title: 252644011436: IFN Treated pig # 10_dpi 6_PBMC

description: Gene expression in PBMC samples  6  days after innoculation of Ebola Kikwit from pig pre-treated with IFN

source_name: PBMC samples from 6  days after innoculation of Ebola Kikwit from pig 10


title: 252644011436: IFN Treated pig # 9_dpi -1_PBMC

status: Public on Dec 09 2020

type: RNA

city: toronto

first: Chandrika

last: Senthilkumaran

state: ON

address: 8, Wisteria RD

country: Canada

institute: Canadian food inspection agency

description: Gene expression in PBMC samples  before pre-treatment of IFN in pigs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Porcine V2 arrays (G2519F-026440) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray slides were scanned on Agilent high resolution C scanner (G2505C) and images processed using the Agilent Feature Extraction software. Quality of samples was analyzed using the ArrayQualityMetrics package and the data imported into GeneSpring 14.8 (Agilent) for further analysis.

data_processing: The data was normalized using a shift to the 75th percentile; thereafter the value was further transformed as log2

molecule: total RNA

organism: Sus scrofa

source_name: PBMC samples before pre-treatment of IFN and (24 hrs) before innoculation of Ebola Kikwit from pig 9

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop.

extract_protocol: Total RNA was extracted from PBMC and BALP pellets and the concentrations were determined using a NanoDrop (NanoDrop Technologies) and shipped to MOGENE LC, St. Louis, MO, USA for the microarray assay.

treatment_protocol: 7 pigs were randomly divided in 2 groups: A (4 pigs) and B (3 pigs). Animals in Group A (# 7, 8, 9, 10) were inoculated subcutaneously (SC) in the neck with 2x1010 pfu/2ml of Ad5-porIFNα. Animals in Group B (Control group #11, 17, 18) were SC inoculated with 2 ml of phosphate-buffered saline (PBS). One day later all pigs were oro-nasally inoculated with 106 pfu/2ml/pig of EBOV (0.5 ml per each nostril, 1ml orally). Arbitrarily, the day of inoculation (dpi) with EBOV was designated as 0 dpi. Clinical signs, behavioral changes and rectal temperature were recorded daily. Nasal washes, oral swabs and blood were collected for each pig the day of Ad5-porIFNα or PBS treatment (-1 dpi), and at 0, 3 and 5 or 6 dpi with EBOV. Blood was collected into BD vacutainer CPTTM cell preparation tubes (Becton Dickinson, New Jersey, USA), plasma and the peripheral blood mononuclear cells (PBMC) were separated according to the manufacturer’s protocol. PBMC pellets diluted four times with PBS

tag: tissue

value: PBMC

tag: gender

value: Male

tag: age

value: 6 weeks


title: 252644011434: IFN Treated pig # 8_dpi 5_PBMC

description: Gene expression in PBMC samples  5  days after innoculation of Ebola Kikwit in pig pre-treated with IFN

source_name: PBMC samples from 5  days after innoculation of Ebola Kikwit from pig 8

value: Female


title: 252644011435: IFN Treated pig # 9_dpi 6_BAP

description: Gene expression in Broncho alvelor pellet samples  5  days after innoculation of Ebola Kikwit from pig pre-treated with IFN

source_name: Broncho alvelor pellet samples from 6  days after innoculation of Ebola Kikwit from pig 9

value: Broncho alvelor pellet


title: HEK-293 transfected cells (pEGFP_hRIZ2) 2

city: Caserta

first: Monica

last: Rienzo

address: Viale  Lincoln

department: Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies

country: Italy

institute: University of Campania “Luigi Vanvitelli”

description: Biological replicate 2 of 3HEK-293 cells overexpressing human RIZ2

hyb_protocol: The hybridized microarrays were then washed according to manufacturer’s instructions, scanned after washing using an Agilent Microarray Scanner (G4845A) at 2μm resolution and 20-bit color-depth

scan_protocol: Images were quantified using Agilent Feature Extraction Software (10.5 Protocol GE2_105_Dec08).

data_processing: Raw data files (unedited)

organism: Homo sapiens

source_name: HEK-293 transfected cells

label_protocol: Samples were processed according to Agilent Two-color Microarray Based Gene Expression Analysis (Low Input Quick Amp Labeling Kit protocol) by Agilent Spike-In Kit, according to the manufacturer’s instructions. The Agilent Two-Color Microarray-based Gene Expression Analysis uses Cyanine 3- and Cyanine 5-labeled targets to measure gene expression in experimental and control samples. Equal amounts of Cyanine 3-labeled (control samples) and Cyanine 5-labeled (experimental samples) cRNA from samples were simultaneously co-hybridized onto the arrayed oligonucleotides on the same Agilent 44k Whole Human Genome chip (Agilent Technologies, 4X44k format) slide at 65°C for 17 h using an Agilent Gene Expression Hybridization Kit in Agilent’s SureHyb Hybridization Chambers (G2545A)

growth_protocol: HEK-293 were maintained at 37 °C with 5% CO2 in humidified atmosphere in DMEM high glucose supplemented with 10% FCS, 1% Non-Essential Amino Acid (NEAA), and antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were transfected with  plasmid DNAs using LipofectamineTM 2000 Reagent in OptiMem I Reduced Serum Medium (Life Technologies, Carlsbad, CA, USA) for 6h, following the manufacturer’s instructions.

tag: cell line

tag: transfection

value: embryonic kidney

value: Fetus


title: 252644011434: control pig # 11_dpi 3_PBMC

description: Gene expression in PBMC samples  3  days after innoculation of Ebola Kikwit in pig not pre-treated with IFN

source_name: PBMC samples from 3  days after innoculation of Ebola Kikwit from pig 11


title: 252644011435: control pig # 11_dpi 5_PBMC

description: Gene expression in PBMC samples  5  days after innoculation of Ebola Kikwit in pig not pre-treated with IFN

source_name: PBMC samples from 5  days after innoculation of Ebola Kikwit from pig 11


title: 252644011436: IFN Treated pig # 9_dpi 6_PBMC

source_name: PBMC samples from 6  days after innoculation of Ebola Kikwit from pig 9


title: 252644011434: IFN Treated pig # 8_dpi 0_PBMC

description: Gene expression in PBMC samples after pre-treatment of IFN but before the innoculation of Ebola Kikwit in pig

source_name: PBMC samples 24 hrs after pre-treatment of IFN and before innoculation of Ebola Kikwit from pig 8


title: 252644011434: IFN Treated pig # 8_dpi-1_PBMC

source_name: PBMC samples before pre-treatment of IFN and (24 hrs) before innoculation of Ebola Kikwit from pig 8


title: RNA-seq in HT55 sgKLF5#3

type: SRA

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

country: USA

institute: University of Utah

library_source: transcriptomic

data_processing:
reads alignment: Bowtie2
read counts calculation: RSEM
Genome_build: hg19
Supplementary_files_format_and_content: RSEM output

molecule: polyA RNA

source_name: colorectal cancer cell line

extract_protocol:
PolyA isolated RNA
NEB Ultra II Directional RNA seq library prep

tag: knockout


title: 252644011437: IFN Treated pig # 10_dpi 3_PBMC

description: Gene expression in PBMC samples  3  days after innoculation of Ebola Kikwit in pig pre-treated with IFN

source_name: PBMC samples from 3  days after innoculation of Ebola Kikwit from pig 10


title: RNA-seq in HT55 sgKLF5#2


title: RNA-seq in HT55 sgKLF5#1


title: 252644011433: control pig # 11_dpi 0_PBMC

description: Gene expression in PBMC samples before the innoculation of Ebola Kikwit in pig not pre-treated with IFN

source_name: PBMC samples from the day of innoculation prior to the innoculation of Ebola Kikwit from pig 11


title: 252644011433: IFN Treated pig # 7_dpi 0_PBMC

source_name: PBMC samples 24 hrs after pre-treatment of IFN and before innoculation of Ebola Kikwit from pig 7


title: 252644011433: IFN Treated pig # 7_dpi 5_PBMC

source_name: PBMC samples from 5  days after innoculation of Ebola Kikwit from pig 7


title: 252644011435: control pig # 11_dpi 5_BAP

description: Gene expression in Broncho alvelor pellet samples  5  days after innoculation of Ebola Kikwit in pig not pre-treated with IFN

source_name: Broncho alvelor pellet samples from 5  days after innoculation of Ebola Kikwit from pig 11


title: 252644011433: IFN Treated pig # 7_dpi -1_PBMC

source_name: PBMC samples before pre-treatment of IFN and (24 hrs) before innoculation of Ebola Kikwit from pig 7


title: RNA-seq in HT55 sgNC3

value: control


title: RNA-seq in HARA sgKLF5#1

source_name: squamous cancer cell line

value: HARA


title: HiChIP of H3K27ac in HARA

description: HiChIP DNA

library_source: genomic

data_processing:
Library strategy: HiChIP
Reads alignment: HiC-Pro
Loop calling: hichipper
Genome_build: hg19
Supplementary_files_format_and_content: bedpe

molecule: genomic DNA

extract_protocol:
HiChIP protocol based on Mumbach et al., 2016, Nature Methods
Illumina Nextera Library preparation

tag: antibody

value: H3K27ac, abcam ab4729


title: RNA-seq in HARA sgNC3


title: ChIP-seq of KLF5 in KATOIII

description: ChIP enriched DNA

data_processing:
Read alignment: Bowtie2
Peak calling and signal normalizaiton: MACS2
UCSC tool bedgraphtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Cancer cell line

extract_protocol:
ChIP-enriched DNA
NEB Ultra II DNA library prep kit

value: KLF5, abcam ab137676

value: KATOIII

tag: genotype

value: wildtype


title: RNA-seq in HT55 sgNC2


title: RNA-seq in HT55 sgNC1


title: RNA-seq in HARA sgKLF5#3


title: gNS/PCs_2H10

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using sailfish version 0.7.6 with default setting.
Low quality samples were removed from data set based on mapping rate and detected gene number.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: WJ cell line

extract_protocol:
nNS/PCs and gNS/PCs were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer.
Whole-transcript amplification was performed as previously described (Hayashi et al; 2018). Amplified cDNA from single cell was processed for library preparation using Nextera XT Library Prep Kit (Illumina).

tag: cell type

value: feeder free iPSC derived gliogenic NS/PCs


title: gNS/PCs_2H06


title: RNA-seq in HARA sgKLF5#2


title: RNA-seq in HARA sgNC2


title: RNA-seq in HARA sgNC1


title: gNS/PCs_2H11


title: gNS/PCs_2G11


title: ChIP-seq of KLF5 in AGS

description: ChIP enriched DNA

value: AGS


title: gNS/PCs_2H02


title: gNS/PCs_2H09


title: gNS/PCs_2G10


title: gNS/PCs_2G08


title: gNS/PCs_2H08


title: gNS/PCs_2G05


title: gNS/PCs_2H04


title: gNS/PCs_2H05


title: gNS/PCs_2G01


title: gNS/PCs_2G03


title: gNS/PCs_2H03


title: gNS/PCs_2F09


title: gNS/PCs_2F08


title: gNS/PCs_2F05


title: gNS/PCs_2F01


title: gNS/PCs_2E03


title: gNS/PCs_2E02


title: gNS/PCs_2E01


title: gNS/PCs_2G07


title: gNS/PCs_2G06


title: gNS/PCs_2H01


title: gNS/PCs_2D09


title: gNS/PCs_2G12


title: gNS/PCs_2F10


title: gNS/PCs_2D11


title: gNS/PCs_2G02


title: HiChIP of H3K27ac in HT55

description: HiChIP DNA


title: gNS/PCs_2F11


title: gNS/PCs_2E04


title: gNS/PCs_2D12


title: gNS/PCs_2D03


title: Pm31

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: SFWvsFFW.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the P_mexicana-1.0 (GCF_001443325.1) genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 10 mapped reads across all samples in the comparison were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: P_mexicana-1.0 (GCF_001443325.1)
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Poecilia mexicana

source_name: red blood cells

growth_protocol: Red blood cells (RBC) from individual fish were collected to assess the environmental impacts of the sulfidic habitats on the fish epigenome. Four female and four male adult individuals were sampled from each location and from both the wild and lab-reared populations, except non-sulfidic males (N=3). Wild-caught samples were obtained from Southern Mexico in proximate H2S-rich (sulfidic) (PSO, Lat: 17.43843, Long: -92.77476) and non-sulfidic springs (Bonita, Lat: 17.42685, Long: -92.75213) in the Tacotalpa Drainage in Southern Mexico.

extract_protocol:
Fish were sacrificed by cervical transection, and blood was immediately extracted by using microhematocrit capillary tubes (Fisher). Tubes were then spun down at 12,000 rpms for 3 minutes using a ZipCombo Centrifuge (LW Scientific) to separate blood cells from serum. After centrifugation, capillaries were broken to retain only red blood cells. The portion of the capillary containing the red blood cells was placed in a 1.5 ml Eppendorf tube for DNA extraction. DNA was extracted using the Qiagen DNeasy Blood & Tissue kit according to manufacturer's instructions. Extracted genomic DNA was used to isolate methylated DNA with a methyl-cytosine antibody precipitation procedure (MeDIP).  Five micrograms of total genomic DNA was sonicated using a Covaris sonicator. Sonicated DNA was diluted with TE buffer to 400 μl, heat denatured for 10 minutes at 95˚C, and cooled on ice for 10 minutes to create single-stranded DNA fragments. A total of 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the fragmented single-stranded DNA. The mixture was incubated on a rotator overnight at 4˚C. Pre-washed magnetic beads (50 μl, Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were added to the 500 μl of DNA-antibody mixture. The mixture was incubated for 2 hours on a rotator at 4˚C. After which the samples were washed three times with 1X IP buffer. Washed samples were resuspended in 250 μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml) and incubated at 55˚ for three hours. A Phenol-Chloroform-Isoamyalcohol extraction was used to clean-up the DNA and the DNA was resuspended in 20μl of H2O. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).
For library preparation, we used the NEBNext Ultra RNA Library Prep Kit for Illumina starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each individual received a unique barcode.

treatment_protocol: Laboratory reared samples were brought from Mexico into a breeding population at Kansas State University for at least two generations. All laboratory reared animals were reared in non-sulfidic water.

tag: source water type

value: non-sulfidic

tag: Sex

value: female

tag: population

value: wild


title: Pm28

description: SFWvsFFW.results.csv.gz


title: gNS/PCs_2C11


title: Pm26

description: SMWvsFMW.results.csv.gz

value: male


title: Pm25

description: SMWvsFMW.results.csv.gz


title: Pm27

description: SMWvsFMW.results.csv.gz


title: gNS/PCs_2F07


title: gNS/PCs_2F03


title: gNS/PCs_2E05


title: gNS/PCs_2E09


title: gNS/PCs_2E10


title: gNS/PCs_2E11


title: gNS/PCs_2F02


title: gNS/PCs_2D10


title: Pm30

description: SFWvsFFW.results.csv.gz


title: Pm29

description: SFWvsFFW.results.csv.gz


title: Pm18

description: SMWvsFMW.results.csv.gz

value: sulfidic


title: gNS/PCs_2E06


title: gNS/PCs_2D04


title: gNS/PCs_2C10


title: Pm14

description: SFLvsFFL.results.csv.gz

value: lab


title: gNS/PCs_2C02


title: gNS/PCs_2D02


title: gNS/PCs_2D01


title: gNS/PCs_2C12


title: gNS/PCs_2C01


title: Pm24

description: SFWvsFFW.results.csv.gz


title: gNS/PCs_2B10


title: Pm23

description: SFWvsFFW.results.csv.gz


title: Pm10

description: SMLvsFML.results.csv.gz


title: gNS/PCs_2B09


title: Pm09

description: SMLvsFML.results.csv.gz


title: Pm22

description: SFWvsFFW.results.csv.gz


title: gNS/PCs_2C09


title: Pm21

description: SFWvsFFW.results.csv.gz


title: gNS/PCs_2C08


title: Pm20

description: SMWvsFMW.results.csv.gz


title: gNS/PCs_2C07


title: gNS/PCs_2B04


title: Pm19

description: SMWvsFMW.results.csv.gz


title: gNS/PCs_2C06


title: gNS/PCs_2C05


title: gNS/PCs_2B02


title: gNS/PCs_2B01


title: Pm07

description: SFLvsFFL.results.csv.gz


title: Pm05

description: SFLvsFFL.results.csv.gz


title: Pm04

description: SMLvsFML.results.csv.gz


title: Pm17

description: SMWvsFMW.results.csv.gz


title: gNS/PCs_2C04


title: gNS/PCs_2A09


title: Pm16

description: SFLvsFFL.results.csv.gz


title: Pm15

description: SFLvsFFL.results.csv.gz


title: gNS/PCs_2C03


title: Pm02

description: SMLvsFML.results.csv.gz


title: Pm13

description: SFLvsFFL.results.csv.gz


title: gNS/PCs_2A01


title: Normal 1

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

description: cultured cells

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10

organism: Mus musculus

source_name: Primary synovial fibroblasts

growth_protocol: Normal ankles from normal mice and swollen ankles obtained from CAIA mouse were dislocated and digested by Collagenase TypeⅣ. To obtain synovial fibroblasts with high purity, obtained synovial cells were seeded to typeⅠcollagen-coated culture dish and cultured for 1 hour. Then, non-adherent cells were removed. Adherent cells were used as synovial fibroblasts. To obtain synovial macrophages with high purity, the non-adherent cells were seeded to normal culture dish. After 1-2 weeks of culturing, stromal cells were detached by trypsinization. Remaining cells was used as synovial macrophage.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 9 were used for library prepairation.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 305-310 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

treatment_protocol: Synovial macrophages and synovial fibroblasts were cultured in DMEM Glutamax supplemented with 10%FBS and 1% antibiotics for 2-3 days

tag: strain

tag: disease state

value: normal

value: fibroblasts derived from normal ankle tissue

tag: passage


title: KOS2_mARKO_ORX_SARM_rep2

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by featureCounts.
Data ware normalized by iDEGES/edgeR and DEGs were deteceted with FDR < 0.05 among Control and mARKO separately.
Genome_build: mm10

source_name: bulbocavernosus muscle

growth_protocol: Mice were generated using AR flox mice and HSA-Cre mice, and littermate were conducted to the treatment.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 8 were used for library prepairation.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 305-310 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

treatment_protocol: Male mARKO and littermate control (ARL2/Y) mice underwent ORX or not. Nine days after ORX, the mice were treated with TEI-SARM2 (10 mg/kg weekly, p.o.) or vehicle (weekly, p.o.) for another 2 weeks.

value: bulbocavernosus muscle

value: mARKO


title: KOS3_mARKO_ORX_SARM_rep3


title: gNS/PCs_1H11


title: gNS/PCs_1H10


title: gNS/PCs_1H09


title: gNS/PCs_2A08


title: KOV3_mARKO_ORX_V_rep3


title: Pm12

description: SMLvsFML.results.csv.gz


title: gNS/PCs_2B11


title: Pm11

description: SMLvsFML.results.csv.gz


title: gNS/PCs_2B07


title: Pm08

description: SFLvsFFL.results.csv.gz


title: gNS/PCs_2B12


title: gNS/PCs_1H06


title: KS3_mARKO_Sham_rep3


title: gNS/PCs_1H05


title: gNS/PCs_2F06


title: gNS/PCs_2B03


title: Pm06

description: SFLvsFFL.results.csv.gz


title: KS2_mARKO_Sham_rep2


title: gNS/PCs_1H04


title: KS1_mARKO_Sham_rep1


title: gNS/PCs_1H02


title: gNS/PCs_2A10


title: Pm01

description: SMLvsFML.results.csv.gz


title: gNS/PCs_1H01


title: Pm03

description: SMLvsFML.results.csv.gz


title: WOS2_Control_ORX_SARM_rep2

value: control


title: gNS/PCs_1G12


title: WOV4_Control_ORX_V_rep4


title: gNS/PCs_2A05


title: gNS/PCs_1G05


title: gNS/PCs_2A04


title: Normal 3

description: cultured cells


title: WS2_Control_Sham_rep2


title: Normal 2

description: cultured cells


title: gNS/PCs_2A03


title: gNS/PCs_1H08


title: KOV2_mARKO_ORX_V_rep2


title: KOS1_mARKO_ORX_SARM_rep1


title: WS1_Control_Sham_rep1


title: gNS/PCs_1F12


title: gNS/PCs_1H07


title: KOV1_mARKO_ORX_V_rep1


title: gNS/PCs_1F08


title: CAIA mice, SM rep3

description:
cultured cells
SM3

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: TMM, FPKM

source_name: Primary synovial macrophages

growth_protocol: Swollen ankle obtained from CAIA mouse was dislocated and digested by Collagenase TypeⅣ. To obtain synovial fibroblasts with high purity, obtained synovial cells were seeded to typeⅠcollagen-coated culture dish and cultured for 1 hour. Then, non-adherent cells were removed. Adherent cells were used as synovial fibroblasts. To obtain synovial macrophages with high purity, the non-adherent cells were seeded to normal culture dish. After 1-2 weeks of culturing, stromal cells were detached by trypsinization. Remaining cells was used as synovial macrophage.

value: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis

value: macrophages derived from CAIA ankle tissue


title: CAIA mice, SM rep1

description:
cultured cells
SM1


title: gNS/PCs_1H03


title: WOS3_Control_ORX_SARM_rep3


title: gNS/PCs_1F06


title: WOS1_Control_ORX_SARM_rep1


title: CAIA mice, SF rep3

description:
cultured cells
SF3

value: fibroblasts derived from CAIA ankle tissue


title: gNS/PCs_1F05


title: gNS/PCs_1G09


title: WOV1_Control_ORX_V_rep1


title: WS3_Control_Sham_rep3


title: PND42 Male Exposed_3

city: Raleigh

first: Scott

middle: M

last: Belcher

state: NC

address: 127 David Clark Labs, Campus box 7617

department: Biological Sciences

institute: North Carolina State University

data_processing:
HiSeq2500 generates real-time base calls and quality metrics
Subsequent quality control of read data was evaluated using FastQC
STAR short read aligner was used to align reads to Mus musculus (mm10) reference genome
Mapped read number was determined using featureCounts software, with data normalized for distortion and depth
Genome_build: mm10
Supplementary_files_format_and_content: comma separate value files include normalized read counts for each sample

source_name: liver

extract_protocol:
Liver tissue was isolated, frozen on powdered dry ice and stored at -80C until prepared for sequencing. RNA was isolated using the Rneasy Mini Kit (Qiagen) and analyzed for RNA integrity using an Agilent 2100 Bioanalyzer. RNA integrity number was >/= 7 for all samples.
Library creation and sequencing were performed using a single-end 125 bp protocol on the Illumina HiSeq2500 sequencer, with ~33 million uniquely mapped reads generated per sample.

value: liver

value: postnatal day 42

tag: exposure

value: 500ppb CdCl2


title: PND42 Male Exposed_2


title: PND42 Male Exposed_1


title: gNS/PCs_1G10

value: feeder free iPSC derived gliogenic NS/PCs


title: PND42 Male Control_3

value: Control


title: PND42 Male Control_4


title: gNS/PCs_1F03


title: gNS/PCs_1E10


title: gNS/PCs_1G11


title: gNS/PCs_1G01


title: CAIA mice, SF rep2

description:
cultured cells
SF2


title: gNS/PCs_1F11


title: WOV2_Control_ORX_V_rep2


title: gNS/PCs_1G04


title: gNS/PCs_1G06


title: PND42 Female Exposed_4

value: female


title: WOV3_Control_ORX_V_rep3

value: male


title: gNS/PCs_1F09


title: CAIA mice, SF rep1

description:
cultured cells
SF1


title: PND42 Female Exposed_3


title: gNS/PCs_1E07


title: CAIA mice, SM rep2

description:
cultured cells
SM2


title: PND42 Male Exposed_4


title: gNS/PCs_1F02


title: gNS/PCs_1E05


title: PND42 Female Exposed_2


title: gNS/PCs_1F07


title: gNS/PCs_1F01


title: PND42 Female Control_1


title: PND42 Male Control_1


title: gNS/PCs_1E09


title: PND42 Male Control_2


title: gNS/PCs_1E03


title: gNS/PCs_1D12


title: PND21 Female Exposed_3

value: postnatal day 21


title: PND21 Female Exposed_2


title: gNS/PCs_1E12


title: gNS/PCs_1E06


title: PND42 Female Control_4


title: PND42 Female Exposed_1


title: PND42 Female Control_3


title: gNS/PCs_1E04


title: PND21 Female Control_2


title: gNS/PCs_1E08


title: PND21 Female Control_1


title: gNS/PCs_1E01


title: PND1 Female Exposed_4

value: postnatal day 1


title: PND42 Female Control_2


title: PND1 Female Exposed_3


title: gNS/PCs_1D10


title: gNS/PCs_1D09


title: PND1 Female Exposed_2


title: gNS/PCs_1E02


title: PND21 Female Control_3


title: PND21 Female Exposed_1


title: PND1 Female Control_4


title: gNS/PCs_1D07


title: gNS/PCs_1D08


title: gNS/PCs_1C10


title: gNS/PCs_1D05


title: gNS/PCs_1C09


title: gNS/PCs_1C12


title: gNS/PCs_1D04


title: gNS/PCs_1C07


title: PND1 Female Exposed_1


title: gNS/PCs_1D06


title: proximalwt-3

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine

country: Netherlands

institute: Academic Medical Center

description: wild type organoid

data_processing:
alignment: HISAT2 (2.0.4), samtools (1.3.1)
quantification:  subread featureCounts (1.5.0-p1)
Genome_build: GRCm38.85
Supplementary_files_format_and_content: raw read counts

source_name: organoid proximal small intestine

growth_protocol: Isolation of small intestine (SI) and colon crypts from wild type mice was adapted from Sato et al. Nature 2009.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA isolation kit (BIOKÉ, Leiden, Netherlands) and the quality of RNA samples was subsequently assessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).
Generation of sequencing libraries was performed using the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA) and 1ug of total RNA.
RNA-sequencing was performed on HiSeq2500 (Illumina) with 50-bp single-end reads.

treatment_protocol: Wild type organoids from proximal SI, distal SI and colon were either transduced with the pWPXL-Ctnnb1(p.S33A;S37A;T41A;S45A)-P2A-dsRed plasmid in order to generate adenoma organoids or not transduced.

tag: location

value: prSI

tag: replicate

tag: lane


title: PND1 Female Control_3

tag: tissue

tag: age


title: PND1 Female Control_2


title: proximalwt-1

description: wild type organoid


title: gNS/PCs_1C06


title: PND1 Female Control_1


title: gNS/PCs_1D02


title: gNS/PCs_1B11


title: proximalbcat-2


title: gNS/PCs_1D03


title: proximalbcat-1


title: proximalwt-2

description: wild type organoid


title: gNS/PCs_1C05


title: proximalbcat-3


title: gNS/PCs_1B10


title: gNS/PCs_1B09


title: gNS/PCs_1B08


title: gNS/PCs_1C03


title: distalwt-2

description: wild type organoid

source_name: organoid distal small intestine

value: diSI


title: distalwt-3

description: wild type organoid


title: distalwt-1

description: wild type organoid


title: distalbcat-2


title: gNS/PCs_1B05


title: distalbcat-1


title: gNS/PCs_1B02


title: gNS/PCs_1B01


title: gNS/PCs_1A10


title: gNS/PCs_1A08


title: colonwt-3

description: wild type organoid

source_name: organoid colon

value: colon


title: gNS/PCs_1A09


title: gNS/PCs_1B12


title: gNS/PCs_1A07


title: colonwt-2

description: wild type organoid


title: colonbcat-1


title: colonbcat-3


title: gNS/PCs_1A06


title: colonwt-1

description: wild type organoid


title: Lymph nodes tuberculosis ID S13-12712

city: Oro Valley

first: Manuel

middle: Leonardo

last: Gonzalez-Garay

state: Arizona

address: 13560 N Vistoso Reserve

department: Medicine

institute: UA

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastq files were analyzed using Salmon version 1.3.0. The template library was prepared using the highQualitySubsetHTGProbes.fasta file and the quantification was performed using the salmon software.
The entire pipeline is available at https://github.com/mlggaray/HTG_Analysis
Genome_build: The sequence of the probes were provided by HTG. Probes without hits or with multiple hits to the Ensembl transcriptome version 90 were removed.  2,430 of the 2,568 original HTG probes were used for the analysis.
Supplementary_files_format_and_content: The Raw_gene_TPM_Abundance_matrix.txt is a tab-delimited text file with TPM values for each Sample
Supplementary_files_format_and_content: Each Salmon Quantification file (_abundance.tsv) is a tab delimited file with the following columns: probe_name, Length,  Effective_Length, TPM, and  NumReads

source_name: lymph nodes

extract_protocol:
Granulomas from formalin fixed, paraffin-embedded tissues were isolated using microdissection by HTG. The genes from the highQualitySubsetHTGProbes.fasta list were isolated using HTG EdgeSeq Nuclease protection
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: tuberculosis granuloma

tag: sample source

value: formalin fixed, paraffin-embedded

tag: sample collection

value: Laser capture microdissection

tag: chemistry

value: HTG EdgeSeq Nuclease protection


title: colonbcat-2


title: distalbcat-3


title: gNS/PCs_1A03

tag: cell type


title: gNS/PCs_1E11


title: gNS/PCs_1A05


title: nNS/PCs_H11

value: feeder free iPSC derived neurogenic NS/PCs


title: Lymph nodes sarcoidosis ID S15-2130

value: sarcoidosis granuloma


title: nNS/PCs_H10


title: gNS/PCs_1A02


title: nNS/PCs_H09


title: Lymph nodes sarcoidosis ID S16-3789


title: Lymph nodes tuberculosis ID S07-1722


title: nNS/PCs_H06


title: Lymph nodes sarcoidosis ID S12-11588


title: nNS/PCs_H05


title: gNS/PCs_1A04


title: nNS/PCs_H08


title: nNS/PCs_H04


title: Lymph nodes tuberculosis ID S11-5890


title: nNS/PCs_H03


title: nNS/PCs_H07


title: nNS/PCs_H01


title: Lymph nodes sarcoidosis ID S11-16399


title: Lymph nodes sarcoidosis ID S11-5747


title: Lymph nodes sarcoidosis ID S11-3356


title: Lymph nodes sarcoidosis ID S12-10867-2


title: Lymph nodes sarcoidosis ID S01-01562


title: Lymph nodes sarcoidosis ID S03-06811


title: Lymph nodes sarcoidosis ID S10-8898


title: nNS/PCs_G11


title: nNS/PCs_H02


title: Lymph nodes tuberculosis ID S10-2574


title: nNS/PCs_G10


title: Lymph nodes sarcoidosis ID S10-5712


title: Lymph nodes sarcoidosis ID S08-11588-2


title: nNS/PCs_G09


title: Lymph nodes healthy control ID LN4

value: healthy tissue


title: nNS/PCs_G05


title: nNS/PCs_G06


title: Lymph nodes healthy control ID LN2


title: Lymph nodes healthy control ID LN5


title: nNS/PCs_G03


title: Lung sarcoidosis ID S01-274

source_name: lung


title: Lung sarcoidosis ID S08-8308


title: nNS/PCs_G01


title: Lung sarcoidosis ID S14-1820


title: nNS/PCs_G04


title: Lung sarcoidosis ID S08-13633


title: nNS/PCs_F11


title: nNS/PCs_G02


title: nNS/PCs_F09


title: nNS/PCs_F12


title: nNS/PCs_F10


title: Lung sarcoidosis ID ng14-2391


title: Lung healthy control ID S16-455


title: Lung healthy control ID S16-430


title: nNS/PCs_F08


title: Lung sarcoidosis ID ng07-1929


title: nNS/PCs_F07


title: nNS/PCs_F06


title: Lung healthy control ID S16-1234


title: nNS/PCs_G08


title: YD-09

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

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 hg38 whole genome using HISAT2
Stringtie was used to assemble transcripts from mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Babao Dan treated xenografts pancreatic cancer sample

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

value: cell line derived xenograft pancreatic cancer

tag: treatment

value: Babao Dan treatment


title: Lung coccidiosis ID S13-15588

value: coccidiosis granuloma


title: Lung coccidiosis ID S15-7163


title: YD-10


title: YD-08


title: nNS/PCs_F04


title: nNS/PCs_F05


title: nNS/PCs_F02


title: nNS/PCs_E11


title: Lung coccidiosis ID S16-1593


title: YD-02

source_name: Control xenografts pancreatic cancer sample

value: Control


title: YD-03


title: nNS/PCs_E09


title: YD-07


title: nNS/PCs_E07


title: Senescent_HS1_Ribo_Seq

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

data_processing:
RNA-Seq analysis: RNA-Seq reads were filtered for rRNAs, tRNAs, microRNAs, and snoRNAs using STAR. The remaining reads were mapped to hg19 version of the human genome using STAR. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values. Ribosome profiling analysis: Ribosome footprint reads were trimmed to maximal size of 34 and polyA sequences from the polyA tailing step were removed, such that footprints of lengths 22-34 were considered. Reads were filtered for rRNAs, tRNAs, microRNAs, and snoRNAs using STAR. The remaining reads were mapped to hg19 version of the genome using RefSeq CDSs. Transcripts shorter that than 100 nucleotides were filtered-out and 30 nucleotides were clipped form the start and end of each CDS, similarly to Ingolia et al.(2017). Expression levels (gene and transcript TPM) were quantified using RSEM after mapping to clipped CDSs using Bowtie2.
TPM values were averaged between sample replicates. Lowly expressed genes with TPM value below four across all samples were filtered out. TPM values of all remaining genes were thresholded to four.
Genome_build: hg19
Supplementary_files_format_and_content: Samples read counts and TPM values

source_name: WI38 cells

growth_protocol: The cells were maintained in growth medium consisted in: MEM Earl’s medium, 10% serum, L-glutamine, 1% Na-pyruvate, 1% nonessential aminoacids and 1% penicillin/streptomycin solution. For the synchronization of the cell cycle, the cells underwent serum starvation for 24 hrs and recovery for another 24 hrs. More specifically, on day 1, cells were plated on 15 cm plates at a confluency of 1.5x10^6 for senescent or 1.3x10^6 for young cells, in growth medium. On day 2, the medium was changed to starvation medium (MEM Earl’s medium +1% penicillin/streptomycin solution), and on day 3 the cells were transferred again into complete medium for recovery.

extract_protocol:
RNA-Seq libraries: RNA was isolated from collected samples using the TRIZOL reagent (Thermo) following treatment with Turbo DNase and phenol chloroform precipitation.
RNA-seq: After quality control, the samples were subjected to Illumina kit (TruSeq RNA) for library preparation. Ribosome footprint profiling libraries:  Ribosome footprinting was mostly performed as described in (Shalgi et al. 2013) with some modifications. Following heat shock, cells were lysed on ice for 10 minutes using the Lysis Buffer (see Cell culture and stress). Then the samples were treated with 20μl Turbo DNase for 5 minutes at 250C while shaking. Nuclei were removed with 10min spin at max speed, at 40C and supernatant was taken. 8 µl NEB RNase If for 2ml lysate at an OD260 of ~10 were added for 55min at 250C, shaking. Ribosomes were pelleted using a sucrose cushion (10ml RP lysis buffer + 12.5 ml 20 mM HEPES pH 7, 100 mM KCl, 5 mM MgCl2, 0.5 M Sucrose), by ultracentrifugation at 60K RPM for 1 hour and 50 minutes, at 40C. Ribosome pellets were subsequently resuspended in 0.5ml 8M guanidinium-HCl, and RNA was precipitated in acid phenol chloroform.

treatment_protocol: On day 4, the day of experiment, the cells were subjected to stress, (heat shock at 440C, for 2 hrs) and then harvested in Lysis Buffer (20mM Hepes pH 7, 100mM KCl, 5mM MgCl2, 0.5% Na DOC, 0.5% NP-40, 1mM DTT, Protease inhibitors (Roche).

tag: cell line

value: human lung fibroblasts

tag: phenotype

value: senescent

value: Heat shock


title: nNS/PCs_F03


title: Senescent2_Ribo_Seq


title: Senescent_HS2_Ribo_Seq


title: nNS/PCs_E06


title: nNS/PCs_E04


title: YD-05


title: nNS/PCs_F01


title: YD-04


title: Young_HS2_Ribo_Seq

value: young


title: nNS/PCs_E08


title: nNS/PCs_E10


title: YD-06


title: nNS/PCs_E01


title: nNS/PCs_D12


title: nNS/PCs_D11


title: nNS/PCs_D10


title: nNS/PCs_E02


title: Senescent_HS2_RNA_Seq


title: nNS/PCs_E12


title: Young1_Ribo_Seq


title: Senescent_HS1_RNA_Seq


title: Senescent2_RNA_Seq


title: Senescent1_RNA_Seq


title: Senescent1_Ribo_Seq


title: nNS/PCs_D05


title: nNS/PCs_E05


title: Young_HS1_RNA_Seq


title: Young1_RNA_Seq


title: nNS/PCs_E03


title: Young_HS2_RNA_Seq


title: YD-01


title: nNS/PCs_D09


title: nNS/PCs_D08


title: nNS/PCs_D03


title: Young2_Ribo_Seq


title: nNS/PCs_D07


title: Young2_RNA_Seq


title: nNS/PCs_D06


title: nNS/PCs_D02


title: Young_HS1_Ribo_Seq


title: nNS/PCs_D01


title: nNS/PCs_C11


title: nNS/PCs_C09


title: nNS/PCs_C08


title: nNS/PCs_C12


title: nNS/PCs_C07


title: nNS/PCs_D04


title: nNS/PCs_C05


title: nNS/PCs_C02


title: nNS/PCs_C04


title: Gsr-KO_P56-Air_biological rep1

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: mouse adult lung (P56), neonatal room air exposure for P0-P5 followed by recovered in room air

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

label: biotin

source_name: Gsr knockout mice, postnatal day 56, air

label_protocol: Two hundred nanograms (200 ng) of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol running the biotin synthesis for 4 hours.

extract_protocol: RNA was isolated from a portion of the lung of each mouse (n = 3 or 4/group) using the RNeasy Mini kit.

treatment_protocol: New born Gsr-WT and Gsr-KO mice were exposed to room air or hyperoxia (100% O2, continusouly) between P0-P5 with dams.  Mice were sacrificed at the end of 5 day exposure or at age P56. Embyronic lungs from same animals were harvested and processed at E19 for microarray.

tag: genotype/variation

value: Gsr knockout

tag: strain

value: lung


title: Gsr-KO_P56-Hyperoxia_biological rep3

description: mouse adult lung (P56), neonatal hyperoxia (100% O2) exposure for P0-P5 followed by recovered in room air

source_name: Gsr knockout mice, postnatal day 56, hyperoxia


title: Gsr-KO_P56-Hyperoxia_biological rep1


title: Gsr-KO_P56-Air_biological rep3


title: Gsr-KO_P5-Hyperoxia_biological rep3

description: mouse neonate lung, hyperoxia (100% O2) exposure from P0-P5 (5 days)

source_name: Gsr knockout mice, postnatal day 5, hyperoxia


title: Gsr-KO_P5-Hyperoxia_biological rep2


title: nNS/PCs_C01

source_name: WJ cell line


title: nNS/PCs_C10


title: nNS/PCs_B12


title: Gsr-KO_P56-Air_biological rep2


title: nNS/PCs_B10


title: nNS/PCs_B08


title: nNS/PCs_C06


title: nNS/PCs_B09


title: nNS/PCs_B11


title: Gsr-KO_P56-Hyperoxia_biological rep2


title: nNS/PCs_B07


title: Gsr-KO_P5-Hyperoxia_biological rep1


title: Gsr-KO_P5-Air_biological rep2

description: mouse neonate lung, room air exposure from P0-P5 (5 days)

source_name: Gsr knockout mice, postnatal day 5, air


title: Gsr-KO_E19_biological rep4

description: mouse embryo lung, no exposure

source_name: Gsr knockout mice, embyronic day 19, air


title: nNS/PCs_B05


title: Gsr-WT_P56-Hyperoxia_biological rep1

source_name: Gsr wildtype mice, postnatal day 56, hyperoxia

value: Gsr wildtype


title: Gsr-KO_P5-Air_biological rep3


title: Gsr-KO_P5-Air_biological rep1


title: Gsr-KO_E19_biological rep3

description: mouse embryo lung, no exposure


title: nNS/PCs_B04


title: nNS/PCs_B06


title: Gsr-KO_E19_biological rep2

description: mouse embryo lung, no exposure


title: Gsr-KO_E19_biological rep1

description: mouse embryo lung, no exposure


title: Gsr-WT_P56-Hyperoxia_biological rep2


title: nNS/PCs_A11


title: nNS/PCs_B03


title: Gsr-WT_P56-Hyperoxia_biological rep3


title: Gsr-WT_P56-Air_biological rep1

source_name: Gsr wildtype mice, postnatal day 56, air


title: Gsr-WT_P56-Air_biological rep2


title: nNS/PCs_B01


title: nNS/PCs_A10


title: nNS/PCs_A09


title: nNS/PCs_A08


title: Gsr-WT_P5-Hyperoxia_biological rep3

source_name: Gsr wildtype mice, postnatal day 5, hyperoxia


title: nNS/PCs_C03


title: Gsr-WT_P5-Air_biological rep2

source_name: Gsr wildtype mice, postnatal day 5, air


title: nNS/PCs_A06


title: nNS/PCs_A05


title: Gsr-WT_P5-Hyperoxia_biological rep1


title: Gsr-WT_P5-Air_biological rep3


title: Gsr-WT_P5-Hyperoxia_biological rep2


title: nNS/PCs_A04


title: nNS/PCs_A07


title: Gsr-WT_E19_biological rep4

description: mouse embryo lung, no exposure

source_name: Gsr wildtype mice, embyronic day 19, air


title: Gsr-WT_P5-Air_biological rep1


title: Gsr-WT_E19_biological rep3

description: mouse embryo lung, no exposure


title: nNS/PCs_A01


title: gNS/PCs_P3_2

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using sailfish version 0.7.6 with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit.
Poly(A)+ RNA was selected and converted to a library of cDNA fragments (200–250 bp) with adaptors attached to both ends for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit Set [Illumina] as per the manufacturer’s instructions.

value: feeder free iPSC derived gliogenic NS/PCs


title: gNS/PCs_P2_1


title: MN_CN4_R1

city: Nijmegen

first: Marlies

last: Noz

state: Nederland

address: Geert grooteplein 8

department: Internal medicine

institute: Radboudumc

description:
CN4
200ng
QuantSeq 3’ mRNA sequencing

data_processing:
Low quality filtering and adapter trimming were performed using Trim Galore!, V0.4.4_dev 9 (Babraham Bioinformatics), a wrapper tool around the tools Cutadapt v1.18 and FastQC tool v0.11.5 (Babraham Bioinformatics).
On average between 8-11 million total reads per individual library were retrieved. Filtered and trimmed reads were mapped to a human reference genome (GRCh38.95, Ensembl) with Star v2.6.0a (19) resulting in BAM. BAM files were counted (number of reads mapped to a feature, e.g. a gene) with HTSeq (HTSeq-count tool v0.11.0 (39)) using a complementary .gtf file, containing annotation for GRCh38.95 (Ensembl).
MultiQC was used to combine results and quality checks of all the samples. Less than 1% of all reads were comprised of overrepresented sequences, and 6-8.5 million reads were uniquely mapped with a mean alignment of 80%.
Given the absence of sample replicates, individuals of the same disease group were considered biological replicates. Hence, differential gene expression analysis was carried out with DESeq2 v1.22.0 in R v3.5 (21), with internal statistical and normalization method (i.e. correction for multiple testing with Benjamini–Hochberg). The average mRNA expression between two groups was analyzed: participants with incident DWI+ lesions were matched to controls without SVD progression for age, sex and hypertension. LogFold shrinkage was performed with apeglm for easier comparison between groups. Genes with a P-adjusted value <0.05 and with log2 fold change of >±2 were considered differentially expressed genes (DEG).
Pathways analysis was performed with Reactome (22). For pathway analysis, a false discovery rate (FDR) corrected P-value <0.05 was considered significant.
Genome_build: GRCh38.95
Supplementary_files_format_and_content: Text files (.counts.txt) containing expression values in counts for each gene. Files are generated by HTSeq-count.

source_name: Monocytes

growth_protocol: Monocytes were isolated from venous blood using Ficoll-Paque density gradient centrifugation (GE Healthcare, Chicago, USA) followed by magnetic activated cell sorting (MACS) using negative bead selection with the Pan Monocyte Isolation kit according to manufacturer's instructions (Miltenyi Biotec, Bergisch Gladbach, Germany). Monocytes with >90% purity in the isolated fraction were used for further RNA extraction.

extract_protocol:
Monocytes were stored in RNAprotect (Qiagen, Venlo, The Netherlands) before processing. RNA was subsequently extracted following manufacturers’ protocol, including an on-column DNase digestion using the RNase-Free DNase set (Qiagen). In short, per 1 mL of RNAprotect 200 µL of chloroform was added, mixed, incubated at room temperature for 5 min and spun down for 15 min at 12000 g at 4°C. The upper aqueous phase was transferred to an RNase free Eppendorf tube, and an equal volume of 70% ethanol was added. After thorough mixing the sample was loaded onto RNeasy mini columns (Qiagen), after which the manufacturer's protocol was followed. After the last manufacturer’s step, 15 µL of RNase free water was added to the columns, incubated for 5 min, and spun down. Quantification and quality assessment of extracted RNA were performed using the Qubit RNA HS assay (Thermo Fisher Scientific) and Nanodrop technology.
Libraries were generated from the extracted RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit-FWD from Lexogen (Lexogen, Vienna, Austria) in accordance to the manufacturers’ protocol. RNA input for all samples was normalized to 200 ng. All samples were processed in a single library preparation. The optimal cycle number for the endpoint PCR was determined on a 1:10 aliquot of the double stranded cDNA libraries. Subsequent quality assessment, i.e. measuring the cDNA concentration using the Qubit dsDNA HS assay (Cat#Q32854, Thermo Fisher Scientific) and the average fragment size with the Agilent 2200 TapeStation (HS-D1000 ScreenTape, Cat#5067-5582, Agilent), enabled the determination of the molar concentration of individual libraries. Equimolar pooling of the libraries was set to 100 fmol, and after final dilution to 4 nM, libraries were sequenced on a NextSeq 500 instrument (Illumina, 1.4 pM loading concentration).

treatment_protocol: Not applicable.

value: Monocytes

tag: diagnosis

value: non-progressive SVD


title: MN_CN2_R1

description:
CN2
200ng
QuantSeq 3’ mRNA sequencing


title: MN_CN3_R1

description:
CN3
200ng
QuantSeq 3’ mRNA sequencing


title: MN_CN5_R1

description:
CN5
200ng
QuantSeq 3’ mRNA sequencing


title: MN_PT4_R1

description:
PT4
200ng
QuantSeq 3’ mRNA sequencing

value: progressive SVD

tag: incident lesion

value: DWI, microbleed


title: gNS/PCs_P3_1


title: MN_PT5_R1

description:
PT5
200ng
QuantSeq 3’ mRNA sequencing

value: DWI


title: nNS/PCs_A02

value: feeder free iPSC derived neurogenic NS/PCs


title: MN_PT1_R1

description:
PT1
200ng
QuantSeq 3’ mRNA sequencing


title: MN_PT2_R1

description:
PT2
200ng
QuantSeq 3’ mRNA sequencing


title: gNS/PCs_P2_2


title: Gsr-WT_E19_biological rep2

description: mouse embryo lung, no exposure


title: 328-4_bd_rep3

city: Hanover

first: Christina

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Align reads: STAR --runThreadN 1 --runMode alignReads --genomeDir /N_crassa_NC12/STAR_genomebuild/ --sjdbGTFfile /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf --readFilesIn ./*_1.fq ./*_2.fq --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFileNamePrefix ./STAR_out/ --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Quantify transcripts: cuffquant --library-type=fr-firststrand /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf Aligned.out.sorted.sam
Normalize samples together: cuffnorm /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf *.cxb
Output: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) at the gene level (i.e. not isoforms) used for analysis.
Genome_build: Neurospora crassa OR74A NC12 genome, accessed 9/28/17: ftp://ftp.broadinstitute.org/pub/annotation/fungi/neurospora_crassa/assembly/
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Neurospora crassa

source_name: N. crassa culture, control

growth_protocol: A mycelial disc was cut from respective strain using a 6 mm cork borer, transferred into a flask containing Bird 1.8% glucose medium, and grown for 48 hours, 25C, constant light, and ~100 RPM shaking.

extract_protocol:
Neurospora tissue was isolated by vacuum filtration and frozen in liquid nitrogen. Frozen tissue was ground under liquid nitrogen using a mortar and pestle. Total RNA was extracted using Trizol (Invitrogen) as described (PMID: 19262566).
Novogene procedures: total RNA QC pass (Agilent 2100 Bioanalyzer), polyA(+) enrichment for mRNA using oligo(dT) beads, NEB directional library preparation kit, library QC pass (concentration & insert size), Illumina NovaSeq 6000 sequencing, 150 bp stranded PE reads returned for each sample

value: 328-4:ras-1bd MAT A

tag: genotype

value: wt


title: 1810_bd_prd-2_rep2

source_name: N. crassa culture, mutant

value: 1810:ras-1bd prd-2::barR MAT A

value: period-2 mutant


title: EB_2

value: feeder free iPSC derived embryoid body


title: nNS/PCs_A03


title: Gsr-WT_E19_biological rep1

description: mouse embryo lung, no exposure


title: EB_1


title: ZNF410 gRNA#2_vector_rep2 (RNA-seq)

city: Philadelphia

first: xianjiang

last: lan

state: Pennsylvania

address: 315A Abramson Research Center 3615 Civic Center Blvd

department: Hematology

institute: children's hospital of philadelphia

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/).
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.
Genome_build: hg38 assembly
Supplementary_files_format_and_content: TSV Files

growth_protocol: HUDEP-2 cells were cultured accrooding to standard protocol (Grevet et al., Science 2018). In vitro primary CD34+ cells were cultured with a three-phase human CD34+ hematopoietic stem and progenitor cells (HSPCs) culture system (Grevet et al., Science, 2018).

extract_protocol:
Total RNA were purified with the RNeasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral vectors containing non-targeting sgRNA or 2 independent ZNF410 sgRNAs were used to infect the human adult type erythroid cell line HUDEP-2 that contained a construct stably expressing spCas9; for primary CD34+ cells, ribonucleoprotein (RNP) Cas9:sgRNAs complexes with non-targeting sgRNA or two independent ZNF410 sgRNAs were used for electroporation at day 3-4 at phase I culture.

value: HUDEP-2 immortalized erythroid cell line

tag: day of isolation

value: Day 7 of culture

value: ZNF410 sgRNA#2 infected cells transduced with empty vector

value: control (vector)


title: 328-4_bd_rep2


title: ZNF410 gRNA#1_CHD4_rep1 (RNA-seq)

value: ZNF410 sgRNA#1 infected cells with CHD4 overexpression

value: CHD4 overexpression


title: iPSC

value: feeder free iPSC


title: ZNF410 gRNA#2_CHD4_rep1 (RNA-seq)

value: ZNF410 sgRNA#2 infected cells with CHD4 overexpression


title: ZNF410 gRNA#1_CHD4_rep2 (RNA-seq)


title: ZNF410 gRNA#2_CHD4_rep2 (RNA-seq)


title: ZNF410 gRNA#1_vector_rep2 (RNA-seq)

value: ZNF410 sgRNA#1 infected cells transduced with empty vector


title: Neg2-vector rep2 (RNA-seq)

value: Non-targeting sgRNA infected cells transduced with empty vector


title: 26_10_TDP_2_S22

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description: 72h TDP-43 treated replicate2

data_processing:
ATACseq analysis
illumina basecalling
adapter trimming
bowtie2
peak calling (macs2)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Primary cortical neurons

growth_protocol: Primary mouse cortical neurons were dissociated into single-cell suspensions from E16.5 mouse cortices with a papain dissociation system (Worthington Biochemical Corporation). Neurons were seeded onto poly-L-lysine–coated plates (0.1% (wt/vol)) and grown in Neurobasal medium (Gibco) supplemented with B-27 serum-free supplement (Gibco), GlutaMAX, and penicillin–streptomycin (Gibco) in a humidified incubator at 37 °C, with 5% CO2. Neurons were cultured for 3 days to let their processes grow before treatment.

extract_protocol:
To probe chromatin accessibility, we harvested neurons 20, 40 and 60h following transduction of (PR)50, TDP-43, or GFP expressing lentiviruses.  We used direct lysis of plated neurons, followed by isolation of released nuclei.
Nuclei were then centrifuged for 10 min at 500 RCF in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was carefully removed with two pipetting steps, as described before, and nuclei were resuspended in 50μl of transposition mix (25μl 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5μl transposase (100 nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20, and 5μl water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator columns.   The complete eluate underwent PCR, as follows. After initial extension, 5 cycles of pre-amplification using indexed primers (Buenrostro et al., 2015) and NEB Next High-Fidelity 2X PCR Master Mix (NEB) were conducted, before the number of additional cycles was assessed by quantitative PCR using SYBR Green. Typically, 7-9 additional cycles were run. The final library was purified using a MinElute PCR kit (QIAGEN) and quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: We transduced the neurons with lentiviruses expressing either a 50-repeat poly(PR) protein, (PR)50, TDP-43, or GFP as a negative control. Both (PR)50 and TDP-43 caused marked cell death and axonal degeneration 72h after transduction. (PR)50 and TDP-43 expressing neurons formed numerous tubulin bIII puncta, indicating that microtubules disassembled, and the axons underwent degeneration

value: Primary cortical neurons

tag: time


title: ZNF410 gRNA#2_rep2 (RNA-seq)

value: ZNF410 sgRNA#2 infected cells

value: ZNF410 depletion (sgRNA targeting)


title: Neg2 gRNA_rep2 (RNA-seq)

value: Non-targeting sgRNA infected cells

value: Control


title: 328-4_bd_rep1

value: 328-4:ras-1bd MAT A

value: wt


title: 1810_bd_prd-2_rep3

value: 1810:ras-1bd prd-2::barR MAT A

value: period-2 mutant


title: ZNF410 gRNA#2_vector_rep1 (RNA-seq)

value: HUDEP-2 immortalized erythroid cell line

value: Day 7 of culture

value: ZNF410 sgRNA#2 infected cells transduced with empty vector


title: ZNF410 gRNA#1_rep2 (RNA-seq)

value: ZNF410 sgRNA#1 infected cells


title: Neg2 gRNA_rep1 (RNA-seq)


title: 26_10_GFP_2_S20

description: 72h GFP treated replicate2

tag: tissue

value: GFP


title: ZNF410 gRNA#1_rep1 (RNA-seq)


title: 26_10_None_2_S18

description: 72h control untreated replicate2


title: ZNF410 gRNA#2_donor2 (RNA-seq)

source_name: Primary CD34+ cell culture

value: Three-phase in vitro culture of CD34+ primay human cells

value: Day 12 of culture

value: ZNF410 sgRNA#2 electroportated cells


title: 26_10_TDP_1_S21

description: 72h TDP-43 treated replicate1

value: Primary cortical neurons


title: 26_10_PR_2_S24

description: 72h (PR)50 treated replicate2


title: 1810_bd_prd-2_rep1


title: ZNF410 gRNA#1_vector_rep1 (RNA-seq)

value: ZNF410 sgRNA#1 infected cells transduced with empty vector

value: control (vector)


title: ZNF410 gRNA#1_donor2 (RNA-seq)

value: ZNF410 sgRNA#1electroportated cells

value: ZNF410 depletion (sgRNA targeting)


title: 25_10_TDP_1_S13

description: 48h TDP-43 treated replicate1


title: 26_10_PR_1_S23

description: 72h (PR)50 treated replicate1


title: 26_10_None_1_S17

description: 72h control untreated replicate1

value: Control


title: 25_10_None_2_S10

description: 48h control untreated replicate2


title: ZNF410 gRNA#2_donor1 (RNA-seq)


title: control gRNA_donor2 (RNA-seq)

value: Non-targeting sgRNA electroportated cells


title: 25_10_PR_1_S15

description: 48h (PR)50 treated replicate1


title: Neg2-vector rep1 (RNA-seq)

value: Non-targeting sgRNA infected cells transduced with empty vector


title: 26_10_GFP_1_S19

description: 72h GFP treated replicate1


title: 25_10_TDP_2_S14

description: 48h TDP-43 treated replicate2


title: 25_10_None_1_S9

description: 48h control untreated replicate1


title: HUDEP-2-HA-ZF1-5_HA (ChIP-seq)

data_processing:
Reads were aligned against reference genome hg38 or mm9 using Bowtie2 (v2.2.9) and the default parameters.
Alignments with MAPQ score lower than 10 and PCR duplicates were removed using Samtools (v0.1.19). Reads aligned to mitochondria, random contigs and ENCODE blacklisted regions were also removed for downstream analysis.
Data were filtered using the following specifications…
Genome coverage files were generated and normalized to 1 million reads per library using bedtools (v2.25.0), and then converted to bigwig format for visualization using the UCSC Toolkit.
Peaks were called using MACS2 (v2.1.0) and a 0.05 q-value cutoff. The final peaks were those overlapped by both ZNF410 replicates but not in control replicates (empty vector and knock-out samples), then manually filtered to exclude peaks near centromere/telomere regions that did not look like peaks on genome browser
Genome_build: hg38 for human and mm9 for mouse
Supplementary_files_format_and_content: bigwig files

growth_protocol: HUDEP-2 cells were cultured and differentiated accrooding to standard protocol (Grevet et al., Science 2018). In vitro primary CD34+ cells were cultured with a three-phase human CD34+ hematopoietic stem and progenitor cells (HSPCs) culture system (Grevet et al., Science, 2018). G1E-ER4 cells were cultured in IMDM supplemented with 15% FBS, 1% penicillin/streptomycin, Kit ligand, monothioglycerol and epoetin alpha.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to standard Illumina protocols

treatment_protocol: 100 nM estradiol was added to induce G1E-ER4 cell differentiation for 24 hours

tag: chip antibody

value: Cells with HA tagged ZF1-5 overexpression


title: HUDEP-2-HA-ZF1-5_ZNF410 (ChIP-seq)

value: HUDEP-2 immortalized erythroid cell line

value: ZNF410 (proteintech, 14529-1-AP)


title: 25_10_GFP_1_S11

description: 48h GFP treated replicate1


title: 24_10_TDP_2_S6

description: 24h TDP-43 treated replicate2


title: HUDEP-2-HA-ZF2-4_ZNF410 (ChIP-seq)

value: Cells with HA tagged ZF2-4 overexpression


title: ZNF410 gRNA#2_rep1 (RNA-seq)

value: Day 7 of culture

value: ZNF410 sgRNA#2 infected cells


title: 24_10_PR_1_S7

description: 24h (PR)50 treated replicate1


title: HUDEP-2C input (ChIP-seq)

value: Cells with Cas9 overexpression


title: CD34+ day9_ZNF410 rep2 (ChIP-seq)

value: Three-phase in vitro culture of CD34+ primay human cells

value: primary human CD34+ cell at day 9 of differentiation


title: CD34+ day9_H3K27ac rep1 (ChIP-seq)

value: H3K27ac (Abcam, ab4729)


title: CD34+ input (ChIP-seq)


title: 25_10_GFP_2_S12

description: 48h GFP treated replicate2

value: Primary cortical neurons

value: GFP


title: 25_10_PR_2_S16

description: 48h (PR)50 treated replicate2


title: 24_10_TDP_1_S5

description: 24h TDP-43 treated replicate1


title: 24_10_GFP_2_S4

description: 24h GFP treated replicate2


title: zin1_DC_rep3_12h

city: Albany

first: Jennifer

last: Lewis

address: 800 Buchanan St

institute: University of California, Berkeley

description:
STAR_edgeR_12h.tsv
HISAT2_edgeR_12h.tsv
STAR_limma-voom_12h.tsv
HISAT2_limma-voom_12h.tsv

data_processing:
Base-calling was performed using CASAVA software.
Read quality was assessed with FastQC, and the first 12 nucleotides of each read were removed with Trimmomatic.
Reads were aligned to the Arabidopsis TAIR10 genome with either STAR or HISAT2 and read counts determined by the program featureCounts.
Normalized abundance measurements were generated by the edgeR and limma-voom algorithms, from which a consensus list of differentially expressed genes was derived.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown in a controlled environment room with a 9-h photoperiod (130 mE∙m^-2s^-1) at constant 22°C and 60% RH

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific, Inc., Waltham, MA) was used to extract RNA from Arabidopsis leaves, according to the manufacturer’s instructions.  Samples were treated with DNase and further purified using RNA Clean and Concentrator kits (Zymo Research Corp.) and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using a needleless 1 mL syringe, the leaves of wild-type and zin1 mutants infiltrated with either 10 mM MgCl2 (Control), 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000, or 1 x 10^8 cfu/mL P. syringae pv. tomato DC3000 ΔhrcC.  Tissues were harvested at 6 and 12 h post-infiltration.

tag: ecotype

value: leaves

tag: plant age

value: six weeks old

tag: agent

tag: time point


title: HUDEP-2C-ZNF410 sgRNA#2 rep2 (ChIP-seq)


title: HUDEP-2-HA-ZNF410 rep2 (ChIP-seq)

value: Cells with HA tagged ZNF410 overexpression


title: control gRNA_donor1 (RNA-seq)

tag: cell type

value: Day 12 of culture

value: Non-targeting sgRNA electroportated cells

value: Control


title: ZNF410 gRNA#1_donor1 (RNA-seq)

tag: treatment

value: ZNF410 sgRNA#1electroportated cells

value: ZNF410 depletion (sgRNA targeting)


title: HUDEP-2-HA-ZF2-4_HA (ChIP-seq)

tag: cell line

value: HUDEP-2 immortalized erythroid cell line

value: Cells with HA tagged ZF2-4 overexpression


title: 24_10_PR_2_S8

description: 24h (PR)50 treated replicate2


title: 24_10_None_1_S1

description: 24h control untreated replicate1


title: CD34+ day9_ZNF410 rep1 (ChIP-seq)

value: ZNF410 (proteintech, 14529-1-AP)


title: HUDEP-2C-Neg2 rep2 (ChIP-seq)

value: Non-targeting sgRNA infected cells


title: HUDEP-2-HA-ZNF410 rep1 (ChIP-seq)


title: 24_10_None_2_S2

description: 24h control untreated replicate2


title: zin1_hrcC_rep3_12h

value: 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000 ΔhrcC


title: HUDEP-2-pSDM101 vector rep2 (ChIP-seq)

value: Cells transduced with empty vector


title: 24_10_GFP_1_S3

description: 24h GFP treated replicate1


title: HUDEP-2C-Neg2 rep1 (ChIP-seq)


title: zin1_hrcC_rep2_12h


title: WT_DC_rep3_12h

value: 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000


title: zin1_Mg_rep3_12h

value: 10 mM MgCl2


title: CD34+ day9_H3K27ac rep2 (ChIP-seq)

value: Three-phase in vitro culture of CD34+ primay human cells

value: H3K27ac (Abcam, ab4729)

value: primary human CD34+ cell at day 9 of differentiation


title: HUDEP-2-pSDM101 vector rep1 (ChIP-seq)


title: WT_hrcC_rep3_12h

value: leaves

value: six weeks old


title: Gsr-WT_P56-Air_biological rep3

value: Gsr wildtype

value: lung


title: zin1_DC_rep2_12h


title: SUM44+BAPN_1

city: Lausanne

first: George

middle: A

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

data_processing:
Raw sequence data quality control performed using FastQC (v0.11.8)
Raw reads were aligned to the human genome (hg38) using Hisat2 (v2.1.0).
Gene counts were generated using FeatureCounts (v1.6.2). Data preprocessing was done using the limma package from Bioconductor (v3.8).
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts from FeatureCounts.

source_name: SUM44 xenograft

growth_protocol: We transcriptionally profiled xenografted mammary glands intraductally injected with SUM44 cells

extract_protocol:
RNA was extracted from RFP+ FACS-sorted cells using miRNeasy Mini Kit (Qiagen).
Libraries were sequenced on Illumina NextSeq 500 instrument with single-end reads of 85 bp.

treatment_protocol: NSG mice were intraductally injected with SUM44 cells and treated either with PBS_vehicle or BAPN using RNA-seq

value: xenografted mammary gland


title: SUM44+BAPN_3


title: Lega_42_scATAC

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-nuclei ATACseq data from BA38 was processed using Cell Ranger ATAC pipeline. Single-nuclei ATAC-seq reads were aligned with BWA-MEM to the reference sequence (hg38 from UCSC). Seurat extension Signac was used for additional filtering, clustering and annotation. MACS2 was used for peak calling.
Human hg38

source_name: Brodmann Area 38

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were washed once in 500 μl of nuclei wash buffer consisting of 10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 1% BSA and, 0.1% Tween-20. Nuclei were resuspended in 500 μl of 1X Nuclei Buffer (10X Genomics). Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich). Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer were first mixed in 9:1 ratio. 500 μl of the resulting sucrose buffer was added to a 2 ml Eppendorf tube. 900 μl of the sucrose buffer was added to 500 μl of isolated nuclei in NSB. 1400 μl nuclei suspension was layered to the top of sucrose buffer. This gradient was centrifuged at 13, 000 x g for 45 min at 4 °C. Nuclei pellet was resuspended and washed once in nuclei wash buffer. Nuclei concentration and integrity was determined using Ethidium Homodimer-1 (EthD-1) (#E1169, Thermo Fisher Scientific). Finally, nuclei were resuspended in 1X Nuclei Buffer at concentration of 4000 nuclei/μl for single-cell ATAC-sequencing.
Droplet-based single-cell ATACseq library was prepared using the Chromium Single Cell ATAC Kit Solution v1.0 (10X Genomics) and following the Chromium Single Cell ATAC Reagent Kits User Guide: CG000168 Rev B. The library was sequenced using an Illumina NextSeq 500 at the McDermott Sequencing Core at UT Southwestern.

value: Resected

value: Healthy

value: Brodmann Area 38

tag: library type

value: 10X single-nuclei ATAC-seq

tag: age (years)

tag: Sex

value: F

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: R

tag: rin

tag: batch

tag: brainbank

tag: protocol

value: Protocol 3


title: Lega_45_scATAC

tag: genotype

tag: diagnosis

tag: tissue

value: L


title: SUM44_PBS_2


title: WT_Mg_rep3_12h

tag: ecotype

tag: plant age

tag: agent

value: 10 mM MgCl2

tag: time point


title: zin1_hrcC_rep1_12h

value: 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000 ΔhrcC


title: SUM44+BAPN_2


title: WT_hrcC_rep2_12h

value: leaves


title: zin1_Mg_rep2_12h

value: six weeks old


title: HUDEP-2C-ZNF410 sgRNA#2 rep1 (ChIP-seq)

tag: cell line

value: HUDEP-2 immortalized erythroid cell line

tag: chip antibody

value: ZNF410 (proteintech, 14529-1-AP)

tag: treatment

value: ZNF410 sgRNA#2 infected cells


title: SUM44_PBS_3

value: xenografted mammary gland


title: SUM44_PBS_1


title: WT_DC_rep2_12h

value: 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000


title: WT_DC_rep1_12h


title: WT_Mg_rep2_12h


title: zin1_DC_rep1_12h


title: zin1_Mg_rep1_12h


title: WT_hrcC_rep1_12h


title: WT_Mg_rep1_12h


title: zin1_DC_rep3_6h

description:
STAR_edgeR_6h.tsv
HISAT2_edgeR_6h.tsv
STAR_limma-voom_6h.tsv
HISAT2_limma-voom_6h.tsv

value: 6 h


title: zin1_hrcC_rep3_6h


title: zin1_Mg_rep3_6h


title: T76_NST_1

source_name: FACS-sorted GFP+ PDX

growth_protocol: we transcriptionally profiled 6 GFP+ FACS-sorted MIND Patient Derived xenografts using RNA-seq

extract_protocol:
RNA was extracted from GFP+ FACS-sorted cells using miRNeasy Mini Kit (#217004) from (Qiagen).
Libraries were prepared in 2 steps and were sequenced on Illumina NextSeq 500 instrument with single-end reads of 85 bp.


title: T73_ILC_2


title: T69_ILC_1


title: T81_NST_2


title: T99_NST_3


title: T78_ILC_3


title: Healthy control replicate 10

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 31) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 31, release June 2019
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 97 (July 2019) (Human genes, GRCh38.p12, download on 09/28/2019). Genes with 0 mean reads in at least one group were removed from analysis. Batch effects were removed by the limma function removeBatchEffect. After principal component analysis, differential gene expression with Benjamini-Hochberg adjusted (adj.) p-values was analyzed using the R package DESeq2 Version 1.22.2 24 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: normalized reads

source_name: Healthy conjunctiva

extract_protocol:
Total RNA was isolated from ten to fifteen formalin-fixed and paraffin-embedded (FFPE) 4-µm-thick sections of all specimens using the Quick-RNA FFPE Kit (Zymo Research, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA). The fragment size of all RNA samples ranged between 120 and 150 bp.
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method. The preparation of MACE libraries was carried out using 1 µg of total RNA, as previously described. The barcoded libraries (seven SCCs, seven papillomas and ten healthy conjunctival samples) were sequenced simultaneously on the NextSeq 500 (Illumina, USA) with 1× 75 bp. PCR bias was removed using an unique molecular identifier.

value: conjunctiva

tag: disease state

value: Healthy


title: WT_DC_rep3_6h


title: Healthy control replicate 9


title: Healthy control replicate 7


title: zin1_DC_rep2_6h


title: zin1_hrcC_rep2_6h


title: WT_DC_rep2_6h


title: zin1_Mg_rep2_6h


title: WT_hrcC_rep3_6h


title: Healthy control replicate 6


title: WT_Mg_rep3_6h


title: WT_Mg_rep2_6h


title: Healthy control replicate 2


title: Healthy control replicate 3


title: Healthy control replicate 4


title: zin1_DC_rep1_6h


title: Healthy control replicate 1


title: Healthy control replicate 5


title: Pap replicate 7

source_name: Conjunctival Pap

value: Conjunctival Pap


title: zin1_hrcC_rep1_6h


title: zin1_Mg_rep1_6h


title: Pap replicate 6


title: WT_DC_rep1_6h


title: Pap replicate 3


title: WT_hrcC_rep1_6h


title: Pap replicate 4


title: WT_Mg_rep1_6h


title: PAL-12-3: Macrophages 12h after treatment with Palmitate #3

city: Madrid

first: Miguel

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 10 ng/ml M-CSF, with cytokine addition every two days.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: At the end of the differentiaton prtocol, macrophages were either untreated (CNT) or treated with 10 ng/ml E. coli 055:B5 lipopolysaccharide (LPS), 100 ng/ml of the TLR7 agonist CL264 (CL264), BSA or 200 mM palmitate (PAL) for 0.5h, 2h, 4h or 12h.

tag: cell type

value: Monocyte-derived M-CSF macrophages

value: Palmitate


title: Healthy control replicate 8


title: PAL-12-2: Macrophages 12h after treatment with Palmitate #2


title: PAL-12-1: Macrophages 12h after treatment with Palmitate #1


title: WT_hrcC_rep2_6h


title: Pap replicate 2


title: Pap replicate 1


title: PAL-4-3: Macrophages 4h after treatment with Palmitate #3


title: PAL-4-1: Macrophages 4h after treatment with Palmitate #1


title: PAL-4-2: Macrophages 4h after treatment with Palmitate #2


title: WT_Veh_exp2_G78

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

description: SRF(WT) alone experiment 2

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data.
PRO-seq datasets were normalized to 10 million tags, and EdgeR (64) was used to compute the significance of the differential gene expression (FDR ≤ 0.05).
Genome_build: rn6
Supplementary_files_format_and_content: bigWig files were generated using the ‘makeUCSCfile’ command in HOMER with setting of ‘-fsize 1e50 -o auto’.

organism: Rattus norvegicus

source_name: rat adult cardiomyocytes

growth_protocol: Cells were cultured in ACCT medium (M199 Medium, Creatine 5 mM, L-carnitine 2 mM, Taurine 5 mM, HEPES 25 mM, 2,3-Butanedione monoxime 10 mM, BSA 0.2% and 1X Insulin-Transferrin-Selenium Supplement) after langendorff perfusion.

extract_protocol: After PE treatment, cells were washed with PBS and resuspened in swelling buffer (Tris-HCl 5 mM pH 7.5, NaCl 5 mM, MgCl2 1.5 mM, NaF 1.0 mM, AEBSF 0.5 mM, DTT 1 mM, Superase In 2 U/ml) for 15-20 min on ice. The swelled cells were passed through a 28.5G needle, then lysed in swelling buffer with 0.3 M Sucrose, 1% NP40 and 2 µM DTT (add freshly). The suspension was passed through a 28.5G needle again and was vortexed briefly to break cell membranes. The cells debris was removed by quick spin at 30g for 3mins. The supernatant was diluted with lysis buffer and filtered using a 40 µm cell strainer. The nuclei were further washed with lysis buffer twice, then resuspended in 1 ml freezing buffer (Tris-HCl 50 mM pH 8.3, glycerol 25%, MgCl2 5 mM, EDTA, 0.1 mM, DTT 5 mM, Superase In 2U/ml). Nuclei were counted by Hoechst staining. 0.7-1.3 million nuclei were acquired per PRO-seq reaction. For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 20 U Superase-In, 1% sarkosyl, 250 μM A/GTP, 50 µM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296-028) according to manufacturer’s instructions. NRO-RNA was fragmented to ∼200-500 nt by alkaline base hydrolysis on ice for 30 min and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732-6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 µl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100). Bound RNA was extracted from the beads using Trizol (Invitrogen, Cat# 15596-018) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation. The RNA fragments were then subjected to poly-A tailing reaction by poly-A polymerase (NEB, Cat# M0276L) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223 primer and superscript III RT kit (Life Technologies, Cat# 18080-044). The cDNA products were separated on a 10% polyacrylamide TBE-urea gel, and only those fragments migrating between 100-400bp were excised and recovered by gel extraction. Next, the first-strand cDNA was circularized by CircLigase (Epicenter, Cat# CL4115K) and relinearized by APE1 (NEB, Cat# M0282L). Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB, Cat# M0530L) according to the manufacturer’s instructions. The oligonucleotide primers oNTI200 and oNTI201 were used to generate DNA library for deep sequencing and the primer sequences were as described previously (56)

treatment_protocol: 1.2 millions adult ventricular ventricular myocytes infected with 300 Multiplicity of Infection (MOI) of adenovirus for 24 hours and/or treated with 20 µM phenylephrine for 1 hour were used for each individual ChIP assay.

value: primary cultured rat adult ventricular cardiomyocytes


title: PAL-2-3: Macrophages 2h after treatment with Palmitate #3


title: SCC replicate 6

source_name: Conjunctival SCC

value: Conjunctival SCC


title: PAL-2-2: Macrophages 2h after treatment with Palmitate #2


title: WT_Veh_exp1_G72

description: SRF(WT) alone experiment 1


title: PAL-0-5-3: Macrophages 0.5h after treatment with Palmitate #3


title: SCC replicate 7


title: Pap replicate 5


title: PAL-2-1: Macrophages 2h after treatment with Palmitate #1


title: SCC replicate 5


title: PAL-0-5-2: Macrophages 0.5h after treatment with Palmitate #2


title: WT_PE_exp1_G73

description: SRF(WT)+PE experiment 1


title: PAL-0-5-1: Macrophages 0.5h after treatment with Palmitate #1


title: SCC replicate 4


title: BSA-12-3: Macrophages 12h after treatment with BSA #3

value: BSA


title: S103D_exp2_G82

description: SRF S103D alone experiment 2


title: FAN1_RNAseq

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

description: processed file is combined into single data matrix

data_processing:
Cell Ranger 2 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
“cellranger count” aligned the Read2 to the mouse reference genome (mm10) using STAR
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (Ensembl GTFs GRCm38.p4)
The output files for 8 samples were aggregated into one gene-cell matrix using “cellranger aggr” with read depth normalization by total number of mapped reads
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <300 genes detected or with >3,000 unique expressed genes (as they are potentially cell duplets). Only genes expressed in 10 or more cells were used for further analysis. Cells were also discarded if their mitochondrial gene percentages were over 50%.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_kidney_scRNAseq_datamatrix.txt.gz: each row corresponds to genes (first row is the cluster number), and each column corresponds to single cell, number in the matrix is the normalized UMI count data  Mouse_kidney_RNAseq_datamatrix.txt.gz: each row corresponds to genes and each column corresponds to sample, number in the matrix is the normalized count data

source_name: whole kidney tissue

extract_protocol:
10X Genomics Chromium Prep. Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.

treatment_protocol: Mice were injected with folic acid (FA) (250 mg/kg once, dissolved in 300 mM NaHCO3) intraperitoneally and sacrificed on day 7

tag: strain

value: adult kidney

tag: age

value: 5-8 weeks

tag: disease

value: folic acid-induced neprophathy


title: FAN3_RNAseq


title: FAN2_RNAseq


title: BSA-12-2: Macrophages 12h after treatment with BSA #2


title: ici-lymphocyte_vp

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 106 Carrigan Drive

department: Biomedical and Health Sciences

institute: University of Vermont

description:
ici-lymphocyte_vp1
ici-lymphocyte_vp2

data_processing:
Library strategy: 4C-Seq
Demultiplexing (Demux) Illumina reads with HiSeq2000 software, MinION reads with oxford nanopore and minibar software.
4C-Seq trimming and alignment with R.4Cker software scripts and STAR aligner for RNA-Seq, RNA counts files generation with featureCounts software.
trans interactions identification and plotting with R.4Cker software and custom bioinformatics, statistical analysis, and plotting scripts using R.
cis interactions identiification with peakC software
read simulation for telomere content analysis with ART software
Visualization: BigWig tracks generation and visualization with Seqsetvis R package and custom scripts using R, as well as IGB.  Circos plots generated with circlize R package and custom R scripts. Ideogram karyotype plots with KareotypeR R package and custom R scripts, as well as IGB.
Genome_build: Human:GRCh38.p1: NC_000012.1 ; HHV6A: NC_001664.4 (iciHHV6A cells) and NC_001664.2 + recombinant elements (293-HHV-6A cells)
Supplementary_files_format_and_content: 4C-Seq peak regions: Bed and BedGraph; 4C-Seq and RNA-Seq signal tracks: BedGraph and BigWig; RNA-Seq transcript counts: RNA-seq counts .

organism:
Homo sapiens
Human betaherpesvirus 6

source_name: iciHHV-6A Lymphocyte cells

growth_protocol: Human smooth muscles cells (SMCs) were isolated from the from the umbilical veins of an iciHHV6A+ subject.  SMCs were immortalized following transduction with a lentiviral vector (pLenti CMV/TO SV40 small + large T (W612-1), a gift form Eric Campeau and obtained from Addgene (plasmid #22298)) and expressing the SV40 T antigens. SMCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum (FBS), 1% penicillin streptomycin (Pen/Strep), and 1% L-Glutamine. Human epithelial kidney 293 T (293 T, ATCC CRL-11268) cells were cultured in the same medium but supplemented with 10% FBS. All cells were maintained in 10 cm2 flasks as a monolayer culture in a humidified 5% CO2 air incubator at 37°C. Bacterial artificial chromosome (BAC)-derived HHV6A (strain U1102) expressing green fluorescent protein (GFP) under the control of the HCMV major immediate early (IE) promoter (293-HHV-6A) was propagated in JJHan cells as described previously [13]. 293 T cells were infected with 293-HHV-6A and GFP positive cells were isolated using a FACS AriaIII cell sorter (BD Biosciences). Clones harboring the integrated 293-HHV-6A genome were identified by quantitative PCR (qPCR) and HHV-6A integration was confirmed by fluorescent in situ hybridization (FISH).

extract_protocol:
RNA-Seq: RNA was extracted from an HHV-6A infected 293T cell line using Trizol Reagent (Life Technologies) and purified using Direct-zol RNA MicroPrep Kit (Zymo Research #R2060) following the manufacturer’s instructions. 4C-Seq: In order to identify the higher order chromatin structure and virus-host DNA contacts, 4C-seq libraries were prepared using both HHV-6A and iciHHV-6A samples as described previously by Krijger et al. 2020.
RNA-Seq: Libraries were quantified using Qubit (Life Technologies), and quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit (Agilent Technologies). Barcoded libraries were pooled and sequenced on an Illumina HiSeq 2000 to obtain 100-bp paired-end reads. 4C-Seq: Library indexing was performed using the DNA HT Dual Index Kit (Illumina) or with custom dual indexing primers with an additional 8 cycles of PCR. Indexing of nanopore libraries was performed with custom 12-nucleotide dual index primers with 8 additional PCR cycles. Libraries were pooled and sequenced with either HiSeq2000 or minION platforms.

treatment_protocol: 293-HHV-6A cells were infected with recombinant HHV6A virus, iciHHV6A+ cells and Lymphocytes were derived from patients samples

value: iciHHV-6A Lymphocyte cells


title: SCC replicate 2


title: BSA-12-1: Macrophages 12h after treatment with BSA #1


title: SCC replicate 3


title: WT_PE_exp2_G79

description: SRF(WT)+PE experiment 2


title: S103A_Veh_exp2_G80

description: SRF S103A alone experiment 2


title: BSA-4-3: Macrophages 4h after treatment with BSA #3


title: control3_RNAseq

value: control


title: control2_RNAseq


title: SCC replicate 1


title: S103A_Veh_exp1_G74

description: SRF S103A alone experiment 1


title: Lega_90_scATAC

description:
10X single-nuclei ATAC-seq
Within_Subject_scATACseq_matrix.h5.gz

data_processing:
Single-nuclei ATACseq data from BA38 was processed using Cell Ranger ATAC pipeline. Single-nuclei ATAC-seq reads were aligned with BWA-MEM to the reference sequence (hg38 from UCSC). Seurat extension Signac was used for additional filtering, clustering and annotation. MACS2 was used for peak calling.
Genome_build: Human hg38
Supplementary_files_format_and_content:H5 format

tag: sample type

value: Resected

value: Brodmann Area 38

tag: age (years)

tag: Sex

value: M

tag: race

value: White

tag: ethnicity

value: Hispanic

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: R

tag: rin

tag: batch

tag: brainbank

value: Protocol 3


title: S103A_PE_exp2_G81

description: SRF S103A+PE experiment 2

tag: cell line


title: BSA-4-2: Macrophages 4h after treatment with BSA #2

value: Monocyte-derived M-CSF macrophages

tag: treatment


title: control1_RNAseq

tag: tissue


title: BSA-4-1: Macrophages 4h after treatment with BSA #1

tag: cell type


title: S103A_PE_exp1_G75

description: SRF S103A+PE experiment 1


title: BSA-2-3: Macrophages 2h after treatment with BSA #3


title: Lega_15_scRNA

description:
10X single-nuclei RNA-seq
Within_Subject_snRNAseq_Counts.txt.gz

data_processing:
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR 2.5.2b to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M24). Gene level expression was calculated using featureCounts. Downstream analysis was performed using Seurat.
Genome_build: Human hg38
Supplementary_files_format_and_content: UMI counts

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol. Libraries and sequencing were performed at the McDermott Sequencing Core at UTSW.

tag: diagnosis

value: Healthy

value: F

value: Non-Hispanic

value: L

tag: protocol

value: Protocol 2


title: Chip8

description: Flag-SRF(S103A) experiment 2, FLAG ChIPs

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the rn6 genome assembly using Bowtie version 2.0.1.
Genome binding peaks for SRF or phospho-Ser103 antibodies were identified using the ‘findPeaks’ command in HOMER with setting of ‘-style factor’: 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
HOMER-IDR program was employed to format the data for the IDR R package to determine the IDR threshold and identify the top peaks above that threshold.
Genome_build: rn6
Supplementary_files_format_and_content: bigWig files were generated using the ‘makeUCSCfile’ command in HOMER with setting of ‘-fsize 1e50 -o auto’.

source_name: Rat adult cardomyocytes

extract_protocol:
The cells for RNA Polymerase II (Pol II) and H3K27ac ChIPs were directly incubated with 1% formaldehyde in PBS for 10 minutes, while all other cells were subjected to cross-linking by disuccinimidyl glutarate for 30 minutes prior to 15 minutes 1% formaldehyde fixation. Cells were washed with PBS for three times, lysed in 1% SDS buffer, and then ChIP assay was performed using the EZ-ChIP kit (Millipore, 17-371), performed as recommended by the manufacturer using 1.4 - 2.9 µg antibody for each immunoprecipitation. To sequence ChIP-enriched DNA, library constructions were performed using KAPA HyperPrep Kits for NGS DNA Library Prep (Kapa Biosystems). Inputs ranged from undetectable via the Qubit dsDNA HS Assay (<10pg/µl) to 5 ng/µl. 14 PCR cycles were adjusted according to input. Samples were barcoded to allow for multiplexing and analysis on an Illumina HiSeq 4000. Cluster generation took place on the Illumina cBot according to the manufacturer's recommendations. Sequencing took place on the Illumina HiSeq 4000 using the reagents provided in the Illumina TruSeq PE Cluster and SBS kits. An average of 15 million single-end 75 base pass-filter reads were generated per sample.
To sequence ChIP-enriched DNA, library constructions were performed using KAPA HyperPrep Kits for NGS DNA Library Prep (Kapa Biosystems).

treatment_protocol: 2.4 millions adult rat ventricular myocytes infected with 300 Multiplicity of Infection (MOI) of adenovirus for 24 hours and/or treated with 20 µM phenylephrine for 1 hour were used for each individual ChIP assay.

value: primary cultured rat adult ventricular cardiomyocytes

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Mouse M2 anti-Flag


title: BSA-2-2: Macrophages 2h after treatment with BSA #2

value: BSA


title: FAN2_scRNAseq

tag: strain

value: adult kidney

tag: age

value: 5-8 weeks

tag: disease

value: folic acid-induced neprophathy


title: S103D_exp1_G75

description: SRF S103D alone experiment 1


title: Tamm_1556

description:
Bulk RNA-seq
Within_Subject_RawCounts.txt
Within_Subject_CPM.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.5.2b to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M24). Uniquely mapped reads were quantified using HTSeq python suite using protein coding genes by gene.
Genome_build: Human hg38
Supplementary_files_format_and_content: CPM and RawCounts included in separate text files.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. Libraries and sequencing were performed at the McDermott Sequencing Core at UTSW.

tag: sample type

value: Post-mortem

value: Brodmann Area 38

tag: age (years)

tag: Sex

value: M

tag: race

tag: ethnicity

value: CTLab

value: Protocol 1