title: Hg3

city: Milan

first: Paolo

last: Gandellini

state: Milan

address: Via celoria 26

department: Bioscience

country: Italy

institute: University of Milan

description: narrowPeak

data_processing:
ChIRP-seq reads were aligned to the UCSC hg19 genome using Bowtie 1.0.1. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.05
For each MACS2 peak, we filtered for regions sharing the same features in more than 2 independent experiments using findConsensusPeakRegions function of consensusSeekeR package in R environment.
Consensus peaks were created with findConsensusPeakRegions function, extending the region of 500 bp on both sides of the position of the peak median and setting expandToFitPeakRegion and shrinkToFitPeakRegion parameters to true.
Assembly: hg19
Supplementary files format and content: narrowPeak files generated using MACS v2
Library strategy: ChIRP-Seq

growth_protocol: RWPE-1 cells were maintained in K-SFM (Thermo Fisher Scientific Inc., Waltham, MA, USA) culture medium supplemented with 5 ng/ml epidermal growth factor and 0.05 mg/ml bovine pituitary extract, and cultured at 37°C at 5% CO2.

extract_protocol:
RWPE-1 cells, grown to 80% confluence in supplemented K-SFM medium, were treated by adding formaldehyde directly to tissue culture medium to a final concentration of 1% and incubated for 10 minutes at room temperature. Cross-linking reactions were stopped by the addition of glycine to a final concentration of 125 mM. Cells were washed three times with ice-cold PBS, scraped, and centrifuged at 2,000 g for 5 minutes. Cell pellets were resuspended in lysis buffer freshly supplemented with protease inhibitor, PMSF and Superase-in (1ml lysis buffer/100 mg cell pellet) and immediately sonicated to an average chromatin length of 500-800 bp. Sonication was performed in a 4°C water bath at highest setting with 30 seconds ON, 45 seconds OFF pulse intervals. Sonicated samples were centrifuged at 16,100 g for 10 minutes at 4°C. 10 µl sonicated chromatin from each sample were stored as inputs for DNA extraction. Remaining chromatin was diluted in two times volume of hybridization buffer freshly supplemented with PMSF, proteinase inhibitor, and Superase-in. 100 pmol probes (LacZ-probes or MIR205HG-probes, sequences of all probes reported in PMID: 30659180) were added to 3 ml of diluted chromatin, which was mixed by end-to-end rotation at 37°C for 4 hours. Streptavidinmagnetic C1 beads (Invitrogen, Carlsbad, CA) were washed three times in lysis buffer and 100 µl washed C1 beads were added per 100 pmol of probes. The whole reaction was mixed for 30 min at 37°C. Beads:biotin-probes:RNA:chromatin adducts were captured by T-1-800 Adna Mag S magnets (AdnaGen, Langenhagen, Germany) and washed five times with wash buffer freshly supplemented with PMSF. After last wash buffer was removed carefully with P-10 pipette so that no trace volume was left behind. For DNA elution all samples including inputs were resuspended in DNA elution buffer and incubated at 37°C for 30 minutes with end-to-end rotation. Beads were captured by T-1-800 Adna Mag S magnets (AdnaGen, Langenhagen, Germany). Eluted DNA from two steps was combined. Chromatin was reverse crosslinked at 65°C overnight with 200 mM NaCl and treated with ProteinaseK at 45°C for 2 hours. DNA was then extracted with equal volume of phenol:chloroform:isoamyl (Invitrogen, Carlsbad, CA) and precipitated with ethanol at 80°C overnight. Isolated DNA was resuspended in elution buffer (19086, Qiagen, Hilden, Germany).
High-throughput sequencing libraries from three independent ChIRP experiments were prepared and indexed using the ThruPLEX® DNA-seq Kit (Rubicon Genomics), using 12 cycles of PCR for all samples (MIR205HG and LacZ). Libriaries were purified on AMPure XP beads, then checked for quality and size range on Agilent Bioanalyzer using the High Sensitivity DNA Assay kit. Samples were then pooled and sequenced on Illumina HiSeq2000 with single read length of 100 bp (SR100).

value: immortalized normal prostate epithelial cells

tag: chirp probes

value: MIR205HG pool


title: KOCXDHPG1

status: Public on Jun 07 2022

type: SRA

city: Edinburgh

first: Emily

last: Osterweil

state: Scotland

address: Hugh Robson Building, 15 George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
Filtering and QC were performed by the sequencing facility
RNA-seq reads were aligned to the GRCm39 genome assembly using STAR version 2.7.1a
GRCm39
Assembly: count files were generating using feature counts

molecule: total RNA

organism: Mus musculus

source_name: Hippocampal slice

growth_protocol: acute hippocampal slices

extract_protocol:
TRAP
Smartseq v4 amplification followed by Nextera library preparation for Illumina sequencing

treatment_protocol: pre-incubation with vehicle or 200nM CX-5461,  stimulated with 50uM S-DHPG 5 minutes, and removed to fresh ACSF (+/- CX-5461) for an additional 25 min.

tag: strain

tag: sample type

value: IP

tag: treatment

value: CX+DHPG

tag: genotype

value: Fmr1 KO


title: IMF-4D-3: Intramuscular  adipocytes-Differentiation day 4-rep3 [mRNA-seq]

city: Beijing

first: Pan

last: Zhang

address: No. 2, Yuanmingyuan West Road, Beijing

country: China

institute: China Agricultural University

data_processing:
The Illumina Novaseq6000 (Illumina, San Diego, CA, USA) platform is used for transcriptome sequencing
Clean reads were mapped to the reference pig genome version scrofa.Sscrofa11.1by using HISAT2tool software for alignment.
We used StringTie (1.3.4d) software to calculate FPKM (Fragments per Kilobase Millon Mapped Reads) values to represent gene expression levels.
DESeq2 (V1.6.3) was used to analyze the differences between group
Genome_build: ss11.1
Supplementary_files_format_and_content: FPKM values for each Sample

molecule: polyA RNA

organism: Sus scrofa

source_name: Intramuscular  adipocytes

extract_protocol:
Total RNA was isolated at various stages of subcutaneous adipocytes and Intramuscular  adipocyte differentiation (0d, 2d, 4d, 8d) using the Trizol reagen. RNase-free DNase was added to total RNA to remove DNA contamination. The integrity of RNA was checked by 1.2% agarose gel electrophoresis and the quality of RNA and the amount of total RNA were determined by Nanodrop 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Longissimus dorsi

tag: age

value: six-day-old

tag: breed

value: Yorkshire


title: KOCX2

value: CX


title: IMF-4D-1: Intramuscular  adipocytes-Differentiation day 4-rep1 [mRNA-seq]


title: Hg1

description: narrowPeak

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: Hg2

description: narrowPeak


title: Renal cell carcinoma_C11W3

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

organism: Rattus norvegicus

source_name: normal kidney cortex

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: Male wild-type and BRCA1+/- rats at 5 weeks of age were injected intraperitonealy with Fe-NTA by the dose of 5 mg iron/kg for the first three times then 7 for the last two times for the first week, and by 7 mg iron/kg for the first time then 5 for four times for the second week, and by 7 mg iron/kg for the first three time then 10 for two times for the third week. The treatment for next 8 weeks was by the dose of 10 mg iron/kg weight, three times per week. The rats were euthanized when they were dying.

value: Jcl:SD wild-type

value: Fe-NTA, 3 months


title: KOCX1


title: Renal cell carcinoma_C5W2


title: Renal cell carcinoma_C5k1

value: Jcl:SD BRCA1+/-


title: Renal cell carcinoma_C5W13


title: Renal cell carcinoma_C10K1


title: IMF-2D-3: Intramuscular  adipocytes-Differentiation day 2-rep3 [mRNA-seq]


title: LacZ

description: narrowPeak

value: LacZ pool


title: IMF-2D-2: Intramuscular  adipocytes-Differentiation day 2-rep2 [mRNA-seq]


title: WTHip4

data_processing:
Library strategy: TRAP-seq
Filtering and QC were performed by the sequencing facility
RNA-seq reads were aligned to the GRCm39 genome assembly using STAR version 2.7.1a
Assembly: GRCm39
Supplementary files format and content: count files were generating using feature counts

source_name: Hippocampus

growth_protocol: Freshly dissected mouse hippocampus

extract_protocol:
TRAP
NuGEN Ovation RNAseq v2

value: WT

value: Hippocampus


title: IMF-2D-1: Intramuscular  adipocytes-Differentiation day 2-rep1 [mRNA-seq]


title: RNAP_1.0X_3

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.36
Trimmed reads were then mapped to the reference genome, E. coli MG1655 (NC_000913.3), using the Bowtie2 v.2.3.5.1 aligner, which outputs BAM files
featureCounts from the Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts
Gene hit counts was then used for the subsequent differential expression analysis. For this, we used the DESeq2 R package (v.1.24.0) to compare gene expression between groups of samples and calculate p-values and log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest). Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10 were removed from further analysis.
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing normalized raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing results from differential expression analysis

growth_protocol: From glycerol stocks (at - 80 ºC), cells were streaked on lysogeny broth (LB) agar plates with appropriate antibiotics and kept at 37 ºC overnight. Next, a single colony was picked and inoculated into fresh LB medium and kept at 30 ºC overnight, with appropriate antibiotics and aeration at 250 rpm. From overnight cultures (ONC), cells were diluted to 1:1000 in tailored LB media (see below), with antibiotics, and incubated at 37 ºC with aeration and allowed to grow until reaching the mid-log phase (with optical density at 600 nm (OD600) ≈ 0.4).   Using this protocol, to attain cells with different intracellular RNAP concentration, starting from LB, we used tailored various media differing in richness, denoted as ‘LB1.0x', ‘LB0.75x, ‘LB0.5x’, ‘LB0.25x’ specifically. Their composition for 100 ml (pH of 7.0) are, respectively: (LB1.0x) 1 g tryptone, 0.5 g yeast extract and 1 g NaCl; (LB0.75x) 0.75 g tryptone, 0.375 g yeast extract and 1 g NaCl; (LB0.5x) 0.5 g tryptone, 0.25 g yeast extract and 1 g NaCl; and (LB0.25x) 0.25 g tryptone, 0.125 g yeast extract and 1 g NaCl.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.

treatment_protocol: Cells from 3 independent biological replicates of MG1655 in each modified LB medium richness were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.

tag: intracellular rnap concentration


title: RNAP_1.0X_2

organism: Escherichia coli str. K-12 substr. MG1655


title: WTHip2


title: IMF-0D-3: Intramuscular  adipocytes-Differentiation day 0-rep3 [mRNA-seq]


title: WTHip3


title: wildtype Fe-NTA 3w injected kidney cortex 3

type: RNA

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074036_D_F_20180103) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Kidney cortex, wild-type Sprague-Dawley rat (CLEA Japan)

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: Male wild-type and BRCA1+/-  rats at 4 weeks of age were injected intraperitonealy with Fe-NTA for 1 or 3 weeks by the dose of 5 mg iron/kg for the first two times then 7 for the last three times for the first week, and by 10 mg iron/kg for 5 times per week for 2 weeks.  The rats were euthanized 48 h after the final injection.  The fresh kidney cortex tissues were excised and processed.

value: Kidney cortex


title: BRCA1+/- Fe-NTA 1w injected kidney cortex 3

source_name: Kidney cortex, BRCA1+/- Sprague-Dawley rat (CLEA Japan)

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).


title: RNAP_1.0X_1


title: WTHip1


title: IMF-0D-2: Intramuscular  adipocytes-Differentiation day 0-rep2 [mRNA-seq]


title: BRCA1+/- Fe-NTA 1w injected kidney cortex 1


title: Renal cell carcinoma_C5W12


title: wildtype Fe-NTA 1w injected kidney cortex 3


title: Olfactory Epithelium,SARSCOV2,31dpi,4

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

country: USA

institute: NYU Langone Health

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)

organism: Mesocricetus auratus

source_name: Olfactory Epithelium

extract_protocol:
Trizol Phenol Chloroform
Poly A tail enrichment and preparation using True Strand RNA-seq Prep

value: Olfactory Epithelium

tag: infection

value: SARS-CoV-2 (1000 PFU)

tag: time

value: 31 dpi


title: BRCA1+/- normal kidney cortex 2


title: KOHipIP4

value: IP


title: wildtype normal kidney cortex 2


title: BRCA1+/- normal kidney cortex 1


title: IMF-0D-1: Intramuscular  adipocytes-Differentiation day 0-rep1 [mRNA-seq]


title: RNAP_0.75X_3


title: Renal cell carcinoma_C8K44


title: wildtype Fe-NTA 1w injected kidney cortex 1


title: BRCA1+/- Fe-NTA 3w injected kidney cortex 1


title: Olfactory Epithelium,SARSCOV2,31dpi,3


title: RNAP_0.75X_2


title: BF-8D-3: Subcutaneous adipocytes-Differentiation day 8-rep3 [mRNA-seq]

source_name: Subcutaneous adipocytes

value: Back subcutaneous fat


title: BRCA1+/- Fe-NTA 1w injected kidney cortex 2


title: RNAP_0.75X_1


title: KOHipIP3


title: KOHipIP2


title: wildtype normal kidney cortex 1


title: Renal cell carcinoma_C1K4


title: Renal cell carcinoma_C8K46


title: BRCA1+/- Fe-NTA 3w injected kidney cortex 2


title: Olfactory Epithelium,SARSCOV2,31dpi,2


title: wildtype Fe-NTA 3w injected kidney cortex 1


title: Renal cell carcinoma_C4W21


title: RNAP_0.5X_3


title: KOHipIP1


title: BF-8D-2: Subcutaneous adipocytes-Differentiation day 8-rep2 [mRNA-seq]


title: Olfactory Epithelium,MOCK,31dpi,4

value: Mock (PBS-treated)


title: RNAP_0.5X_2


title: Olfactory Epithelium,SARSCOV2,31dpi,1


title: wildtype Fe-NTA 1w injected kidney cortex 2


title: wildtype Fe-NTA 3w injected kidney cortex 2


title: DT_72h_scATAC

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: single cell ATAC seq

data_processing:
10X Genomics
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-seq: raw matrix files with corresponding barcodes and features from cellranger; scATAC-seq: cellranger filtered matrix files with corresponding barcodes and features

source_name: Small intestine

extract_protocol:
Small Intestine were removed, dissociated to make single cells, FACS sorted for tdTomato positive cells, and the cells processed using 10x Genomics Kit (Cat# for scRNA seq and Cat# for scATAC seq).
RNA libraries were prepared for sequencing using 10X Genomics  (Cat# for scRNA seq and Cat# for scATAC seq).
10X Genomics kit

treatment_protocol: Normal Control mice harvested after 2 daily doses of Tamoxifen; for stem cell ablation/ DT samples mice harvested after 2 daily doses of Tamoxifen plus one dose of DT before harvest

value: Small Intestine

tag: hour

value: 2 daily doses of Tamoxifen and one dose of DT before harvest

value: Aligned using Cellranger ATAC software v1.1.0


title: BF-4D-3: Subcutaneous adipocytes-Differentiation day 4-rep3 [mRNA-seq]

value: six-day-old

value: Yorkshire


title: Renal cell carcinoma_C9W4

value: Jcl:SD wild-type

value: Fe-NTA, 3 months


title: DT_72h_scRNA

description: single cell RNA seq

value: Aligned using Cellranger RNA software v3.0.2


title: BF-4D-2: Subcutaneous adipocytes-Differentiation day 4-rep2 [mRNA-seq]


title: Renal cell carcinoma_C10W2


title: Olfactory Epithelium,MOCK,31dpi,2

value: WT


title: Renal cell carcinoma_C6K2

value: Jcl:SD BRCA1+/-


title: RNAP_0.25X_3


title: DT_48h_scATAC_rep2

description: single cell ATAC seq


title: Olfactory Epithelium,MOCK,31dpi,1


title: BF-4D-1: Subcutaneous adipocytes-Differentiation day 4-rep1 [mRNA-seq]


title: Renal cell carcinoma_C8W712


title: BF-2D-3: Subcutaneous adipocytes-Differentiation day 2-rep3 [mRNA-seq]


title: DT_48h_scATAC_rep1

description: single cell ATAC seq


title: RNAP_0.25X_2


title: RNAP_0.25X_1


title: BF-2D-1: Subcutaneous adipocytes-Differentiation day 2-rep1 [mRNA-seq]


title: Olfactory Epithelium,IAV,31dpi,4

value: Influenza (100,000 PFU)


title: Olfactory Epithelium,IAV,31dpi,3

value: Olfactory Epithelium


title: DT_48h_scRNA_rep3

description: single cell RNA seq


title: RNAP_0.5X_1


title: αMHC-GFP positive ADRCs after transfection of 6 factors rep1

city: Showa-ku, Nagoya

first: Shingo

last: Narita

address: 65 Tsurumai-cho

department: Cardiology

institute: Nagoya University Graduate School of Medicine

description: Passage 2 / 3 weeks after transfection

data_processing:
CLC Genomics Workbench (CLC bio/QIAGEN, Version: 21.0.5)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCM38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values or Normalized expression values for each Sample

source_name: ADRCs

growth_protocol: ADRCs were isolated from the inguinal and axillary fat pads of mice. The adipose tissues were treated with 5 ml of collagenase type 1 (FUJIFILM, Cat# 037-17603) solution; subsequently, 2 mg/ml Hank's balanced salt solution was added. Enzyme treatment was performed with gentle rocking at 37 ℃ for 30 to 45 min. The digested tissues were filtered through a 100 μm mesh filter and centrifuged at 500  g for 5 min. The supernatant was removed and the pellet was stirred with 10 ml Dulbecco’s modified Eagle medium (DMEM; Sigma Aldrich, Cat# D6046-500ML) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. The suspension was plated in 10 cm dishes (passage 0), and the medium was exchanged the day after isolating the ADRC. ADRCs were cultured under 5% CO2 at 37 ℃ conditions. The medium was changed every 2–3 days. After achieving the desired confluency of 80–90%, ADRCs were harvested by trypsinization for 5 min at 37 ℃  and pipetting to passage 1. The passage 2 process was same as Passage 1.

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (QIAGEN, Cat# 217084) and the TURBO DNA-freeTM Kit (Thermo Fisher Scientific, Cat# AM1907) to remove contaminating DNA.
Complementary DNA synthesis and library preparation were performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEW ENGLAND Biolabs, Cat# E6310) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEW ENGLAND Biolabs, Cat# E7770)

value: ADRCs

value: mesenchymal cells

value: C57BL/6-Tg (Myh6-EGFP) MG3Tm; MG3

value: Reprogramming using lentiviral 6 factors gene transfer / FACS sorting of GFP-positive cells


title: αMHC-GFP positive ADRCs after transfection of 6 factors rep2

description: Passage 2 / 3 weeks after transfection


title: BF-2D-2: Subcutaneous adipocytes-Differentiation day 2-rep2 [mRNA-seq]

value: Back subcutaneous fat


title: Olfactory Epithelium,IAV,31dpi,2

value: 31 dpi


title: BF-0D-3: Subcutaneous adipocytes-Differentiation day 0-rep3 [mRNA-seq]


title: DT_48h_scRNA_rep2

description: single cell RNA seq

value: Small Intestine

value: 2 daily doses of Tamoxifen and one dose of DT before harvest


title: ADRCs from 8 weeks mouse adipose tissue (αMHC-GFP positive control), Passage 2 rep2

description: Passage 2


title: DT_24h_scATAC_rep2

description: single cell ATAC seq

value: Aligned using Cellranger ATAC software v1.1.0


title: Olfactory Epithelium,MOCK,31dpi,3

value: Mock (PBS-treated)


title: Olfactory Epithelium,IAV,31dpi,1


title: ADRCs from 8 weeks mouse adipose tissue (αMHC-GFP positive control), Passage 2 rep1

description: Passage 2


title: DT_24h_scATAC_rep1

description: single cell ATAC seq


title: BF-0D-2: Subcutaneous adipocytes-Differentiation day 0-rep2 [mRNA-seq]

value: six-day-old

value: Yorkshire


title: HFD Rag1-Tbet-DKO IRI [SAMPLE 8]

city: Washington, DC

first: Alexander

last: Kroemer

state: DC

address: 3800 Reservoir Road NW, Pasquerilla Healthcare Center (PHC), 2nd Floor,

department: Center for Translational Transplant Medicine (CTTM)

institute: MedStar Georgetown Transplant Institute

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/
For the normalization, we used an automatically selected housekeeping gene panel (Actb, Hsp90ab1, Gapdh) for Rag1-KO mice and automatically selected reference genes from the entire cataloged array (Nodal, IL-9, and Csf1) for Rag1-Tbet-DKO mice.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (e.g., (HFD Rag1-KO non-IRI) / (ND Rag1-KO non-IRI)) ratios.

label: SYBR Green

source_name: Mouse liver tissue.

label_protocol: PCR assays were performed using mouse liver specimens stored in Allprotect Tissue Reagent (Qiagen) and the Mouse Cytokines & Chemokines PCR Array panel (Qiagen) following the manufacturer’s instructions. cDNA was synthesized utilizing RT² First Strand kit (Qiagen) using 1.25ug pooled total RNA from at least three separate mice livers in an equal proportion. Quantitative real-time PCR were performed using StepOnePlus (Applied Biosystems) thermocycler, the qPCR cycling conditions were 95°C for 10 minutes for 1 cycle, followed by 40 cycles of 95°C for 15 seconds and 60°C for 1 minute.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Mixed

tag: diet

value: High fat diet (HFD)

tag: hepatic injury

value: Ischemia re-purfusion injury (IRI)


title: HFD Rag1-Tbet-DKO non-IRI [SAMPLE 7]

description: Test

value: No injury


title: Embryonic (E11.5) whole heart rep1

growth_protocol: ADRCs were isolated from the inguinal and axillary white adipose fat pads of mice. The adipose tissues were treated with 5 ml of collagenase type 1 (FUJIFILM, Cat# 037-17603) solution; subsequently, 2 mg/ml Hank's balanced salt solution was added. Enzyme treatment was performed with gentle rocking at 37 ℃ for 30 to 45 min. The digested tissues were filtered through a 100 μm mesh filter and centrifuged at 500  g for 5 min. The supernatant was removed and the pellet was stirred with 10 ml Dulbecco’s modified Eagle medium (DMEM; Sigma Aldrich, Cat# D6046-500ML) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. The suspension was plated in 10 cm dishes (passage 0), and the medium was exchanged the day after isolating the ADRC. ADRCs were cultured under 5% CO2 at 37 ℃ conditions. The medium was changed every 2–3 days. After achieving the desired confluency of 80–90%, ADRCs were harvested by trypsinization for 5 min at 37 ℃  and pipetting to passage 1. The passage 2 process was same as Passage 1.

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (QIAGEN, Cat# 217084) and the TURBO DNA-freeTM Kit (Thermo Fisher Scientific, Cat# AM1907) to remove contaminating DNA.
Complementary DNA synthesis and library preparation were performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEW ENGLAND Biolabs, Cat# E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEW ENGLAND Biolabs, Cat# E7770)


title: DT_48h_scRNA_rep1

description: single cell RNA seq

value: Aligned using Cellranger RNA software v3.0.2


title: DT_24h_scRNA_rep3

description: single cell RNA seq


title: RNAP_1.0X_125min_3

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.39.
Trimmed reads were then mapped to the reference genome, E. coli MG1655 (NC_000913.3), using the Bowtie2 v.2.3.5.1 aligner, which outputs BAM files.
Then, featureCounts from the Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts. Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10 were removed from further analysis.
Unique gene hit counts were then used for the subsequent differential expression analysis. For this, we used the DESeq2 R package (v.1.24.0) to compare gene expression between groups of samples and calculate p-values and log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest).
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure).
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing raw counts, normalized counts, or results from differential expression analysis

growth_protocol: From glycerol stocks (at - 80 ºC), cells were streaked on lysogeny broth (LB) agar plates with antibiotics and kept at 37 ºC overnight. Next, a single colony was picked, inoculated into fresh LB medium and, kept at 30 ºC overnight with appropriate antibiotics and aeration at 250 rpm. From overnight cultures (ONC), cells were diluted to 1:1000 in tailored LB media (see below) with antibiotics, incubated at 37 ºC with aeration, and allowed to grow until reaching the mid-log phase (with optical density at 600 nm (OD600) ≈ 0.4).   Using this protocol, to attain cells with different intracellular RNAP concentration, starting from LB, we used tailored media, denoted as ‘LB1.0x’ and ‘LB0.5x’, specifically. Their composition for 100 ml (pH of 7.0) are, respectively: (LB1.0x) 1 g tryptone, 0.5 g yeast extract and 1 g NaCl; (LB0.5x) 0.5 g tryptone, 0.25 g yeast extract and 1 g NaCl.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen). RNA was treated twice with DNase (Turbo DNA-free kit, Ambion) and quantified using Qubit 2.0 Fluorometer RNA assay (Invitrogen, Carlsbad, CA, USA). Total RNA amounts were determined by gel electrophoresis, using a 1% agarose gel stained with SYBR safe (Invitrogen). RNA was detected using UV with a Chemidoc XRS imager (Biorad).
RNA-seq libraries were constructed according to the Illumina's protocol.
Library strategy established by GENEWIZ, Inc. (Leipzig, Germany) for RNA-seq

treatment_protocol: Cells from 3 independent biological replicates of MG1655 in each modified medium were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.

tag: sample group


title: Embryonic (E11.5) whole heart rep2


title: BF-0D-1: Subcutaneous adipocytes-Differentiation day 0-rep1  [mRNA-seq]


title: ADRCs from 8 weeks mouse adipose tissue , Passage 2 rep2

description: Passage 2

value: ADRCs


title: BF-8D-1: Subcutaneous adipocytes-Differentiation day 8-rep1 [mRNA-seq]


title: DT_24h_scRNA_rep2

description: single cell RNA seq


title: ND Rag1-Tbet-DKO IRI [SAMPLE 6]

description: Test

value: Normal diet (ND)


title: RNAP_1.0X_125min_1


title: DT_24h_scRNA_rep1

description: single cell RNA seq


title: ADRCs from 8 weeks mouse adipose tissue , Passage 2 rep1

description: Passage 2

value: mesenchymal cells


title: RNAP_1.0X_60min_3


title: ND Rag1-Tbet-DKO non-IRI [SAMPLE 5]

description: Control


title: DT_12h_scATAC

description: single cell ATAC seq


title: RNAP_1.0X_60min_2


title: HFD Rag1-KO non-IRI [SAMPLE 3]

description: Test


title: HFD Rag1-KO IRI [SAMPLE 4]

description: Test


title: DT_12h_scRNA

description: single cell RNA seq


title: WTVEHIP6

extract_protocol:
TRAP
NuGeN Ovation RNAseq v2

treatment_protocol: DHPG stimulation for LTD

value: IP

value: Vehicle

value: WT

value: Ribosome bound mRNA


title: RNAP_1.0X_60min_1


title: Normal 72h_scATAC

description: single cell ATAC seq

value: Small Intestine

value: 2 daily doses of Tamoxifen before harvest


title: WTVEHIP4


title: Normal 48h_scATAC

description: single cell ATAC seq

value: Aligned using Cellranger ATAC software v1.1.0


title: RNAP_0.5X_125min_2


title: Normal12h_scATAC

description: single cell ATAC seq


title: WTVEHIP2


title: ND Rag1-KO IRI [SAMPLE 2]

description: Test


title: WTVEHIP3


title: RNAP_0.5X_125min_1


title: RNAP_0.5X_60min_3


title: WTVEHIP5


title: ND Rag1-KO non-IRI [SAMPLE 1]

description: Control


title: HEK293_no_RNaseH_spKAS-seq.rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
First, the trim-galore package was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters.
Sam files were subsequently converted and sorted to bam files using samtools (v1.9). Duplicated mapped reads were removed using picard MarkDuplicates (v1.141).
For paired-end spKAS-seq data, SAMtoBED.py was used to combine “properly paired” alignments into a single BED interval. For single-end spKAS-seq data, deduplicated unique mapped reads were extended to 150 bp to match the average length of DNA fragments (awk command).
Bed files were converted to bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Assembly: hg19
Supplementary files format and content: bigWig, spKAS-seq density on plus and minus strands.
Library strategy: strand-specific KAS-seq (spKAS-seq)

growth_protocol: HEK293T were purchased from ATCC (CRL11268 for HEK293T, HB8065 for HepG2) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco 10378) and grown at 37 °C with 5% CO2. K562 cells were purchased from ATCC (CCL243) and were cultured in RPMI 1640 (Gibco 11875) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 °C with 5% CO2. All cell lines were routinely checked to be free of mycoplasma.

extract_protocol:
After labeling, cells were harvested for genomic DNA isolation by using the PureLink Genomic DNA mini kit (Thermo, K182002). Around 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin (Sigma, 760749). The mixture was gently shacked at 37 °C for 1.5 h, after which 5 µL RNase A (Thermo, 12091039) was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit (Zymo, D4013) and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. Save 5% of the sonicated DNA as input and use the rest for enrichment with 10 µL Dynabeads MyOne Streptavidin C1 (Thermo, 65001). The beads were washed by 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were washed once in 1× B&W buffer and then washed twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal. A final wash with 1× B&W buffer was followed, and DNA was eluted in 10 µL H2O by heating the beads at 95 °C for 10 min.
Input and enriched DNA were used for library construction by using the Accel-NGS Methyl-seq DNA library kit (Swift, 30024). Libraries were sequenced on Illumina platforms with pair-end more with around 60 million reads per library.

treatment_protocol: Cells were treated with 5 mM N3-kethoxal dissolved in their culture media for 10 min at 37 °C, 5% CO2.

value: Human embryonic kidney cells

value: wild type

value: no RNaseH


title: RNAP_1.0X_125min_2


title: WTDHPGIP4

value: DHPG


title: RV_CAV_4

city: Nashville

first: Kaushik

last: Amancherla

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

description: 10x Genomics single-nuclear RNA sequencing (snRNA-seq)

library_source: transcriptomic single cell

data_processing:
The raw FASTQ files were first individually trimmed using CutAdapt to remove homopolymers and the template switch oligo. Trimmed reads were aligned to the GRCh38 human genome reference using CellRanger v6.0.2 with the default settings, except for r1_length = 26, include_introns = TRUE, and recovered_cells = 8000. All CellRanger output was then processed by CellBender v0.2.0 to remove ambient background RNA contamination. The CellBender output was imported into R v4.1.0 Patched and underwent quality control filtering with Seurat v4.0.3 at the individual sample level. Nuclei were removed from an experiment if 1) the number of genes detected was less than 100 or greater than the 3rd quartile plus 1.5 times the interquartile range, or 2) the number of UMI per nucleus was greater than the 3rd quartile plus 1.5 times the interquartile range, or 3) the mitochondrial gene content was greater than 5%. We also excluded droplets containing more than one nucleus as identified by Scrublet. Samples were merged together, underwent normalization via SCTransform, and % mitochondrial reads were regressed out. The normalized data was corrected for batch effects using Harmony v0.1.0 with each sample considered a unique batch.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human myocardium

extract_protocol:
Approximately 3-10 mg of endomyocardial biopsy tissue and 25 mg of explanted cardiac tissue underwent was first cryosectioned into 100um sections until at least 25 sections were obtained per sample. Tissue sections were then placed in a cold lysis buffer solution and underwent gentle pipette mixing, followed by homogenization via several rounds of douncing with loose and tight pistons. Subsequently, the samples underwent multiple rounds of filtering through a 100um and 20um filter. The supernatant was centrifuged at 500G for 5 minutes at 4⁰ C followed by resuspension in a cold nuclear resuspension buffer.
Nuclei were counted on a hemocytometer and loaded into the 10X Genomics single cell 3’ v3.1 platform for an estimated recovery of 8,000 nuclei per sample at 25,000 reads per nucleus.

tag: condition

value: CAV (from right ventricle)

value: Human myocardium


title: LV_CAV_3

value: CAV (from left ventricle)


title: HEK293_no_RNaseH_spKAS-seq.rep1


title: RNAP_0.5X_125min_3


title: Normal 72h_scRNA

description: single cell RNA seq

tag: strain

value: Aligned using Cellranger RNA software v3.0.2


title: Normal 48h_scRNA

description: single cell RNA seq


title: WTDHPGIP6

tag: sample type


title: WTDHPGIP5

tag: treatment


title: RV_CAV_2


title: Odc_Delta_Epi-Infected3

first: Keith

middle: T

last: Wilson

address: 2215 Garland Ave

department: Medicine

data_processing:
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts of each gene for each sample

source_name: Gastric tissue

growth_protocol: Littermates Odc fl/fl and Odc_Delta_Epi male mice (6 to 12 weks old)

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen).
Librabry preparation was performed using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs)

treatment_protocol: Mice were gavaged on day 0 and day 2 with 1x10^9 H. pylori strain PMSS1. Stomachs were harvested after 4 weeks and gastric tissues used for RNA isolation

value: Gastric tissue

tag: infected

value: Yes

tag: genotype


title: Odc_Delta_Epi-Infected4

tag: tissue


title: WTDHPGIP3

value: IP


title: Normal 24h_scRNA

description: single cell RNA seq


title: Odc_Delta_Epi-Infected1


title: LV_CAV_2


title: KOVEHIP4

value: Vehicle

value: KO (Fmr1-/y)


title: RNAP_0.5X_60min_2


title: RV_CAV_1


title: KOVEHIP5

value: Ribosome bound mRNA


title: RNAP_0.5X_60min_1


title: Odc_Delta_Epi-Infected2


title: LV_CAV_1


title: KO IFNa+ RUX 3

city: Hannover

first: Frank

last: Pessler

state: Niedersachsen

address: Feodor Lynen Str. 7

country: Germany

institute: Twincore

hyb_protocol: Hybridization was done for 16 hrs at conditions recommended by the manufacturer. Clariom™ S  chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000. Image analysis was done by Affymetrix® GeneChip® Command Console® Software (AGCC) and  Affymetrix® Expression Console™ Software

data_processing: Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions.

label: biotin

source_name: iPSC derived endothelial cells

label_protocol: Complementary RNA (cRNA) amplification and coversion to biotinylated double-stranded cDNA (ds-cDNA) was done by Clariom™ S Pico Assay, human Affymetrix protocol from10 ng total RNA (GeneChip® Pico UserGuide 703308 Rev. 4 Affymetrix).

growth_protocol: Endothelial cells were cultured in fibronectin coated 6-well plates.

extract_protocol: mRNA was extracted and purified from endothelial cells using MN NucleoSpin RNA kit.

treatment_protocol: Endothelial cells  were stimulated with interferon-a for 8 hours and treated with IA, DI, 4OI and RUX for 16 hours.

tag: genotype/variation

value: ISG15 KO

value: 1 uM RUX


title: Flox-Infected4

value: Flox


title: RV_CAV_3


title: RV_Control_3

value: control


title: RV_Control_2


title: Flox-Infected3


title: KOVEHIP6


title: WTDHPGIP2

value: WT


title: Flox-Infected2


title: KOVEHIP2


title: Flox-Infected1


title: Odc_Delta_Epi-Uninfected4

value: No


title: KO IFNa+ RUX 1


title: KO IFNa+ RUX 2


title: RV_Control_1


title: KODHPGIP4

value: DHPG


title: KODHPGIP5


title: mRNA-seq data HCT116 DROSHA-KO miR-148a-3p, rep 3

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with miR-148a-3p, replicate 3

data_processing:
The sequencing reads of mRNA were also adapter-trimmed and refined by cutadapt (Martin 2011) (-a 'A{18}AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC') and  FASTX-Toolkit (fastq_quality_filter -q 30 -p 70,  http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.14), respectively. The resulting sequencing reads were mapped to the human genome (GRCh38) using STAR, which was set to permit splice junction mapping (Dobin et al., 2013). Mapped reads were labeled using the human gene transfer format (GTF) file downloaded from Ensembl. Read distribution across the gene body was obtained using RSeQC (Wang et al., 2012).
The DNA libraries of small RNAs were sequenced by Illumina Nextseq 500. The resulting DNA sequencing reads were processed by cutadapt (Martin 2011) (-a AGATCGGAAGAG CACACGTC -A GATCGTCGGACTGTAGAACTCTGAAC), removing the adaptes. Next, the sequencing reads were refined by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.14) (fastq-join, fastq_quality_filter -q 30 -p 90), which merged pair-end reads, and discarded low quality. The refined sequencing reads were finally aligned to the human genome (GRCh38) using Bowtie2, which was set to allow unmatched nucleotides only at their 3'-end (Langmead and Salzberg 2012). The aligned reads were annotated using the miRNA annotation data from miRBase version 22 (Kozomara et al., 2019).
Assembly: human genome (GRCh38)
Supplementary files format and content: Bed files containing read count of each mRNA or miRNA

source_name: HCT116 DROSHA-KO cells

growth_protocol: The parental HCT116 and HCT116 DROSHA-KO cells were cultured in McCoyʼs 5A medium (Gibco, 16600082) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells by using 1 mL TRIzol Reagent (Invitrogen, 15596018) per 10^6 cells following the manufacturer's mannual.
Transfected cells were harvested 48 h post-transfection and total RNA was extracted using Trizol (Ambion, #15596018). Collibri™ 3' mRNA Library Prep Kit for Illumina (Invitrogen, #A38110024) was used for library preparation. In brief, 500 ng of extracted total RNA were reverse-transcribed with the oligodT-containing reverse primers, specifically targeting polyA-RNAs, generating cDNAs. RNAs were then degraded by the RNA removal reagents at 95ºC. The complementary strands of cDNAs were then synthesized with the random forward primers in one-cycle PCR reaction. The resulting double-stranded DNAs were then purified using magnetic beads and amplified with a pair of primers containing i5 and i7 indexes to generate the DNA libraries. The concentration and size distribution of the DNA libraries were examined by Qubit dsDNA HS Assay Kit (Invitrogen, #Q32854) and Fragment Analyzer system, respectively. Finally, the examined DNA libraries were subjected to the next-generation sequencing (NGS).  The small RNA construction and analysis were performed similarly as previously described (Li et al., 2020a, Nguyen et al., 2022). In brief, the small RNA sequencing libraries were constructed from total RNA samples isolated from HCT116 cells by using the TruSeq Small RNA Library Prep Kits (Illumina). The DNA libraries of small RNAs were sequenced by Illumina Nextseq 500.

tag: cell line

value: HCT116 DROSHA-KO

tag: transfection


title: KOVEHIP3


title: small RNA sequencing data, HCT116 wild-type

description:
endogenous small RNAs
small RNA sequencing library of HCT116 cells


title: Odc_Delta_Epi-Uninfected2


title: mRNA-seq data HCT116 DROSHA-KO miR-148a-3p, rep 2

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with miR-148a-3p, replicate 2


title: Odc_Delta_Epi-Uninfected3


title: Odc_Delta_Epi-Uninfected1


title: mRNA-seq data HCT116 DROSHA-KO miR-148a-3p, rep 1

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with miR-148a-3p, replicate 1


title: KO IFNa+ 4OI 3

value: 25 uM 4OI


title: mRNA-seq data HCT116 DROSHA-KO control miRNA, rep 3

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with control miRNA, replicate 3

value: control miRNA


title: KODHPGIP6


title: KO IFNa+ DI 3

value: 0.5 mM DI


title: KODHPGIP3


title: KODHPGIP2


title: KO IFNa+ 4OI 2


title: KO IFNa+ 4OI 1


title: KO IFNa+ DI 1


title: mRNA-seq data HCT116 DROSHA-KO control miRNA, rep 2

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with control miRNA, replicate 2


title: KO IFNa+ DI 2


title: KO IFNa+ IA 3

value: 10 mM IA


title: KO IFNa+ IA 2


title: Flox-Uninfected2

value: Gastric tissue


title: Flox-Uninfected4


title: WTVEHIN1

value: Input

value: Hippocampal slice


title: mRNA-seq data HCT116 DROSHA-KO control miRNA, rep 1

description:
endogenous mRNAs
mRNA tail cloning of HCT116 DROSHA-KO cells transfected with control miRNA, replicate 1


title: Flox-Uninfected3


title: ORmusRNAseqHOM4

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: bulk RNAseq

data_processing:
Bulk RNAseq:
fastq reads were trimmed from the adapter with cutadapt, and aligned to the genome with STAR_2.5.2b. Read count was also performed with STAR
MARSseq:
fastq reads were trimmed from the adapter with cutadapt, and aligned to the genome with STAR_2.5.2b. Umi reduction was performed with custom home script followed by read count with htseq-count
scRNAseq:
Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.).
Genome_build: mm10
Supplementary_files_format_and_content: MEX format file with the scRNAseq feature cellular barcodes
Supplementary_files_format_and_content: tsv file with the scRNAseq feature list
Supplementary_files_format_and_content: tsv file with the scRNAseq cellular barcodes
Supplementary_files_format_and_content: Matrix table with the raw gene counts for the bulk RNAseq and for the MARSseq experiments

source_name: Hnrnpu mutant

growth_protocol: For scRNA seq, cortices of E13 embryos were dissected in oxygenated dissection media (cold L15 supplemented with Glucose (0.6%)). After meninges removal, the cortices were mechanically dissociated and immediately plate in low adherence plates in NeuroBasal media containing B27 (x1) GlutaMAX (x1) Gentamicin (25ug/ml), EGF (20ng/ml), bFGF (20ng/ml) and Heparin (2ug/ml).

extract_protocol:
For the Bulk MARS-Seq and total RNAseq experiments E13 embryos were removed and their cortices dissected in cold PBS and immediately flash frozen in liquid nitrogen and kept in -80C until RNA extraction. RNA was harvested using RNeasy Mini kit, Quiagen
The 10x Genomics© Chromium system was used to capture 5000 single cells. The sequencing library was generated using the 10x Genomics© Single Cell 3′ Solution kit and subjected to Illumina NextSeq 500.
Bulk MARS-Seq library preparation was done according to MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9, Keren-Shaul et al. 2019 Nature Protocols) and sequenced using NextSeq 500 High Output Kit v2.0  75 Cycles (Illumina).
For the Bulk RNA-Seq libraries we applied ribosomal RNA-depletion using Illumina's RiboZero, followed by library preparation with Illumina's TruSeq Stranded Total RNA library preparation kit.
libraries were sequenced using NextSeq 500/550 High Output Kit v2.0  75 Cycles (Illumina)

treatment_protocol: After two days in culture, Neurospheres were dissociated with Accutase, washed with OptiMEM and mixed with a DNA solution (4ug of each pX330 CRISPR/CAS9 plasmid, 1ug of pCAG::GFP). Dissociated cells (1-2x106) were electroporated in 2mm cuvettes, in Nepa21 Electroporator (poring parameters: 2x150V, 3ms long pulses, with a 50ms interval and 10% decay rate. Transfer: 5x20 volts pulses, 50ms long, with 50ms intervals and 40% decay rate. Cells were collected 24 hours post electroporation, dissociated using Accutase and passed through a 40 micron strainer.

tag: cell type

value: E13 embryo dissected cortices

value: mixed

value: embryonic mouse cortex

tag: age

value: Emx1 Cre/+, Hnrnpu fl/fl


title: WTDHPGIN2

data_processing:
Filtering and QC were performed by the sequencing facility
RNA-seq reads were aligned to the GRCm39 genome assembly using STAR version 2.7.1a
GRCm39
Assembly: count files were generating using feature counts


title: KO IFNa 3

value: ISG15 KO

value: IFNa


title: SARS-CoV-2-Spike reactive B cells, healthy donor 8

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

data_processing:
Demultiplexing of raw base call (BCL) files, alignment, read filtering, barcode and UMI counting of the gene expression and feature barcode (10 hashtag oligos (HTOs) to discriminate individual donors and two antibody-derived tags (ADTs) for IgD/CD27 phenotyping) libraries was performed with the 10X Genomics Cell Ranger analysis pipeline using ‘cellranger count’ (Cell Ranger v4.0.0). Sequence assembly of the V(D)J library was performed using ‘cellranger vdj’ (Cell Ranger v4.0.0).
During sequencing, Read 1 was assigned 28 base pairs and was used for identification of the Illumina library barcodes, cell barcodes and UMIs. Read 2 was used to map to the human reference transcriptome (GRCh38, version 3.0.0) and the Cell Ranger human V(D)J reference (GRCh38, version 5.0), respectively
Filtered feature-barcode matrices were imported in R (version 4.0.3) using the Seurat package (version 4.0.2). HTO and ADT UMI counts were normalized using centered log ratio (CLR) transformation. The Seurat function ‘MULTIseqDemux’ was used to demultiplex samples from the 10 healhy donors using the HTOs and identify singlets, doublets and negative cells (McGinnis et al. 2019, Nat Methods 16, 619–26).
RESEDA (https://bitbucket.org/barbera/reseda/;commit 8f12c292cf6b7f05d510b20ce8c7e8655f080a6e) was used to further analyze the BCR repertoire. Sequences assembled by Cell Ranger v4.0.0 were aligned to the IMGT gene database (version Nov 2015)(Giudicelli et al. 2005, Nucleic Acids Research 33 (Database issue): D256–61) with BWA v0.7.12 (default settings) (Li and Durbin 2010, Bioinformatics 26 (5): 589–95). Variants were called with samtools (v1.7) mpileup (Li et al. 2009, Bioinformatics 25 (16): 2078–79) and VarScan v2.3.7 (Koboldt et al. 2009,Bioinformatics 25 (17): 2283–85) with minimum coverage set to 1 read to avoid missing mutations from antibody parts covered by a single sequence read. Consequently, any differences with respect to the IMGT sequences were considered as SHM. The CDR3 sequences were determined by translating the nucleotide sequences to peptide sequences and searching for conserved motifs in the V and J genes. The information from RESEDA was merged with the results obtained with Seurat.
Genome_build: GRCh38 (refdata-cellranger-GRCh38-3.0.0 and refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0)
Supplementary_files_format_and_content: Cell Ranger filtered counts for gene expression (countsGEX.tab), HTO (countsHTO.tab) and ADT (countsADT.tab) libraries in tab delimited format. Suppl_GEX_HTO_ADT_VDJ_withRESEDA.xlsx: combined file linking information from Seurat and RESEDA.

source_name: SARS-CoV-2-Spike reactive B cells

extract_protocol:
Single cell suspensions were kept at 4°C and processed within 2 h upon completion of single cell sorting. Cells were then filtered to prevent clumping and counted to assess cell integrity and concentration. Out of 10,000 cells that were sorted, approximately 8,000 cells were loaded. Single-cells were embedded in gel beads-in-emulsion (GEMs) and generation of barcoded cDNA was performed on a 10X Genomics Chromium Controller, following the 10X Genomics v1.1 single-cell V(D)J Next GEM with Feature Barcoding technology for cell surface protein chemistry.
Sequencing libraries were prepared following standard 10X Genomics protocols, generating a transcriptome, cell surface protein marker and a V(D)J library from each experiment. The cDNA libraries were paired-end sequenced on an Illumina NovaSeq S4 with a 2x150 bp Illumina kit.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll-Paque Plus. Isolated PBMCs were cryopreserved at -80°C for future usage. B cells were magnetically enriched  from 4×10^7 PBMCs of 10 healthy donors. Enriched B cells were stained with Human TruStain FcX Fc Blocking Reagent (BioLegend, 422302) for 10 min at 4 °C. For each donor a mix of Abs linked to feature barcodes, containing one specific hashtag barcode together with CD27 and IgD, was centrifuged at 14,000g at 4 °C for 10 min and supernatant harvested. Barcoded antibody mix, anti-CD19-AF700, Live/DEAD dye, and labelled SARS-CoV-2 S (AF647 and BV421) were added to the cells and stained for 30min at 4 °C. Cells were then washed twice and resuspended in FACS buffer. Live B cells positives for the SARS-CoV-2 S protein (AF647 and BV421) were bulk sorted, for a total of 10,700 cells, and used for downstream 10X Genomics analysis

tag: status

value: healthy donor

value: B cells

tag: Sex

value: M

tag: hto id


title: SARS-CoV-2-Spike reactive B cells, healthy donor 7

value: F


title: WTVEHIN3

source_name: Hippocampal slice

value: Vehicle

value: WT


title: WTDHPGIN3

value: DHPG


title: WTVEHIN2


title: SARS-CoV-2-Spike reactive B cells, healthy donor 10


title: SARS-CoV-2-Spike reactive B cells, healthy donor 9


title: Flox-Uninfected1

value: No

value: Flox


title: ORmusRNAseqHOM3

description: bulk RNAseq


title: WTDHPGIN1

value: Input


title: SARS-CoV-2-Spike reactive B cells, healthy donor 6


title: ORmusRNAseqHOM1

description: bulk RNAseq


title: KO IFNa+ IA 1

value: 10 mM IA


title: KO IFNa 2


title: KO con 3

value: Control


title: SARS-CoV-2-Spike reactive B cells, healthy donor 5


title: KO con 2


title: ORmusRNAseqHET4

description: bulk RNAseq

source_name: Hnrnpu Het

value: E13 embryo dissected cortices

value: mixed

value: Emx1 Cre/+, Hnrnpu +/fl


title: ORmusRNAseqHET3

description: bulk RNAseq

value: embryonic mouse cortex


title: KO con 1

value: ISG15 KO


title: SARS-CoV-2-Spike reactive B cells, healthy donor 4

value: healthy donor


title: KOVEHIN2

value: KO (Fmr1-/y)

value: Hippocampal slice


title: KO IFNa 1

value: IFNa


title: KODHPGIN3


title: WT IFNa+ RUX 3

value: 1 uM RUX


title: BRCA1+/- Fe-NTA 3w injected kidney cortex 3

value: Kidney cortex

value: Jcl:SD BRCA1+/-


title: ORmusRNAseqWT3

description: bulk RNAseq

value: Emx1 Cre/+, Hnrnpu +/+


title: KODHPGIN2

value: DHPG


title: ORmusRNAseqHET1

description: bulk RNAseq


title: WT IFNa+ RUX 1

value: WT


title: KOVEHIN3

value: Input

value: Vehicle


title: KODHPGIN1


title: MSC/AVIL-B3

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 345 Crispell Dr,  Charlottesville

institute: University of Virginia

data_processing:
STAR aligner (version 020201) with default parameters was used to align the raw reads to human genome (hg38).
featureCounts software (version 1.6.2) was used to get raw gene counts from bam file obtained by running STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

source_name: MSC/AVIL

growth_protocol: MEM Alpha medium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AVIL virus infected MSC cells, and use G418 selet stable cell line.

value: Mesenchymal Stem Cells

value: AVIL overexpress in MSC


title: ORmusRNAseqWT2

description: bulk RNAseq

value: E13 embryo dissected cortices

value: mixed


title: WT IFNa+ RUX 2


title: ORmusRNAseqHET2

description: bulk RNAseq

value: embryonic mouse cortex

value: Emx1 Cre/+, Hnrnpu +/fl


title: SARS-CoV-2-Spike reactive B cells, healthy donor 1

value: healthy donor

value: B cells

value: F


title: C3.1_-pTX-long-127860

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

data_processing:
RNA-seq reads were first trimmed using trimgalore v0.5.0 and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (rDNA, mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) and parameter -s 0. Differential gene-expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Assembly: mm10
Supplementary files format and content: tsv of read counts per gene

source_name: stem cells

extract_protocol:
Smart-Seq protocol
Smart-Seq
Bulk RNA-seq

value: stem cells

tag: sorting definition cdx2-gfp expression

value: no-sort

tag: culture condition

value: pTX-long


title: WT IFNa+ 4OI 3

value: 25 uM 4OI


title: SARS-CoV-2-Spike reactive B cells, healthy donor 2


title: KOVEHIN1

first: Emily

last: Osterweil

address: Hugh Robson Building, 15 George Square

value: KO (Fmr1-/y)

value: Hippocampal slice


title: scRNA Hnrnpu KO Neurospheres

description: 10x Genomics

source_name: Hnrnpu sgRNA treated mouse Neurospheres

value: Cultured mouse Neurospheres

value: ICR

value: E13+2DIV (EP)+1DIV

value: wild type


title: SARS-CoV-2-Spike reactive B cells, healthy donor 3


title: ORmusRNAseqWT1

description: bulk RNAseq

value: E13 embryo dissected cortices

value: Emx1 Cre/+, Hnrnpu +/+


title: C3.1_-pTX-127857

value: pTX


title: MSC/AVIL-B2

value: Mesenchymal Stem Cells

value: AVIL overexpress in MSC


title: C3.1_-pTX-long-127859


title: batch 21b, negative control 4x 10 nM (21b_NegCtrl_4x)

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Expression values were computed using STAR and featureCounts
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: text files holding raw counts

source_name: spleen and lymph nodes

growth_protocol: The spleen and lymph nodes from wild-type C57BL/6 female mice were used to isolate naïve CD4+ T cells (magnetic beads). Cells were put in culture and allowed to differentiate into Th2 cells over 4 days, in RMPI-1640 containing FCS, penicillin and  streptomycin, in the presence of α-CD28 and α-CD3 (coating wells), IL-4, IL-2, and α-IFN-γ. After 72 h, culture media contained only IL-2 and α-IFN-γ until restimulation.

extract_protocol:
After restimulation with α-CD3 for 4 h, RNA was collected using the Rneasy Plus RNA extraction kit, including a gDNA elimination step.
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

treatment_protocol: 1x 50 nM at experiment start, or 4x 10 nM at 0 h, 24 h, 48 h, and 72 h.

value: spleen and lymph nodes

value: differentiating CD4+ T cell (Th2)

value: universal negative control, 4x


title: WT IFNa+ 4OI 1

value: WT


title: MSC/AVIL-B1


title: MSC/CT-A2

source_name: MSC/CT

value: Control cells


title: C3.1_-pTX-long-127858

value: stem cells

value: no-sort

value: pTX-long


title: MSC/CT-A3


title: batch 21b, miR-71, 4x 10 nM (21b_miR71_4x)

value: hpo-miR-71-5p, 4x


title: batch 21b, miR-81, 4x 10 nM (21b_miR81_4x)


title: C3.1_-pTX-127856


title: WT IFNa+ 4OI 2

value: 25 uM 4OI


title: MSC/CT-A1


title: C3.1_-TX-127854

value: TX


title: batch C, miR-1, 1x 50 nM (C9)

value: hpo-miR-1-3p, 1x


title: iPSC derived KO macrophages interferon-a+ 4-octyl itaconate

description:
Single cell transcriptome from total 2279 human-iPSC derived KO macrophages IFNa stimulated and 4-octyl itaconate treated
all_samples_seurat.rds/stim/KO_4OI

data_processing:
Cell Ranger 1.3 (http://10xgenomics.com) was used to process Chromium  single  cell  3’  RNA-seq  output
cellranger count aligned to the pre-built human reference genome (hg19, GRCh38)
Raw counts were normalized by the global-scaling normalization method “LogNormalize”.
Principal component analysis score was used to determine the ‘dimensionality’ of all cells.
Scatter plots were obtained using the UMAP method. Cell clusters were identified as different cell populations based on the expression of recently published canonical markers
Genome_build: human reference genome (hg19, GRCh38)
Supplementary_files_format_and_content: filtered_feature_bc_matrix, tsv and mtx files
Supplementary_files_format_and_content: Seurat object

source_name: iPSC derived macrophages

extract_protocol:
Cells were stained with propidium iodide and dead cells and doublets were removed by FACS. Live cells (including those undergoing apoptosis) were used to make single cell suspensions using the 10x Genomics platform.
The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer’s instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode.
The  cDNA  libraries  were  constructed  using  the  10x  ChromiumTM  Single  cell  3’  Library  Kit  according  to  the  manufacturer’s  original  protocol.   Libraries were sequenced on an Illumina NovaSeq 6000 2x50 paired-end kits using the following read length

treatment_protocol:
Embryoid bodies were prepared from hiPSCs and macrophages were harvested from embryoid bodies. Macrophages were used for further experiment.
WT and ISG15 KO macrophages were seeded in 6-well plate and stimulated with 1000 IU/ ml of IFN-a for 8 hours and treated with itaconic acid 10 mM, 4-octyl itaconate 25 µM and ruxolitinib 1 µM for 16 hours.

value: Human iPSC derived cells

value: ISG15 KO

value: IFNa stimulated+ 4OI treated


title: WT IFNa+ IA 2

value: 10 mM IA


title: WT IFNa+ IA 3


title: WT IFNa+ DI 3

value: 0.5 mM DI


title: batch C, combo, 4x 10 nM (C8)

value: spleen and lymph nodes

value: combination miR-71, miR-10021, miR-100, 4x


title: WT IFNa+ DI 2


title: iPSC derived KO macrophages interferon-a+itaconic acid

description:
Single cell transcriptome from total 2378 human-iPSC derived KO macrophages IFNa stimulated and itaconic acid treated.
all_samples_seurat.rds/stim/KO_IA

value: IFNa stimulated+ IA treated


title: F4-GFP_iCDX2_pTX-long-127850


title: iPSC derived KO macrophages interferon-a

description:
Single cell transcriptome from total 2107 human-iPSC derived KO macrophages IFNa stimulated.
all_samples_seurat.rds/stim/KO_IFN

value: IFNa stimulated


title: batch C, combo, 1x 50 nM (C7)

value: differentiating CD4+ T cell (Th2)

value: combination miR-71, miR-10021, miR-100, 1x


title: WT IFNa+ DI 1

value: WT


title: iPSC derived KO macrophages control

description:
Single cell transcriptome from total 2364 human-iPSC derived KO macrophages untreated.
all_samples_seurat.rds/stim/KO_CT

value: untreated


title: C3.1_-TX-127852

value: stem cells

value: no-sort


title: WT IFNa 3

value: IFNa


title: batch 21b, lipofectamine 4x (21b_Lipo_4x)

value: Lipofectamine RNAiMax, 4x


title: WT IFNa+ IA 1


title: C3.1_-pTX-127855

value: pTX


title: iPSC derived WT macrophages interferon-a+ 4-octyl itaconate

description:
Single cell transcriptome from total 3045 human-iPSC derived WT macrophages IFNa stimulated and 4-octyl itaconate treated
all_samples_seurat.rds/stim/WT_4OI

value: Human iPSC derived cells


title: C3.1_-TX-127853

value: TX


title: F4-GFP_iCDX2_pTX-long-127851

value: pTX-long


title: iPSC derived WT macrophages interferon-a+ ruxolitinib

description:
Single cell transcriptome from total 2114 human-iPSC derived WT macrophages IFNa stimulated and ruxolitinib treated
all_samples_seurat.rds/stim/WT_RUX

value: IFNa stimulated+ RUX treated


title: batch C, miR-81, 4x 10 nM (C6)

value: spleen and lymph nodes


title: batch C, miR-81, 1x 50 nM (C5)


title: WT con 2

value: Control


title: iPSC derived WT macrophages interferon-a+itaconic acid

description:
Single cell transcriptome from total 2590 human-iPSC derived WT macrophages IFNa stimulated and itaconic acid treated.
all_samples_seurat.rds/stim/WT_IA

value: IFNa stimulated+ IA treated


title: WT IFNa 2


title: batch C, miR-71, 4x 10 nM (C4)

value: hpo-miR-71-5p, 4x


title: batch C, miR-100, 4x 10 nM (C2)

value: differentiating CD4+ T cell (Th2)


title: batch C, miR-71, 1x 50 nM (C3)

value: hpo-miR-71-5p, 1x


title: WT IFNa 1

value: WT


title: WT con 3


title: F4-GFP_iCDX2_pTX-long-127849


title: F4-GFP_iCDX2_HI_FGF-127848


title: F4-GFP_iCDX2_HI_FGF-127847


title: EOC_63_S28

city: columbia

first: Hongyu

last: Liu

state: mo

address: 920 east campus drive.

institute: university of missouri

data_processing:
We performed pair-end sequencing on each sample, FastQC (v 0.11.9) and MultiQC (v 1.10.1) were used to evaluate the quality of the sequence. Trimmomatic (v 1.10.1) was used to remove adapters and low-quality bases from the reads.
Then they aligned to the bovine genome (ARS-UCD1.2.103) by applying STAR aligner (v 2.7.0e) with an average unique mapping rate of 88.54% and a average read length of 201 bp. Gene quantification were calculated by using StringTie package (v 2.1.3b). Assembled transcripts for each sample were merged and created a uniform set of transcripts for all samples. Counts calculate for the samples is provided by the StringTie python script. Count matrix were used to perform differential gene analysis in R (version 4.0.2) using package DESeq2(v 1.30.1). Design formula (sample ~ condition) as a factor to account for variation in the data.
Assembly: ARS-UCD1.2.103
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: Endometrial explant

extract_protocol:
Total RNA was isolated from frozen explant endometrium (∼40 mg) by homogenizing in 1 mL of TRIzol reagent and a Qiagen RNeasy Mini Kit (Qiagen). RNA quantity and quality were determined using an Agilent Bioanalyzer (Agilent Technology). To eliminate DNA contamination, samples were treated with Dnase. RNA concentrations and integrity were determined by quantitative high-sensitivity RNA analysis on the Fragment Analyzer instrument (Catalog # DNF-472, Advanced Analytical Technologies, Inc., Ankeny, IA).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Sequencing was performed on an Illumina NextSeq 500 sequencer to a depth of 30–40 million raw reads per sample.

treatment_protocol: Culture wells with endometrial explants placed epithelial side up were incubated in 5% CO2 in air at 38.8◦C for 4 h. The media was aspirated and replaced with 1 mL of pre-warmed fresh media (RPMI with 1% ABAM). Then, eight explants from each heifer were cultured individually in RPMI for 6 h in 5% CO2 in air at 38.8◦C with either (i) nothing (control; n = 4), (ii) 100 ng/mL recombinant ovine IFNT (provided by G. Charpigny, INRAE, France; n = 4), or (iii) a single Day 15 conceptus from one of each of the six bulls (HF: n=12; LF: n=12).

value: Endometrial explant

tag: group

value: control

tag: explant donor heifer

value: Heifer 4


title: iPSC derived WT macrophages control

description:
Single cell transcriptome from total 1894 human-iPSC derived WT macrophages untreated.
all_samples_seurat.rds/stim/WT_CT

value: untreated


title: batch B, lipofectamine, 4x (C14)

value: Lipofectamine RNAiMax, 4x


title: batch C, untreated control (C15)

value: no treatment


title: F4-GFP_iCDX2_HI_FGF-127846

value: stem cells

value: no-sort


title: batch B, lipofectamine, 1x (C13)

value: Lipofectamine RNAiMax, 1x


title: iPSC derived WT macrophages interferon-a

description:
Single cell transcriptome from total 741 human-iPSC derived WT macrophages IFNa stimulated.
all_samples_seurat.rds/stim/WT_IFN

value: Human iPSC derived cells

value: IFNa stimulated


title: F4-GFP_iCDX2_TX_DOX-127844


title: EOC_60_S31

value: low fertility bull


title: KO_untreated3

description: deseq2 normalized counts.csv

data_processing:
Large sets of high‐throughput sequencing reads were mapped against the Homo sapiens hg38 reference genome via STAR 2.7.3a tool.
DESeq2 was used to normalize the counts of each gene to account for differences in sequencing depth and low count variability. The DESeq2 normalization metric is based on the median of ratios method.
Following normalization, DESeq2 was run in a pairwise manner, identifying significantly differentially expressed genes with higher levels of expression in the unstimulated group in comparison to the stimulated group of both WT and KO cells.
Genome_build: human reference genome (hg19, GRCh38)
Supplementary_files_format_and_content: normalized count csv file

growth_protocol: Embryoid bodies were prepared from hiPSCs and macrophages were harvested from embryoid bodies. Macrophages were used for further experiment.

extract_protocol:
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 5 x107 reads per RNA sample.

treatment_protocol: WT and ISG15 KO macrophages were seeded in 6-well plate and stimulated with 1000 IU/ ml of IFN-a for 24 hours.

value: ISG15 KO

value: KO


title: KO_IFNa1

description: deseq2 normalized counts.csv


title: KO_untreated2

description: deseq2 normalized counts.csv


title: F4-GFP_iCDX2_TX_DOX-127843


title: F4-GFP_iCDX2_TX_DOX-127845


title: EOC_64_S40

value: interferon tau


title: EOC_62_S29


title: WT con 1

value: Control


title: batch C, negative control, 4x 10 nM (C12)

value: spleen and lymph nodes

value: differentiating CD4+ T cell (Th2)

value: universal negative control, 4x


title: WT_IFNa3

description: deseq2 normalized counts.csv

value: WT


title: F4-GFP_iCDX2_pTX-127842

value: pTX


title: EOC_57_S34

value: Endometrial explant

value: high fertility bull

value: Heifer 4


title: EOC_56_S35

value: Heifer 3


title: F4-GFP_iCDX2_pTX-127840

value: stem cells

value: no-sort


title: EOC_61_S30


title: batch C, miR-1, 4x 10 nM (C10)

value: hpo-miR-1-3p, 4x


title: KO_untreated1

description: deseq2 normalized counts.csv

value: Human iPSC derived cells

value: untreated


title: batch C, negative control, 1x 50 nM (C11)

value: universal negative control, 1x


title: EOC_59_S32


title: F4-GFP_iCDX2_TX-127839

value: TX


title: batch B, miR-1, 1x 50 nM (B9)

value: hpo-miR-1-3p, 1x


title: WT_IFNa1

description: deseq2 normalized counts.csv

value: IFNa stimulated


title: batch B, combo, 4x 10 nM (B8)

value: spleen and lymph nodes

value: differentiating CD4+ T cell (Th2)

value: combination miR-71, miR-10021, miR-100, 4x


title: F4-GFP_iCDX2_pTX-127841

value: pTX


title: F4-GFP_iCDX2_TX-127837


title: EOC_55_S36

value: Endometrial explant

value: control


title: WT_untreated3

description: deseq2 normalized counts.csv

value: WT


title: KO_IFNa2

description: deseq2 normalized counts.csv

value: ISG15 KO

value: KO


title: EOC_50_S41

value: high fertility bull

value: Heifer 3


title: EOC_48_S43

value: interferon tau

value: Heifer 2


title: EOC_49_S42


title: G4_ES-127834

value: stem cells

value: no-sort


title: batch B, miR-71, 4x 10 nM (B4)

value: hpo-miR-71-5p, 4x


title: G4_ES-127835


title: WT_IFNa2

description: deseq2 normalized counts.csv

value: Human iPSC derived cells

value: IFNa stimulated


title: EOC_52_S39

value: low fertility bull


title: C3.1_no-sort-127833

value: TX


title: EOC_53_S52


title: batch C, miR-100, 1x 50 nM (C1)

value: spleen and lymph nodes

value: differentiating CD4+ T cell (Th2)


title: siCTRL_4

city: Portland

first: Jonathan

last: Brody

state: OR

address: 2730 S. Moody Ave CL6JB

institute: Oregon Health & Science University

data_processing:
Base calling was done by Novogene Co., Ltd. (CASAVA)
Conversion to FASTQ was done by Novogene Co., Ltd. (bcl2fastq2)
Paired-end fastq sequences were trimmed using trim-galore ver 0.6.3 and default parameters.
Pseudoalignment was done  with kallisto ver 0.44.0 using genome assembly GRCh38.p5 gencode v24 annotation, default parameters were used other than the number of threads.
The Bioconda package bioconductor-tximport ver 1.12.1 was used to create gene level counts and abundances (TPMs).
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: tab-delimited text files with gene level counts and TPM values from the kallisto based pipeline described above.

growth_protocol: Cells were cultured in standard DMEM(+++) with 10% FBS, 1% Pen-Strep, 1%L-glutamine

extract_protocol:
RNA was extracted using Qiagen RNAseEasy Kit as per manufacturer's instructions
Libraries were constructed by Novogene Co., Ltd.

treatment_protocol: Cells were transfected using [30nM] siRNAs complexed in RNAiMax

value: siCTRL


title: batch B, combo, 1x 50 nM (B7)

value: combination miR-71, miR-10021, miR-100, 1x


title: batch B, miR-81, 1x 50 nM (B5)


title: batch B, miR-100, 4x 10 nM (B2)


title: siYAP1_3


title: EOC_51_S27

value: Endometrial explant


title: siHuR_4

value: siHuR


title: WT_untreated1

description: deseq2 normalized counts.csv

value: WT

value: untreated


title: siHuR_3


title: C3.1_LHL-127830

value: LHL


title: WT_untreated2

description: deseq2 normalized counts.csv


title: EOC_44_S47

value: Heifer 2


title: batch B, miR-81, 4x 10 nM (B6)


title: EOC_46_S45


title: G4_ES-127836

value: stem cells


title: siYAP1_4


title: batch B, lipofectamine, 1x (B13)

value: Lipofectamine RNAiMax, 1x


title: C3.1_LLL-127832

value: LLL


title: C3.1_LLH-127831

value: LLH


title: siHuR_2


title: F4-GFP_iCDX2_TX-127838

value: no-sort


title: batch B, miR-71, 1x 50 nM (B3)

value: hpo-miR-71-5p, 1x


title: EOC_43_S48

value: high fertility bull


title: siCTRL_2


title: EOC_41_S50


title: C3.1_HLH-127827

value: HLH

value: TX


title: EOC_47_S44

value: control


title: batch B, negative control, 4x 10 nM (B12)

value: spleen and lymph nodes

value: differentiating CD4+ T cell (Th2)

value: universal negative control, 4x


title: batch B, untreated control (B15)

value: no treatment


title: batch B, miR-1, 4x 10 nM (B10)

value: hpo-miR-1-3p, 4x


title: batch B, lipofectamine, 4x (B14)

value: Lipofectamine RNAiMax, 4x


title: EOC_42_S49

value: Endometrial explant

value: Heifer 2


title: EOC_40_S51

value: interferon tau

value: Heifer 1


title: C3.1_HLL-127828

value: stem cells

value: HLL


title: batch B, negative control, 1x 50 nM (B11)

value: universal negative control, 1x


title: siYAP1_2


title: EOC_45_S46

value: low fertility bull


title: siCTRL_3

value: siCTRL


title: C3.1_HHL-127826

value: HHL

value: TX


title: batch B, miR-100, 1x 50 nM (B1)

value: spleen and lymph nodes


title: siCTRL_1


title: C3.1_LHH-127829

value: LHH


title: C3.1_LL-127824

value: LL


title: C3.1_LH-127823

value: LH


title: siHuR_1

value: siHuR


title: JH58_WT_female_lacrimal_scRNAseq_R4

city: Baltimore

first: Jacob

middle: S

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Dissociated lacrimal gland cells.

data_processing:
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v3.0.1; 10x Genomics) with default settings. Cell barcodes were determined using the DropletUtils R/Bioconductor package. The normalized gene x cell matrix was used as input for the Monocle R/Bioconductor package (Trapnell et al., 2014). Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis. For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP. Initial clusters were identified from the 2-D embedding using k-means clustering. Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Adult dissociated WT lacrimal gland

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Dissociated single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits v2 (10X Genomics, Pleasanton) as per the manufacturer’s protocol. In brief, single cells were sorted into 0.4% BSA–DPBS. Approximately 14,000 single retinal cells were added to a channel. The cells were then partitioned into Gel Beads in Emulsion in the 10x Genomics Chromium Controller, where cell lysis occurred.
Cell lysis was followed by barcoded oligo-DT priming and reverse transcription of poly-adenylated RNA, amplification, shearing and 5′ adaptor and sample index attachment.

tag: genotype/strain

value: WT/BALB/cJ

value: 4 months

value: Female

value: Exorbital lacrimal gland


title: JH57_WT_male_lacrimal_scRNAseq_R4

description: Dissociated lacrimal gland cells.

value: Male


title: EOC_37_S38

value: Endometrial explant

value: Heifer 1


title: ATACSeq_Non-CMS_iPSCErythroid_Hypoxia-rep3

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

description: NEBH.gappedPeak

data_processing:
ATAC-Seq data preprocessing was performed with TrimGalore (v0.6.5)!, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>20)
Trimmed reads were aligned to the hg19 human genome (1000 Genomes reference) using BBMap (v37.95) in the BBtools suite with the options maxindel=20 ambig=random
Sorting and indexing of bam files was performed with SAMTools (v1.35)
GenRich (v0.6) was used to call peaks on the ATAC-Seq data in order to determine regions of accessible chromatin, using all three replicates to generate a consensus list of peaks for each condition
Genome_build: hg19
Supplementary_files_format_and_content: gappedPeak

source_name: hiPSC-derived erythroid cells from human non-CMS cells

growth_protocol: The Non-CMS and CMS fibroblasts were derived from skin biopsies in accordance with the UC San Diego IRB approval. The iPS cell lines have been well characterized by us as described in our previous publications. In brief:  iPS cell line were generated using Retroviral vectors containing the Yamanaka factors (OCT4, cMYC, KLF4, and SOX2 human cDNAs). DNA-fingerprinting analysis and stem array, a high-resolution karyotyping as well as standard staining procedures were used to characterize the iPS cell lines. The erythroid cells were generated from these iPS using our in-vitro protocol previously described by us in detail (Azad et al. 2016).  Briefly, Human iPSC passages 9–20 were grown in Matrigel (BD)-coated dishes supplemented with mTeSR media (STEMCELL Technologies). . For all generating the errythroid cells, the cultures were started with approximately 107 iPS cells. Human iPSCs were differentiated by formation of EBs (hEB) during 27 d in a liquid culture medium on the basis of IMDM (Biochrom), 450 µg/ml holo human transferrin (Sigma-Aldrich), 10 µm g/ml recombinant human insulin (Roche), 2 IU/ml heparin, and 5% human plasma in the presence of 100 ng/ml SCF, 100 ng/ml TPO, 100 ng/ml FLT3 ligand, 10 ng/ml rhu bone morphogenetic protein 4 (BMP4), 5 ng/ml rhu VEGF (VEGF-A165), 5 ng/ml IL-3, 5 ng/ml IL-6 (PeproTech), and 3 U/ml Epo. The resulting erythroid cells were characterized by flow cytometric analysis of CD markers (Eg. CD235a).

extract_protocol:
For ATAC-Seq, transposition reactions were performed on 50,000 non-CMS and non-CMS with ARID1B KD (replicates, n = 3) hiPSC-derived erythroid cells grown under hypoxic and normoxic conditions for two weeks as previously described Buenrostro et al., 2013 (52). Briefly Cells were washed with PBS followed by lysis with cold lysis buffer. Cells were then suspended in 50 μl 1X reaction buffer. Transposase reactions were carried out at 37°C for 30 minutes and DNA was purified using ChIP DNA Clean & Concentrator kits.
DNA was amplified and library was generated using the dual barcoded primers (Illumina) using NEBNext High-Fidelity 2XPCR Master Mix for 14 cycles.

treatment_protocol: The iPSC-derived erythroid cells were exposed to normoxia or hypoxia (5% O2).

value: hiPSC-derived erythroid cells

tag: knockdown

tag: oxygen status

value: hypoxia


title: EOC_39_S14

value: control


title: EOC_38_S12

value: low fertility bull


title: C3.1_HL-127822

value: stem cells

tag: treatment

value: HL

value: TX


title: JH56_WT_female_lacrimal_scRNAseq_R3

description: Dissociated lacrimal gland cells.

tag: tissue


title: C3.1_HHH-127825

value: HHH


title: EOC_36_S3


title: ATACSeq_Non-CMS_iPSCErythroid_Hypoxia-rep2

description: NEBH.gappedPeak


title: C3.1_HH-127821

value: HH


title: EOC_35_S4

value: high fertility bull


title: ATACSeq_ARID1BKD_iPSCErythroid_Hypoxia-rep3

description: AEBH.gappedPeak

source_name: hiPSC-derived erythroid cells from human non-CMS cells with ARID1B-KD


title: ATACSeq_Non-CMS_iPSCErythroid_Hypoxia-rep1

description: NEBH.gappedPeak


title: C3.1_L-127820

value: L


title: EOC_34_S5


title: ATACSeq_ARID1BKD_iPSCErythroid_Hypoxia-rep2

description: AEBH.gappedPeak


title: JH50_NOD.H2b_male_lacrimal_scRNAseq_R2

description: Dissociated lacrimal gland cells.

source_name: Adult dissociated NOD.H2b lacrimal gland

value: 4 months


title: EOC_33_S6


title: JH48_NOD.H2b_male_lacrimal_scRNAseq_R1

description: Dissociated lacrimal gland cells.


title: ATACSeq_ARID1BKD_iPSCErythroid_Hypoxia-rep1

description: AEBH.gappedPeak


title: IMB-NR-008_HM5V5BGXC_TSC_24hours

data_processing:
To analyze CEL-Seq single cell sequencing experiments, mouse genomic sequence and annotation from NCBI GRCm38.p6 were used. Reads were trimmed using trim_galore v0.6.4 and subsequently aligned to the mouse genome (GRCm38.p6) using STAR v2.7.6a. UMI quantification and raw count matrixes generation were performed using umi_tools v1.0.1.
Assembly: GRCm38.p6
Supplementary files format and content: tsv of read counts per gene

source_name: Mouse trophoblast stem cells

extract_protocol:
CEL-Seq protocol
CEL-Seq2
Single cell RNA seq

value: Mouse trophoblast stem cells

value: removal of FGF4/TGFβ1 growth factors

tag: differentiation time

value: differentiation 24 hours


title: EOC_27_S33

value: Endometrial explant

value: Heifer 4


title: C3.1_H-127819

value: H


title: JH55_WT_male_lacrimal_scRNAseq_R3

description: Dissociated lacrimal gland cells.

value: WT/BALB/cJ

value: Male

value: Exorbital lacrimal gland


title: ATACSeq_Non-CMS_iPSCErythroid_Normoxia-rep3

description: NEBN.gappedPeak

value: hiPSC-derived erythroid cells

value: normoxia


title: ATACSeq_Non-CMS_iPSCErythroid_Normoxia-rep2

description: NEBN.gappedPeak


title: EOC_22_S37

value: low fertility bull

value: Heifer 3


title: IMB-NR-006_HM5V5BGXC_TSC_4hours

value: differentiation 4 hours


title: IMB-NR-007_HM5V5BGXC_TSC_12hours

value: differentiation 12 hours


title: JH47_WT_male_lacrimal_scRNAseq_R1

description: Dissociated lacrimal gland cells.


title: ATACSeq_Non-CMS_iPSCErythroid_Normoxia-rep1

description: NEBN.gappedPeak


title: JH46_MRL_lpr_female_lacrimal_scRNAseq_R2

description: Dissociated lacrimal gland cells.

source_name: Adult dissociated MRL/MpJ-Fas<lpr>/J lacrimal gland

value: MRL/MpJ-Fas<lpr>/J

value: Female


title: IMB-NR-005_HM5V5BGXC_TSC_0hours

value: Mouse trophoblast stem cells

value: differentiation 0 hours


title: IMB-NR-003_HM5V5BGXC_TSC_48hours

value: removal of FGF4/TGFβ1 growth factors

value: differentiation 48 hours


title: JH45_WT_female_lacrimal_scRNAseq_R2

description: Dissociated lacrimal gland cells.

value: 4 months


title: ATACSeq_ARID1BKD_iPSCErythroid_Normoxia-rep3

description: AEBN.gappedPeak


title: JH49_WT_male_lacrimal_scRNAseq_R2

description: Dissociated lacrimal gland cells.


title: JH44_MRL_lpr_female_lacrimal_scRNAseq_R1

description: Dissociated lacrimal gland cells.


title: JH43_WT_female_lacrimal_scRNAseq_R1

description: Dissociated lacrimal gland cells.


title: ATACSeq_ARID1BKD_iPSCErythroid_Normoxia-rep1

description: AEBN.gappedPeak


title: IMB-NR-001_HM5V5BGXC_TSC_36hours

value: differentiation 36 hours


title: ATACSeq_ARID1BKD_iPSCErythroid_Normoxia-rep2

description: AEBN.gappedPeak


title: 4KR 12 hr

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: LGP2-4KR Tg HEK293

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: LGP2 and LGP2-4KR Tg HEK293 cells were cultured in MEM with heat-inactivated 10% FCS in a 24-well plate.

extract_protocol: Total RNA was extracted using TRIZOL reagents according to the manufacture's protocol.

treatment_protocol: short poly I:C (LMW poly I:C) was purchased from Invivogen. 100 ng/ml of short polyI:C was trasnfected into cells using Lipofectaimin 2000 according to manufacture's protocol. 12 hr after trasnfection, total RNA was extracted.

tag: cell line background

value: Human immortalized cells

tag: genotype/variation

value: LGP2-4KR Tg

value: 100 ng/ml of short poly I:C for 12 h


title: Kai_235_rep2

status: Public on Jun 06 2022

city: Jena

first: Maximilian

last: Colatz

address: Leutragraben 1

institute: Friedrich-Schiller-University Jena

data_processing:
The reads were trimmed using prinseq (v0.20.3) with default parameters and a quality string of 20.
Mapping was done using segemehl (v0.2.0) with default parameters and an accuracy value of 80.
Bedtools intersect (v2.23.0) was used to remove remaining rRNAs to cope with overrepresentation.
Read counting was done using htseq-count (v0.6.0) with default parameters in strand-specific union mode.
The read counts were normalized by DESeq2.
Genome_build: GCA_000340785.1
Supplementary_files_format_and_content: One tab-delimited file for all samples with normalized expression values. The file contains additional information about gene names and corresponding GO terms.

organism: Cyanobacterium

source_name: Kai_235_complete cell

growth_protocol: Grown under continuous illumination.

extract_protocol:
The RNA was isolated according to Doerrich et al. (https://www.ncbi.nlm.nih.gov/pubmed/25139948)
RNA libraries were treated for rRNA depletion and the Illumina TruSeq kit was used for library construction.

tag: strain

value: Synechocystis sp. PCC 6803

tag: genotype/varaition

value: kai

tag: light period

value: light

tag: sample extraction time point


title: Kai_175_rep2

source_name: Kai_175_complete cell


title: Kai_125_rep2

source_name: Kai_125_complete cell


title: Kai_55_rep2

source_name: Kai_55_complete cell

value: dark


title: SW626.3D

city: Saugus

first: Michael

last: Raabe

address: 3214 Founders Way

institute: Massachusetts General Hospital

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

source_name: cell line

growth_protocol: For PDAC and CRC cell lines 3D media contained serum free RPMI supplemented with 20 ul/ml B27 (Invitrogen/Life Technologies), 20 ng/ml EGF (Invitrogen/Life Technologies), 20 ng/ml bFGF (Invitrogen/Life Technologies) and 1% Pen/Strep (Gibco/Life Technologies).  For EOC cell lines, standard growth media (see Supplementary Table 1 of manuscript) was used for 3D cultures in non-adherent tissue culture dishes.

extract_protocol:
RNA was isolated using Trizol reagent (ThermoFisher) or the AllPrep DNA/RNA/protein mini kit (Qiagen #80004) according to manufacturer recommendations.
Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for RNA-seq.

treatment_protocol:
OVCAR4, IGROV1, OAW28, and OVSAHO cells were plated at a density of 120,000 cells/well in 6 well tissue culture treated plates (Corning). OVCAR4 and IGROV1 cells were grown in RPMI medium and OAW28 and OVSAHO cells were grown in DMEM/F12, both containing 1% Pen/Strep and 10% FBS. After 2 days, 500 nM Negative control (Scramble) or HSATII custom designed LNA were transfected into the cells with Lipofectamine 2000 (Invitrogen/Life Technologies) following the manufacturer’s recommendations.
IGROV1, OV90, OAW28 and CaOV3 cells were plated at 300,000 cells per well in 6 well ultra-low attachment cell culture dishes (Sigma-Aldrich, Cat #CLS3471) in standard growth media.  Cells were incubated for 48-72 hours to allow tumorsphere formation, then treated with 500 nM 5-azacytidine (Sigma-Aldrich, Cat #A2385), 250 nM Trichostatin A (Sigma-Aldrich, Cat #T1952) or DMSO for vehicle control and incubated for 72 hours.

tag: cell line

tag: agent


title: RP.37


title: RP.38


title: SW620.3D


title: SW837.3D


title: RP.39


title: LGP2 0 hr

source_name: LGP2 HEK293

tag: cell type

value: LGP2 Tg


title: RP.35


title: LGP2 12 hr


title: RP.29


title: SKOV3.3D


title: RP.28


title: 4KR 0 hr


title: RP.27


title: RP.36


title: wt_125_rep2

source_name: wt_125_complete cell

value: wt


title: wt_175_rep2

source_name: wt_175_complete cell


title: wt_235_rep2

source_name: wt_235_complete cell


title: RP.26


title: wt_115_rep2

source_name: wt_115_complete cell


title: Kai_115_rep2

source_name: Kai_115_complete cell


title: RP.25


title: RP.18


title: kai_05_rep2

source_name: kai_05_complete cell


title: Kai_235_rep1


title: RP.16


title: Kai_175_rep1


title: RP.14


title: Kai_55_rep1


title: wt_05_rep2

source_name: wt_05_complete cell


title: kai_05_rep1


title: RP.15


title: Kai_125_rep1


title: PKD1


title: PKD2


title: wt_125_rep1


title: RP.13


title: PDAC2.cells.Veh.2

value: Veh


title: wt_55_rep2

source_name: wt_55_complete cell


title: wt_115_rep1


title: Kai_115_rep1


title: wt_235_rep1


title: wt_175_rep1


title: RP.17


title: wt_05_rep1


title: OVKATE.3D

value: OVKATE


title: wt_55_rep1


title: OV90


title: Panc1.DMSO

value: DMSO


title: OVCAR4.3D


title: OAW28


title: NS84.H.121418


title: NS84.BD.121418


title: OVSAHO.3D

value: OVSAHO


title: NS84.W.121418


title: NS84.Ay.121418


title: PA.1.3D


title: NS84.BI.121418


title: NS84.AS.121418


title: NS84.Av.121418


title: NS84.D2.121418


title: NS84.Au.121418


title: NS84.AO.121418


title: NS84.AM.121418


title: NX90d-1

city: changsha

first: LI

last: Biao

address: Nongda South Road

department: College of Animal Science and Technology

institute: Hunan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Sus scrofa (pig)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Ningxiang

value: spleen

tag: developmental stage

value: post natal day 90


title: NS178.OVCAR4


title: NS84.AK.121418


title: NX30d-2

value: post natal day 30


title: NS178.OVSAHO.D3


title: NS178.IGROVI.D3


title: Naive_D5_3

first: Erna

middle: A

last: van Niekerk

data_processing:
Reads were aligned to the latest mouse_mm10 reference genome using the STAR spliced read aligner.
No read trimming or filtering was done with this dataset because the quality distribution and variance appear normal.
Assembly: mm10

source_name: Primary Cortical Neurons isolated from Adult C57/BL6 mice

extract_protocol:
RNA was harvested using Agilent absolute RNA nanoprep kit (catalog #400753)
RNA libraries for RNA-seq were prepared using Nugen RNA Ultra Low Input (500 pg) + Kapa Hyper over 2 lanes by HiSeq4000.

value: primary cortical culture

value: Adult Neuron

tag: genotype

value: WT

tag: time

value: Day 5


title: Lesion_D7_1

value: Conditioning lesion

value: Day 7


title: Lesion_D5_2


title: Lesion_D5_3


title: Naive_D7_2


title: Lesion_D5_1


title: Lesion_D7_2


title: Lesion_D7_3


title: NX30d-3


title: NS178.Kumarochi


title: NX30d-1


title: Naive_D7_1


title: Naive_D5_2


title: Naive_D5_1


title: NS178.CaOV3.D3


title: Lesion_D3_3

value: Day 3