title: rep2_shRING1B_45min_atacseq

description: 04_shRING1B_E2_pooled.atac.fc.signal.bigwig

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were collected for the transposase reaction.

extract_protocol:
ATAC-seq experiments were performed as previously described (Buenrostro et al., 2013). 50,000 alive cells were used for the experiment. Samples were purified with a MinElute Reaction Cleanup kit (Qiagen cat# 28206) and DNA eluted in 10μl of EB Buffer.
The ATAC-seq library construction was performed as previously described (Buenrostro et al, 2013) with the additional following step: size selection was performed by using the AMPure XP beads (Beckman Coulter #A63881) at 1.8x the PCR volume to remove fragments smaller than 100 bp. To determine the average fragment size of each library, samples were run through a High-sensitivity DNA screentape (Agilent Technologies cat# 5067-5584) following the manufacturer’s instructions on an Agilent Technologies 2200 TapeStation machine. To determine the concentration of each library, Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific cat# Q32851) were used following the manufacturer’s instructions on a Qubit 3 fluorometer.

value: pLKO-shRING1B stable


title: WT-24 hr O3 Replicate 3

status: Public on Sep 29 2021

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Comparisons: Genotype effect & exposure effect on lung gene expression

hyb_protocol: The biotinylated RNA was fragmented and hybridized to the Affymetrix array (MOE430A) for 16 hr at 45 degree C in a hybridization oven rotating at 60 rpm. The array was washed and stained with streptavidin–phycoerythrin using an Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: WT-24 hr O3_homogenized mouse lung tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from left lung homogenates of each mouse (n= 3 per group) using Trizol (Invitrogen, Waltham, MA) and RNA quality was evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Tnfr1/2-deficient (Tnfr-/-) and wild-type (Tnfr+/+, C57BL/6J) mice were exposed to air or 0.3-ppm O3 continuously for 24, 48, or 72 hr in individual stainless-steel wire cages within a Hazelton 1000 chamber  (Lab Products, Maywood, NJ) equipped with a charcoal and high-efficiency particulate air-filtered air supply. Mice had free access to water and diet. O3 was generated from ultra-high purity air (<1 ppm total hydrocarbons; National Welders, Inc., Raleigh, NC) using a silent arc discharge O3 generator (Model L-11, Pacific Ozone Technology, Benicia, CA). Constant chamber air temperature (72 ± 3° F) and relative humidity (50 ± 15%) were maintained. O3 concentration was continually monitored (Dasibi model 1008-PC, Dasibi Environmental Corp.). Parallel exposure to filtered air was done in a separate chamber. Immediately following the end of exposure, mice were euthanized by sodium pentobarbital overdose (104 mg/Kg).

tag: genotype

value: Tnfr+/+ (WT, B6)

tag: exposure

tag: tissue

value: Homogenized mouse lung tissues


title: WT-48 hr O3 Replicate 3

source_name: WT-48 hr O3_homogenized mouse lung tissue


title: T_004

type: SRA

city: Washington

first: Rency

middle: S

last: Varghese

state: District of Columbia

address: 4000 Reservoir Rd NW, Building D

department: Oncology

institute: Georgetown University

library_source: transcriptomic

data_processing:
The fastq files were imported into Partek Flow for quality assessment, alignment, and estimating transcript abundance.
Alignment was performed using the spliced transcripts alignment (STAR) algorithm. The aligned reads were quantified to the transcriptome through Expectation Maximization (E/M) method implemented in Partek Flow and normalized using the TMM method.
Supplementary_files_format_and_content: gene counts

organism: Homo sapiens

source_name: Liver

extract_protocol:
RNA samples from the 32 fresh-frozen samples (16 HCC and 16 adjacent normal) were isolated using the RNeasy Plus Universal Mini Kit (Qiagen) with on-column RNase-free DNase treatment. The RNA quality and quantity were estimated based on ultraviolet-visible (UV-VIS) spectrophotometry using the NanoDrop ND-1000 spectrophotometer. The RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.
Aliquots of the RNA samples described above were indexed using the TruSeq RNA Access Library Prep Kit prior to sequencing by Illumina HiSeq 4000 using 150 bp pair end (PE150). The mRNA-seq data contained an average of 33M reads per sample

tag: disease status

value: HCC

tag: race

value: EA


title: RNA-seq of Tumor WT 2

city: Cambridge

first: Daniel

middle: Robert

last: Goulet

state: MA

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
RNA-seq of mCh+ tumor cells isolated from the bone marrow of wild-type C57BL/6J mouse
processed data file:
Tumor_Normalized_Counts.txt
Tumor_DESeq_Results.txt

data_processing:
Fastq files were aligned to mm10 genome using salmon (version 1.3.0). The salmon quant command was executed with the following flags: --validateMappings --gcBias --seqBias
Salmon quant files were normalized and differentially expressed genes were identified using the DESeq2 R package (version 1.28.1). The DESeq command was executed with default options.
Table of read counts normalized by DESeq2 was output to a tab-delimited txt file.
Results of DESeq analysis of WT ~ IL6KO was output to a tab-delimited txt file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts and DESeq2 analysis output to tab delimited txt

source_name: RNA-seq of Tumor WT

growth_protocol: 500,000 BCR-ABL+ B-ALL cells were injected into the tail vein of wild-type or IL6KO C57BL/6J mice.

extract_protocol:
Extracted RNA as directed using Qiagen RNeasy Kit (Qiagen cat. # 74134)
Prepared library as directed using NEB Ultra II Directional RNA with rRNA Depletion Kit (NEB cat. # E7400)

tag: strain background

value: BCR-ABL+, Arf-/-

value: Bone marrow

tag: cell type

value: Bone-marrow derived mCh+ transplanted ALL


title: RNA-seq of Tumor WT 1


title: HF EWD

city: Oklahoma City

first: Elizabeth

middle: A

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

data_processing:
scRNA-seq UMI count matrices were generated using the kallisto (0.46.2) and bustools (0.39.4).
The Seurat package in R was then used to aggregate the matrices, which were further filtered to exclude cells not passing the following QC measures: fewer than 5% of UMIs derived from mitochondi and greater than 200 genes detected.
Genome_build: GRCm38
Supplementary_files_format_and_content: count_matrix.tsv contains UMI counts per gene per cell.

molecule: polyA RNA

source_name: Adipose stromal cells

extract_protocol:
Adipose tissue was digested in collagenase buffer. Stromal pellet was washed and resuspended for FACS staining of CD45, CD31, CD29. All CD29+ cells were retrieved.
Chromium Single Cell 3' Reagent Kit v3

tag: strain

value: Adipose stromal cells

tag: diet

value: High fat

tag: treatment

value: E2 Withdrawal


title: rep2_shCtrl_45min_atacseq

city: Miami

first: Lluis

last: Morey

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

description: 03_shCtrl_E2_pooled.atac.fc.signal.bigwig

library_source: genomic

data_processing:
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
DRIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 using the "histone" setting, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Besides using the "histone" setting, all other parameters used default values.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.29.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

molecule: genomic DNA

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were collected for the transposase reaction.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: pLKO-shCtrl stable


title: WT-Air Replicate 3

source_name: WT-Air_homogenized mouse lung tissue

value: Air


title: WT-Air Replicate 2


title: rep2_shRING1B_0hr_atacseq

description: 02_shRING1B_HD_pooled.atac.fc.signal.bigwig

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior being used for the transposase reaction.


title: rep2_shCtrl_0hr_atacseq

description: 01_shCtrl_HD_pooled.atac.fc.signal.bigwig

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to being used for the transposase reaction.


title: WT-24 hr O3 Replicate 1


title: dbm_t5

city: Wuhan

first: Luo

last: Qiang

state: Hubei

address: Zhang Zhidong Road

country: China

institute: Renmin hospital of wuhan university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Genome_build: NCBI, Mus, GCA_000001635.9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Mouse renal tubules

growth_protocol: Normal laboratory feeding

extract_protocol:
RNA of kidney glomeruli and renal tubules extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the 24-week-old mice were sacrificed, the kidneys were taken out and cut into pieces to extract the glomeruli and tubules.

value: db/m mice

tag: age (weeks)

tag: disease state

value: non-diabetic

value: untreated

value: Mouse renal tubules


title: dbm_t6


title: WT-Air Replicate 1

value: Tnfr+/+ (WT, B6)

value: Homogenized mouse lung tissues


title: rep1_shRING1B_45min_atacseq

value: pLKO-shRING1B stable


title: T_005

value: Adjacent Normal

value: EA


title: dbm_t4


title: HF E2+TAM


title: dbm_g6

source_name: Mouse glomeruli

value: Mouse glomeruli


title: HF E2

value: Adipose stromal cells


title: LF EWD

value: Low fat


title: WT-24 hr O3 Replicate 2


title: dbm_g4


title: LF E2+TAM


title: Nfkb1KO-O3 Replicate 3

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

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

source_name: Nfkb1KO-O3_homogenized mouse lung tissue

label_protocol: Gene expression analysis was conducted using Affymetrix Mouse Genome 430 2.0 GeneChip® arrays (Affymetrix, Santa Clara, CA). One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol.

extract_protocol: Total RNA was extracted from left lung homogenates of each mouse (n= 3 per group) using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) and RNA quality was evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Nfkb1-deficient (Nfkb1-/-) and wild-type (Nfkb1+/+) mice were exposed to 0.3-ppm O3 continuously for 48 hr in individual stainless-steel wire cages within a Hazelton 1000 chamber  (Lab Products, Maywood, NJ) equipped with a charcoal and high-efficiency particulate air-filtered air supply. Mice had free access to water and diet. O3 was generated from ultra-high purity air (<1 ppm total hydrocarbons; National Welders, Inc., Raleigh, NC) using a silent arc discharge O3 generator (Model L-11, Pacific Ozone Technology, Benicia, CA). Constant chamber air temperature (72 ± 3° F) and relative humidity (50 ± 15%) were maintained. O3 concentration was continually monitored (Dasibi model 1008-PC, Dasibi Environmental Corp.). Parallel exposure to filtered air was done in a separate chamber. Immediately following the end of exposure, mice were euthanized by sodium pentobarbital overdose (104 mg/Kg).

value: Nfkb1-/- (KO)


title: rep1_shCtrl_0hr_atacseq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site


title: dbdb_t3

value: db/db mice

value: type-2 diabetic


title: Nfkb1KO-O3 Replicate 2


title: male WT Entolimod 30min [RS-03284069]

city: Buffalo

first: Andrei

last: Gudkov

state: NY

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina bcl2fastq2/2.20 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mouse reference genome (UCSC mm10/GRCm38) using  STAR RNA-seq aligner v2.6.0 using annotation from the same source with default parameters. Reads were counted per gene using featureCounts as part of Subread package, version 1.6.2 with parameters -Q 10 -t exon -g gene_id.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: neutrophils

growth_protocol: Pathogen-free BALB/c mice were obtained from The Jackson Laboratories and housed in microisolator cages in a laminar flow unit under ambient light.

extract_protocol:
Neutrophils were isolated by magnetic isolation from the bone marrow of 12 week old mice. Following treatment, neutrophils were washed once with PBS, resuspended in Qiazol, and flash frozen. Total and small RNA was extracted using the miRNeasy mini kit (Qiagen) following the manufacturer’s recommended protocol. DNAse digestion was performed to remove any residual genomic DNA followed by additional washes prior to elution of high-quality RNA in RNase-free water. The purified RNA was quantitatively assessed using a Qubit Broad Range RNA kit (Thermofisher) and its concentration was determined by Ribogreen fluorescent binding. The RNA was further evaluated qualitatively using RNA Nanotape on the 4200 Tapestation (Agilent technologies), where sizing of the RNA was determined, and a qualitative numerical score (RINe) was assigned.
Sequencing libraries were prepared with the KAPA mRNA HyperPrep Kit (Roche Sequencing Solutions) from 100 ng total RNA following the manufacturer’s recommended protocol. The resulting pool of DNA libraries was then loaded into the appropriate NovaSeq Reagent cartridge for 100 cycle single end sequencing and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina, Inc.).

treatment_protocol: Neutrophils were suspended in media and treated with vehicle (PBS-T) or entolimod (1 ng/mL) for 30 minutes in a humidified chamber at 37°C and 5% C02.

value: wild type

tag: Sex

value: male

value: entolimod

tag: time

value: neutrophils


title: Nfkb1KO-O3 Replicate 1


title: molm14 cells treated with 500 uM TFMB-2HG rep2

city: Chicago

first: Jing

last: Chen

state: Illinois

address: 5801 South Ellis Avenue

institute: The University of Chicago

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  human GRCh38 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: exp.txt  (table delimited text file containing the expression of genes)

source_name: Peripheral blood

growth_protocol: cells were cultured in RPMI 1640 medium with 10% FBS

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: indicated TFMB-2HG was added to cell culture medium and cells were cultured for 6 days

value: Acute myeloid leukemia

tag: cell line

value: 500 uM TFMB-2HG


title: male WT Vehicle 30min [RS-03284068]

tag: genotype

value: vehicle


title: rep1_shRING1B_0hr_atacseq

value: ATCC #HTB-133

value: pLKO-shRING1B stable


title: molm14 cells treated with 1000 uM TFMB-2HG rep1

value: 1000 uM TFMB-2HG


title: dbm_g5

value: db/m mice

value: non-diabetic

value: untreated

value: Mouse glomeruli


title: LF E2

value: Adipose stromal cells

value: Low fat


title: molm14 cells treated with 250 uM TFMB-2HG rep2

value: 250 uM TFMB-2HG


title: rep1_shCtrl_45min_atacseq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: pLKO-shCtrl stable


title: molm14 cells treated with 500 uM TFMB-2HG rep1


title: dbdb_t1

value: db/db mice

value: type-2 diabetic

value: Mouse renal tubules


title: female WT Entolimod 30min [RS-03284066]

value: wild type

value: female

value: entolimod

value: neutrophils


title: molm14 cells treated with 1000 uM TFMB-2HG rep2

value: Acute myeloid leukemia

value: 1000 uM TFMB-2HG


title: WT-O3 Replicate 1

source_name: WT-O3_homogenized mouse lung tissue

value: Nfkb1+/+ (WT)

tag: exposure

value: Homogenized mouse lung tissues


title: Nfkb1KO-Air Replicate 3

source_name: Nfkb1KO-Air_homogenized mouse lung tissue

value: Nfkb1-/- (KO)

value: Air

tag: tissue


title: dbdb_g1

value: untreated

value: Mouse glomeruli


title: Nfkb1KO-Air Replicate 1


title: KO4_hipp

city: New Haven

first: Barbara

middle: E

last: Ehrlich

state: CT

address: 333 Cedar Street

department: Department of Pharmacology

institute: Yale University

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_KO4_361_216_S44_L001

data_processing:
Real Time Analysis (RTA) software on the Illumina NovaSeq 6000 system was used for basecalling
Pre-alignment quality control and aligment to the mm10 reference genome using STAR, version 2.7.3a, were performed using Partek® Flow® (v 9, 2020) software.
Raw gene counts were quantified using the Partek E/M (expectation maximization) model in the Partek® Flow® (v 9, 2020) software (annotation: RefSeq release 94, 2020; strict pair-end compatibility: yes; minimum read overlap with feature: 100%; minimum reads: 10).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Mouse brains were dissected, tissues were flash frozen, total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain; hippocampus


title: WT-O3 Replicate 3


title: WT-Air Replicate 1


title: Nfkb1KO-Air Replicate 2


title: female WT Vehicle 30min [RS-03284065]

value: vehicle


title: WT-Air Replicate 3


title: molm14 cells treated with 250 uM TFMB-2HG rep1

value: 250 uM TFMB-2HG


title: s_veh3

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

description: processed data file: pia_vehicle_normalized_counts.txt

data_processing:
Reads from generated FASTQ files were quality checked, trimmed with CutAdapr v1.6, and mapped to the mouse reference genome (mm10) using STAR2.5.0.a. The expression count matrix of uniquely mapped reads was computed with HTseq v0.5.3.
Expression count matrix was processed through DESeq2 v1.22.1 pipeline in Bioconductor, resulting in generation of normalized count matrix (provided as processed data file).
Genome_build: mm10
Supplementary_files_format_and_content: pia_vehicle_raw_counts.txt: Tab-delimited text file containing raw counts.

source_name: pia enriched fraction

extract_protocol:
Mouse leptomeninges were microdissected, dissociated and FACS sorted. RNA was extracted from lysates using RNeasy Mini columns (Qiagen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng of total RNA (RIN 9.7 - 10)  underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

value: pia enriched fraction

tag: derivative

value: vehicle-treated mice


title: dbdb_g2

value: db/db mice

value: type-2 diabetic


title: WT-O3 Replicate 2


title: WT-Air Replicate 2


title: HeLa with 10mM magnesium

city: Suwon-si

first: Jeong Hwan

last: Hur

state: No State

address: 2066, Seobu-ro, Jangan-gu, Rm 6317

country: South Korea

institute: Sungkyunkwan University

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Expression Console software. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Expression Console software was used.

source_name: HeLa

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Wild-type and genome-engineered mutant HeLa cells were cultured in 6-well plates. 5.0 x 105 cells were cultured in DMEM growth media (WELGENE Inc., Gyeongsangbuk-do, Republic of Korea) without Mg2+ for 24 hours. The media was changed with Mg2+-containing media after 24 hours of culture

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

treatment_protocol: Magnesium-containing media was substituted after 24 hrs, and cultured another 24 hrs at 37oC. Cells were collected and washed with PBS

value: HeLa

value: 10mM magnesium supplemented during the growth


title: s_veh1


title: KO2_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_KO2_302_275_S41_L001


title: KO1_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_KO1_290_287_S42_L001


title: dbdb_g3


title: molm14 cells treated with 125 uM TFMB-2HG rep1

value: Acute myeloid leukemia

value: 125 uM TFMB-2HG


title: molm14 cells control rep2

value: DMSO control


title: s_veh2


title: molm14 cells control rep1


title: KO5_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_KO5_314_263_S40_L001


title: RNA seq for nlp_KNO3_3

city: Qingdao

first: Xiaoqian

last: Chu

address: No. 72 Binhai Road

department: School of Life Sciences

institute: Shandong University

description: biological replicate 3

data_processing:
The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software.
The gene reads count were calculated by htseq-count with default parameters, and differential gene expression was analysed using DESeq2 tool with generalized linear model.
Genome_build: tair 10
Supplementary_files_format_and_content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Arabidopsis thaliana

source_name: nlp7-1_10 mM KNO3  for 3h

growth_protocol: Wild-type Col-0 seedlings, nlp7-1 and hbi-q mutants growing on medium with 7 mM KNO3 under a 16/8 h light/dark cycle at 22-24 °C.

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Genomics Institute.

treatment_protocol: Wild-type Col-0 seedlings, nlp7-1 and hbi-q mutants growing on medium with 7 mM KNO3 for 7 days were transferred to nitrogen-free medium for 2 days then treated with 10 mM KNO3 for 3 hours. To analyse the effects of H2O2 on nitrate regulated gene expression, Col-0 seedlings growing on medium with 7 mM KNO3 for 7 days were transferred to nitrogen-free medium for 2 days then treated with 10 mM KNO3 with or without 0.5 mM H2O2 for 3 hours or treated with H2O2 for 3 hours.

tag: ecotype background

value: Seedlings

value: 10 mM KNO3  for 3h


title: RNA seq for nlp_KNO3_2

description: biological replicate 2


title: WT4_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_WT4_338_239_S38_L001

source_name: wild type_hippocampus

tag: strain background

value: wild type


title: Brain organoids, ADRC28_3821

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to hg19 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger (V3.0.0)'s default settings
Genome_build: hg19
Supplementary_files_format_and_content: text files containing the raw gene expression count

source_name: ADRC28 brain organoids: BO3

growth_protocol: The brain organoids were cultured in a low adherent T25 flask with the differentiation medium containing DMEM/F12 basal medium, 1× N2 supplement (Life Technologies), 1× B27 supplement (Life Technologies), 2.5 μg/ml Insulin, 1× Glutamax, 0.5× MEM-NEAA, and 3.5 μl/L (V/V) 2-Mercaptoethanol on an Orbi-Shaker (Benchmark Scientific) at 50 rpm. Medium was changed every 2-3 days.

extract_protocol:
Total RNA
Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v3 User Guide (10x Genomics). Approximately 10,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: Before collecting the brain organoids at Day 93 or Day 94 for scRNA-seq, brain organoids were treated without (control) or with 10% human serum for 13 or 14 days.

value: iPSC-derived brain organoids

value: 10% human serum 3821 for 14 days

tag: Stage

value: Day 95


title: WT5_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_WT5_326_251_S39_L001

value: brain; hippocampus


title: KO3_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_KO3_373_204_S43_L001


title: molm14 cells treated with 125 uM TFMB-2HG rep2

tag: cell type


title: Brain organoids, 14048_8748

source_name: 14048 brain organoids: BO2

value: 10% human serum 8748 for 13 days

value: Day 94


title: WT3_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_WT3_350_227_S37_L001


title: Ser2_Dox_r1

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs

tag: growth condition

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

tag: antibody

value: Rat 3E10 anti-CTD Ser2-P (Chromotek)


title: RNA seq for nlp_KCl_2

description: biological replicate 2

tag: treatment

value: mock


title: Reprogramming MEFs(OSKA)_8 dpi_+4OHT

city: Sagamihara

first: Yoichi

last: Sekita

state: Kanagawa

address: 1-15-1 Kitasato, Minami-ku

department: Biosciences

country: Japan

institute: Kitasato University School of Science

description: 4OHT administration, AKT-MER not activate.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (Cy3-CTP incorporation > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent according to the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Microarray 8x60k (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green, Green PMT is set to 100% and TIFF file dynamic range is 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MEFs with reprogramming factors (Oct4, Sox2, and Klf4) and AKT-MER

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: OE-MEFs were transduced with reprogramming factors (Oct4, Sox2 and Klf4) with or without AKT-MER by retrovirus vectors.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen).

treatment_protocol: 4OHT or mock was administrated to the reprogramming cells 3 days after transduction, and cells were sampled at day 8.

tag: strain

value: Oct4-EGFP transgenic mouse

value: male

value: Isolated from E13.5 embryos


title: HeLa with No magnesium

value: HeLa

value: 0mM magnesium supplemented during the growth


title: Reprogramming MEFs(OSKA)_8 dpi_-4OHT

description: Mock administration, AKT-MER was not activate.


title: RNA seq for nlp_KCl_1

description: biological replicate 1

value: Seedlings


title: MIAPACA2_sh49_rep1

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: MIAPACA2 cells

growth_protocol: MV4;11 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics; MIA PaCa-2 cells were grown in DMEM plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used with 1 ug of total RNA for the construction of the multiplexed sequencing libraries.

treatment_protocol: For the WDR5 knockdown (KD) experiments, MV4;11 or MIA PaCa-2 cells bearing an inducible WDR5-targeted shRNA or empty vector mock (shEV) were subjected to treatment with 0.5 µg/mL of doxycycline (Dox) for four days. For compound treatment studies, MV4;11 cells were subjected to treatment with 0.1µM of either DMSO, OICR-9429, MS67 or MS67N for three days; MIA PaCa-2 cells were subjected to treatment with 1.0 µM of either DMSO, OICR-9429, MS67 or MS67N for six days.

tag: shRNA


title: Human PMN

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

description: Human polymorphonuclear (PMN) leukocytes were isolated from venous blood collected from four healthy donors and pooled. Briefly, blood was centrifuged (250 g, 20 min, at room temperature), the platelet-rich plasma was discarded, and the erythrocytes were removed by dextran sedimentation. Mononuclear cells were then separated from the granulocytes by centrifugation on Ficoll-Paque cushions. Hypotonic lysis was performed on the granulocyte cell pellet to remove the remaining erythrocytes. The resulting suspensions contained mainly PMN leukocytes (≥95%) with eosinophils as the major contaminant. PMN leukocytes were then re-suspended at 1x10e7 cells/ml in Hanks' balanced salt solution containing 1.6 mM CaCl2.

data_processing:
Adaptor were trimmed using Cutadapt V1.7.1
Quality Control was performed with fastqc V0.11.3
Identical sequences were collapsed into a single fasta sequence and were filtered to keep only those detected at least twice using a custom script
Genome_build: NA
Supplementary_files_format_and_content: Fasta files containing the aligned sequences that were detected at least twice in the dataset, separated in 2 groups based on the size (8-15nt and 16-30nt)

source_name: Human polymorphonuclear (PMN) leukocytes isolated from venous blood collected from healthy adult volunteers

growth_protocol: Please refer to the Samples section above

extract_protocol:
Total RNA samples were prepared using TRIzol® reagent or TRIzol LS® reagent for liquid samples (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s recommendations. Contaminating DNA was degraded by DNase I (M0303S, New England Biolabs, MA, USA) treatment following manufacturer’s instructions. Total RNA was shipped on dry ice and analyzed by Arraystar Inc. RNA sequencing service (Rockville, MD).
The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser. Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, USA), as per the manufacturer's instructions.

tag: sample type

value: Human PMN


title: MIAPACA2_sh49_rep2


title: Reprogramming MEFs(OSK)_8 dpi_+4OHT

description: 4OHT administration, AKT-MER was not activate.

source_name: MEFs with reprogramming factors (Oct4, Sox2, and Klf4)

tag: Sex


title: RNA seq for nlp_KCl_3

description: biological replicate 3


title: KO4_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_KO4_058_135_S111_L002

source_name: Ncs1-/-_frontal cortex

value: brain; frontal cortex


title: KO3_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_KO3_070_123_S110_L002


title: Brain organoids, ADRC28_control

value: iPSC-derived brain organoids

value: untreated


title: RNA seq for T_N_2

description: biological replicate 2

source_name: hbi-q_10 mM KNO3  for 3h

value: hbi-q

value: 10 mM KNO3  for 3h


title: RNA seq for T_N_1

description: biological replicate 1


title: HEK393 cells

description: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine in a humidified incubator under 5% CO2 at 37˚C.

source_name: Human embryonic kidney 293 (HEK293) cells

value: HEK393 cells


title: RNA seq for nlp_KNO3_1

description: biological replicate 1


title: Ser2_H2O_r1

treatment_protocol: Uninduced control cells

value: DMEM 10% FCS, +hygromycin, +blasticidin


title: Brain organoids, 14048_control

value: Day 94


title: MIAPACA2_sh47_rep2


title: RNA seq for T_N_3

description: biological replicate 3


title: KO1_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_KO1_094_099_S108_L002


title: MIAPACA2_shEV_rep1

value: shEV


title: Reprogramming MEFs(OSK)_8 dpi_-4OHT


title: WT5_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_WT5_035_158_S105_L002

source_name: wild type_frontal cortex

value: wild type


title: KO2_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_KO2_082_111_S109_L002


title: HUVEC

description: Cells were cultured in endothelial growth medium (Lonza, Basel, Switzerland) supplemented with bovine brain extract (Lonza, Basel, Switzerland) and maintained at 37°C under 5% CO2. HUVEC were used between passages 2 to 6.

source_name: Human umbilical vein endothelial cells (HUVEC)

value: HUVEC


title: WT2_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_WT2_362_215_S36_L001

value: brain; hippocampus


title: MIAPACA2_MS67_rep1

tag: agent


title: MIAPACA2_sh47_rep1

tag: cell line


title: OV2008

city: Sacramento

first: Dennis

middle: J

last: Montoya

address: 2700 Stockton Blvd

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Alignment STAR-2.7.3a: -alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignSoftClipAtReferenceEnds Yes --chimJunctionOverhangMin 15 --chimMainSegmentMultNmax 1 --chimOutType Junctions SeparateSAMold WithinBAM SoftClip --chimSegmentMin 15 --limitSjdbInsertNsj 1200000 --outFilterIntronMotifs None --outFilterMatchNminOverLread 0.33 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.33 --outFilterType BySJout --outSAMattributes NH HI AS nM NM ch --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outSAMunmapped Within --twopassMode Basic
Gene Counts HTSeq 0.6.1p1 -f bam -r name -s no -a 10 -t exon -i gene_id -m intersection-nonempty gencode.v34.annotation.gtf
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Comma-delimited matrix table with raw gene counts for every gene and every sample from HTSeq

source_name: ovarian cancer cell line

growth_protocol: 70% confluency

extract_protocol:
RNA stored in TRIzol (Ambion, Carlsbad, CA)/chloroform (Sigma-Aldrich) was isolated  using Qiagen RNA extraction kit
RNA sequencing library prepared with TruSeq RNA library kit (Illumina, San Diego, CA).

treatment_protocol: Each cell line was treated with 8 µM quinacrine (Sigma-Aldrich, Saint Louis, MO) for 6 hours in growth medium [4]. Parallel treatment with buffer in each cell line served as controls

tag: chemotherapy resistance

value: sensitive

value: control


title: OV2008_QC

value: quinacrine 8uM


title: KO5_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_KO5_023_170_S106_L002

tag: genotype


title: MIAPACA2_shEV_rep2


title: MIAPACA2_MS67N_rep2


title: SKOV3_TR

value: resistant


title: WT2_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_WT2_071_122_S102_L002

tag: tissue


title: WT1_hipp

description:
processed data file: Hippocampus_NCS1_WT_KO_mm10_gene_counts_matrix.txt
HIP_WT1_374_203_S35_L001


title: RNA seq for T_Cl_3

description: biological replicate 3

value: Seedlings

value: mock


title: MIAPACA2_MS67N_rep1


title: OV2008_C13_QC


title: WT1_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_WT1_083_110_S101_L002

value: brain; frontal cortex


title: WT4_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_WT4_047_146_S104_L002


title: RNA seq for N_H_2

description: biological replicate 2

source_name: wild type_10 mM KNO3 and 0.5 mM H2O2  for 3h

value: 10 mM KNO3 and 0.5 mM H2O2  for 3h


title: MIAPACA2_OICR-9429_rep1


title: RNA seq for T_Cl_1

description: biological replicate 1

value: hbi-q


title: dbdb_t2

source_name: Mouse renal tubules

value: db/db mice

tag: age (weeks)

tag: disease state

value: type-2 diabetic

value: untreated

value: Mouse renal tubules


title: SKOV3_TR_QC


title: OV2008_C13


title: RNA seq for N_M_3

description: biological replicate 3

source_name: wild type_10 mM KNO3  for 3h

tag: ecotype background

value: 10 mM KNO3  for 3h


title: WT3_cortex

description:
processed data file: Cortex_NCS1_WT_KO_mm10_gene_counts_matrix.txt
Cortex_WT3_059_134_S103_L002

tag: strain background

value: wild type


title: MIAPACA2_MS67_rep2


title: RNA seq for N_H_1

description: biological replicate 1


title: MIAPACA2_DMSO_rep2

value: DMSO


title: RNA seq for N_M_2

description: biological replicate 2


title: hnRNPDL-KD rep2

city: Hefei

first: Qingyang

last: Zhang

state: Anhui

address: No.443, HuangShan Road Shushan District

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China for School of Life Sciences

description: hnRNP DL-/- mouse hippocampus

data_processing:
Bcl2fq software used for basecalling.
Bowtie-1.1.2 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.1
Alternative splicing analyzationwas conducted with rMATS v4.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include genes with differential alternative splicingpatterns

source_name: hippocampus

growth_protocol: Standard protocol for mouse experiment for RNA-seq

extract_protocol:
Total RNA was extracted by Trizol.Total amount of 2 μg RNA per sample was used as input material for the RNA   sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library  Prep  Kit  for  Illumina following the manufacturer’s   recommendations  and  index  codes  were  added  to  attribute  sequences  to  each  sample
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Standard protocol for Adeno-associated virus injection in hippocampus

value: hnRNP DL KD


title: RNA seq for T_Cl_2

description: biological replicate 2


title: HeyA8_QC

value: sensitive


title: MIAPACA2_DMSO_rep1


title: HeyA8

value: control


title: RNA seq for N_M_1

description: biological replicate 1


title: MIAPACA2_OICR-9429_rep2


title: RNA seq for Cl_M_1

description: biological replicate 1

source_name: wild type_mock


title: SKOV3


title: RNA seq for Cl_M_2

description: biological replicate 2


title: HeyA8_MDR


title: RNA seq for Cl_M_3

description: biological replicate 3


title: hnRNPDL-KD rep3

description: hnRNP DL-/- mouse hippocampus


title: KI

city: Hershey

first: Bowen

last: Yan

state: PA

address: HERSHEY MED CTR 500 UNIVERSITY DRIVE 500 UNIVERSITY DRIVE

institute: PENNSYLVANIA STATE UNIV

data_processing:
Single Cell 10x Chromium analysis gene count matrix for each sample was performed using Cell Ranger pipeline (10x Genomics) according to 10x genomics workflow.
pooled samples were demultiplexed with cellranger mkfastq program (10x genomics), and demultiplexed FASTQ files were then performed the alignment with reference mm10 genome, filtering, barcode counting, and unique molecular identifier (UMI) counting with cellranger count under the default parameters (10x genomics).
output of cellranger were uploaded as processed data files _barcodes.tsv, _genes.tsv and _matrix.mtx files from individual group.
Genome_build: mm10

source_name: bone marrow

extract_protocol:
Flow cytometry sorting cells (Lin- Kit+) were examined under a microscope and counted with a hemocytometer.
Then, these Cells were loaded in each channel with a target output of 6,000 cells. Reverse transcription and library preparation were performed on C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA and final libraries were examined with the Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies).
scRNA-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations.

value: GATA-1 mutation Knockin

value: bone marrow

tag: cell type

value: lin-kit+ cells


title: RNA seq for N_H_3

description: biological replicate 3

value: Seedlings


title: WT

value: WT


title: WT rep2

description: wild type mouse hippocampus


title: MV4;11_sh49_rep1

source_name: MV4;11 cells


title: HeyA8_MDR_QC

value: resistant

value: quinacrine 8uM


title: B-CyPA-3

city: Xi'an

first: Jiejie

last: Geng

state: Shanxi

address: Changle West road

department: Cell biology department

institute: The Fourth Military Medical 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 (RPKM) 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.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: B-CyPA

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and 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

value: CyPA stimulation


title: dSG-ife replicate 3

status: Public on Sep 28 2021

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

data_processing:
Illumina bcl2fastq software was used for basecalling
Partek Flow software was used for quality assessment and control and for alignment to the mm10 genome using the 2.5.3a STAR algorithm with default settings on Partek servers
Aligned reads were quantified (MM10, Ensembl Transcripts release 83) using the Partek E/M annotation model using default settings on Partek servers
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: dSG_ifetroban treated

extract_protocol:
At sacrifice, hearts were perfused with PBS and RNA was isolated from freshly harvested left ventricle using Lysing Matrix D (MP Biomedicals) and RNeasy (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wildtype or delta-sarcoglycan knockout mice were treated from weaning with normal drinking water or water containing 25 mg/kg/day of the TP receptor antagonist ifetroban. Mice were periodically supplied with running wheels to instigate cardiomyopathy phenotype. At 6 months mice were sacrificed and hearts isolated.

tag: genotype/variation

value: delta-sarcoglycan (dSG) knockout

tag: age

value: 6 months

value: ifetroban

value: cardiac left ventricle


title: SKOV3_QC

tag: treatment


title: MV4;11_shEV_rep2

value: shEV


title: B-control-3

source_name: B-control


title: WT rep3

description: wild type mouse hippocampus

value: wild type


title: B-control-1


title: RNA seq for Cl_H_2

description: biological replicate 2

source_name: wild type_0.5 mM H2O2 for 3h

value: 0.5 mM H2O2 for 3h


title: dSG-veh replicate 1

source_name: dSG_vehicle treated

value: vehicle


title: RNA seq for Cl_H_3

description: biological replicate 3


title: RNA seq for Cl_H_1

description: biological replicate 1


title: dSG-ife replicate 2


title: hnRNPDL-KD rep1

description: hnRNP DL-/- mouse hippocampus

value: hnRNP DL KD


title: MV4;11_sh49_rep2


title: B-CyPA-2


title: dSG-veh replicate 2


title: MV4;11_shEV_rep1


title: wt-veh replicate 2

source_name: wild-type_vehicle treated


title: wt-veh replicate 1


title: wt-ife replicate 1

source_name: wild-type_ifetroban treated


title: dSG-ife replicate 1


title: WT rep1

description: wild type mouse hippocampus


title: mTEChi sample

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

data_processing:
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Paired-end reads were concatenated and trimmed to 50bp. Single-end reads were 50bp length
Alignment to the mm9 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution. RPKM were generated taking into account the total number of mapped reads and the RefSeq length
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include RPKM for each RefSeq

source_name: medullary thymic epithelial cells

extract_protocol:
Total RNA was extracted by Trizol
Non-directionnal TruSeq V3 RNA Sample Prep Kit on PolyA+ mRNA

treatment_protocol: MHC-II high or low mTECs were isolated from pooled thymic of B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure.

value: thymus

tag: type

value: MHCII high medullary epithelial cells

value: WT B6


title: wt-ife replicate 2


title: mTEClo sample

value: MHCII low medullary epithelial cells


title: IgG_G5

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description: IgG IP_sMPNST5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with lumi in R
After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package.

label: Biotin

source_name: Cancer Tissue

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Frozen tissue samples from human cancer panel (n=8 neurofibroma and n=12 for MPNST) were homogenized in polysome lysis buffer [100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 7.0, 0.5% NP-40, 1 mM DTT, 100 units/ml RNase OUT, 1X Protease Inhibitor Cocktail), incubated for 30 min on ice, and centrifuged at 13 000 rpm, 4ºC for 30 minutes.

extract_protocol: Phenol chloroform extraction

treatment_protocol: Immunoprecipitation (IP) protocol of endogenous mRNA-HuR complexes was performed as described by (Jayaseelan et al., 2014; Keene et al., 2006).   For RIP-ChIP analyses, frozen tissue samples from human cancer panel (n=8 neurofibroma and n=12 for MPNST) were homogenized in polysome lysis buffer [100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 7.0, 0.5% NP-40, 1 mM DTT, 100 units/ml RNase OUT, 1X Protease Inhibitor Cocktail), incubated for 30 min on ice, and centrifuged at 13 000 rpm, 4ºC for 30 minutes. 500 l of lysates were pre-cleared by incubating with 25 l of protein A-sepharose 4B beads (Merck) and anti-mouse IgG (BD Biosciences) in 1 ml of NT2 buffer [50 mM Tris pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40] and incubating under rotation for 30 min. The pre-cleared extracts were then divided and incubated with 50 l of protein A-sepharose 4B beads, pre-coated with anti-HuR or anti-mouse IgG antibodies. After incubation, beads were washed 5 times with 1 ml NT2 buffer and bound RNA recovered after proteinase K digestion (Roche) and phenol chloroform extraction. RNAs were then submitted to the Genomics Analysis Platform at CIC bioGUNE for analysis on HUMAN HT-12 V4 arrays (Illumina).

value: IgG IP


title: IgG_G6

description: IgG IP_sMPNST6


title: IgG_G3

description: IgG IP_sMPNST3


title: IgG_F4

description: IgG IP_NF-MPNST4


title: IgG_G2

description: IgG IP_sMPNST2


title: HuR_G6

description: HuR IP_sMPNST6

value: HuR IP

tag: antibody

value: Anti-HuR (3A2) Mouse mAb, Santa Cruz Biotechnology, Cat# sc-5261, RRID:AB_627770


title: IgG_G4

description: IgG IP_sMPNST4


title: IgG_F6

description: IgG IP_NF-MPNST6


title: IgG_F2

description: IgG IP_NF-MPNST2


title: IgG_E4

description: IgG IP_pNF4

value: plexiform neurofibroma


title: IgG_F1

description: IgG IP_NF-MPNST1


title: HuR_G7

description: HuR IP_sMPNST7


title: HuR_G5

description: HuR IP_sMPNST5


title: IgG_F3

description: IgG IP_NF-MPNST3


title: IgG_E5

description: IgG IP_pNF5


title: IgG_D4

description: IgG IP_dNF4

value: dermal neurofibroma


title: IgG_D1

description: IgG IP_dNF1


title: IgG_G7

description: IgG IP_sMPNST7


title: IgG_D2

description: IgG IP_dNF2


title: HuR_G4

description: HuR IP_sMPNST4


title: IgG_F7

description: IgG IP_NF-MPNST7


title: HuR_G3

description: HuR IP_sMPNST3


title: HuR_G2

description: HuR IP_sMPNST2


title: HuR_F3

description: HuR IP_NF-MPNST3


title: IgG_D5

description: IgG IP_dNF5


title: HuR_F7

description: HuR IP_NF-MPNST7


title: IgG_E2

description: IgG IP_pNF2


title: Urine_DU_1mo_rep7

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Single-end reads for miRNA were mapped to miRbase version 21 using BowTie aligner with the following parameters: Number of Mismatches: 2, Length of the Seed: 20, Alignment Type: -n, Maximum Allowed Multiple Mappings: 10. The alignment was performed by Norgen Biotek using sRNAbench and sRNAtoolbox.
Supplementary_files_format_and_content: Tab-delimited matrix table with raw read counts for every miRNA

organism: Rattus norvegicus

source_name: Urine

growth_protocol: Male Sprague–Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol:
Total RNA was isolated from urine samples using the Urine Cell-Free Circulating RNA Purification Mini Kit (Cat. 56900, Norgen Biotek, Thorold, ON, Canada) following manufacturer's protocol. Briefly, 2 ml of cell-free urine was mixed with Binding Solution K and transferred to spin column. RNA within the sample was bound to the spin column while the urine was discarded as flow-through. Following application of Lysis Buffer A, the flow-through was precipitated with isopropanol and subjected to repeat centrifugation through the column to allow maximum RNA binding. The column was then washed twice with Wash Solution A, centrifuged to remove left over alcohol, and transferred to a new RNAse-free tube for elution. The concentration of total RNA was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation and sequencing was performed by Norgen Biotek. Briefly, library preparation was done using the Norgen Biotek Small RNA Library Prep Kit (Cat. 63600). Sequencing was performed using the NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cycle Kit) on the Illumina NextSeq 500 platform.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

tag: gender

value: Male

tag: strain

value: Sprague-Dawley

tag: metal

value: DU

tag: time


title: Urine_DU_1mo_rep4


title: Urine_DU_1mo_rep3


title: Urine_DU_1mo_rep6


title: Urine_DU_1mo_rep2


title: HuR_D4

description: HuR IP_dNF4


title: HuR_F1

description: HuR IP_NF-MPNST1


title: ATACseq_SARSCoV2_Rep1

city: Hannover

first: Benjamin

middle: Erik

last: Nilsson-Payant

address: Feodor-Lynen-Straße 7

department: Experimental Virology

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Research

description:
Sample 46
Nextera DNA Library Prep Kit
ATACseq_SARSCoV2_1.bw

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 (Samples 1-49) or NextSeq 2000 (Samples 50-54) platform.
Samples 1-42: Raw sequencing reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA) or to the SARS-CoV-2 genome using Bowtie2. Differential gene expression analysis was performed using DESeq2 comparing infedcted samples to mock-infected samples.
Sample 43: Sequencing data were processed with CellRanger v4.0.0 (10X Genomics, Inc). Reads were mapped to a combined human (GRCh38) and SARS-CoV-2 (WuhCor1, NC_045512.2, modified to reflect the USA-WA1/2020 strain, MT246667.1) genome reference using CellRanger count. Raw gene x cell counts matrices were analyzed using Seurat (v4.0.1). After an initial filter to remove cells with fewer than 4,000 UMIs (empty droplets) or greater than 65,000 UMIs (doublets) and percent mitochondrial gene expression less than 5% or greater than 40%, counts data were subject to natural logarithm normalization, cell cycle scoring, highly variable gene selection, gene expression scaling, and dimensional reduction by principal component analysis using the developer’s defaults. UMIs, mitochondrial gene expression percentage, S cell cycle phase score, and G2M cell cycle phase score were regressed during gene expression scaling. Further processing included unsupervised clustering analysis using the FindClusters function (resolution: 0.4) and visualization with Uniform Manifold Approximation and Projection (developer’s defaults). All gene expression violin plots were plotted using natural logarithm normalized counts and heatmaps with z-scaled counts. Cells were classified as infected or uninfected by performing hierarchical clustering using Ward’s minimum variance method on a distance matrix of z-scaled, log normalized viral gene expression per cell with k set to 2. Comparing total viral UMIs per cluster separated cells into high and low viral gene expressing cells, and the cluster with higher viral gene expression was classified as infected.  Differential gene expression (DGE) analyses were conducted using edgeR v3.30.3, with additional modifications for scRNA-Seq data. Gene x cell count matrices were extracted from Seurat objects with infection information as metadata. SARS-CoV-2 viral genes were excluded from all differential gene expression analyses and cell cycle scores were calculated using Seurat’s CellCycleScoring function. For all analyses, genes expressed (i.e. greater than or equal to 1 UMI) in less than 10% of cells for at least one group were excluded from differential gene expression testing. To identify the transcriptional signature in infected cells, differential expression analysis was conducting comparing bystander cells versus infected cells. To mitigate the dramatic differences in host gene expression between infected cells and bystander cells, transcript counts from infected and bystander cells were randomly downsampled to the median transcript counts/cell of the infected cells group. All cells with counts below this value were excluded from differential expression analyses. edgeR linear models included factors for cell cycle score (S phase and G2M phase scores), cellular gene detection rate, and infection status. The resulting significant differentially expressed genes were defined by an adjusted p-value < 0.0001 and an absolute log2 fold-change of > +/-1. Gene set enrichment testing was conducted using the HALLMARK gene sets from the Molecular Signatures database (MSigDB) with the CAMERA function. The parameter ‘use.ranks’ was set to TRUE to minimize assumptions about data structure of scRNA-seq data as compared to bulk RNA-seq or microarray data. Gene set enrichment contrasts were set to compare infected cells versus bystander cells and significantly enriched gene sets were identified using an adjusted p-value of less than 0.001.
Samples 44-48: Quality and adapter filtering was applied to raw reads using ‘trim_galore’ before aligning to human assembly hg38 with bowtie2 using the default parameters. The Picard tool MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove reads with the same start site and orientation. The BEDTools suite (http://bedtools.readthedocs.io) was used to create read density profiles. Enriched regions were discovered using MACS2 and scored against matched input libraries (fold change > 2 and FDR-adjusted p-value < 0.1). A consensus peak atlas was then created by filtering out blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/) and then merging all peaks within 500 bp. A raw count matrix was computed over this atlas using featureCounts (http://subread.sourceforge.net/) with the ‘-p’ option for fragment counting. The count matrix and all genome browser tracks were normalized to a sequencing depth of ten million mapped fragments. DESeq2 was used to classify differential peaks between two conditions using fold change > 2 and FDR-adjusted p-value < 0.1. Peak-gene associations were made using linear genomic distance to the nearest transcription start site with Homer (http://homer.ucsd.edu).
Genome_build: human (hg19 or hg38), SARS-CoV-2 (MN985325.1 or MT246667.1)
Supplementary_files_format_and_content: Comma-separated value files (csv) for raw read count table, raw feature-cell matrux files and bigwig ATAC-seq peak files.

source_name: A549-ACE2 cells

extract_protocol:
Samples 1-42: Cells were homogenized in TRIzol reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit according to the manufacturer's instructions. Sample 43: Cells were trypsinized with 0.25% trypsin and collected as a single cells suspension. Cells were then washed twice with ice cold 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and viability were determined using trypan blue stain and a Countess II automatic cell counter (Thermfisher Scientific). Based on this cell count, a target cell input volume of 3,000 cells was loaded into a Chromium Controller using Chromium Next Gem (Gel Bead-In Emulsion) Single Cell 5’ Library & Gel Bead Kit v1.1 (10x Genomics) according to manufacturer’s instructions.. Samples 44-48: Cells were trypsinized and collected as a single cell suspension in complete DMEM. 50,000 cells were isolated and washed twice with ice cold PBS. Nuclei from washed cell pellets were extracted using lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was performed at 37°C for 30 min using the Nextera DNA Library Prep Kit (Illumina) and transposed DNA was purified using the QIAgen MinElute PCR Purification kit according to the manufacturers’ instructions.
Samples 1-42: TruSeq Stranded mRNA Library Prep Kit (Illumina); Sampls 43: Chromium Single Cell 5’ Library Kit v1.1 (10x Genomics); Samples 44-48: Nextera DNA Library Prep Kit (Illumina)
Samples 1-42: RNA-seq; Sample 43: scRNA-seq; Samples 44-48: ATAC-seq

treatment_protocol: Cells were infected with SARS-CoV-2 (USA-WA1/2020) at the indicated MOI and for the indicated amount of time. Alternatively, mock infected cells were treated with

value: Lung adenocarcinoma

tag: virus

tag: time point


title: ATACseq_Mock_Rep2

description:
Sample 45
Nextera DNA Library Prep Kit
ATACseq_Mock_2.bw

value: Mock


title: ATACseq_SARSCoV2_Rep3

description:
Sample 48
Nextera DNA Library Prep Kit
ATACseq_SARSCoV2_3.bw


title: HuR_E5

description: HuR IP_pNF5


title: HuR_F6

description: HuR IP_NF-MPNST6


title: ATACseq_SARSCoV2_Rep2

description:
Sample 47
Nextera DNA Library Prep Kit
ATACseq_SARSCoV2_2.bw


title: ATACseq_Mock_Rep1

description:
Sample 44
Nextera DNA Library Prep Kit
ATACseq_Mock_1.bw


title: IgG_E3

description: IgG IP_pNF3


title: THP-1 shDF1#1 mRNA

city: Zhanjiang

first: Yun-Guang

last: Hong

state: Guangdong

address: #236 Yuanzhu Road, Chikan District, Zhanjiang

department: Zhanjiang Institute of Clinical Medicine

institute: Zhanjiang Central Hospital, Guangdong Medical 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 mm10 mRNA index using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for every Sample.

source_name: Peripheral blood

growth_protocol: THP-1 human leukemia cells were obtained from ATCC. THP-1 cells were cultured in RPMI Medium 1640 basic (Gibco) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 1mM sodium pyruvate (Gibco).

extract_protocol:
Total RNA was isolated from control cells or YTHDF1 knockdown THP-1 cells using TRIzol reagent. m6A-antibody was used for capturing m6A-modified mRNA. Ultracentrifugation was used for collecting ribosome-protected mRNA fragments.
1 ug of total RNA was used for the construction of sequencing libraries accroding to TruSeq Small RNA Sample Preparation Kit (Illumina).

treatment_protocol: silenced YTHDF1 using two independent short hairpins targeting YTHDF1 (hereafter referred to as shDF1#1, shDF1#2).

tag: tissue

value: Peripheral blood

value: YTHDF1 knockdown


title: THP-1 shDF1#1 ribo

data_processing:
Library strategy: Ribo-seq
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 mm10 mRNA index using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for every Sample.


title: THP-1 CTL ribo

value: untreated


title: Urine_Pb_1mo_rep2

value: Pb


title: HuR_E3

description: HuR IP_pNF3


title: HuR_F4

description: HuR IP_NF-MPNST4


title: HuR_E4

description: HuR IP_pNF4


title: HuR_F2

description: HuR IP_NF-MPNST2


title: HuR_D5

description: HuR IP_dNF5


title: THP-1 shDF1#2 m6A

value: anti-m6A (Synaptic Systems, 202003)


title: THP-1 shDF1#1 m6A


title: HuR_E2

description: HuR IP_pNF2


title: MI

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases . scRNA-seq data was processed using stander CellRanger pipeline.
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12. scRNA-seq data was processed using stander CellRanger pipeline.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1. scRNA-seq data was processed using stander CellRanger and Seurat pipeline.
Genome_build: Anas_platyrhynchos.BGI_duck
Supplementary_files_format_and_content: The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

organism: Anas platyrhynchos

source_name: PWBC scRNA-seq

growth_protocol: Seperated cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols

treatment_protocol: Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks and removed erythrocytes from blood samples using erythrocyte lysis solution. Then, cells were first separated by density gradient centrifugation using a duck lymphocyte isolation kit.The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs.

value: Duck peripheral white blood cells


title: HuR_D2

description: HuR IP_dNF2


title: Urine_DU_1mo_rep5


title: Urine_DU_1mo_rep1


title: Urine_Al_1mo_rep1

value: Al


title: Urine_Pb_1mo_rep4


title: HuR_D1

description: HuR IP_dNF1


title: THP-1 CTL mRNA


title: Urine_Cu_1mo_rep3

value: Cu


title: FI


title: Urine_Cu_1mo_rep2


title: Urine_Pb_1mo_rep3


title: Urine_Cu_1mo_rep1


title: Urine_Fe_1mo_rep5

value: Fe


title: Urine_Fe_1mo_rep4


title: HeLa LENG8-GFP-2

city: Shanghai

first: Feng

last: Liu

address: 600 Yishan Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Shanghai JiaoTong University Affiliated Sixth People's Hospital

data_processing:
the adaptor sequence were revoved by cutadapt
clean date were generated by removing the reads of low quality using Trimmomatic programe
the rRNA reads were mapped using  bowtie2 programe
the non-rRNA reads were mapped to human genome version hg38 by Hisat2 version  v2.0.4 with default setting
peak-calling were performed by MACS2
Genome_build: hg38
Supplementary_files_format_and_content: excel files containing annotaion to each peaks

source_name: Hela cells

growth_protocol: Hela were obtained from cell bank of Shanghai Institute for Biological Sciences (CAS) and maintained in standard conditions (37℃, 5% CO2) in DMEM/High Glucose medium with 10% FBS, 100 U/ml penicillin and100 mg/ml streptomycin (Life Science). All cell lines have been tested negative for mycoplasma contamination.

extract_protocol:
HeLa cells expressing GFP-tagged human THOC1 or LENG8 were pelleted by centrifugation at 500g for 10 min at 4 °C and washed twice with ice-cold PBS. Cells were lysed in an equal volume of RIP lysis buffer (10 mM HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 25 mM EDTA, 0.5% (v/v) Nonidet-P40, 1 mM dithiothreitol, protease inhibitor cocktail (EDTA-free, Beyotime) for 30 min on ice in the presence of 100 U ml−1 RNase inhibitor (Sangon)) and lysates clarified by centrifugation at 9,000g and 4 °C for 10 min. Clarified lysates were incubated with anti-GFP with a final concentration at 0.2ug ml-1 and the binding reactions were conducted for 2 hours at 4 °C with continuous gentle rotation.
NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) was used for library construction.

treatment_protocol: Hela were transfected with Lentivirus encoding LENG8-GFP or THOC1-GFP for 48 hours, and the stably transfected cells were selected with 1 uM puromycin.

value: Hela cells stably expressed LENG8-GFP

tag: rip antibody

value: anti-GFP


title: Urine_Fe_1mo_rep6


title: HeLa LENG8-GFP-1


title: Urine_Al_1mo_rep2


title: Urine_Al_1mo_rep3


title: THP-1 CTL m6A Input


title: Urine_Pb_1mo_rep1


title: Urine_Fe_1mo_rep3


title: Urine_Fe_1mo_rep2


title: Urine_Al_1mo_rep4


title: HeLa THOC1-GFP-2

value: Hela cells stably expressed THOC1-GFP


title: Urine_Fe_1mo_rep1

value: Male


title: βH1 CM omental stromal cells differentiated in Adipocyte (Ad) from patient 1

city: PARIS

first: Blandine

last: SECCO

address: PORT ROYAL

institute: INSERM

data_processing:
After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5)
Bioinformatic Alignment were performed with STAR Version 2.5.2b and Ensembl Homo GRCh38p12 release 93 as reference.
Differential analysis was done with R version 3.5.1 (2018-07-02).
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustement, and genes with at least 10 reads in at least 3 different samples). Following the package recommendations, we used the Wald test with the contrast function and the Benjamini-Hochberg FDR control procedure to identify the differentially expressed genes. R scripts and parameters are availables on GitHub (https://github.com/BSGenomique/genomic-rnaseq-pipeline/releases/tag/v1.0420).
Genome_build: Ensembl, Homo sapiens, GRCh38p12 release 93
Supplementary_files_format_and_content: Results Matrix with RSEM genes results

growth_protocol: Human pancreatic beta cell line EndoC-βH1 cells was cultured in low glucose DMEM medium supplemented with 2% BSA fraction V, 50 μM β-mercaptoethanol, 10 mM nicotinamide, 5.5 μg/ml human transferrin, 6.7 ng/ml selenite, 100 U/ml penicillin 100 μg/ml streptomycin. Cells were seeded at 8.10^4 cells/cm2 on plates coated with 1.2% Matrigel, 3ug/mL fibronectin and passaged once a week.

extract_protocol:
Total RNA was isolated using RNeasy Micro kit (Qiagen). The quality of the RNA was assessed by a bioanalyzer 2100 (Agilent).
100ng of total RNA was used for each library. The RNA samples were processed with the TruSeq mRNA Stranded kit (Illumina) according to manufacturer’s instructions.
Libraries were sequenced with the NextSeq 500 on a High Output flow cell. 38±6 millions of read pairs were obtained for each sample.

treatment_protocol: We obtained human omental adipose tissue biopsies from morbidly obese people candidate for bariatric surgery. We isolated and amplified stromal cells. They were cultured until confluence in the absence or presence of TNF-α to create a pro-inflammatory environment, or differentiated into adipocytes. Conditioned media (CM) were next prepared by incubating adipose tissue-derived cells for 48h in EndoC-βH1 culture medium, filtered and frozen. Next human beta cell line EndoC-βH1 was cultured with omentum-derived CMs diluted by half for 48h and effects on gene expression was quantified by RNA-sequencing.

value: Human beta cell line generated from human fetal pancreas

tag: conditions cm


title: Urine_Cu_1mo_rep4

value: Sprague-Dawley


title: βH1 CM omental stromal cells pretreated TNFa (D0TNFa) from patient 1


title: Urine_Cu_1mo_rep5


title: HeLa THOC1-input


title: βH1 CM omental stromal cells (D0) from patient 2


title: βH1 CM omental stromal cells (D0) from patient 1


title: βH1 CM omental stromal cells differentiated in Adipocyte (Ad) from patient 3


title: HeLa LENG8-input


title: HeLa THOC1-GFP-1


title: Urine_Ni_1mo_rep6

value: Ni


title: Urine_Ni_1mo_rep5


title: Urine_Co_1mo_rep1

value: Co


title: βH1 CM omental stromal cells differentiated in Adipocyte (Ad) from patient 2


title: Urine_Co_1mo_rep2


title: βH1 CM omental stromal cells pretreated TNFa (D0TNFa) from patient 3


title: Urine_Ni_1mo_rep3


title: βH1 CM omental stromal cells pretreated TNFa (D0TNFa) from patient 2


title: Urine_Ni_1mo_rep2


title: βH1 CM omental stromal cells (D0) from patient 3


title: BOEC 1

city: College Station

first: Tanmay

last: Mathur

state: TX

address: 101 Bizzell St

department: Biomedical Engineering

institute: Texas AM University

description:
endothelial cell
B1

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Post sequencing, raw single end reads (1x75) were analyzed for quality using FastQC
HISAT2 was then to splice align the reads to latest ENSEMBL-release-102 human genome/transcriptome and generate sequence alignment map (SAM) files
Raw counts were then generated from alignment files (SAM) using the Bioconductor package SUBREAD.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for all samples

source_name: Blood outgrowth endothelial cells

growth_protocol: Endothelial cells were cultured under normal media conditions consisting of endothelial growth media 2 (EGM2, Promocell) supplemented with 10% fetal bovine serum (Gibco, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, culture media was replaced with fresh media. Cells were passaged with 0.25% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~15000 cells/cm2. All experiments were completed with cell populations under P5.

extract_protocol:
After cells reached 70% confluence, total RNA was isolated (Monarch® Total RNA Miniprep Kit, New England Biolabs) and converted to cDNA (>1 µg)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Endothelial progenitor cells


title: Urine_Co_1mo_rep4


title: iPSC-EC 4

description:
endothelial cell
I4

source_name: iPSC derived endothelial cells

value: iPSC derived endothelial cells


title: BOEC 2

description:
endothelial cell
B2


title: Urine_Ni_1mo_rep1


title: BOEC 4

description:
endothelial cell
B4


title: Urine_Co_1mo_rep5


title: iPSC-EC 3

description:
endothelial cell
I3


title: Urine_Co_1mo_rep3


title: βH1 CM Ctr rep3

value: betaH1 Control


title: βH1 CM Ctr rep1


title: Urine_W_1mo_rep6

value: W


title: Urine_Ni_1mo_rep4


title: BOEC 3

description:
endothelial cell
B3


title: βH1 CM Ctr rep2


title: Urine_W_1mo_rep5


title: Urine_W_1mo_rep2


title: HUVEC 1

description:
endothelial cell - control
H1

source_name: Human umbilical vein endothelial cells

value: Primary endothelial cells


title: Urine_Ta_1mo_rep6

value: Ta


title: scRNAseq_SARSCoV2

description:
Sample 43
Chromium Single Cell 5’ Library Kit v1.1
scRNAseq_matrix.mtx.gz

value: Lung adenocarcinoma


title: iPSC-EC 2

description:
endothelial cell
I2


title: iPSC-EC 1

description:
endothelial cell
I1


title: Urine_DU_12mo_rep4

value: DU


title: mRNAseq_IFNb_12h_Rep3

description:
Sample 39
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: Mock

value: IFN-β (100 U/ml)


title: Urine_W_1mo_rep1


title: HUVEC 3

description:
endothelial cell - control
H3


title: HUVEC 4

description:
endothelial cell - control
H4


title: Urine_W_1mo_rep4


title: Urine_DU_12mo_rep3


title: Urine_W_1mo_rep3


title: mRNAseq_TNFa_12h_Rep3

description:
Sample 42
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: TNF-α (100 ng/ml)


title: mRNAseq_TNFa_12h_Rep2

description:
Sample 41
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_DU_12mo_rep2


title: Urine_Ta_1mo_rep5


title: Urine_Ta_1mo_rep7


title: Urine_Ta_1mo_rep2


title: mRNAseq_IFNb_12h_Rep1

description:
Sample 37
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Ta_1mo_rep3


title: HUVEC 2

description:
endothelial cell - control
H2


title: mRNAseq_TNFa_12h_Rep1

description:
Sample 40
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_SARSCoV2_24h_Rep1

description:
Sample 34
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: SARS-CoV-2 (USA-WA1/2020), MOI=2


title: Urine_Pb_12mo_rep7

value: Male

value: Pb


title: Urine_Ta_1mo_rep1

value: Sprague-Dawley


title: Urine_DU_12mo_rep5


title: mRNAseq_SARSCoV2_24h_Rep3

description:
Sample 36
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_SARSCoV2_24h_Rep2

description:
Sample 35
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Pb_12mo_rep5


title: Urine_Pb_12mo_rep4


title: mRNAseq_IFNb_12h_Rep2

description:
Sample 38
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Pb_12mo_rep2


title: mRNAseq_SARSCoV2_12h_Rep3

description:
Sample 33
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Pb_12mo_rep3


title: Urine_Ta_1mo_rep4


title: mRNAseq_SARSCoV2_9h_Rep1

description:
Sample 28
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: 9 h


title: mRNAseq_SARSCoV2_9h_Rep2

description:
Sample 29
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Al_12mo_rep7

value: Al


title: Urine_DU_12mo_rep1


title: Urine_Al_12mo_rep8


title: mRNAseq_SARSCoV2_6h_Rep1

description:
Sample 25
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: 6 h


title: Urine_Al_12mo_rep6


title: mRNAseq_SARSCoV2_4h_Rep3

description:
Sample 24
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: 4 h


title: mRNAseq_SARSCoV2_6h_Rep2

description:
Sample 26
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_SARSCoV2_9h_Rep3

description:
Sample 30
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Pb_12mo_rep6


title: mRNAseq_SARSCoV2_4h_Rep1

description:
Sample 22
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_SARSCoV2_12h_Rep2

description:
Sample 32
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Pb_12mo_rep1


title: mRNAseq_SARSCoV2_6h_Rep3

description:
Sample 27
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Al_12mo_rep5


title: mRNAseq_SARSCoV2_2h_Rep1

description:
Sample 19
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: 2 h


title: Urine_Al_12mo_rep2


title: Urine_Cu_12mo_rep5

value: Cu


title: mRNAseq_SARSCoV2_4h_Rep2

description:
Sample 23
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_12h_Rep3

description:
Sample 15
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_24h_Rep1

description:
Sample 16
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Al_12mo_rep4


title: mRNAseq_SARSCoV2_12h_Rep1

description:
Sample 31
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_SARSCoV2_2h_Rep3

description:
Sample 21
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Cu_12mo_rep2


title: Urine_Al_12mo_rep3


title: mRNAseq_Mock_12h_Rep1

description:
Sample 13
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_9h_Rep3

description:
Sample 12
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Cu_12mo_rep6


title: mRNAseq_SARSCoV2_2h_Rep2

description:
Sample 20
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Fe_12mo_rep5

value: Fe


title: Urine_Fe_12mo_rep6


title: Urine_Al_12mo_rep1


title: Urine_Fe_12mo_rep4


title: Urine_Cu_12mo_rep4


title: Urine_Cu_12mo_rep1


title: mRNAseq_Mock_24h_Rep2

description:
Sample 17
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Cu_12mo_rep3


title: mRNAseq_Mock_6h_Rep2

description:
Sample 8
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_6h_Rep3

description:
Sample 9
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_24h_Rep3

description:
Sample 18
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_9h_Rep1

description:
Sample 10
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_9h_Rep2

description:
Sample 11
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Fe_12mo_rep7


title: Urine_Fe_12mo_rep2


title: Urine_Fe_12mo_rep3


title: Urine_Co_12mo_rep6

value: Co


title: mRNAseq_Mock_4h_Rep2

description:
Sample 5
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: Lung adenocarcinoma


title: mRNAseq_Mock_6h_Rep1

description:
Sample 7
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_2h_Rep3

description:
Sample 3
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: mRNAseq_Mock_4h_Rep1

description:
Sample 4
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Co_12mo_rep7


title: Urine_Co_12mo_rep3


title: mRNAseq_Mock_2h_Rep1

description:
Sample 1
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Co_12mo_rep5


title: HEK293T_benzamide_rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

data_processing:
(Replicate 1 only) Paired-end reads were merged using Ngmerge v0.2.
Reads were split according to the sample barcodes (ACGAT for benzamide-treated samples and TTACG for CHX-treated samples) using fastx-toolkit v0.0.14. Barcodes were trimmed and the resulting reads were filtered by length (>8 bp) by cutadapt v1.8.1.
UMIs were trimmed from the reads and attached to the fastq headers using a custom Python code (see McGlincy, N. J.; Ingolia, N. T. Methods 2017, 126, 112–129. for details).
Bases whose quality is below 15 were trimmed, and then the resulting reads shorter than 6 bp were removed by cutadapt v1.8.1. Then, artifacts were removed by fastx-toolkit v0.0.14 using fastx_artifacts_filter command.
Reads were aligned to libraries of human ribosomal RNAs, tRNAs (source: GtRNAdb) and other noncoding RNAs (source: Noncode v6 and Ensembl GRCh38) using Bowtie2 (v.2.3.2) in this order, and reads that aligned to any of those libraries were removed.
Remaining reads were aligned to hg38 genome using STAR v2.7.0e and then sorted using samtools v1.5. PCR duplicates were removed using UMI-tools v1.0.0.
Genome_build: hg38
Supplementary_files_format_and_content: Differential ribosome occupancy was analyzed by DESeq2. The baseMean, log2FoldChange, lfcSE, stat, pvalue and padj of each detected gene were summarized in a csv file.

growth_protocol: HEK293T cells were grown in DMEM supplemented with 100 U mL-1 penicillin, 100  μg mL-1 streptomycin and 10% fetal bovine serum.

extract_protocol:
Ribosome profiling was carried out according to the previously described protocol (McGlincy, N. J.; Ingolia, N. T. Methods 2017, 126, 112–129.) with minor modificationsCells were lysed and the lysates were clarified by centrifugation for 10 min at 20,000g, 4 °C. For each condition, lysate containing 30 μg total RNA (determined by Qubit RNA BR Assay Kit, Thermo Fisher Scientific) was used for nuclease footprinting. The digestion was transferred to 8 x 34 mm thick wall polycarbonate ultracentrifuge tube (Beckman 343776) on top of 0.25 mL sucrose cushion. Ribosome recovery was carried out by centrifugation in a TLA 100.1 rotor at 100,000 rpm, 4 °C for 3 h 40 min. The RNA from the pelleted ribosomes was purified first using the Direct-zol RNA Miniprep kit (Zymo Research) and then by precipitating with isopropanol. Size selection by running a 15% polyacrylamide TBE-Urea gel for 65 min at 200 V in 1X TBE, staining the gel for 3 min with 1X SYBR Gold in TBE, and excising the 17 nt – 34 nt region. The size-selected RNA was extracted in the gel extraction buffer and purified by isopropanol precipitation.
The extracted RNA was resuspended in 10 μL 10 mM Tris pH 8, and end repaired by T4 polynucleotide kinase (New England Biolabs, hereafter NEB). Linker ligation was performed using T4 RNA ligase 2 truncated K227Q (NEB) and linkers preadenylated using 5’ DNA adenylatioin kit (NEB). NI-812 linker (barcode CGTAA) was used for footprints from CHX-treated cells and NI-810 (barcode ATCGT) was used for footprints from 8- treated cells. Depletion of the unligated linker from the ligation reaction was carried out by adding 1 μL yeast 5’-deadenylase 10 U/μL and 1 μL RecJ exonuclease 10 U/μL (epicenter definition) directly to the ligation reaction and incubating for 45 min at 30 °C. After pooling and purification of ligations, ribosomal RNA was depleted using RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific) according to the manufacturer’s instruction. The resulting RNA was reverse transcribed using SuperScript III RT (Invitrogen) and the reverse transcription products were separated from the unextended primers and no-insert background products by running a 15% polyacrylamide TBE-Urea gel for 40 min at 180 V. The reverse transcription products were extracted from the excised bands in the DNA gel extraction buffer and were purified by isopropanol precipitation. The resulting cDNA was circularized by CircLigase II (EpiCentre) and was quantified by qPCR. Library construction was carried out by 9 cycles of PCR using Q5 Hot Start High-Fidelity DNA Polymerase (NEB). After purification of the DNA library, library length distribution was analyzed by TapeStation 2200 (Agilent) using High Sensitivity D1000 ScreenTape. The first technical replicate was sequenced for 51 cycles (paired end) on an Illumina MiSeq, and the second replicate was sequenced for 150 cycles (single read) on an Illumina NextSeq.
Ribosome profiiling

treatment_protocol: Cells were grown on 10cm2 tissue culture plates to approximately 90% confluency and were treated for 1 minute with 350 μM benzamide or 350 μM cycloheximide (solution in 0.1% DMSO in PBS) at 37 °C.

value: kidney

tag: developmental stage

value: embryonic

value: C13-benzamidyl cycloheximide


title: mRNAseq_Mock_2h_Rep2

description:
Sample 2
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

value: Mock