title: BJABs 180 min aIg +Ibru PROT

city: Nijmegen

first: Francesca

last: Rivello

address: Heyendaalseweg 135

department: Physical-Organic Chemistry

country: Netherlands

institute: Radboud University

description: the polyA RNA and the protein are composed by the same cells barcoded with QuRIE-seq technology

data_processing:
Library strategy: QuRIE-seq
bcl2Fastq v2.16.0.10 used for base-calling
code used to analyze data: https://github.com/indrops/indrops
Reads were filtered based on having correct structure: R1 biological read and R2 metadata read
R2 includes barcode1+adaptor+barcode2+UMI and it is 51 bp
R1 is the transcript read for the RNA libraries and the Ab barcode read including 4 bp random sequence + 18 bp Nextera read + Ab BC and it is 35 bp.
Trimmomatic was used on the read 1 (R1) of the protein libraries in order to retain only the first 8 bases (Ab barcode) and in the RNA libraries to filter low-complexity and low-quality sequences (leading=28, slidingwindow=4:20, minlen=16)
Abundant barcodes were identified and a threshold representing real cells was set (barcodes with less reads than the set threshold are not considered real cells and their reads are discarded)
Reads were aligned using Bowtie with the following settings: RNA - m = 10, n = 1, l = 15, e = 1000 and proteins - m = 1, n = 1, l = 8, e = 75.
Reads were then quantified to UMIFM
Genome_build: GRCh38.85
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (RNA) or protein and every cell

molecule: other

source_name: Lymphocyte cell line

growth_protocol: BJAB cells were obtained from DSMZ, Germany (acc 757). Cells were cultured in RPMI medium (Thermo Fisher Scientific, USA) supplemented with 20% FBS (Biowest, France) and 1% Penicillin-Streptomycin (Thermo Fisher Scientific, USA). Before stimulation, cells were harvested, centrifuged at 200 g for 5 minutes and re-suspended in complete medium at a concentration of 3*106 cells/ml.

extract_protocol:
The chip design described by Klein et al. for single-cell barcoding was used, with four inlets (reverse transcription mix, beads, cell suspension and oil phase with surfactant). After microfluidic emulsification, the cells were de-crosslinked by the action of DTT present in the RT mix which reduced the disulphide bonds present and the barcoding primers were released from the hydrogel beads by 8-minute UV exposure at 10 mW/cm2 from a photolithography machine (ABN Inc, USA). Subsequently, the poly(dT) tail of the barcoding primers annealed both to the poly(A) tail of the mRNA and the poly(dA) tail of the Ab tags and the single cells-derived material was barcoded by reverse transcription: incubation of 2 hours at 50 ℃, followed by 15 minutes at 70 ℃. The emulsion was then broken by adding 3 µL  of 20% (vol/vol) PFO on the top of the emulsion, and then 40 µL of  HFE-7500 fluorinated fluid (3M).  The samples were stored until further use at -80°C.
After microfluidic single-cell barcoding, samples were thawed, centrifuged at 4 °C for 5 minutes at 19000 g to pellet cell debris, then the aqueous post-RT material (top layer) was separated from the bottom oil layer and transferred to a nucleic acid purification column (Corning Costar Spin-X column, 0.45 µm, Sigma-Aldrich, USA). Tubes were centrifuged for 1 minute at 16000 g at 4 °C. Subsequently, 100 µL of digestion mix was added per each 70 µL of the sample (final concentrations were 0.5x FastDigest Buffer (Thermo Fisher Scientific, USA) and 0.6 U/µL ExoI (Thermo Fisher Scientific, USA)) and incubated for 30 minutes at 37 °C. After digestion of unused primers and primer dimers, the mix was size separated using 0.6x volume of AMPure XP magnetic beads (Beckman Coulter, USA). The short fragments (the proteomic library that were retained in supernatant) were separated from the long fragments (the transcriptomic library kept by beads) and each library was then processed independently. mRNA library: After the size separation of the mRNA library from the protein library, the mRNA library was processed for second-strand synthesis (SSS) and linear amplification by In Vitro Transcription (IVT). Briefly, 2 µL of 10x SSS buffer and 1 µL of SSS Enzyme (NEBNext mRNA Second Strand Synthesis Module, New England Biolabs, USA) were added to the 17 µL of the purified sample, mixed, and incubated at 16 °C for 1.5 hour, and 20 min at 65 °C. Subsequently, 60 µL of IVT mix was added to each of the 20 µL SSS product, and incubated at 37 °C for 15 hours. The IVT reaction was composed by 1x reaction buffer, 10mM each of ATP, CTP, GTP and UTP, and 10x diluted T7 RNA Polymerase mix (HiScribe™ T7 High Yield RNA Synthesis Kit, New England Biolabs, USA). After linear amplification, the amplified RNA material was purified with 1.3x AMPure XP magnetic beads (Beckman Coulter, USA), and fragmented by adding 1 µL of 10X RNA fragmentation Reagents (Thermo Fisher Scientific, USA) to 10ul of purified IVT, mixing and immediately incubating at 70 °C for exactly 3 minutes. Thereafter, the mix was transferred on ice and 34 µl of STOP mix (8.9 µl nuclease-free water, 24 µl AMPure XP magnetic beads, and 1.1 µl STOP solution) were added to it. Purification using AMPure XP magnetic bead was followed by sample elution in 8 µl nuclease-free water. The following step of the library preparation consisted of the reverse transcription (RT) of the amplified RNA material using random hexamers. This was performed by first addition of 1 µL of 10 nM of each dNTP (Thermo Fisher Scientific, USA) and 2 µL of 100 µM of PE2-N6 primer (Biolegio, The Netherlands), and incubation of the mix at 70 °C for 3 minutes, followed by cooling down the mixture on ice. Next, 3.5 µL nuclease-free water was added to 4 µL of 5x PrimeScript buffer (Takara, USA), 1 µL RNAse OUT (Thermo Fisher Scientific, USA) and 0.5 µL PrimeScript RT (Takara, USA), and the reaction mix was incubated at 30 °C for 10 minutes, followed by 42 °C for 1 hour and by 15 minutes at 70 °C. The RT product was then purified with 1.2x AMPure XP magnetic beads and eluted in 10 µL of nuclease-free water ands amplified by PCR. The number of required cycles was determined by qPCR using 0.5 µL of purified material with the addition of 6.5 µL nuclease-free water, 10 µL of 2x Kapa HiFi HotStart PCR mix (Roche, Switzerland), 1 µL of 20x EvaGreen Dye (Thermo Fisher Scientific, USA), and 2 µL of PE1/PE2 primer mix (5 µM each) (Biolegio, The Netherlands). Final material was obtained by mixing  0.5 µL of nuclease-free water, 12.5 µL of 2x Kapa HiFi HotStart PCR mix (Roche, Switzerland), and 2 µL of PE1/PE2 primer mix (5 µM each) (Biolegio, The Netherlands) and  the 9.5 µL of sample. The PCR thermal cycling was as follows: 2 minutes at 98 °C, followed by 2 cycles of: 20 seconds at 98 °C, 30 seconds at 55 °C and 40 seconds at 72 °C, preliminary to a number of thermocycles (number previously determined by qPCR) of: 20 seconds at 98 °C, 30 seconds at 65 °C and 40 seconds at 72 °C, and terminated with 5 minute-incubation at 72 °C. After PCR, the sample was purified by addition of 0.7x AMPure XP magnetic beads and eluted in 10 µl of water. The  quality of the final libraries was verified by ds-DNA concentration measurement using Qubit ds-DNA High Sensitivity assay (Thermo Fisher Scientific, USA) and BioAnalyzer (Agilent 2100, USA), following manufacturer's instructions. If the quality of the samples was sufficient, the mRNA libraries were sequenced together with the protein libraries on with NextSeq500 (targeting 50 million reads per sample). Protein library: After size separation of the protein and mRNA libraries, the protein library was amplified by IVT reaction. 20 µL of product was mixed with 60 µL of IVT mix and amplified  for 15 hours at 50 °C. The IVT mix was composed of 1x reaction buffer, 10 mM each dNTP (ATP, CTP, GTP and UTP), and 10x diluted T7 RNA Polymerase mix (HiScribe™ T7 High Yield RNA Synthesis Kit, New England Biolabs, USA). After linear amplification, the sample was purified by addition of 1.5x AMPure XP magnetic beads and eluted in 20 µl of water. 10 µl of the sample were stored at -80 °C as post-IVT backup and the other 10 µl were mixed with 1 µL of 10 nM of each dNTP (Thermo Fisher Scientific, USA), 1 µL of 10 µM PE2-NNNN-Next1 primer (Biolegio, The Netherlands), and 1 µL of 10 µM PE2-NNNN-BioHash2 primer (Biolegio, The Netherlands) and reversely  transcribed by incubation for 3 minutes at 70 °C followed by cooling down the mixture on ice. Next, 1.5 µL nuclease-free water, 4 µL of 5x PrimeScript buffer (Takara, USA), 1 µL RNAse OUT (Thermo Fisher Scientific, USA) and 0.5 µL of 200 U/µL PrimeScript RT (Takara, USA) was added to the reaction mix that was incubated: at 30 °C for 10 minutes, followed by 42 °C for 1 hour and by 15 minutes  at 70 °C. After reverse transcription, the product was purified with 1.5x AMPure XP magnetic beads and eluted in 10 µL of nuclease-free water. Subsequently, the sample was PCR amplified after prior determination of the number of cycles needed by qPCR: 0.5 µL of purified material was mixed with 6.5 µL nuclease-free water, 10 µL of 2x Kapa HiFi HotStart PCR mix (Roche, Switzerland), 1 µL of 20x EvaGreen Dye (Thermo Fisher Scientific, USA), and 2 µL of PE1/PE2 primer mix (5 µM each) (Biolegio, The Netherlands). Then the PCR reaction was started by adding: 0.5 µL of nuclease-free water, 12.5 µL of 2x Kapa HiFi HotStart PCR mix (Roche, Switzerland), and 2.5 µL of PE1/PE2 primer mix (5 µM each) (Biolegio, The Netherlands) to the 9.5 µL of sample. The PCR thermal cycling was as follows: 2 minutes at 98 °C, followed by 2 cycles of: 20 seconds at 98 °C, 30 seconds at 55 °C and 40 seconds at 72 °C, preliminary to a number of thermocycles (number previously determined by qPCR) of: 20 sec at 98 °C, 30 sec at 65 °C and 40 sec at 72 °C, and terminated with 5-minute incubation at 72 °C. PCR

treatment_protocol: For each time point, 500 µl cell suspension was dispensed in 3 ml FACS tubes (BD biosciences, USA). For cells treated with inhibitor 1 µM Ibrutinib was added directly to the cell suspension. Subsequently, cells were allowed to rest in complete medium for one hour at 37°C with or without an inhibitor. Cells were then stimulated with 10 µg/ml F(ab')₂ Fragment Goat Anti-Human IgA + IgG + IgM (H+L) (Jackson ImmunoResearch, USA) for the indicated time points. After incubation, cells were immediately fixated by adding two times concentrated fixative (5 mM dithiobis(succinimidyl propionate) (DSP) (Thermo Fisher Scientific, USA) and 5 mM succinimidyl 3-(2-pyridyldithio)propionate (SPDP) (Thermo Fisher Scientific, USA) in PBS (Thermo Fisher Scientific, USA), and incubated for one hour at room temperature. Fixated cells were quenched and permeabilized with 100 mM Tris-HCl pH 7.5, 150 mM NaCl and 0.1% Triton X100 (Thermo Fisher Scientific, USA) for 10 minutes at room temperature. After permeabilization, cells were washed once and blocked for 45 minutes in 0.5x protein-free blocking buffer (Thermo Fisher Scientific, USA) with 0.2mg/ml dextran sulfate (Sigma Aldrich, USA) and 0.5 U/ml RNasin plus (Promega, USA) in PBS (Thermo Fisher Scientific, USA). Cells were stained in a blocking buffer containing DNA-tagged antibodies (Ab list in Supplementary Table 1) for one hour at room temperature. Following staining, cells were washed twice with the blocking buffer and re-suspended in PBS containing 5 mg/ml BSA (Thermo Fisher Scientific, USA) and 0.5 U/ml RNsing plus (Promega, USA).

value: BJAB

value: Lymphocyte

value: 180 min polyclonal anti-immunoglobulin antibody + Ibrutinib


title: AB61

status: Public on Mar 03 2022

type: SRA

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

country: USA

institute: Washington University In St Louis

description:
h3k4me1.pooled.fc.signal.bigwig
h3k4me1.epic2.naive_overlap_peaks.txt.gz

library_source: genomic

data_processing:
Sequencing reads were demultiplexed and processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with the “histone” option (https://github.com/ENCODE-DCC/chip-seq-pipeline2, version v1.1.6-10-gd4f6442) (Roadmap Epigenomics et al., 2015), which aligns reads to human genome (hg19) by bowtie2, and generates signal strength relative to the control samples using MACS2
epic2 were used to call peaks for the histone markers.
The stables sets of peaks were determined using the "naive ovelap" strategy as used in the ENCODE-chipseq pipline, i.e.,  peaks were called with the pooled reads, and 2 partions of the pooled psuedoreplicates, separately, using relaxed threshold of p<0.05; stable peaks are subset of the peaks from the pooled reads, which overlap at least 50% with peaks from both pseudoreplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for signal strength, tab-delimited text files for called peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: human induced pluripotent stem cells

extract_protocol:
Cells extracted after 70% confluency, sonicated by using COVARIS, Histone -DNA complex extracted by using antibdy.
ChIPmentation protocol bySchimdl et al.,2015
ChIPmentation

tag: cell type

value: human induced pluripotent stem cells

tag: genotype

value: KDM6A KO


title: Patient_12_CRC_Tissue

city: Kaunas

first: Rokas

last: Lukosevicius

address: Eiveniu str. 4

department: Institute for Digestive Research

country: Lithuania

institute: Lithuanian University of Health Sciences

description: small RNA

library_source: transcriptomic

data_processing:
Trimming of adapter sequences: cutadapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -q 30 –discard-untrimmed (cutadapt v1.9.dev6)
Filtering of reads mapped to viral genome (RefSeq), human tRNAs, rRNAs, snRNAs and sRNAs (Rfam) : blastn  -word_size=18 (BLASTN v2.2.30)
Quantification of miRNAs: miraligner -sub 1 -trim 3 -add 3 -s hsa -i $reads -db miRBase_v21 -o "isomir_$sample" -freq (SeqBuster)
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

molecule: total RNA

source_name: colon

extract_protocol:
Standard protocol of miRNeasy Mini Kit (Qiagen).
Standard protocol of TruSeq Small RNA Sample Preparation Kit (Illumina)

tag: tissue

value: CRC tissue

tag: gender

value: Female

tag: age

tag: side

value: right

tag: smoking

value: Current

tag: Stage

tag: tnm classification


title: B108-Brain (WGBS)

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: mm10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

organism: Mus musculus

source_name: Brain

growth_protocol: Fetal brain and placenta were harvested on gestational day 18

extract_protocol:
Tissue was flash frozen and nucleic acids were extracted using the Qiagen TissueLyser and AllPrep DNA/RNA/miRNA kit
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit

treatment_protocol: Pregnant dams were exposed to 1.0 mg/kg/d of a PCB mixture or a vehicle control

tag: treatment

value: Control

tag: Sex

value: female

tag: embryo

tag: litter

value: Brain


title: AB40

value: igg


title: RNA-seq G401 scr DMSO rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 1e-15.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per condition

source_name: G401 cells

growth_protocol: G401 cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin.TTC549, cells were grown in RPMI with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
For ChIP-seq experiments, chromatin was extracted from nuclear pellets and frozen until ready for immunoprecipitation with antibodies. Immunoprecipitated DNA was extracted using a PCR purification kit. For RNA-seq, Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 3 days. For ChIP-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 4 hours.

tag: cell line

value: G401 cells

tag: condition

value: scr shRNA

value: 0.01% DMSO for 3 days


title: BJABs  180 min aIg PROT

value: 180 min polyclonal anti-immunoglobulin antibody


title: D201-Placenta (WGBS)

source_name: Placenta

value: Placenta


title: RNA-seq G401 p53 DMSO rep3

value: p53 shRNA


title: RNA-seq G401 p53 DMSO rep2


title: RNA-seq G401 p53 DMSO rep1


title: Patient_10_CRC_Tissue

description: small RNA

tag: height

tag: weight (kg)

value: Ex-Smoker


title: 2_3

description:
h3k4me3.pooled.fc.signal.bigwig
h3k4me3.epic2.naive_overlap_peaks.txt.gz

tag: cell type

value: human induced pluripotent stem cells


title: D104-Placenta (WGBS)

value: male


title: AB21

tag: genotype

value: KDM6A KO


title: B107-Brain (WGBS)

tag: tissue


title: D102-Placenta (WGBS)


title: RNA-seq G401 scr C16 rep2

value: 500 nM C16 for 3 days


title: B105-Brain (WGBS)


title: Patient_7_CRC_Tissue

description: small RNA

value: CRC tissue

tag: gender

value: Female

value: right

value: Never


title: Patient_8_CRC_Tissue

description: small RNA

value: Male

tag: age

value: left


title: Patient_4_CRC_Tissue

description: small RNA

tag: side


title: D103-Placenta (WGBS)

value: Control


title: Patient_5_CRC_Tissue

description: small RNA

tag: smoking


title: B104-Brain (WGBS)

value: Brain


title: ChIP-seq TTC549 WDR5 C16 rep3

source_name: TTC549 cells

value: TTC549 cells

tag: antibody

value: 500 nM C16 for 4 hours


title: BJABs  60 min aIg PROT

value: BJAB

value: Lymphocyte

value: 60 min polyclonal anti-immunoglobulin antibody


title: RNA-seq G401 scr DMSO rep2

value: G401 cells

value: scr shRNA

value: 0.01% DMSO for 3 days


title: BJABs 6 min aIg PROT

value: 6 min polyclonal anti-immunoglobulin antibody


title: BJABs 6 min aIg + Ibru PROT

value: 6 min polyclonal anti-immunoglobulin antibody + Ibrutinib


title: Patient_2_CRC_Tissue

description: small RNA

value: CRC tissue

value: Ex-Smoker

tag: Stage

tag: tnm classification


title: RNA-seq G401 scr DMSO rep1

tag: treatment


title: Patient_1_CRC_Tissue

description: small RNA


title: B103-Brain (WGBS)

tag: Sex

value: female

tag: embryo


title: ChIP-seq TTC549 C16 IgG rep3

tag: cell line

value: IgG


title: B102-Brain (WGBS)

value: male

tag: litter


title: ChIP-seq TTC549 WDR5 C16 rep1


title: BJABs 2 min aIg PROT

value: 2 min polyclonal anti-immunoglobulin antibody


title: Healthy_control_32

description: small RNA

value: healthy colon

value: Female

tag: height

value: Never


title: BJABs 0 min aIg PROT

value: BJAB

value: Untreated


title: BJABs 4 min aIg PROT

value: Lymphocyte

value: 4 min polyclonal anti-immunoglobulin antibody


title: A103-Brain (WGBS)

value: PCB

value: Brain


title: Patient_3_CRC_Tissue

description: small RNA

value: left

tag: weight (kg)


title: ChIP-seq TTC549 C16 IgG rep2

value: TTC549 cells

value: 500 nM C16 for 4 hours


title: BJABs 180 min aIg +Ibru  RNA

description:
the polyA RNA and the protein are composed by the same cells barcoded with QuRIE-seq technology
inDrop V3

data_processing:
bcl2Fastq v2.16.0.10 used for base-calling
code used to analyze data: https://github.com/indrops/indrops
Reads were filtered based on having correct structure: R1 biological read and R2 metadata read
R2 includes barcode1+adaptor+barcode2+UMI and it is 51 bp
R1 is the transcript read for the RNA libraries and the Ab barcode read including 4 bp random sequence + 18 bp Nextera read + Ab BC and it is 35 bp.
Trimmomatic was used on the read 1 (R1) of the protein libraries in order to retain only the first 8 bases (Ab barcode) and in the RNA libraries to filter low-complexity and low-quality sequences (leading=28, slidingwindow=4:20, minlen=16)
Abundant barcodes were identified and a threshold representing real cells was set (barcodes with less reads than the set threshold are not considered real cells and their reads are discarded)
Reads were aligned using Bowtie with the following settings: RNA - m = 10, n = 1, l = 15, e = 1000 and proteins - m = 1, n = 1, l = 8, e = 75.
Reads were then quantified to UMIFM
Genome_build: GRCh38.85
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (RNA) or protein and every cell

molecule: polyA RNA

tag: cell type

value: 180 min polyclonal anti-immunoglobulin antibody + Ibrutinib


title: ChIP-seq TTC549 WDR5 C16 rep2


title: A101-Brain (WGBS)


title: A104-Brain (WGBS)


title: ChIP-seq TTC549 WDR5 DMSO rep3

value: 0.01% DMSO for 4 hours


title: BJABs  60 min aIg  RNA

value: 60 min polyclonal anti-immunoglobulin antibody


title: BJABs  180 min aIg  RNA

value: 180 min polyclonal anti-immunoglobulin antibody


title: A102-Brain (WGBS)

value: female


title: E207-Brain (WGBS)

value: Control


title: ChIP-seq TTC549 C16 IgG rep1

value: IgG


title: Healthy_control_29

description: small RNA

value: healthy colon

value: Female

value: Never


title: E206-Brain (WGBS)

value: male


title: Healthy_control_30

description: small RNA

value: Male


title: Healthy_control_28

description: small RNA

value: Current


title: BJABs 6 min aIg RNA

value: BJAB

value: Lymphocyte

value: 6 min polyclonal anti-immunoglobulin antibody


title: E205-Brain (WGBS)

value: Brain


title: BJABs 6 min aIg + Ibru RNA

value: 6 min polyclonal anti-immunoglobulin antibody + Ibrutinib


title: Healthy_control_31

description: small RNA


title: F208-Brain (WGBS)

value: PCB


title: F207-Brain (WGBS)


title: ChIP-seq TTC549 WDR5 DMSO rep1

value: TTC549 cells

value: 0.01% DMSO for 4 hours


title: ChIP-seq TTC549 DMSO IgG rep1


title: ChIP-seq TTC549 WDR5 DMSO rep2


title: Healthy_control_23

description: small RNA


title: Healthy_control_26

description: small RNA


title: Healthy_control_25

description: small RNA


title: BJABs 4 min aIg RNA

value: 4 min polyclonal anti-immunoglobulin antibody


title: Healthy_control_24

description: small RNA


title: ChIP-seq TTC549 DMSO IgG rep2


title: BJABs 2 min aIg RNA

value: 2 min polyclonal anti-immunoglobulin antibody


title: ChIP-seq TTC549 DMSO IgG rep3

value: IgG


title: F203-Brain (WGBS)

value: female


title: Clod-lip rep1

city: Toon

first: Yukihiro

last: Kohrara

state: Ehime

address: Sitsukawa

country: Japan

institute: Ehime University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using Tophat
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample after FPKM normalization

source_name: Repair tissue_Clod-lip

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), and purified using RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: periosteum and quandriceps on the surface of injured bone


title: F202-Brain (WGBS)

tag: tissue


title: Healthy_control_20

description: small RNA

value: healthy colon

tag: gender

value: Female

value: Never


title: Healthy_control_27

description: small RNA

value: Male

tag: age

value: Current


title: Empty-lip rep 3

source_name: Repair tissue_Empty-lip


title: RNA-seq (DMSOvsNutlin-3a) TTC642 Nutlin rep1

description: RNAseq-DMSOvsNutlin-G401-KYM1-TTC642-proteincoding-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per condition
Supplementary_files_format_and_content: PRO-seq: tab-delimited text file include raw counts for proximal-promoter and gene body region, and density for gene body

source_name: TTC642 cells

growth_protocol: G401 cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. TTC642, KYM-1, TTC549, and TM87-16 cells were grown in RPMI with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
For ChIP-seq experiments, chromatin was extracted from nuclear pellets and frozen until ready for immunoprecipitation with antibodies. Immunoprecipitated DNA was extracted using a PCR purification kit. For PRO-seq, run-on biotinylated RNA from nuclei were extracted using trizol and streptavidin Dynabeads, and then processed and continually purified through multiple rounds of streptavidin Dynabead addition. For RNA-seq, Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 3 days.For ChIP-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 4 hours. For PRO-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 2 hours.

value: TTC642 cells

value: 500 nM Nutlin-3a for 3 days


title: RNA-seq (DMSOvsNutlin-3a) TTC642 DMSO rep3

value: 0.01% DMSO for 3 days


title: Healthy_control_21

description: small RNA


title: RNA-seq (DMSOvsNutlin-3a) TTC642 Nutlin rep3


title: RNA-seq (DMSOvsNutlin-3a) TTC642 Nutlin rep2


title: Clod-lip rep2


title: C206-Brain (WGBS)

value: Brain


title: BJABs 0 min aIg RNA

value: BJAB

value: Lymphocyte

value: Untreated


title: Healthy_control_22

description: small RNA


title: RNA-seq (DMSOvsNutlin-3a) TTC642 DMSO rep1


title: Clod-lip rep3


title: Healthy_control_19

description: small RNA

value: Ex-Smoker


title: Empty-lip rep 2


title: C205-Brain (WGBS)

value: PCB


title: Healthy_control_18

description: small RNA


title: Healthy_control_17

description: small RNA


title: C207-Brain (WGBS)


title: RNA-seq (DMSOvsNutlin-3a) KYM1 Nutlin rep3

source_name: KYM-1 cells

value: KYM-1 cells


title: RNA-seq (DMSOvsNutlin-3a) TTC642 DMSO rep2


title: F201-Brain (WGBS)

value: male


title: C203-Brain (WGBS)

value: female


title: Empty-lip rep 1

value: periosteum and quandriceps on the surface of injured bone


title: C204-Brain (WGBS)


title: RNA-seq (DMSOvsNutlin-3a) KYM1 Nutlin rep2


title: Healthy_control_16

description: small RNA

value: healthy colon

value: Female


title: C202-Brain (WGBS)


title: C201-Brain (WGBS)


title: Healthy_control_14

description: small RNA

value: Male

value: Never


title: RNA-seq (DMSOvsNutlin-3a) KYM1 DMSO rep3


title: F108-Brain (WGBS)


title: RNA-seq (DMSOvsNutlin-3a) KYM1 DMSO rep2


title: PVC FGF biological rep1

type: RNA

city: STOCKHOLM

first: Kayoko

last: Hosaka

state: Solna

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska institutet

description: Isolated perivascular cells from FGF group

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US).

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: TdT

source_name: Perivascular cells FGF overexpressing 1

label_protocol: TdT DNA labeling reagent was applied.

extract_protocol: Tumor cells were injected subcutaneously dorsal back on C57BL/6 mouse. Perivascular cells were isolated using enzymatic digestion of tumor tissues followed by an anti-NG2 antibody labeling isolation.

treatment_protocol: FGF = fibroblast growth factor

tag: background strain

value: Isolated perivascular cells

tag: injected tumor cells

value: mouse fibrosarcoma


title: F106-Brain (WGBS)


title: Healthy_control_11

description: small RNA

tag: smoking


title: RNA-seq (DMSOvsNutlin-3a) KYM1 DMSO rep1

value: 0.01% DMSO for 3 days


title: F107-Brain (WGBS)

value: Brain


title: PVC FGF biological rep2

source_name: Perivascular cells FGF overexpressing 2

growth_protocol: Tumor cells were injected subcutaneously dorsal back on C57BL/6 mouse


title: RNA-seq (DMSOvsNutlin-3a) G401 Nutlin rep3

value: G401 cells

value: 500 nM Nutlin-3a for 3 days


title: WGBS_TALL-1

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Whole genome bisulfite sequencing

data_processing:
Paired-end reads from sequencing were trimmed using trimgalore (v0.4.4, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), removing low quality (Q30) bases and adapter sequences, and clipping 10 bases from each end of the read pairs.
Trimmed reads were then mapped to hg19 using BSMAP (v2.90) with default parameters to report unique pairs with a 17 base pair minimal insert size and 600 base pair maximum insert size
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Only CpGs covered by at least 10 reads were considered for downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph file containing methylation rates for CpGs covered by at least 10 reads: <chr> <start> <end> <methylation rate>

source_name: TALL-1 T-ALL cell line

growth_protocol: ALL cell lines were maintained in RPMI 1640 medium containing 10% or 20% fetal bovine serum (HyClone), penicillin/streptomycin (100 U/mL), and glutamine (100 µM) at 37°C, 5% CO2. Cell identity was confirmed by short tandem repeat (STR) profiling using a PowerPlex Fusion System (Promega). All of the cell lines were confirmed as Mycoplasma spp. free using the Universal Mycoplasma Detection Kit (American Type Culture Collection, Manassas, VA).

extract_protocol:
Cells at exponential growth phase were spun down at 1500 rpm for 3 minutes and cell pellet was used to extract genomic DNA.
Whole genome bisulfite sequencing was performed on bisulfite-modified DNA-sequencing library generated according to Illumina’s instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). 200ng of genomic DNA, including 0.2% Lambda DNA (N6-methyladenine-free; NEB) was bisulfite converted in a single reaction using the EZ DNA Methylation Gold Kit (Zymo Research) as outlined by the manufacturer. The bisulfite converted DNA (bsDNA) was split into four aliquots per sample. Four single indexed WGBS libraries were constructed with the EpiGnome Methyl-Seq kit (EGMK81312, Epicentre) according to the manufacturer’s recommendations. The final concentration of each library was accurately determined through qPCR (KAPA Biosystems). The four independent libraries were normalized, pooled, and loaded across three lanes of the HiSeq 2000 instrument (Illumina).

tag: condition

value: WT


title: F105-Brain (WGBS)


title: WGBS_RPMI-8402

description: Whole genome bisulfite sequencing

source_name: RPMI-8402 T-ALL cell line


title: Healthy_control_10

description: small RNA

value: Ex-Smoker


title: PVC Control biological rep2

description: Isolated perivascular cells from control group

source_name: Perivascular cells Control2


title: Healthy_control_15

description: small RNA


title: PVC Control biological rep3

source_name: Perivascular cells Control3


title: F104-Brain (WGBS)

value: PCB


title: RNA-seq (DMSOvsNutlin-3a) KYM1 Nutlin rep1

value: KYM-1 cells


title: PVC FGF biological rep3

source_name: Perivascular cells FGF overexpressing 3


title: Healthy_control_9

description: small RNA


title: WGBS_PER-117

description: Whole genome bisulfite sequencing

source_name: PER-117 T-ALL cell line


title: PVC Control biological rep1

source_name: Perivascular cells Control1


title: WGBS_PEER

description: Whole genome bisulfite sequencing

source_name: PEER T-ALL cell line

value: PEER


title: F103-Brain (WGBS)

source_name: Brain

value: male


title: Healthy_control_13

description: small RNA

source_name: colon

value: Current


title: RNA-seq (DMSOvsNutlin-3a) G401 Nutlin rep1

source_name: G401 cells


title: RNA-seq (DMSOvsNutlin-3a) G401 DMSO rep3


title: RNA-seq (DMSOvsNutlin-3a) G401 Nutlin rep2


title: Healthy_control_8

description: small RNA

value: healthy colon


title: Healthy_control_12

description: small RNA

value: Female


title: F102-Brain (WGBS)


title: B204-Brain (WGBS)

value: Control

value: female


title: Healthy_control_6

description: small RNA

value: Never


title: WGBS_NALM-6_Rep2

description: Whole genome bisulfite sequencing

source_name: NALM-6 B-ALL cell line


title: RNA-seq (DMSOvsNutlin-3a) G401 DMSO rep1


title: B203-Brain (WGBS)


title: Healthy_control_5

description: small RNA

value: Male


title: B202-Brain (WGBS)


title: Healthy_control_4

description: small RNA


title: WGBS_NALM-6_Rep1

description: Whole genome bisulfite sequencing


title: RNA-seq (DMSOvsC16) TM87-16 C16 rep3

description: RNAseq-DMSOvsC16-TTC549-TM87-16-proteincoding-count.txt

source_name: TM87-16 cells

value: TM87-16 cells

value: 500 nM C16 for 3 days


title: WGBS_MUTZ5

description: Whole genome bisulfite sequencing

source_name: MUTZ5 B-ALL cell line


title: RNA-seq (DMSOvsC16) TM87-16 C16 rep2


title: RNA-seq (DMSOvsC16) TM87-16 DMSO rep2

value: 0.01% DMSO for 3 days


title: WGBS_MOLT-16

description: Whole genome bisulfite sequencing

source_name: MOLT-16 T-ALL cell line


title: B201-Brain (WGBS)

value: Brain


title: Healthy_control_3

description: small RNA


title: D203-Brain (WGBS)


title: D207-Brain (WGBS)


title: Healthy_control_2

description: small RNA


title: Healthy_control_1

description: small RNA


title: D206-Brain (WGBS)


title: WGBS_MHH-CALL-2

description: Whole genome bisulfite sequencing

source_name: MHH-CALL-2 B-ALL cell line

value: WT


title: RNA-seq (DMSOvsC16) TM87-16 DMSO rep3


title: Healthy_control_7

description: small RNA

value: Ex-Smoker


title: RNA-seq (DMSOvsC16) TM87-16 C16 rep1


title: WGBS_LOUCY

description: Whole genome bisulfite sequencing

source_name: LOUCY T-ALL cell line

value: LOUCY


title: WGBS_MHH-CALL-4

description: Whole genome bisulfite sequencing

source_name: MHH-CALL-4 B-ALL cell line


title: D201-Brain (WGBS)


title: RNA-seq (DMSOvsC16) TM87-16 DMSO rep1


title: RNA-seq (DMSOvsNutlin-3a) G401 DMSO rep2

value: G401 cells


title: WGBS_NALM-16

description: Whole genome bisulfite sequencing

source_name: NALM-16 B-ALL cell line


title: WGBS_ALL-SIL

description: Whole genome bisulfite sequencing

source_name: ALL-SIL T-ALL cell line

value: ALL-SIL


title: RNA-seq (DMSOvsC16) TTC549 C16 rep3

source_name: TTC549 cells

value: TTC549 cells


title: RNA-seq (DMSOvsC16) TTC549 C16 rep2


title: D103-Brain (WGBS)

value: male


title: D104-Brain (WGBS)


title: Male, aorta, PPE 7d #5

city: Stanford

first: Joshua

middle: M.

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

description:
Gene expression from murine aortic tissue with or without AAA
MTA-1_0.r3.na36.mm10.a1.transcript.csv

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Thermo Fisher).

data_processing: Analysis was performed using Transcriptome Analysis Console (TAC) 4.0.2.15 - appliedbiosystems/Thermo Fisher Scientific. Exclusions were performed based on principal components analysis, hierarchical clustering and technical QC. Annotation: MTA-1_0.r3.na36.mm10.a1.transcript.csv, Map File: MTA-1_0_MappingFile.r1.map, Genome Version: mm10 (Mus musculus).

label: biotin, streptavidin conjugated to phycoerythrin

source_name: infrarenal aorta, aneurysm, PPE operated, 7d

label_protocol: Un-pooled total RNA (100 ng) was isolated as described from the affected infra-renal region of murine aorta.  Affymetrix GeneChip WT PLUS reagent kits were used for array sample preparation. Total RNA was amplified, labeled, and hybridized to Clariom D/MTA-1_0 mouse whole transcriptome microarrays following manufacturer's instructions (Thermo-Fisher/Affymetrix), one mouse per array. Washing and labeling was performed on GeneChip Fluidics station 450.

extract_protocol: Total RNA was isolated using a TRIzol-based (Invitrogen) RNA isolation protocol. RNA was quantified by Nanodrop (Agilent Technologies), and RNA and miRNA quality were verified using an Agilent 2100 Bioanalyzer (Agilent Technologies). Samples required 260/280 ratios >1.8, and sample RNA integrity numbers >9 for inclusion.

treatment_protocol:
The PPE infusion model to induce mouse AAA was performed as previously described at 10 weeks of age (PMID: 19629030). The proximal and distal aorta was temporarily ligated or clamped, followed by an aortotomy above the iliac bifurcation. A catheter was used to infuse the aorta for 5 minutes at 120 mmHg with saline (sham), or saline containing type I porcine pancreatic elastase (PPE, 2.5 U/mL; Sigma Aldrich), and the aortotomy was then repaired. The induced AAA aortic segment (between the left renal artery and the bifurcation) was harvested at 7 days post-surgery
After 7 days, all mice were sacrificed with an inhalation overdose of isoflurane (Vet One, Meridian, ID, USA) and cervical dislocation or heart puncture followed by cervical dislocation.  The aorta was transected and flushed via the left ventricle with ice cold phosphate buffered saline (PBS; pH 7.4). The aorta was then dissected from fat and connective tissue from the left renal artery to the bifurcation using a microscope (Leica, Wetzlar, Germany). Aortae were snap-frozen individually in liquid nitrogen and stored at -80°C before further processing


title: D102-Brain (WGBS)


title: RNA-seq (DMSOvsC16) TTC549 C16 rep1


title: RNA-seq (DMSOvsC16) TTC549 DMSO rep2


title: RNA-seq (DMSOvsC16) TTC549 DMSO rep3


title: D101-Brain (WGBS)


title: Male, aorta, PPE 7d #6

hyb_protocol: Un-pooled total RNA (100 ng) was isolated as described from the affected infra-renal region of murine aorta.  Affymetrix GeneChip WT PLUS reagent kits were used for array sample preparation. Total RNA was amplified, labeled, and hybridized to Clariom D/MT


title: Male, aorta, PPE 7d #7


title: Male, aorta, PPE 7d #4


title: RNA-seq (DMSOvsC16) TTC549 DMSO rep1


title: NCM MI day7_2

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

data_processing:
The dataset was aligned and quantified using the CellRanger software package with default parameters.
Cells with >300 expressed genes were retained, resulting in 1,783 cells from 2 mice (sham operation) for the subsequent analysis using Seurat v3.
SCTransform normalization was implemented separately for each dataset, after which the top 500 feature genes were selected and used for data integration.
The integrated data were used for dimensionality reduction and cluster detection.
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: Non-cardiomyocytes

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 19-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences).
Single-cell cDNA libraries were generated using the Chromium 3′ v2 chemistry kit (10x Genomics) according to the manufacturer’s instruction.

treatment_protocol: Myocardial infarction (MI) was induced as previously described. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

value: Non-cardiomyocytes

tag: operation

value: MI

value: heart

tag: name in supplementary file

tag: molecule subtype

tag: protocol

value: Chromium (10X Genomics)


title: NCM MI day7_1


title: RNA-seq (DMSOvsC16) TTC642 C16 rep2

description: RNAseq-DMSOvsC16-G401-KYM1-TTC642-proteincoding-count.txt

source_name: TTC642 cells

tag: cell line

value: TTC642 cells

tag: treatment


title: NCM MI day1_2


title: RNA-seq (DMSOvsC16) TTC642 C16 rep1


title: Male, aorta, PPE 7d #3

value: Male


title: Male, aorta, PPE 7d #2


title: NCM MI day1_1


title: Male, aorta, sham 7d #5

source_name: infrarenal aorta, control, sham operated, 7d


title: Male, aorta, sham 7d #4


title: RNA-seq (DMSOvsC16) TTC642 DMSO rep2


title: Mock-expressing-CEM-4

first: Kazumi

last: Nakano

state: Kanto

address: 4-6-1, Shirokanedai, Minatoku

department: Department of Computational Biology and Medical Sciences

institute: Grad. Sch. Frontier Sci., The University of Tokyo

description: Expression level of each exon in mRNAs from whole human genome

hyb_protocol: 3.75 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Exon 2x400K Microarray (G4848A)  for 17 hours at 65C 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 37C GE Wash buffer 2 (Agilent), then air-dried for >5min before scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using one color scan setting for 2x400K array slides (Scan area: 61x21.6 mm, Scan resolution: 3um, Dye channel: Green,Green PMT gain: 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1-107_Sep9 and Grid: 028680_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TALL patient derived T-cell line

label_protocol: The Cy3 labeling was performed using the Low Input Quick Amp WT Labeling Kit  (Agilent Technologies Inc.).

growth_protocol: CEM cells were maintained in RPMI (Gibco, Thermo Fisher Scientific, Inc.) containing 10% FBS (Gibco, Thermo Fisher Scientific, Inc.) at 37 ℃ with 5% CO2.

extract_protocol: Total RNA was extracted using TRI-Zol (Invitrogen, Thermo Fisher Scientific, Inc.).

treatment_protocol: CEM cells were infected with recombinant retrovirus expressing Rex or nothing (mock).  After 48 h, puromycin selection (0.5 μg / mL) was started and the cells (CEM-Rex and CEM-Emp) were used for experiments after 10-12 days.

value: T cell

tag: modification

value: CEM cells infected with mock expressing retrovirus


title: Male, aorta, sham 7d #3


title: Mock-expressing-CEM-2


title: NCM sham2

treatment_protocol: Sham surgery was performed in mice randomly selected from among those weighing 20–23 g at the age of 9–11 weeks.

value: sham


title: RNA-seq (DMSOvsC16) TTC642 DMSO rep1

value: 0.01% DMSO for 3 days


title: NCM sham1


title: Rex-expressing-CEM-4

value: CEM cells infected with Rex expressing retrovirus


title: Spatial Htra3KO MI

data_processing:
Library strategy: Spatial transcriptomics
Differentially expressed genes were detected by using FindMarkers in Seurat (log2fc.threshold > 0.25, p_val_adj < 0.05).
Genome_build: mm10

source_name: heart

extract_protocol:
Frozen samples were embedded in OCT (TissueTek Sakura) and cryosectioned at −14℃ (Leica CM1860). Sections were placed on chilled Visium Spatial Gene Expression Slides (2000233, 10X Genomics), and adhered by warming the back of the slide. Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics). For gene expression samples, tissue was permeabilized for 15 minutes, which was selected as the optimal time based on tissue optimization time course experiments (CG000238 Rev D, 10X Genomics). Brightfield histology images were taken using a 10X objective on a BZ-X700 microscope (Keyence Corporation, Itasca, Illinois). Raw images were stitched together using BZ-X analyzer software (Keyence Corporation) and exported as TIFF files.
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics).

value: Spatial

value: Visium


title: RNA-seq (DMSOvsC16) KYM1 DMSO rep2

source_name: KYM-1 cells

value: KYM-1 cells


title: Male, aorta, sham 7d #1


title: Spatial Htra3KO sham


title: Rex-expressing-CEM-3


title: Rex-expressing-CEM-1


title: Male, aorta, PPE 7d #1


title: RNA-seq (DMSOvsC16) KYM1 DMSO rep1


title: Rex-expressing-CEM-2


title: Mock-expressing-CEM-3


title: Male, aorta, sham 7d #2


title: Female, aorta, PPE 7d #3

value: Female


title: Female, aorta, PPE 7d #4


title: Spatial WT sham


title: 87_miRNA

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

institute: University Medicine Halle (Saale)

data_processing:
Low quality read ends as well as remaining parts of sequencing adapters were clipped off using Cutadapt (v 1.14)  with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the mouse genome (mm10 UCSC) using Bowtie2 (v 2.3.2) with parameters  -N 1
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 1 -t miRNA -g ID and miRBase annotations (mirbase 22 GRCm38)
Differential gene expression was assessed using R/edgeR (v 3.26.8) using TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file containing raw counts for each sample

growth_protocol: Cells were cultured according to ATCC recommendations.

extract_protocol:
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared by Novogene according to Illumina's instructions accompanying the NEB Next Ultra RNA Library Prep Kit.

treatment_protocol: The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LTA (0.5 µg/mL; from Staphylococcus aureus).

value: macrophage

value: unsupplemented/LTA stimulated


title: RNA-seq (DMSOvsC16) G401 C16 rep2

source_name: G401 cells

value: G401 cells

value: 500 nM C16 for 3 days


title: Mock-expressing-CEM-1


title: RNA-seq (DMSOvsC16) KYM1 C16 rep2


title: RNA-seq (DMSOvsC16) KYM1 C16 rep1


title: 84_miRNA


title: Female, aorta, PPE 7d #2


title: Female, aorta, sham 7d #3


title: Female, aorta, PPE 7d #1


title: RNA-seq (DMSOvsC16) G401 DMSO rep1


title: Spatial WT MI

value: heart

value: MI


title: Female, aorta, sham 7d #2


title: DHA+LTA3_miRNA

value: DHA supplemented/LTA stimulated


title: PRO-seq KYM1 C16 rep2

molecule: nuclear RNA

value: 500 nM C16 for 2 hours


title: RNA-seq (DMSOvsC16) G401 C16 rep1


title: Female, aorta, sham 7d #1


title: Mock-expressing-CEM-4

description: Expression level of mRNAs from whole human genome

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 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 following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human GE 4x44K v2 Microarray Kit  (G4845A)  for 17 hours at 65C 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 37C GE Wash buffer 2 (Agilent), then air-dried for >5min before scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using one color scan setting for 4x44K array slides (Scan area: 61x21.6 mm, Scan resolution: 5um, Dye channel: Green,Green PMT gain: 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v7 (Agilent) using default parameters (protocol GE1-107_Sep9 and Grid:026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: The Cy3 labeling was performed using the Low Input Quick Amp Labeling Kit  (Agilent Technologies Inc.).

value: T cell


title: DHA+LTA1_miRNA


title: PRO-seq KYM1 DMSO rep2

value: 0.01% DMSO for 2 hours


title: DHA+LTA2_miRNA


title: PRO-seq KYM1 DMSO rep1


title: PRO-seq KYM1 C16 rep1


title: PRO-seq G401 C16 rep2


title: 92_miRNA

value: AA supplemented/LTA stimulated


title: Mock-expressing-CEM-1

value: CEM cells infected with mock expressing retrovirus


title: 93_miRNA


title: 91_miRNA


title: Mock-expressing-CEM-2


title: PRO-seq G401 DMSO rep2


title: Mock-expressing-CEM-3


title: 2_miRNA

value: unsupplemented/unstimulated


title: Rex-expressing-CEM-3

value: CEM cells infected with Rex expressing retrovirus


title: RAW LTA1_miRNA


title: 3_miRNA


title: Rex-expressing-CEM-4


title: PRO-seq G401 DMSO rep1


title: RNA-seq (DMSOvsC16) G401 DMSO rep2

value: 0.01% DMSO for 3 days


title: pc12_10d_α1ACT_1

city: Chicago

first: Christopher

last: Gomez

state: IL

address: 5812 S Ellis Ave Room J219

department: Neurology

institute: University of Chicago

data_processing:
adatper trimming by Cutadapter
The miRNA raw readings were then mapped to miRBase version 22 using two web-based tools Chimira and sRNAbench.
[22-24]. Both Chimira and sRNAbench read counts were normalized and analyzed using Bioconductor R package EdgeR with a deciding criterion |fold change| > 1.5 and FDR < 0.1 to identify differentially expressed miRNAs
Supplementary_files_format_and_content: read counts

organism: Rattus norvegicus

source_name: pc12 cells

growth_protocol: pc12 was established from ATCC and cultured in F-12K medium (ATCC, Manassas) supplemented with 10% horse serum and 2.5% fetal bovine serum (FBS) in a 37 °C, 5% CO2 incubator on a plate coated with 0.01% poly-L-lysine. For stable cell line generation, when pc12 cells reached 60% confluence they were transfected with pcDNA3 vectors expressing C-terminal 3xFlag tag α1ACT with 11 polyglutamine repeats and empty pcDNA3 vector using TransIT 1(Mirus, Pittsburgh, PA, USA) by following the manufacturer’s instruction. Transfected cells were selected with 150 mg/ml G418(GIBCO) and then stable clones were obtained. The pc12 cells are male.

extract_protocol:
Total cellular RNA and total mouse brain and cerebellum RNA was isolated by RNeasy mini Kit and RNeasy lipid mini Kit (QIAGEN, Valencia, CA, USA), respectively, according to the manufacturer’s instructions. The flow through obtained from the total RNA extraction was used for purifying the miRNA-enriched fraction by using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA, USA), following the manufacturer’s instructions
Small-RNA-seq was performed using Illumina TrueSeq Small RNA protocol at the University of Chicago Genomics Facility

tag: stable expression

value: stably expressing pcDNA3 alpha1ACT

tag: time after split

value: 10 days


title: pc12_10d_α1ACT_3


title: Rex-expressing-CEM-2

tag: cell type


title: ChIP-seq KYM1 WDR5 C16 rep1

value: KYM-1 cells

value: 500 nM C16 for 4 hours


title: pc12_10d_pcDNA3_3

value: stably expressing pcDNA3 blank vector


title: ChIP-seq KYM1 WDR5 C16 rep2


title: pc12_10d_α1ACT_2


title: ChIP-seq KYM1 WDR5 DMSO rep3

value: 0.01% DMSO for 4 hours


title: Rex-expressing-CEM-1


title: 1_miRNA

value: macrophage


title: 87_mRNA

data_processing:
Low quality read ends as well as remaining parts of sequencing adapters were clipped off using Cutadapt (v 1.14)  with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the mouse genome (mm10 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 0 -M -t exon -g gene_id and Ensembl gene annotations (GRCm 38.79)
Differential gene expression was assessed using R/edgeR (v 3.26.8) using TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file containing raw counts for each sample

value: unsupplemented/LTA stimulated


title: DHA+LTA2_mRNA

value: DHA supplemented/LTA stimulated


title: 84_mRNA


title: S-46717

city: Amsterdam

first: Rodrigo

last: Leite de Oliveira

address: De Boelelaan 1118

institute: Amsterdam UMC / location VUmc

data_processing:
Reads were aligned to the prebuilt reference GRCh38 genome_snp_tran using HiSAT2 version 2.2.1
Genecounts were generated by counting mapped reads overlapping genes defined in Ensembl GTF release 95 using a Htseq-count union strategy
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files with genecounts for Ensembl gene id's

source_name: SUM159 P+I R1

growth_protocol: A549 cells were grown in RPMI (Gibco) supplemented with 10% FBS, 1% P/S and 2 mM L-glutamine. SUM159  was grown in DMEM/F12 (Gibco) supplemented with 10% FBS, 1% P/S, 5 µg/ml insulin (Sigma-Aldrich) and 1µg/ml hydrocortisone (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen, cat# 74106) including a column DNase digestion (Qiagen, cat#79254).
Illumina stranded mRNA prep

treatment_protocol: The cells were treated with 2µM Palbociclib,  3µM of indisulam and the combniation for 16h.

tag: tissue

value: breast cancer

value: Palbocicilib + Indisulam


title: RAW LTA1_mRNA


title: S-46716

source_name: SUM159 IN R2

value: Indisulam


title: S-46718

source_name: SUM159 P+I R2


title: pc12_10d_pcDNA3_1


title: ChIP-seq KYM1 WDR5 DMSO rep2


title: pc12_3d_α1ACT_3

value: 3 days


title: ChIP-seq KYM1 WDR5 DMSO rep1


title: ChIP-seq KYM1 IgG rep3


title: pc12_3d_α1ACT_2


title: DHA+LTA3_mRNA


title: ChIP-seq KYM1 WDR5 C16 rep3


title: ChIP-seq KYM1 IgG rep2


title: S-46715

source_name: SUM159 IN R1


title: 93_mRNA

value: AA supplemented/LTA stimulated


title: 91_mRNA


title: 3_mRNA

value: unsupplemented/unstimulated


title: 92_mRNA


title: pc12_3d_pcDNA3_2


title: PRO-seq G401 C16 rep1

value: G401 cells

value: 500 nM C16 for 2 hours


title: pc12_3d_α1ACT_1

value: stably expressing pcDNA3 alpha1ACT


title: ChIP-seq KYM1 IgG rep1


title: S-46712

source_name: SUM159 UT R2

value: untreated


title: ChIP-seq G401 WDR5 C16 rep2


title: ChIP-seq G401 WDR5 C16 rep3


title: S-46713

source_name: SUM159 PD R1

value: Palbociclib


title: pc12_10d_pcDNA3_2

value: 10 days


title: S-46711

source_name: SUM159 UT R1


title: ChIP-seq G401 WDR5 DMSO rep3


title: 2_mRNA


title: ChIP-seq G401 WDR5 C16 rep1

value: 500 nM C16 for 4 hours


title: pc12_3d_pcDNA3_1

value: stably expressing pcDNA3 blank vector


title: S-46710

value: lung cancer


title: pc12_24h_α1ACT_3

value: 24 hour


title: S-46709


title: DHA+LTA1_mRNA

value: macrophage

value: DHA supplemented/LTA stimulated


title: 1_mRNA


title: pc12_24h_α1ACT_2


title: pc12_3d_pcDNA3_3


title: pc12_24h_α1ACT_1


title: S-46708

source_name: A549 IN R2


title: ChIP-seq G401 WDR5 DMSO rep1

value: 0.01% DMSO for 4 hours


title: pc12_24h_pcDNA3_3


title: RAW LPS1

description: RAW.counts

data_processing:
Low quality read ends as well as remaining parts of sequencing adapters were clipped off using Cutadapt (v 1.14)  with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the mouse genome (mm10 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file containing raw counts for each sample

treatment_protocol: The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LPS (1 µg/mL; from E. coli serotype 0111:B4).

tag: supplemented

value: unsupplemented

tag: stimulated

value: LPS


title: pc12_24h_pcDNA3_2


title: RAW LPS3

description: RAW.counts


title: ChIP-seq G401 IgG rep2


title: S-46714

source_name: SUM159 PD R2

value: breast cancer


title: pc12_24h_pcDNA3_1


title: RAW LPS2

description: RAW.counts


title: S-46705

source_name: A549 PD R1


title: ChIP-seq G401 WDR5 DMSO rep2


title: ChIP-seq G401 IgG rep3


title: RAW DHA+LPS3

description: RAW.counts

value: DHA supplemented


title: S-46707

source_name: A549 IN R1

value: Indisulam


title: S-46706

source_name: A549 PD R2


title: pc12_6h_α1ACT_3

value: 6 hour


title: RAW DHA+LPS2

description: RAW.counts


title: S-46704

source_name: A549 UT R2


title: ChIP-seq G401 IgG rep1

value: G401 cells


title: RNAseq_Jurkat_WT_Rep3

description: RNA sequencing

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25 –interleaved --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --interleaved --overlap 20 --minimum-length --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the human reference genome (hg19) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts).
Transcripts were assembled using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (release 19).
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts from STAR output: <gene ID> <counts for unstranded RNA-seq> <counts for the 1st read strand aligned with RNA> <counts for the 2nd read strand aligned with RNA>
Supplementary_files_format_and_content: Gene abundance from stringtie output: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>

source_name: Jurkat T-ALL cell line

growth_protocol: Cells were maintained in suspension culture at a density between 0.3X10^6 and 1X10^6 in 90% GlutaMAX supplemented RPMI 1640, 10%FBS. Cells were split 1:2 to 1:4 every 2-4 days.

extract_protocol:
Cells were harvested by centrifugation and RNA was extracted using the Qiagen RNeasy Mini Kit.
500 ng of RNA was used going into the KAPA stranded mRNA-seq library preparation kit used according to manufacturer's recommendations

value: Jurkat

tag: genotype

value: WT


title: RAW54

description: RAW.counts

value: AA supplemented


title: RNAseq_Jurkat_WT_Rep2

description: RNA sequencing


title: S-46703

source_name: A549 UT R1

value: untreated


title: pc12_6h_α1ACT_1

value: stably expressing pcDNA3 alpha1ACT


title: RNAseq_Jurkat_WT_Rep1

description: RNA sequencing


title: RAW53

description: RAW.counts


title: Biliary epithelial cells - HL11 CD133-

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
HL11minus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt

data_processing:
Base call data generated by Illumina NextSeq 550, NextSeq 2000
Read quality assessed using FastQC (v.0.11.9) and MultiQC (v.1.3.dev0).
Adapter and poly-G trimming with Cutadapt (v.1.16).
Read alignment with STAR (v.2.7.1a).
Read counting with featureCounts (Rsubread Bioconductor package v.2.0.1).
Differential expression computed using DESeq2 (v.1.26.0).
Genome_build: GRCh38.99
Supplementary_files_format_and_content: Tab separated matrix tables with raw gene counts for all genes and every sample

source_name: biliary epithelium

growth_protocol: Sorted hBEC were grown as organoids by plating onto low-adherence plates (Greiner) in hemispheres of growth factor reduced Matrigel (Corning) and grown in hBEC Expansion Medium: Advanced DMEMF12 +1%P/S, 1% Glut containing 10%FCS, 10 mM HEPES pH7, 10 mM Nicotinamide, 1x N2 Supplement, 1x B27 Supplement, 50 ng/ml EGF, 10 nM Gastrin, 100 ng/ml FGF-10, 25 ng/ml HGF, 500 ng/ml R-Spondin 1, 1.25 mM NAC, 5 uM A-83-01 and 10 uM Forskolin. For the first three days of culture medium was supplemented with 100 ng/ml Noggin, 100 ng/ml Wnt and 10 uM Y27632. Medium was changed every three days and cells passaged once confluent every 7 to 10 days. Cells were routinely tested for mycoplasma contamination using MycoAlert Assay Control set (Lonza).

extract_protocol:
Cryopreserved sections (or fresh samples of tissue) were defrosted at room temperature and digested for 30 min at 37°C in a solution of Collagenase (2 ug/ml, Gibco)-Dispase (1 ug/ml, Gibco)-Bovine Fetal Calf Serum (2% FCS, Gibco) in Advanced DMEMF12 (LifeTech) supplemented with 1% Penicillin/Streptomycin (P/S, Gibco) and 1% L-Glutamine (Glut, Gibco). When the intrahepatic bile ducts could be observed by microscope inspection the sample was centrifuged at 100g for 5 mins, resuspended in Versene (Thermo Fisher) and incubated at 37°C for 1 hour. Dissociated cells were filtered through a 40 um cell strainer and washed in Advanced DMEMF12. Cells were resuspended in Advanced DMEMF12 underlayered with an equal volume of 20% and 50% (v/v) Percoll (Sigma). Following centrifugation at 1800g for 30 mins at 4°C, the HPC rich fraction lying between the 20 and the 50% Percoll layers was collected, washed and re-suspended in PBS with 2% FCS and 100 mmol EDTA (Sigma) for FACS staining procedure. Cells were incubated for 1 hour with EpCAM-BV650 conjugated antibody, CD24-BV421, CD133-APC, CD45-488 and CD31-488 at the concentrations stated in Table 1. Samples were stained with SYTOX-AADvanced dead cell stain kit (ThermoFisher) prior analysis in a FACSAria Fusion (BD Biosciences). Trigger pulse width was used to exclude cell doublets from analysis and collection.
For library preparation, 1ng of each total RNA sample was fragmented to a size appropriate for sequencing based on the level of degradation assessed using an Agilent Bioanalyser (Agilent), and cDNA was generated using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio, # 634411). AMPure XP beads (Beckman Coulter) were then used to purify the cDNA library. Depletion of ribosomal cDNA was achieved using ZapR and R-probes. The library fragments originating from rRNA (18S and 28S) and mitochondrial rRNA (m12S and m16S) were cut by ZapR in the presence of R-probes (mammalian-specific). R-probes were hybridized to ribosomal RNA and mitochondrial rRNA sequences derived from the human mitochondrial genome and are therefore strictly human specific. Uncleaved fragments were then enriched by 15 cycles of PCR before a final purification using AMPure XP beads (Beckman Coulter). Completed libraries were quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA HS assay and assessed for quality and size distribution of library fragments using the Agilent Bioanalyser and the DNA HS kit (Agilent).

value: CD133- biliary epithelial cells

tag: disease state

value: steatotic

tag: individual


title: pc12_6h_pcDNA3_2

source_name: pc12 cells

value: stably expressing pcDNA3 blank vector


title: pc12_6h_pcDNA3_1


title: RAW50

description: RAW.counts

value: macrophage


title: Biliary epithelial cells - HL9 CD133-

description:
HL9minus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt


title: RNAseq_Jurkat_TET2KO_Rep3

description: RNA sequencing

treatment_protocol: TET2 KO cells were generated by transfecting JURKAT cells with px 458 (Addgene) containing a guide RNA targeting exon 3 near the start of the catalytic domain. Transfected cells were single cell sorted into a 96 well plate and clonally expanded before genotyping by PCR and sanger sequencing to confirm the KO.

value: TET2 KO


title: Biliary epithelial cells - HL11 CD133+

description:
HL11plus
Biliary epithelial cells of biliary origin.
Due to a corrupted file, only three lanes (1,2,4) available for sample HL11plus.
hBEC_gene_counts_matrix.txt

value: CD133+ biliary epithelial cells


title: RAW10

description: RAW.counts

value: unstimulated


title: RNAseq_Jurkat_TET2KO_Rep2

description: RNA sequencing


title: RAW9

description: RAW.counts


title: Biliary epithelial cells - HL9 CD133+

description:
HL9plus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt


title: RNAseq_Jurkat_TET2KO_Rep1

description: RNA sequencing


title: RAW8

description: RAW.counts


title: RNAseq_DND41_WT_Rep3

description: RNA sequencing

source_name: DND41 T-ALL cell line


title: WT 37C B [SB1405G]

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

data_processing:
Relative abundances (reported as TPM values [Li et al PMID 21816040]) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the preprocessed reads and mRNA sequences using KALLISTO version 0.46.0 [Bray et al PMID 27043002]. Further analysis was restricted to transcripts with TPM ≥ 10 in at least one sample.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.30.8 [Ritchie et al PMID 25605792, Smyth et al PMID 16646809].  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change ≥ 1) for a given contrast.
Genome_build: GCA_000170175.2
Supplementary_files_format_and_content: All processed data files are tab-delimited text (generated as abundance.tsv by kallisto)

organism: Coccidioides posadasii str. Silveira

source_name: WT 37C_liquid culture

growth_protocol: Duplicate mycelial cultures of each strain were grown by inoculation of 5 x 107 arthroconidia into 100 ml of 2X GYE and then incubated with shaking at 180 rpm for 48 h at 28°C. Spherule cultures of Silveira and Δryp1 were also grown in duplicate by inoculating 100 ml of modified Converse liquid medium with 3 x 108 arthroconidia and growing them at 38°C with 20% CO2, with shaking at 180 rpm for 48 h (Mandel et al 2006 PMID: 16857399).

extract_protocol:
RNAs were isolated using a modified acid-phenol prep as described previously (Mandel et al 2006 PMID: 16857399) with the modification that liquid N2 grinding was used to initially disrupt the cells. RNAs were resuspended in diethyl pyrocarbonate-treated dH2O prior to assessment of their quality and concentration with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA-seq libraries were prepared as previously described (Rodriguez et al 2019, PMID 31568523). Briefly, for the isolation of mRNAs, five μg total RNA from each sample was subjected to poly-A purification using Dynabeads Oligo (dT)25(Invitrogen-ThermoFisher). RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit (NEB). Quality of the total RNA, mRNA and library was confirmed using Bioanalyzer (Agilent).

tag: temperature

tag: replicate

value: B


title: ryp1 37C B [SB1405H]

source_name: ryp1 37C_liquid culture


title: RAW DHA6

description: RAW.counts

value: DHA supplemented


title: Biliary epithelial cells - HL6 CD133+

description:
HL6plus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt


title: RNAseq_DND41_WT_Rep2

description: RNA sequencing


title: RAW DHA+LPS1

description: RAW.counts

value: LPS


title: pc12_6h_α1ACT_2

value: 6 hour


title: WT 37C A [SB1405E]

value: A


title: Biliary epithelial cells - HL5 CD133-

description:
HL5minus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt

value: healthy


title: RNAseq_DND41_WT_Rep1

description: RNA sequencing

value: WT


title: RAW DHA4

description: RAW.counts


title: WGBS_Jurkat

description: Whole genome bisulfite sequencing

data_processing:
Paired-end reads from sequencing were trimmed using trimgalore (v0.4.4, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), removing low quality (Q30) bases and adapter sequences, and clipping 10 bases from each end of the read pairs.
Trimmed reads were then mapped to hg19 using BSMAP (v2.90) with default parameters to report unique pairs with a 17 base pair minimal insert size and 600 base pair maximum insert size
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Only CpGs covered by at least 10 reads were considered for downstream analyses.
genome build: hg19
processed data files format and content: Bedgraph file containing methylation rates for CpGs covered by at least 10 reads: <chr> <start> <end> <methylation rate>

extract_protocol:
Cells were harvested by centrifugation and genomic DNA was extracted using the PureLink Genomic DNA Mini Kit.
100 ng of gDNA was sheared by sonication and then bisulfite converted using the Zymo EZ DNA Methylation Gold Kit. Bisulfite converted DNA was then immediately processed using the Swift Biosciences Accel-NGS Methyl-Seq library kit according to manufacturer's instructions

value: Jurkat


title: RAW27

description: RAW.counts


title: ryp1 RT B [SB1405D]

source_name: ryp1 RT_liquid culture

value: RT


title: ryp1 RT A [SB1405C]


title: RAW3

description: RAW.counts

value: unsupplemented


title: Biliary epithelial cells - HL4 CD133-

description:
HL4minus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt

value: CD133- biliary epithelial cells


title: WT RT B [SB1405B]

source_name: WT RT_liquid culture


title: WGBS_Jurkat_TET2KO

description: Whole genome bisulfite sequencing


title: RAW2

description: RAW.counts


title: Biliary epithelial cells - HL4 CD133+

description:
HL4plus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt


title: WGBS_DND41

description: Whole genome bisulfite sequencing


title: WT RT A [SB1405A]


title: RAW1

description: RAW.counts


title: Tob5d

status: Public on Mar 02 2022

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: P. aeruginosa PA14 clone obtained under selective pressure of the antibiotic tobramycin

data_processing:
Rockhopper was used for aligning reads and for calculating Reads per Kylobase per Million (RPKM). Default parameters for paired-end, strand-specific reads
Those genes with a level of expression below 15 Reads per Kilobase per Million (RPKM) in the wild-type strain or in the mutant were discarded for further analysis.
The fold change threshold for the genes up- or down-regulated in the mutants compared to the wild-type was settled at 1.5 and 0.75, respectively.
Genome_build: NC_008463
Supplementary_files_format_and_content: Excel file with with raw gene counts and RPKM, as calculated by Rockhopper, for every gene and every sample, and fold changes for every gene of each mutant compared to the WT strain. Additional sheets containing only with genes with significative changes in expression in each mutant

organism: Pseudomonas aeruginosa

source_name: Laboratory evolution experiment

growth_protocol: Overnight cultures of P. aeruginosa PA14, Tgc5d, Tob5d and Caz5d were used to inoculate 20 ml of LB medium to a final OD600nm of 0.01 and were grown until exponential phase (OD600nm = 0.6).

extract_protocol:
Ten milliliters of each culture was centrifuged at 7,000 rpm and 4°C for 20 min. Five hundred seventy microliters of TE buffer (10 mM Tris-HCl, 1 mM EDTA [pH 8.0]) and 30 μl of lysozyme (Sigma) from a 20 mg/ml stock, for a final concentration of 1 mg/ml, were added to each sample. Afterwards, the samples were mixed by vortexing for 10 s and were incubated at room temperature for at least 10 min with regular vortexing. A volume of 2,100 μl of buffer RLT (Qiagen) was added, and samples were sonicated twice for 5 to 10 s (constant frequency, 0.45 Hz). Then, 1,410 μl of ethanol was added and the protocol continued using the RNeasy minikit (Qiagen), according to the manufacturer's instructions. In order to eliminate any residual DNA, a DNase I (Qiagen) treatment was carried out, according to the manufacturer's instructions. A second treatment was performed using Turbo DNA-free (Ambion).
RNAs obtained from three independent cultures of each strain were pooled and RNA-sequencing (RNA-seq) was performed at the Next Generation Sequencing Service of the Centre for Research in Agricultural Genomics by using paired end format lectures (2x75bp) in an Ion PGM™ Sequencer

tag: strain

tag: antibiotic resistant

value: tobramycin


title: Caz5d

description: P. aeruginosa PA14 clone obtained under selective pressure of the antibiotic ceftazidime

value: ceftazidime


title: orfN*

description: P. aeruginosa PA14 clone obtained under selective pressure of the antibiotic tigecycline in plate

data_processing:
Rockhopper was used for aligning reads and for calculating Reads per Kylobase per Million (RPKM). Default parameters for paired-end, strand-specific reads
Those genes with a level of expression below 15 Reads per Kilobase per Million (RPKM) in the wild-type strain or in the mutant were discarded for further analysis.
The fold change threshold for the genes up- or down-regulated in the mutants compared to the wild-type was settled at 1.5 and 0.75, respectively.
Genome_build: NC_008463
Supplementary_files_format_and_content: Excel file with raw gene counts and RPKM, as calculated by Rockhopper, for every gene and every sample, and fold changes for every gene of each mutant compared to the WT strain. Additional sheets containing only with genes with significative changes in expression in each mutant

source_name: Single-step tigeclycine resistant mutant selected in plate

growth_protocol: Overnight cultures of P. aeruginosa PA14, Tgc5d, Tob5d, Caz5d and orfN* were used to inoculate 20 ml of LB medium to a final OD600nm of 0.01 and were grown until exponential phase (OD600nm = 0.6).

value: tigecycline, tobramycin, ceftazidime


title: Tgc5d

description: P. aeruginosa PA14 clone obtained under selective pressure of the antibiotic tigecycline

value: tigecycline


title: Biliary epithelial cells - HL6 CD133-

description:
HL6minus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt

value: steatotic


title: ryp1 37C A [SB1405F]


title: PA14(WT)

description: P. aeruginosa wild-type PA14 strain

source_name: Laboratory collection


title: ΔsbrH1-R,6 day

city: Harbin

first: Lan

last: Ye

address: No. 59 Mucai Street

country: China

institute: Northeast Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Genomic localization analysis of sequence using Bowtie 2.2.3
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were estimation of gene expression level (Trapnell, Cole, et al., 2010)
Genome_build: GCF_000092385.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Streptomyces bingchenggensis

source_name: Soil

extract_protocol:
The mycelia were collected,flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: High-yielding strain


title: ΔsbrH1-R,3 day


title: BC-101-4,6 day

value: wild type


title: BC-101-4,3 day


title: Biliary epithelial cells - HL5 CD133+

description:
HL5plus
Biliary epithelial cells of biliary origin.
hBEC_gene_counts_matrix.txt

value: CD133+ biliary epithelial cells


title: 04_3D_FGF2_1_01292020

city: Albany

first: Susan

middle: Ellen

last: LaFlamme

state: New York

address: 47 New Scotland Ave

department: Regenerative and Cancer Cell Biology

institute: Albany Medical Center

description: spheroids expressing proacinar markers

hyb_protocol: Samples were hybridized to the Affymetrix Clariom D Assay, Mouse for 16-18 h at 45°C.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000

data_processing: Data were processed using Transcriptome Analysis Console software and R/Rstuio. The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method. Values are presented according to log2 RMA signal intensity. We defined the genes with a fold-change of more than 1.99 or less than 1.99 and a p-value of less than 0.05 as different expression genes

label: biotin

source_name: Spheroids cultured in Pro-A

label_protocol: Samples were enzymatically fragmented and biotinylated by terminal deoxynucleotidyl transferase (TdT) (Clariom D Kit)

growth_protocol: mSG-PAC1 cells were cultued in matrigel as spheroid in medium that promoted myoepithelial differentiation (Pro-M-medium) or proacinar differentiation (Pro-A medium)

extract_protocol: Total RNA was extracted using RNeasy Mini-Kit (Qiagen), then cDNA synthesis and amplification (Clariom D Kit)

treatment_protocol: Pro-M medium - DMEM containing 10%FBS; Pro-A medium - modified MCF10A medium consisting of DMDMF12, 5% horse serum and 100ng/ml FGF2

value: pro-acinar


title: SL_19_F_3D_2_10102119

description: spheroids expressing proacinar markers


title: proQ mutant with empty vector 2

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

country: Australia

institute: Monash University

data_processing:
raw fastq files were aligned to the Pasturella multocida reference VP191,(NZ_CP048792.1) and aligned using R subread (Liao, Smyth, and Shi 2019).
Reads were quantified with featureCounts (Liao, Smyth, and Shi 2014) producing the raw gene count matrix. The QC for the raw genes counts matrix and various quality control metrics were summarised in a MultiQC report (Ewels et al. 2016).
Raw counts were then analyzed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: Pasturella multocida reference VPM191,(NZ_CP048792.1)
Supplementary_files_format_and_content: raw gene counts, text file, comma separated

organism: Pasteurella multocida

source_name: Bacterial cells

growth_protocol: Grown to OD600=0.6 in Heart Infusion Broth

extract_protocol:
Phenol:Choloform extraction
Agilent SureSelect Strand-Specific RNA Library Prep kit

value: AL2973 proQ mutant with vector pPBA1100S; SpecR

value: proQ mutant

tag: expression

value: lack of ProQ protein


title: proQ mutant with empty vector 1

tag: treatment


title: proQ mutant with empty vector 3


title: 03_3D_FGF2_1_01292020

description: spheroids expressing proacinar markers


title: Complemented proQ mutant 2

value: AL2973 proQ mutant provided with an intact copy of proQ on pAL1449; SpecR

value: complemented proQ mutant

value: overexpression of ProQ protein


title: Wild-type with empty vector 2

value: Wild type strain VP161 containing vector pPBA1100S; SpecR

value: control


title: Complemented proQ mutant 1


title: SL_13_DMEM_1_10102019

description: spheroid expressing myoepithelial markers

source_name: Spheroids cultured in Pro-M

value: myoepithelial like


title: SL_14_DMEM_1_10102019


title: S3C

city: Yangzhou

last: Zhang

address: 48 Wenhui Road

institute: Yangzhou university

description: Pyrus calleryana Decne

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
The resulting clean data was mapped to the P. betuleafolia genome (https://ngdc.cncb.ac.cn/gwh/Assembly/647/show) with the Hisat2 program
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
Genome_build: Pyrus betulifolia Genome v1.0
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.xls)

organism: Pyrus calleryana

source_name: Callery pear

growth_protocol: Fifteen-year-old callery pears growing in the garden of the College of Horticultural and Plant Protection, Yangzhou University, Jiangsu province, China

extract_protocol:
Total RNA was extracted by the ethyl ammonium bromide (CTAB) method using seeds collected at 0, 20 and 50 days after cold stratification with three biological replicates.
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Seeds were separated from mature fruits, washed to remove pulp, and dried in the shade with ambient temperature. After 24 h water uptake (imbibition), the imbibed pear seeds were placed on petri dishes with wet filter paper and then held in cold storage (4°C) for fifty days. The filter paper was moistened with water every 2–3 d. Seed samples were harvested at 0, 20 and 50 days after cold stratification

value: imbibed pear seeds, sampled 50 days after cold stratification

value: seed


title: Wild-type with empty vector 1


title: 01_3D_DMEM_1_01292020


title: S3B

description: Pyrus calleryana Decne


title: S2A

description: Pyrus calleryana Decne

value: imbibed pear seeds, sampled 20 days after cold stratification


title: S1C

description: Pyrus calleryana Decne

value: imbibed pear seeds without cold stratification


title: S1B

description: Pyrus calleryana Decne


title: S2C

description: Pyrus calleryana Decne


title: S1A

description: Pyrus calleryana Decne


title: Wild-type with empty vector 3


title: M. incognita RNA-seq M-1

city: Kunming

first: Chao-Jun

last: Lu

state: Yunnan

address: No. 2 Cuihu North Road

institute: Yunnan University

description: Meloidogyne incognita middle stage of second stage juveniles replicate1

data_processing:
CASAVA was used  for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M.incognita whole genome using TopHat2 with defaul parameters
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced were calculated using a protocol from Trapnell, Cole, et al., 2010.
Genome_build: M. incognita reference genome: PRJEA28837(BioProject)
Supplementary_files_format_and_content: fpkm

organism: Meloidogyne incognita

source_name: second stage juveniles

extract_protocol:
Total RNA of individual sample was extracted with Trizol reagent from TaKaRa
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: middle stage juveniles


title: M. incognita RNA-seq M-3

description: Meloidogyne incognita middle stage of second stage juveniles replicate3

value: wild type


title: M. incognita RNA-seq E-2

description: Meloidogyne incognita early stage of second stage juveniles replicate2

value: early stage juveniles


title: M. incognita RNA-seq E-1

description: Meloidogyne incognita early stage of second stage juveniles replicate1


title: Complemented proQ mutant 3


title: M. incognita RNA-seq E-3

description: Meloidogyne incognita early stage of second stage juveniles replicate3


title: S68 Sample3 [S3]

city: Beijing

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

data_processing:
Illumina HiSeq software used for basecalling.
Data were filtered using the fastp to delete adaptor, 10% N reads and Get rid of more than 50% of READs with a mass value below 20.
RNA-seq reads were aligned to the Stropharia rugosoannulata S68 genome assembly using E hisat2.
The transcript of sample was assembled by StringTie.
Peaks were called using PeaksFind version 2.2 with the following setting, StringTie was used statistis.
Genome_build: Stropharia rugosoannulata S68
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Stropharia rugosoannulata

source_name: Fungi

growth_protocol: The mycelium was cultivated on PDA plates at 25 °C

extract_protocol:
Total RNA  was extracted using Plant RNA kit (OMEGA), following the manufacturer’s instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mycelia were harvested by filtering and ground in liquid nitrogen

tag: locality

value: Heilongjiang province, China

value: Heinong No.1

tag: development stage

value: mycelium


title: S68 Sample2 [S2]


title: Plasmodium single-nucleus RNA-seq (snRNAseq_PrimeB)

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

institute: EMBL Heidelberg

description: single-nucleus RNA-seq

data_processing:
10xGenomics' Cellranger software package (v3.0.2) was used for all preprocessing steps for 10xGenomics data.
The basecaller "freeIbis" was used for SmartSeq2 samples (Bioinformatics. 2013 May 1;29(9):1208-9) and "leeHom" was used to trim adapters and merge Illumina sequencing reads afterwards (Nucleic Acids Res. 2014 Oct;42(18):e141). "deML" was used for robust demultiplexing of Illumina sequences for SmartSeq2 samples (Bioinformatics. 2015 Mar 1;31(5):770-2).
Sequencing reads were mapped against the Physarum polycephalum reference transcriptome (Glockner & Marwan 2017 Sci Rep) using STAR with either Cellranger's built in function for 10xGenomics samples or with a local STAR installation for SmartSeq2 samples (Dobin et al. 2013 Bioinformatics).
Gene expression levels were estimated by custom Perl scripts as TPM values for SmartSeq2 samples or based on UMI counts for 10x Genomics samples, respectively.
Genes without an UniProt annotation (Glockner & Marwan 2017 Sci Rep) were removed from all sample/gene matrices and final data sets were loaded and analyzed using Seurat (Stuart et al. 2019 Cell).
Genome_build: Physarum polycephalum transcriptome (Glockner & Marwan 2017 Sci Rep)
Supplementary_files_format_and_content: Matrix and tsv files are cellranger outputs ready to be loaded by Seurat (Stuart et al. 2019 Cell)
Supplementary_files_format_and_content: RDS files are Seurat objects containing all relevant information for Spatial Transcriptomics data files.

organism: Badhamia polycephala

source_name: Single plasmodium nuclei

growth_protocol: Physarum polycephalum was cultivated as Microplasmodia in a liquid culture and 100-500 uL of microplasmodia suspension was placed on Agar to induce plasmodium network formation as recently described (Bauerle et al. 2017 Journal of Physics D: Applied Physics).

extract_protocol:
Dounce homogenization to obtain nuclei suspension / FACS / 10x Genomics 3' chemistry kit v3
10x Genomics 3' chemistry kit v3

tag: life cycle stage

value: Plasmodium

tag: plasmodium part

value: Whole plasmodium


title: Plasmodium single-nucleus RNA-seq (snRNAseq_SecNet)

description: single-nucleus RNA-seq

value: Network enriched


title: Plasmodium single-nucleus RNA-seq (snRNAseq_PrimeA)

description: single-nucleus RNA-seq


title: Amoeba single-cell RNA-seq (scRNAseq_AmoebaA)

description: single-cell RNA-seq

source_name: Single amoeba cells

extract_protocol: 10x Genomics 3' chemistry kit v3


title: Spatial Transcriptomics 384 well plate (Spatial_T_H7B)

description:
bulk RNA-seq
Spatial_T.RDS

source_name: Plasmodium pieces

extract_protocol:
SmartSeq2 (Wollny et al. 2016 bioRxiv / Picelli et al. 2013 Nat Methods)
Illumina Nextera


title: Spatial Transcriptomics 384 well plate (Spatial_T_H7A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Amoeba single-cell RNA-seq (scRNAseq_AmoebaB)

description: single-cell RNA-seq


title: Plasmodium single-nucleus RNA-seq (snRNAseq_SecFan)

description: single-nucleus RNA-seq

value: Fan enriched


title: Spatial Transcriptomics 384 well plate (Spatial_T_H9B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H8B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H5B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H8A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H3B)

description:
bulk RNA-seq
Spatial_T.RDS


title: S3A

first: Jing

description: Pyrus calleryana Decne

tag: tissue


title: M. incognita RNA-seq M-2

description: Meloidogyne incognita middle stage of second stage juveniles replicate2


title: Spatial Transcriptomics 384 well plate (Spatial_T_H6A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H6B)

description:
bulk RNA-seq
Spatial_T.RDS


title: S2B

description: Pyrus calleryana Decne


title: Spatial Transcriptomics 384 well plate (Spatial_T_H5A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H2B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H4B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H2A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H3A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H1B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H1A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H12B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G9A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H11B)

description:
bulk RNA-seq
Spatial_T.RDS


title: S68 Sample1 [S1]


title: Spatial Transcriptomics 384 well plate (Spatial_T_G8B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H10A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H10B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G8A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G6A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H9A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G6B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G7B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G7A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G5A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G5B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G4B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_H4A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G3B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G4A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G2B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G2A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G1B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G3A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G1A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G12B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G11B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G10B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G10A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F9B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_G9B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F8A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F7B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F6A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F6B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F5A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F5B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F7A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F4B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F2A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F2B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F1B)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F3A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F4A)

description:
bulk RNA-seq
Spatial_T.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_T_F12B)

description:
bulk RNA-seq
Spatial_T.RDS