: Capture Hi-C, Primary CD4+ T-cells, 24hr stimulated, pool1, replicate 1

description:
Sample name: T24H_CHiC pool1
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz

value: 24hr CD3/CD28 Dynabeads


title: AT-04-SAT


title: RNA-seq, Primary CD4+ T-cells, 4hr stimulated, replicate 2

description:
Sample name: T4H_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz

molecule: nuclear RNA

extract_protocol:
Five million CD4+ T-cells were harvested, stored in Qiagen RNAprotect solution and the nuclear RNA isolated using a Qiagen RNeasy kit and quantified. Samples were either pooled in equal amounts (same individuals as for Hi-C to create matched samples), or processed individually to give duplicate samples. Libraries for RNA-seq were prepared using the NEB Next Ultra Directional RNA-seq reagents and protocol using 100ng of nuclear RNA as Input.
Primary human CD4+ T-cells were isolated from PBMCs using an EasySep T-cell isolation kit (StemCell)


title: RNA-seq, Primary CD4+ T-cells, unstimulated, replicate 2

description:
Sample name: T0_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: Capture Hi-C, Primary CD4+ T-cells, 20min stimulated, replicate 1

description:
Sample name: T20_CHiC pool1
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: RNA-seq, Primary CD4+ T-cells, 2hr stimulated, replicate 2

description:
Sample name: T2H_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz

value: 2hr CD3/CD28 Dynabeads


title: RNA-seq, Primary CD4+ T-cells, 20min stimulated, replicate 2

description:
Sample name: T20_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1

description:
Sample name: T0_CHiC pool1
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: RNA-seq, Primary CD4+ T-cells, 24hr stimulated, replicate 2

description:
Sample name: T24H_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: RNA-seq, Primary CD4+ T-cells, 24hr stimulated, replicate 1

description:
Sample name: T24H_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: Capture Hi-C, Primary CD4+ T-cells, 1hr stimulated, replicate 1

description:
Sample name: T1H_CHiC pool1
This Sample represents 1 pool of 3 individuals
bait_fragments.bed.gz


title: RNA-seq, Primary CD4+ T-cells, 4hr stimulated, replicate 1

description:
Sample name: T4H_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: RNA-seq, Primary CD4+ T-cells, 1hr stimulated, replicate 2

description:
Sample name: T1H_RNA pool2
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: Hi-C, Primary CD4+ T-cells, 24hr stimulated, replicate 1

description:
Sample name: T24H_HiC  pool1
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1

description:
Sample name: T0_HiC  pool1
This Sample represents 1 pool of 3 individuals
merged_TADS.bed.gz
merged_A_compartments.bed.gz
merged_B_compartments.bed.gz


title: RNA-seq, Primary CD4+ T-cells, 1hr stimulated, replicate 1

description:
Sample name: T1H_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: RNA-seq, Primary CD4+ T-cells, 2hr stimulated, replicate 1

description:
Sample name: T2H_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: ATAC-seq, Primary CD4+ T-cells, 4hr stimulated, replicates 1-3

description:
Sample name: T4H_ATAC
This Sample represents 3 replicates

extract_protocol:
ATAC-seq libraries were generated from 50,000 CD4+ T-cells from three individual samples using the protocol detailed in Buenrostro et al using the Illumina Nextera DNA Sample Preparation Kit.
Primary human CD4+ T-cells were isolated from PBMCs using an EasySep T-cell isolation kit (StemCell)


title: ATAC-seq, Primary CD4+ T-cells, 2hr stimulated, replicates 1-3

description:
Sample name: T2H_ATAC
This Sample represents 3 replicates


title: RNA-seq, Primary CD4+ T-cells, unstimulated, replicate 1

description:
Sample name: T0_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: ATAC-seq, Primary CD4+ T-cells, 24hr stimulated, replicates 1-3

description:
Sample name: T24H_ATAC
This Sample represents 3 replicates


title: ATAC-seq, Primary CD4+ T-cells, 1hr stimulated, replicates 1-3

description:
Sample name: T1H_ATAC
This Sample represents 3 replicates


title: ATAC-seq, Primary CD4+ T-cells, 20min stimulated, replicates 1-3

description:
Sample name: T20_ATAC
This Sample represents 3 replicates


title: RNA-seq, Primary CD4+ T-cells, 20min stimulated, replicate 1

description:
Sample name: T20_RNA pool1
This Sample represents 1 pool of 3 individuals
combined_RNA-seq_counts.csv.gz


title: ATAC-seq, Primary CD4+ T-cells, unstimulated, replicates 1-3

description:
Sample name: T0_ATAC
This Sample represents 3 replicates


title: RNA_GFP+_rep3

status: Public on Oct 18 2019

first: Eric

last: Engelbrecht

address: 1 Blackfan Street

department: Vascular Biology Program

institute: Boston Children's Hospital

description:
processed data file:
RNAseq.aorta.GEO.edgeR.xls
Supplementary.File.1.Bulk.RNA-seq.GFP.and.ECKO.xls

data_processing:
ATAC-seq: Read alignment to the MGSCv37 (mm9) genome assembly was performed with bowtie2 (Langmead & Salzberg, 2012) and the options: --very-sensitive –X 2000 –no-mixed –no-discordant. Duplicated fragments were removed using the Picard “MarkDuplicates” script with the options: Remove_Duplicates=true Validation_stringency=lenient (http://broadinstitute.github.io/picard/).   Paired-end reads were separated, centered on Tn5 cut sites, and trimmed to 10 bp using a custom in-house script. Peaks were called using the MACS2 “callpeak” script (Zhang et al., 2008) with options: -B –keep-dup all –nomodel –nolambda –shift -75 –extsize 150. Reads mapping to murine blacklisted regions and mitochondrial DNA were masked out of peak lists using the Bedtools “intersect -v” script (Quinlan & Hall, 2010).   Replicates from each biological group were merged using the bedops “merge” script to generate one high-confidence peak set for each of the four biological groups (GFPhigh, GFPlow, S1pr1-ECKO, S1pr1-WT) (Neph et al., 2012). These four peak sets were then merged to generate a merged, consensus peak set of 123,473 peaks. For each replicate, reads covering consensus peak intervals were counted using the Bedtools “coverage” script with the “-counts” option (Quinlan & Hall, 2010). The resultant count table was input to edgeR (M. D. Robinson et al., 2010) to determine differentially accessible peaks (DAPs).
Base calls were performed using Illumina CASAVA 1.8.2
bigWig files:  Nucleotide-resolution coverage (bigWig) tracks were generated by first combining trimmed reads from each replicate, then inputting the resultant .bam files to the DeepTools (Ramirez et al., 2016) “bamCoverage” script with options “—normalizeUsing RPGC –binSize 1”.
bulk RNA-seq: Reads from each sample were aligned to the MGSCv37 (mm9) genome assembly using STAR (Dobin et al., 2013) with the options: --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM. Gene-level counts over UCSC annotated exons were calculated using the Rsubread package and “featureCounts” script (Liao, Smyth, & Shi, 2013) with options: -M –O –p –d 30 –D 50000. The resultant count table was input to edgeR (M. D. Robinson, McCarthy, & Smyth, 2010) for differential gene expression analysis.
bulk RNA-seq: The .bam files from STAR were input to the RSEM (B. Li & Dewey, 2011) script “rsem-calculate-expression” with default parameters to generate FPKMs for each replicate. FPKMs are located in the Supplementary File called "Supplementary.File.1.Bulk.RNA-seq.GFP.and.ECKO.xls"
single-cell RNA-seq: 1152 Fastq files (one per cell) were aligned to the GRCm38 (mm10) genome assembly using STAR with options –runThreadN 4 –outSAMstrandField intronMotif –twopassmode Basic. Bam files were input to the velocyto (http://velocyto.org/velocyto.py/) command-line script “run-smartseq2” (La Manno et al., 2018). Expressed repetitive elments were downloaded from the UCSC genome browser and masked from analysis using the “-m” option of the “run-smartseq2” script. The resultant table of read counts per transcript (“loom” file) was input to the PAGODA2 (https://github.com/hms-dbmi/pagoda2) R package for further analysis (Fan et al., 2016; La Manno et al., 2018).
Genome_build: mm9 (all bulk sequencing experiments); mm10 (single-cell RNA-seq only)
Supplementary_files_format_and_content: Excel files include edgeR outputs from bulk RNA-seq and ATAC-seq experiments. the bigWig files were generated as described in "data processing". The file "Supplementary.File.1.Bulk.RNA-seq.GFP.and.ECKO.xls" includes FPKMs and lists of differentially expressed genes, in addition to the edgeR output. The file "aorta.GFP.scRNAseq.cell.info.updated.xlsx" includes information about individual sorted cells, including GFP fluorescence (GFP+ or GFP-) and cluster annotation among the 9 clusters identified by Pagoda2 clustering. The loom file (scRNAseq.Aorta_GFP_EC.loom) was generated using the velocyto package (http://velocyto.org/velocyto.py/) and the “run-smartseq2” script. This files contains a matrix of transcript counts for each single cell.

growth_protocol: Mice were housed in our animal facility with food ad libitum and 12 hr light/dark cycles. Animals were used in accordance with protocols approved by the Institutional Animal Care and Use Committees (IACUC) of Boston Children’s Hospital and the French Department of Education.

extract_protocol:
bulk RNA-seq: Cells were sorted into either 0.1% FAF-BSA/PBS or buffer RLT (Qiagen) supplemented with beta-mercaptoethanol for ATAC-seq and RNA-seq, respectively. Cells sorted into buffer RLT were subjected to total RNA extraction using the RNeasy Micro Kit (Qiagen).
scRNA-seq: Library preparation from single cells was performed as previously described (Vanlandewijck et al., 2018). Briefly, cells were deposited into individual wells of 384-well plates containing 2.3 µL of lysis buffer (0.2% Triton-X (Sigma, T9284), 2U/μL RNase inhibitor (ClonTech, 2313B), 2 mM dNTP’s (ThermoFisher Scientific, R1122), 1 μM Smart-dT30VN (Sigma), ERCC 1:4 × 107 dilution (Ambion, # 4456740)) prior to library preparation using the Smart-seq2 protocol (Picelli et al., 2014).
ATAC-seq: ATAC-seq libraries were prepared according to the previously described fast-ATAC protocol (Corces et al., 2016). Briefly, 800-4,000 FACS-isolated cells in 0.1% FAF-BSA/PBS were pelleted by centrifugation at 400  g at 4 ˚C for 5 min. Supernatant was carefully removed to leave the cell pellet undisturbed, then cells were washed once with 1 mL ice-cold PBS. The transposition mix [25 µL buffer TD, 2.5 µL TDE1 (both from Illumina FC-121-1030), 1 µL of 0.5% digitonin (Promega, G9441) and 16 µL nuclease-free water] was prepared and mixed by pipetting, then added to the cell pellet. Pellets were disrupted by gently flicking the tubes, followed by incubation at 37 ˚C for 30 minutes in an Eppendorf ThermoMixer with constant agitation at 300 rpm. Tagmented DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, 28204), and subjected to cycle-limiting PCR as previously described (Buenrostro et al., 2013). Transposed fragments were purified using the MinElute PCR Purification Kit (Qiagen, 28004) and Agilent DNA Tapestation D1000 High Sensitivity chips (Agilent) were used to quantify libraries.
bulk RNA-seq: Double-stranded cDNA was synthesized from 5-10 ng RNA using the SMART-Seq2 v4 Ultra Low RNA Kit for Sequencing (Takara) according to the manufacturer’s instructions.
single-cell RNA-seq: mRNA was converted to cDNA by a reverse transcription (RT) reaction using oligo(dT) primers and the SuperScript II RT enzyme (ThermoFisher Scientific, cat: 18064-071), as previously described (Picelli et al., 2014). This cDNA was amplified with 22 cycles of PCR, then cDNA was fragmented and tagged (i.e. tagmented) with the Tn5 transposase (Nextera XT library kit, Illumina, cat: FC-131-1096)8, and individual wells indexed using the Illumina Nextera XT indexing kits (Illumina, FC-131-2001).

treatment_protocol: "WT" and "ECKO" mice were given intraperitoneal injections of tamoxifen (2 mg/day) at 5-6 weeks of age for five consecutive days. Tamoxifen treated mice were rested for a minimum of 2 weeks prior to experiments.

tag: strain background

tag: genotype/variation

value: young adult (8-12 weeks)

value: male

value: endothelial cell

value: FACS-sorted adult mouse aortic endothelial cells (MAECs)


title: aorta.GFP.scRNAseq

value: female


title: Non Tumor NT_WW_034

status: Public on Oct 08 2019

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg/GRCh38.p12 whole genome using hisat2 v2.1.0.
'featureCounts'' v1.6.4 was used for counting reads to genomic features mapped to GENCODE v30. Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using gfold v1.1.4. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the library.
Genome_build: hg/GRCh38.p12
Supplementary_files_format_and_content: Microsoft Excel files include RPKM and TPM values for each Sample.


title: Non Tumor NT_VV_033


title: Non Tumor NT_UU_032


title: RNA_GFP+_rep2


title: ATAC_GFP+_rep3

description:
processed data file:
ATACseq.aorta.GEO.edgeR.xls
ATAC.GFP+.merged.sortedbinsize1.bw

value: S1PR1-GS (GFPlow)


title: ATAC_GFP+_rep1


title: RNA_GFP-_rep3

value: S1PR1-GS (GFPhigh)


title: ATAC_GFP-_rep3

description:
processed data file:
ATACseq.aorta.GEO.edgeR.xls
ATAC.GFP-.merged.sorted.binsize1.bw


title: RNA_GFP-_rep1


title: RNA_GFP+_rep1


title: RNA_ECKO_rep1


title: ATAC_GFP-_rep1


title: ATAC_GFP+_rep2


title: RNA_GFP-_rep2


title: RNA_WT_rep2


title: RNA_ECKO_rep3


title: RNA_WT_rep1


title: RNA_ECKO_rep2


title: ATAC_GFP-_rep2


title: ATAC_WT_rep1

description:
processed data file:
ATACseq.aorta.GEO.edgeR.xls
ATAC.WT.merged.sorted.binsize1.bw


title: ATAC_ECKO_rep3

description:
processed data file:
ATACseq.aorta.GEO.edgeR.xls
ATAC.ECKO.merged.sorted.binsize1.bw


title: ATAC_WT_rep3


title: ATAC_ECKO_rep2


title: ATAC_WT_rep2


title: ATAC_ECKO_rep1


title: Non Tumor NT_SS_030


title: Non Tumor NT_TT_031


title: Non Tumor NT_RR_027


title: RNA_WT_rep3


title: Non Tumor NT_QQ_026


title: Non Tumor NT_PP_025


title: Non Tumor NT_OO_023


title: Non Tumor NT_NN_021


title: Non Tumor NT_MM_020


title: Non Tumor NT_EE_010


title: Non Tumor NT_DD_009


title: Non Tumor NT_LL_019


title: Non Tumor NT_II_014


title: Non Tumor NT_KK_018


title: Non Tumor NT_JJ_017


title: Non Tumor NT_GG_012


title: Non Tumor NT_BB_005


title: Tumor T_R_027


title: Non Tumor NT_FF_011


title: Tumor T_S_030


title: Tumor T_T_031


title: Tumor T_U_032


title: Tumor T_V_033


title: Non Tumor NT_AA_004


title: Tumor T_P_025


title: Tumor T_O_023


title: Tumor T_N_021


title: Tumor T_Q_026


title: Non Tumor NT_HH_013


title: Tumor T_M_020


title: Tumor T_L_019


title: Tumor T_I_014


title: Tumor T_J_017


title: Tumor T_K_018


title: Tumor T_H_013


title: Tumor T_G_012


title: Non Tumor NT_CC_007


title: Tumor T_F_011


title: Tumor T_E_010


title: Tumor T_D_009


title: Tumor T_A_004


title: Omentum_non_endothelial_stroma

status: Public on Sep 18 2019

city: Edinburgh

first: Cecile

last: Benezech

address: 47 Little france Crescent

department: Centre for Cardiovascular Sciences

institute: University of Edinburgh

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.0.2.
Genome_build: mm10 (Ensembl 93)
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Omentum

extract_protocol:
Enzymatic digestion and FACS
10X Genomics Single cell 3' gene expression V2

value: omentum

tag: cell markers

tag: disease status

value: Unchallenged

value: Female