title: sbrotila

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

data_processing:
cellranger pipeline using default parameters with forced recovery of 10000 cells for each library
cells filtered for minimum 250 (vs2) or 350 (vs3) detected genes
library names were appended to barcodes from individual libraries
Assembly: Reads were mapped to a customized transcriptome generated by cellranger::mkref with AUR.transcripts.gtf and AUR.transcripts.fa as input files
Assembly: AUR.transcripts.gtf mapping coordinates for generating the mapping tool
Assembly: AUR.transcripts.fa : transcriptome sequences for generating the mapping tool in fasta format
Supplementary files format and content: polyp.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: polyp2.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: polyp.clover.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: strobila.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: ephyra.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: medusa.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: mT.gastrodermis.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: mT.manubrium.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: mT.margin.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: mT.umbrella.matrix.mtx: Matrix Market format count matrix after demultiplexing, mapping, UMI reduction and filtering
Supplementary files format and content: polyp.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: polyp2.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: polyp.clover.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: ephyra.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: strobila.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: medusa.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: mT.manubrium.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: mT.margin.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: mT.umbrella.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: mT.gastrodermis.samples.csv ; sample (column) names for corresponding mtx file
Supplementary files format and content: genes.csv ; gene (row) names for all mtx files

organism: Aurelia coerulea

source_name: 5 individuals

extract_protocol:
Whole embryos, animals, or dissected tissues were  incubated in calcium-magnesium free artificial sea water, followed by an incubation in 300μl Collagenase/Dispase Blend I (Merck) at RT for 30 minutes.  Mechanical force was used to disrupt the tissues and obtain single-cell suspensions. Cell suspensions were washed with 0.1% BSA (bovine serum albumin), and cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted to 1000 cells/ microliter and loaded into a 10x Genomics single cell platform using vs2 or vs3 reagents.
10X Genomics Chromium v2/v3 chemistry according to manufacturer protocols

value: 5 individuals

value: wild type lab strain


title: ephyra

status: Public on Dec 31 2025

type: SRA

library_source: transcriptomic single cell

molecule: total RNA

tag: tissue

tag: genotype


title: mT_gastrodermis

source_name: Tissue dissection from 8-10cm animal: gastrodermal tissue including gonadal region

value: Tissue dissection from 8-10cm animal:gastrodermal tissue including gonadal region


title: AML_190

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR and quantified with HT-Seq using the GRCh38 human assembly.
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions.
Libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform in accordance with the manufacturer’s protocol (paired-end 2 × 150 bp).

value: Bone marrow

tag: disease state

value: AML

tag: treatment


title: polyp


title: AML_189


title: polyp_clover


title: Col-0 12°C RNA-seq (replicate 1)

city: Austin

first: Sibum

last: Sung

state: TX

country: USA

institute: University of Texas at Austin

data_processing:
Reads generated by Illumina NovaSeq platform were checked for quality using FastQC
After quality assessment, reads were aligned on TAIR10 genome using HISAT2 for RNA-seq and Bowtie2 for ChIP-seq
SAM files generated from mapping were then converted into BAM files and sorted using Samtools
For the gene counting bedtools program was used which generates raw count using BAM files
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Assembly: TAIR10
Supplementary files format and content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample

organism: Arabidopsis thaliana

source_name: Whole rosettes

extract_protocol:
RNA was extracted using Qiagen, Rneasy Plant Mini kit.
Library was prepared using NEB illumina library preparation kit

value: Whole rosettes

value: Continous 12°C in short-day


title: AML_195


title: AML_187


title: AML_186


title: Col-0 22°C RNA-seq (replicate 2)

value: Continous 22°C in short-day


title: AML_185


title: AML_182


title: Col-0 22°C RNA-seq (replicate 1)


title: AML_193


title: AML_183


title: AML_184


title: Col-0 22°C RNA-seq (replicate 3)


title: vil1-1 22°C RNA-seq (replicate 1)


title: AML_172


title: mT_umbrella

source_name: Tissue dissection from 8-10cm animal: umbrellar tissue

value: Tissue dissection from 8-10cm animal:umbrellar tissue


title: mT_manubrium

source_name: Tissue dissection from 8-10cm animal: manubrial arm including stomodeum

value: Tissue dissection from 8-10cm animal:manubrial arm including stomodeum


title: AML_181


title: +P-HT root - 2

city: Higashi-Hiroshima

first: Lydia

middle: Ratna

last: Bunthara

state: Hiroshima

address: Kagamiyama 1-7-1

department: Graduate School of Integrated Sciences for Life

country: Japan

institute: Hiroshima University

description: Library name: Sample14

data_processing:
Preprocessing steps included trimming and cutting adapter using Trimmomatic ver. 0.39.2, followed by quality control assessment using FastQC ver. 0.14.0. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
RSEM ver. 1.3.3  was used for counting, producing the expected counts (Raw count) of gene for subsequent analyses. Then, differential expression genes (DEGs) analysis was conducted using the DESeq2 ver.1.44.0 package in R Statistical Software version 4.4.2. DESeq2 provide statistical routines for determining differential expression in coding sequence expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
The gene sequences and protein sequences were aligned against Swiss-Prot database (Apweiler et al., 2004), Eggnog ver.5.0 (Huerta-Cepas et al., 2019), and KEGG (Kanehisa et al., 2019) databases using BLASTX and BLASTP with an E-value threshold of 1E-5. Additionally, the amino acid sequences of proteins were annotated against the Pfam database (Finn et al., 2016) using HMMER (Eddy, 1998) with an E-value threshold of 1E-10.
Assembly: The clean data from each sample were mapped to GCF_012489685_LjGifu_v1.2_genomic.fna using star ver. 2.7.11a, generating BAM files for counting.
Supplementary files format and content: This file contains the results of differential gene expression analysis performed using DESeq2. Each row represents a gene, and the columns include the following information: Gene ID; The unique identifier for each gene. baseMean; The average normalized expression value of the gene across all samples in the comparison. log2FoldChange; The log₂-transformed fold change in gene expression between experimental conditions. Genes with values greater than 2 are considered upregulated, and values less than -2 are considered downregulated. lfcSE; The standard error of the log₂ fold change, indicating the variability of the fold change estimate. stat; The test statistic used to compute the p-value. pvalue; The unadjusted p-value, representing the probability that the observed difference in expression occurred by chance. padj; The adjusted p-value (false discovery rate, FDR), calculated using the Benjamini-Hochberg method to correct for multiple testing. Only genes with an absolute log₂ fold change greater than 2 and an adjusted p-value less than 0.05 were considered significantly differentially expressed.

organism: Lotus japonicus

source_name: whole root

growth_protocol: After germinating Lotus japonicus in agar medium, seedlings were transplanted into hydroponic container containing 1.5 L nutrient solution. Three plants were pooled to form one replicate, and five replicates were included for each treatment.

extract_protocol:
RNA extraction of shoot and root samples were performed using Favorgen Plant Total RNA Mini Kit (Favorgen Biotech, Ping-Tung, Taiwan), following the manufacturer's protocol.
Library preparation was performed by Rhelixa (Tokyo, Japan) using NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection; New England Biolabs, Ipswich, MA, USA) and NEBNext® Ultra™ ll Directional RNA Library Prep Kit (New England Biolabs). Sequencing was performed by Rhelixa using the NovaSeq 6000 (Illumina; San Diego, CA, USA) with 150 bp paired end.

treatment_protocol: Growth chambers were maintained under 16 h light (200 μmol m-2 s-1)/8 h at 23°C /22°C photoperiod for FT treatment and 16 h light (200 μmol m-2 s-1)/8 h dark at 30°C /29°C for HT treatment. Two P treatments were applied to represent P-deficient and P-sufficient conditions: 6.4 and 64 µM NaH2PO4-2H2O, designated respectively as -P and +P treatments.

value: whole root

value: sufficient P and high temperature


title: AML_180


title: mT_margin

source_name: Tissue dissection from 8-10cm animal: margin including rhopalium and tenatcles

value: Tissue dissection from 8-10cm animal:margin including rhopalium and tenatcles


title: +P-HT root - 1

description: Library name: Sample13


title: AML_177


title: medusa


title: Col-0 12°C RNA-seq (replicate 2)


title: -P-HT root - 1

description: Library name: Sample15

value: low P and high temperature


title: AML_176


title: polyp2


title: AML_174


title: AML_175


title: -P-HT root - 2

description: Library name: Sample16


title: AML_169


title: AML_173


title: AML_168


title: +P-FT root - 2

description: Library name: Sample10

value: sufficient P and favorable temperature


title: AML_170


title: AML_171


title: -P-HT shoot - 2

description: Library name: Sample8

source_name: whole shoot

value: whole shoot


title: -P-FT root - 2

description: Library name: Sample12

value: low P and favorable temperature


title: AML_163


title: AML_161


title: AML_162


title: -P-FT root - 1

description: Library name: Sample11


title: AML_167


title: +P-HT shoot - 2

description: Library name: Sample6


title: +P-FT root - 1

description: Library name: Sample9


title: AML_164


title: -P-HT shoot - 1

description: Library name: Sample7


title: AML_165


title: AML_159


title: AML_160


title: +P-HT shoot - 1

description: Library name: Sample5


title: -P-FT shoot - 2

description: Library name: Sample4


title: Retina, hemizygote, replicate 2 scRNAseq

city: Guangzhou

first: Jiamin

last: Ouyang

state: Guangdong

address: 7 Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

description:
Library name: Sample 8
10x Genomics

data_processing:
Bioinformatic analysis was performed using Omicsmart, a real-time interactive online platform for data analysis (http://www.omicsmart.com).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for all samples.

organism: Rattus

source_name: Retina

extract_protocol:
Retinas for rats at P14 were extracted and digested with 200 units papain (Worthington, LS003126) at 37℃ for 30min after perfusing transcardially with ice-cold saline. Retinas were submitted to BerryGenomics Co. Ltd for the scRNA-seq.
Briefly, single cells were captured to reverse transcription for library construction, partitioned through gel beads in emulsion (GEMs), barcoded cDNA, and sequenced on an NovaSeq platform (Illumina) to generate 150 bp paired-end Reads.

value: Retina

tag: cell type

value: Retinal cells

value: hemizygote

tag: Sex

value: Male

tag: time

value: postnatal day (P) 14


title: AML_166

value: Bone marrow

value: AML


title: Undifferentiated SH-SY5Y Neuronal Cell line, p10, DLD_17

city: Leipzig

first: Linnaeus

middle: Tapia

last: Bundalian

address: 15 Albert-Scwheitzer Str.

country: Germany

institute: Universitatklinikum Leipzig

data_processing:
nf-core rnaseq pipeline
extract counts from the DESeq2 dds object from the final output of the pipeline
Assembly: GRCh38
Supplementary files format and content: comma separated values of normalized counts extracted from dds object

growth_protocol: SH-SY5Y cells were purchased from the Leibniz Institute DSMZ − German Collection of Microorganisms and Cell Cultures. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 15% fetal calf serum (FCS) and glutamine (2 mM) in a humidified atmosphere containing 5% CO2 at 37°C. Cells were sub-cultured every 2−3 days once they reached a density of ~ 75%. Cells were discarded once they reached passage fifteen to prevent senescence.

extract_protocol:
Trizol based total RNA extraction with Promega columns. 500ng were used for library preparation
TruSeq RNA Library Prep v2

treatment_protocol: To ensure optimal cell growth cells were re-seeded at a density of ~ 3.500 cells/cm2 one day before transfection. Cells were collected via trypsinisation, counted, divided into the different experimental groups, and washed once with DPBS, which was removed afterwards. For transfection the NeonTM Transfection system (Invitrogen) was used according to the manufacturer’s instructions. We added either control siRNA or a pool of four WDFY3 siRNAs (see Supplementary Tab.  1) to the cell pellet to achieve an siRNA concentration of 10 nM in the culture medium following transfection. After transfection cells were added to pre-warmed medium and seeded in multiwell plates for further analysis and/or treatment.

tag: cell line

value: Neuronal Cell Line

value: control siRNA


title: +P-FT shoot - 2

description: Library name: Sample2


title: AML_158


title: Retina, heterozygote, replicate 1 scRNAseq

description:
Library name: Sample 4
10x Genomics

value: heterozygote

value: Female


title: +P-FT shoot - 1

description: Library name: Sample1


title: Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_13


title: Undifferentiated SH-SY5Y Neuronal Cell line, p19, DLD_18

value: WDFY3 siRNA


title: Retina, control, replicate 3 scRNAseq

description:
Library name: Sample 3
10x Genomics

value: WT


title: -P-FT shoot - 1

description: Library name: Sample3


title: Undifferentiated SH-SY5Y Neuronal Cell line, p9, DLD_06


title: Retina, control, replicate 2 scRNAseq

description:
Library name: Sample 2
10x Genomics


title: Retina, heterozygote, replicate 3 scRNAseq

description:
Library name: Sample 6
10x Genomics


title: Undifferentiated SH-SY5Y Neuronal Cell line, p11, DLD_10


title: Retina, hemizygote, replicate 1 scRNAseq

description:
Library name: Sample 7
10x Genomics


title: Undifferentiated SH-SY5Y Neuronal Cell line, p11, DLD_09


title: GS_M_180_Rep2

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

data_processing:
The RNA-seq analysis program in CLC Genomics Workbench v7.0 (CLC Bio-Qiagen, Aarhus, Denmark) was used for mapping and expression computation using default parameters except for paired-end distance (min distance = 200 and max distance = 400). Forward and reverse reads were interleaved, and the matched reads were counted as one paired read. Reads were imported into CLC Genomics Workbench and mapped to the reference transcriptome using CLC Map Reads to Reference tool. Mismatch score was set to one with a mismatch cost of two. A linear gap cost model was used with insertion and deletion costs set to three. The length fraction parameter was set to 0.5 and the similarity fraction parameter set to 0.8. For non-specific match handling, the “map randomly” setting was selected. Normalized measures of expression intensity, FPKM values, were computed from the read counts, the length of the targeted region, and total number of mapped reads.
Differential gene expression was investigated using the empirical differential gene expression (EDGE) test in CLC (Robinson & Smyth, 2008). Twelve two-group pairwise comparisons between three biological replicates of one condition and three biological replicates of another condition were made between the untreated, 15, 60, and 180 MAT time points of GR RR young tissue and GS young tissue, GR RR mature tissue and GS mature tissue, and GR RR young tissue and GR RR mature tissue. These three comparisons were made to investigate differences between GR and GS biotypes as well as developmental differences between young and mature tissue to investigate the resistance mechanism resulting in the rapid-response phenotype after glyphosate treatment. DEG lists were further narrowed using the following cutoffs: expression threshold of ≥3 FPKM in at least one sample to be considered transcriptionally active, log2 fold change ≥2 between compared groups and False Discovery Rate (FDR) adjusted P ≤0.05 at any time point from each of the three comparison groups described above
Genome_build: TSA GIMT00000000
Supplementary_files_format_and_content: Microsoft Excel worksheet file containing FPKM values and statistical analysis for each sample

organism: Ambrosia trifida

source_name: Leaf tissue

growth_protocol: All plants were grown in the greenhouse in commercial potting mix (Fafard Custom Mix, Sun Gro Horticulture, 770 Silver Street, Agawam, MA 01001), and a photoperiod of 14 h light, 25 °C/10h dark, 20 °C.

extract_protocol:
Leaf samples were frozen immediately in liquid nitrogen and ground separately for total RNA extraction using the RNeasy kit and protocols (Qiagen, Hilden, Germany).
Library preparation, sequencing and quality filtering was completed by Fasteris DNA Sequencing Service (Geneva, Switzerland). Illumina sequencing for 150 bp paired-end reads was conducted for the 48 samples using bar-coded adapters with six samples multiplexed in each lane of an eight-lane flow cell on an Illumina HiSeq2500.

treatment_protocol: All glyphosate treatments were 0.84 kg ae ha-1 applied using a laboratory track sprayer calibrated at 187·L ha-1 spray volume with an 8002EVS single even flat-fan nozzle (TeeJet, Spraying Systems Co., Wheaton, IL).

tag: ecotype

value: Glyphosate susceptible

tag: leaf type

value: Mature


title: Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_01


title: GS_M_180_Rep1


title: GS_M_180_Rep3


title: Undifferentiated SH-SY5Y Neuronal Cell line, p9, DLD_05


title: Retina, control, replicate 1 scRNAseq

description:
Library name: Sample 1
10x Genomics


title: Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_14


title: Retina, heterozygote, replicate 2 scRNAseq

description:
Library name: Sample 5
10x Genomics


title: si-SOX5_H3K4me1, CUT&Tag seq

city: Shenzhen

first: Jiajie

last: Lin

address: 3025# Shennan Road

institute: The Eighth Affiliated Hospital, Sun Yat-sen University

description: CUT&Tag seq

library_source: genomic

data_processing:
The sequencing adaptors and low-quality reads were removed using TrimGalore with the parameters -q 20 --phred33--stringency 3. The clean reads were then mapped to a reference genome (GRCh38.p12). MACS2 was employed to call peaks with the parameter -q 0.05 --call-summits --nomodel--shift -100 --extsize 200 --keep-dup all.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Human spinal entheseal fibroblasts

extract_protocol:
CUT&Tag assay was performed using NovoNGs CUT&Tag 4.0 High-Sensitivity Kit following the manufacturer’s instructions. Briefly, a total of 1×105 cells were harvested and bound to ConA magnetic beads. The cells were incubated with primary H3K27ac antibody or primary H3K4me1 antibody at 4 ℃ overnight, and then incubated with Goat Anti-Rabbit IgG H&L at room temperature for 1 h. After washing with wash buffer, the cells were incubated with pAG-Transposome at room temperature for 1 h. Subsequently, the cells were washed with wash buffer, incubated with tagmentation buffer at 37℃ for 1 h, and then the reaction was terminated with stop buffer at 55℃ for 10 min. DNA was extracted using the tagment DNA extract beads.
PCR was performed with index primers using extracted DNA to construct CUT&Tag library. The CUT&Tag libraries were performed sequencing using an Illumina NovaSeq 6000 platform.

value: Human spinal entheseal fibroblasts

tag: chip antibody


title: GS_M_60_Rep2


title: GS_M_60_Rep1


title: Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_02


title: si-SOX5_H3K27ac, CUT&Tag seq

description: CUT&Tag seq


title: GS_M_15_Rep3


title: si-NC_H3K4me1, CUT&Tag seq

description: CUT&Tag seq

value: si-NC


title: human LAA, Paro-AF Z1811

first: Xi

last: Fan

state: --- Select One ---

address: No.12, Urumqi Middle Road, Shanghai, China

institute: Huashan Hospital of Fudan university

data_processing:
The sequencing process was controlled by Illumina's data collection software, and real-time data analysis was performed.
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.
FASTQs generated from Illumina sequencing output were aligned to the human genome GRCh38 using the STAR algorithm.
Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-nucleus associated barcodes.
A gene-nucleus-barcode matrix containing the barcoded nucleus and gene expression counts was generated and then imported into the Seurat (v2.3.0).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

molecule: nuclear RNA

source_name: heart

extract_protocol:
Cell nuclei were isolated using the nuclear isolation kit (Shanghai Bohao, Cat No. 52009-10) following the manufacturer’s instruction.Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). GEM was transferred into PCR for reverse transcription.
The library construction was performed according to the standard manufacturer’s protocol (CG000206 Rev D).

value: heart


title: GS_M_0_Rep3


title: human LAA, No-AF 3832


title: human LAA, No-AF 0410


title: human LAA, No-AF 0616


title: GS_M_0_Rep2


title: human LAA, Paro-AF Z6663


title: GS_M_0_Rep1


title: GS_Y_180_Rep3

value: Young


title: si-NC_H3K27ac, CUT&Tag seq

description: CUT&Tag seq


title: GS_M_60_Rep3


title: GS_Y_180_Rep2


title: GS_Y_180_Rep1


title: human LAA, Pe-AF 4517


title: human LAA, Pe-AF 9446


title: GS_Y_60_Rep2


title: GS_Y_60_Rep3


title: Mock-infected HIE 1 dpi, scRNAseq

city: Ann Arbor

first: Andres

last: Rivera Ruiz

state: MI

address: 5737A Med Sci II 1137 Catherine St

department: Microbiology & Immunology

institute: University of Michigan

description: 10x Genomics

data_processing:
Cell Ranger (10X Genomics)
scanpy
Assembly: custom (GRCh38  + VA1)
Supplementary files format and content: processed: h5 files
Supplementary files format and content: raw: fastq.gz

molecule: polyA RNA

source_name: HT-124-I (fetal ileum organoid)

extract_protocol:
10X Genomics scRNAseq protocol
10X Genomics

value: HT-124-I (fetal ileum organoid)


title: human LAA, Pe-AF 9513


title: VA1-infected HIE 3 dpi, scRNAseq

description: 10x Genomics


title: GS_Y_60_Rep1


title: Mock-infected HIE 3 dpi, scRNAseq

description: 10x Genomics


title: GS_Y_15_Rep3


title: GS_M_15_Rep1


title: GS_M_15_Rep2


title: GS_Y_15_Rep2


title: GS_Y_15_Rep1


title: GS_Y_0_Rep3


title: X173, skin (NRML)

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Counts for sample sequenced with multiple lanes were added to produce a single column of value
Assembly: GRCh37
Supplementary files format and content: Tab delimited raw gene counts of each sample

source_name: skin (NRML)

extract_protocol:
Total RNA was extracted from skin biopsies by the Qiagen miRNeasy Mini Kit (Valencia, CA, USA)
Libraries prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Pluskit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Nova 6000 with pair-end 100 cycles. Our sequencing depth ranged 50M reads, Image analysis and bases calling was conducted in real-time by the lllumina analysis pipeline.

value: skin (NRML)

tag: timepoint

value: Control

tag: condition

value: Healthy

tag: gender

value: female

tag: subjectid


title: X174, skin (NRML)

value: male


title: X172, skin (NRML)


title: GS_Y_0_Rep2


title: GS_Y_0_Rep1


title: human LAA, Paro-AF 4462


title: X170, skin (NRML)


title: VA1-infected HIE 1 dpi, scRNAseq

description: 10x Genomics


title: X169, skin (NRML)


title: GR_M_180_Rep1

value: Glyphosate resistant


title: X168, skin (NRML)


title: X166, skin (NRML)


title: GR_M_180_Rep2


title: GR_M_60_Rep3


title: X167, skin (NRML)


title: GR_M_60_Rep2


title: X165, skin (NRML)


title: GR_M_60_Rep1


title: X164, skin (NRML)


title: GR_M_15_Rep3


title: X163, skin (NRML)


title: X162, skin (NRML)


title: GR_M_15_Rep1


title: X161, skin (NRML)


title: X171, skin (NRML)


title: X160, skin (NRML)


title: GR_M_180_Rep3


title: GR_M_0_Rep2


title: GR_M_0_Rep1


title: X157, skin (NRML)


title: X159, skin (NRML)


title: GR_Y_180_Rep2


title: X155, skin (NRML)


title: X154, Lesional skin

source_name: Lesional skin

value: Lesional skin

value: Psoriasis


title: X156, skin (NRML)


title: GR_Y_180_Rep3


title: GR_Y_60_Rep3


title: X153, Lesional skin


title: GR_Y_180_Rep1


title: GR_Y_60_Rep2


title: GR_M_15_Rep2


title: X150, Lesional skin


title: GR_Y_15_Rep3


title: X148, Lesional skin

value: BL


title: GR_Y_15_Rep2


title: X149, Lesional skin


title: GR_Y_60_Rep1


title: X151, non-lesional skin

source_name: non-lesional skin

value: non-lesional skin


title: GR_Y_0_Rep3


title: GR_M_0_Rep3


title: X146, Lesional skin


title: X147, non-lesional skin


title: GR_Y_0_Rep2


title: GR_Y_15_Rep1


title: GR_Y_0_Rep1


title: X144, Lesional skin


title: X143, non-lesional skin


title: T-D-2

city: Jinan

first: MA

last: Haizhen

state: Shandong

address: Daxue Road

institute: Qilu University of Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Further, we also can perform deep analysis based on DEGs (We use 'FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' as the threshold to judge the significance of gene expression difference), including Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: leaf

tag: developmental stage

value: 3-leaf stage

tag: line

value: KN5585 maize inbred line

value: transgenic

tag: stress

value: drought


title: CK-D-3

tag: tissue

tag: genotype

value: control


title: X145, Lesional skin


title: T-D-3


title: CK-D-2


title: X141, Lesional skin


title: CK-D-1


title: X139, non-lesional skin


title: T-D-1


title: X136, Lesional skin


title: X138, Lesional skin


title: Mouse heart, F_NM 5

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Boulevard

department: Internal Medicine

institute: UTMB

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

organism: Mus musculus

source_name: Heart

growth_protocol: Nineteen two-month-old male and female C57BL/6NTac germ-free mice were housed in the UTMB Germ-Free Mouse Facility with a 12-hour light/dark cycle, temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and a piece of cardiac tissue was snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen heart tissue using the PureLink RNA Mini Kit (Thermo Fisher). RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: There were four groups of 4 or 5 mice receiving the following treatments: (1) males with normal microbiome (M_NM), (2) males with dysbiotic microbiome (M_DM), (3) females with normal microbiome (F_NM), and (4) females with dysbiotic microbiome (F_DM).

value: Heart

value: Cardiocytes

value: WT

tag: treatment

value: NM FMT


title: Mouse heart, F_NM 2

tag: cell type


title: X135, non-lesional skin


title: X137, Lesional skin


title: Mouse heart, F_NM 1


title: X132, Lesional skin


title: Mouse heart, M_DM 5

value: DM FMT


title: X131, non-lesional skin

value: male


title: Mouse heart, F_DM 1


title: Mouse heart, M_DM 4


title: Mouse heart, M_DM 3


title: X133, Lesional skin


title: X142, Lesional skin


title: Mouse heart, F_NM 4


title: X130, Lesional skin


title: X129, Lesional skin


title: Mouse heart, M_DM 2


title: Mouse heart, M_DM 1


title: X128, Lesional skin


title: Mouse heart, M_NM 4


title: X127, non-lesional skin


title: X126, Lesional skin


title: X140, Lesional skin


title: X134, Lesional skin


title: Mouse heart, M_NM 2


title: X125, Lesional skin


title: Mouse heart, M_NM 3


title: Mouse heart, F_NM 3


title: X124, Lesional skin


title: Mouse heart, M_NM 1


title: X123, non-lesional skin


title: X122, Lesional skin


title: 2689-2, muMT uninfected

city: Oxford

first: Aminul

last: Islam

state: OH

address: 700 E High street

department: Microbiology

institute: Miami University

data_processing:
CLC Genomics Workbench 23.0.3
Low quality sequence were trimmed using CLC Genomics Workbench
Trimmed sequence reads were mapped to Mus musculus sequence mm10 (parameters: maximum of 2 mismatches, a minimum length and similarity fraction of 0.8, and a minimum of 10 hits per read
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung

extract_protocol:
RNA was extracted using Direct-zol RNA microprep kit using the manufacturer's instructions
RNA libraries for RNA-Seq were prepared using PerkinElmer NEXTFLEX Rapid Directional RNA-Seq Kit 2.0

value: Lung

value: muMT

value: Uninfected


title: 2689-3, muMT uninfected


title: 2721-1, WT uninfected


title: X121, Lesional skin

value: Lesional skin

value: Psoriasis


title: 2689-1, muMT uninfected


title: X119, non-lesional skin

value: non-lesional skin

value: BL


title: X117, Lesional skin

value: female


title: X116, Lesional skin


title: 2671-2, WT uninfected


title: 2685-1, WT uninfected


title: X115, non-lesional skin


title: 2671-1, WT uninfected


title: 2686-4, muMT infected

value: Infected


title: 2686-3, muMT infected


title: 2686-1, muMT infected


title: X113, Lesional skin


title: X112, Lesional skin


title: 2686-2, muMT infected


title: 2669-4, WT infected


title: X111, non-lesional skin


title: 2669-3, WT infected


title: 2669-2, WT infected


title: X108, Lesional skin


title: X107, non-lesional skin


title: X110, Lesional skin


title: G:K:TG014

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description: 10X Genomics

data_processing:
Fastq data was put into the 10X Cell Ranger platform for alignment and data processing into HDF5 files
Assembly: mm39
Supplementary files format and content: Cell Ranger HDF5 Feature-Barcode Matrix Format

growth_protocol: All mice were be housed in microisolator cages within the specific pathogen-free (SPF) environment in Hoffman Medical Research Center (HMR) at USC. All animal protocols are reviewed semiannually and annually and monitored continuously by an Institutional Animal Care and Use Committee (IACUC). Veterinary care is provided by USC’s Animal Resources Center. The facility has received full AAALAC accreditation.

extract_protocol:
Mice were euthanized with 100 uL Euthasol by IP injection. Lungs were perfused with 20 mL PBS to flush peripheral blood from lungs. Lungs were snap frozen in liquid nitrogen, and 10x genomics nuclei isolation kit (1000494) was use to isolate, purify and enrich nuclei from tissues.
10X Genomics Next GEM 3' Gene Expression Library Construction

treatment_protocol: Oncogenic KRASG12D was induced by tamoxifen through IP injection. Control mice received corn oil administration by IP injection.

value: Tamoxifen


title: X109, Lesional skin


title: X103, Lesional skin


title: 2669-1, WT infected


title: X118, Lesional skin


title: X102, Lesional skin


title: X101, Lesional skin


title: G:K:TG007

description: 10X Genomics

value: Corn Oil


title: G:K:TG005

description: 10X Genomics


title: X114, Lesional skin


title: S:K:TG010

description: 10X Genomics


title: X100, non-lesional skin


title: G:K:TG004

description: 10X Genomics


title: X99, Lesional skin


title: X98, Lesional skin


title: X97, Lesional skin


title: S:K:TG008

description: 10X Genomics


title: X96, non-lesional skin


title: S:K:TG005

description: 10X Genomics


title: X95, Lesional skin


title: X94, Lesional skin


title: G:TG001

description: 10X Genomics


title: S:K:TG003

description: 10X Genomics


title: X92, non-lesional skin


title: G:K:TG011

description: 10X Genomics


title: S:TG001

description: 10X Genomics


title: WT001

description: 10X Genomics


title: X90, Lesional skin


title: X91, Lesional skin


title: mTmG001

description: 10X Genomics

value: ROSAmTmG


title: UBE4AKO_6

first: FengFeng

last: Rao

address: 1088 Xueyuan Road

institute: Southern University of Science and Technology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: liver

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver

value: Ube4a LKO


title: UBE4AKO_7


title: X88, non-lesional skin


title: X89, Lesional skin


title: UBE4AKO_5


title: X87, Lesional skin


title: UBE4AKO_4


title: S:K:TG009

description: 10X Genomics


title: UBE4AKO_3


title: UBE4AKO_2


title: X86, Lesional skin


title: X84, non-lesional skin


title: X85, Lesional skin


title: X93, Lesional skin


title: UBE4AKO_1


title: X82, Lesional skin


title: WT_4

value: Ube4a flox/flox


title: WT_3


title: X78, Lesional skin


title: X79, Lesional skin


title: WT_5


title: WT_2


title: X76, non-lesional skin


title: X75, Lesional skin


title: proximal small intestine, Standard_Diet_D14

city: Solna

first: Ning

last: He

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

data_processing:
Visium libraries were sequenced on a NovaSeg S1 flow cell (Illumina)
Fastq files were processed with SpaceRanger (10X Genomics) v1.2.0 mapped to 2 reference genomes.
Assembly: Reads were aligned to reference genomes compiled from mouse reference files (FASTA and GTF, mm10 version 32, enssmbl 98) and Heligmosgides, polygur.s reference files (FASTA and GTF, PRJEB1203) utilizing the spaseranger mkref command line tool
Supplementary files format and content: Matrix with raw counts for every gene and every spot, filtered to include spots under tissue
Supplementary files format and content: High/low resolution Hematoxylin and Eosin (HE) image in PNG format
Supplementary files format and content: Scalefactors in json format
Supplementary files format and content: Table with array and pixel coordinates
Library strategy: Spatial Transcriptomics (Visium)

source_name: proximal small intestine

extract_protocol:
Mouse proximal 4-6cm small intestines were collected either on day 6 or on day14 after infection, Swisrolled and frozen in OCT. Tissues (day6 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide.
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

treatment_protocol: Wild type male C57BL/6Jmice were under standard of GW3965 diet for 10 days then mice were infected with 200 L3 Heligmosomoides polygyrus via oral gavage.

value: proximal small intestine

tag: strain

value: Wild type

tag: diet

value: Standard

tag: infection

value: H.polygyrus 14dpi


title: X74, Lesional skin


title: proximal small intestine, GW3965_Diet_D6

value: H.polygyrus 6dpi


title: Tumor cells, Cold, rep4

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt files include TPM values for each sample.

source_name: Tumor cell

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor cell

value: Cold exposure


title: X72, non-lesional skin

value: non-lesional skin

value: Psoriasis


title: X77, Lesional skin

value: Lesional skin

value: BL

value: male


title: X73, Lesional skin

value: female


title: proximal small intestine, Standard_Diet_D6


title: Tumor cells, Cold, rep3


title: WT_1


title: X70, Lesional skin


title: X69, Lesional skin


title: X81, Lesional skin


title: Tumor cells, Control, rep5

value: Control


title: X68, non-lesional skin


title: X80, non-lesional skin


title: X71, Lesional skin


title: Tumor cells, Cold, rep1


title: X64, Lesional skin


title: X63, Lesional skin


title: X62, Lesional skin


title: Tumor cells, Control, rep1


title: X61, non-lesional skin


title: Tumor cells, Control, rep2


title: proximal small intestine, GW3965_Diet_D14


title: CD8TILs, Cold, rep4


title: X59, Lesional skin


title: Tumor cells, Cold, rep2


title: CD8TILs, Cold, rep2


title: CD8TILs, Cold, rep3


title: CD8TILs, Cold, rep1


title: X57, non-lesional skin


title: X58, Lesional skin


title: CD8TILs, Control, rep3


title: X55, Lesional skin


title: Tumor cells, Control, rep4


title: X56, Lesional skin


title: CD8TILs, Control, rep1


title: Tumor cells, Control, rep3


title: X53, non-lesional skin


title: Tumor tissues, Cold, rep4

source_name: tumor tissue

value: tumor tissue


title: X54, Lesional skin


title: Tumor tissues, Cold, rep6


title: X51, Lesional skin


title: X52, Lesional skin


title: Tumor tissues, Cold, rep5


title: X50, Lesional skin


title: X60, Lesional skin


title: X49, non-lesional skin


title: Tumor tissues, Cold, rep2


title: Tumor tissues, Control, rep6


title: X48, Lesional skin


title: Tumor tissues, Cold, rep1


title: CD8TILs, Control, rep2


title: X47, Lesional skin


title: X46, Lesional skin


title: Tumor tissues, Control, rep5


title: X45, non-lesional skin


title: Tumor tissues, Control, rep4


title: Tumor tissues, Control, rep3


title: Tumor tissues, Control, rep2


title: Tumor tissues, Cold, rep3


title: X43, Lesional skin


title: X41, non-lesional skin


title: X40, Lesional skin


title: HV1 CD4+ and CD8+ T-cells, TCR

city: Minneapolis

first: Allison

middle: M.

last: Haaning

state: MN

address: 117 Pleasant St. SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: TCR library: Read 1 file contains cell barcodes and UMIs; read 2 file contain T-cell receptor sequences

data_processing:
For GEX, ADT, and HTO data, the kallisto and bustools (kb) count function was used to produce a matrix with counts per feature and feature and barcode files.
For TCR data, the CellRanger vdj pipeline was used to call clonotypes for TCR profiling.
Assembly: mm10
Supplementary files format and content: kb count output files (equivalent to CellRanger count output): HV1_CD4_CD8_T_Cells_GEX_barcodes.tsv.gz, HV1_CD4_CD8_T_Cells_GEX_features.tsv.gz, HV1_CD4_CD8_T_Cells_GEX_matrix.mtx.gz
Supplementary files format and content: kb count output files (ADT and HTO counts done separately using same input fastq files): HV1_CD4_CD8_T_Cells_ADT_barcodes.tsv.gz, HV1_CD4_CD8_T_Cells_ADT_features.tsv.gz, HV1_CD4_CD8_T_Cells_ADT_matrix.mtx.gz, HV1_CD4_CD8_T_Cells_HTO_barcodes.tsv.gz, HV1_CD4_CD8_T_Cells_HTO_features.tsv.gz, HV1_CD4_CD8_T_Cells_HTO_matrix.mtx.gz
Supplementary files format and content: output of CellRanger vdj pipeline (T-cell profiling): HV1_CD4_CD8_T_Cells_TCR_filtered_contig_annotations.csv
Library strategy: CITE-seq

source_name: CD4+ CD8+ T-cells

extract_protocol:
A 50:50 mixture of CD45.2+ HV1 CD4 T cells as well as CD44+ CD8 T cells were sorted from the indicated experimental treatment arms.
The sorted T cells were labeled with treatment arm-specific hashtag oligonucleotide (HTO) antibodies, as well as CITE-Seq antibody derived oligonucleotide tag (ADT) antibodies to CD4, CD39, CD4b, PD1, TIM3 and LAG3. Cells were captured and single cell sequencing for gene expression (GEX), sample-specific hashtag and protein feature barcodes, and T-cell receptor (TCR) repertoires was performed using the 10X Genomics Chromium Next GEM Single Cell 5' (ver. 1.1) reagents

treatment_protocol: CD45.1+ mice were injected with CD45.2+ HV1 CD4 T cells via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day. Some of the CD45.1+ mice were treated with the tyrosine kinase inhibitor nilotinib five days/week for one week starting at day 14 post-leukemia-establishment, as well as treatment with an isotype control or IL10R blocking or PDL1 blocking antibody on days 14, 16 and 18 post-leukemia-establishment.

value: CD4+ CD8+ T-cells

value: Mixed treatments corresponding to hashtags:Naïve HV1 T-cells, Leukemia challenged T-cells, and Leukemia challenged T-cells treated with Nilotinib + Isotype, Nilotinib + aPDL1, or Nilotinib + aIL10R

tag: library type

value: scTCR-seq


title: X42, Lesional skin


title: Tumor tissues, Control, rep1


title: HV1 CD4+ and CD8+ T-cells, combined ADT and HTO

description:
TotalSeq™-C0001 anti-mouse CD4 Antibody, TotalSeq™-C0834 anti-mouse CD39 Antibody, TotalSeq™-C0421 anti-mouse CD49b Antibody, TotalSeq™-C0004 anti-mouse CD279 (PD-1) Antibody, TotalSeq™-C0003 anti-mouse CD366 (Tim-3) Antibody, TotalSeq™-C0378 anti-mouse CD223 (LAG-3) Antibody
TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody, TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody, TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody
ADT and HTO library: Read 1 file contains cell barcodes and UMIs; read 2 file contains antibody-derived and hashtag antibody-derived tag reads

library_source: other

molecule: protein

value: scADT/HTO


title: HV1 day 17-post-leukemia challenge CD4+ T-cells, ATAC

description: Single cell ATAC sequencing

library_source: genomic single cell

data_processing:
ATAC-seq fastq files were processed using the cellranger-atac-2.1.0 pipeline
Data for all treatments was integrated into a single Seurat object using Seurat (v4) and Signac, and gene activity was calculated using the Signac GeneActivity function.
Assembly: mm10
Supplementary files format and content: Output of 10XGenomics cellranger-atac: singlecell.csv (cell metadata)
Supplementary files format and content: Output of 10XGenomics cellranger-atac: filtered_peak_bc_matrix.h5 (data for creating Seurat object)

source_name: CD4+ T-cells

extract_protocol:
HV1 CD4 T cells from leukemic CD45.1+ mice at days 9, 13, and 17 post-leukemia challenge were sorted. As a control, HV1 CD4 T cells from naïve leukemia-specific TCR transgenic mice were also sorted.
Nucleii from the sorted T cells were isolated and captured on the 10x Chromium, and library preparation was generated using the Chromium Next GEM Single Cell ATAC library kit (ver. 1.1), following the manufacturer’s recommendations.

treatment_protocol: CD45.1+ mice were injected with CD45.2+ CD4 T cells from a leukemia-specific TCR transgenic mouse (HV1 CD4 T cells) via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day.

value: CD4+ T-cells

value: CD45.1+ mice injected with CD45.2+ HV1 CD4 T cells followed by injection with LM138 leukemia cells the next day. HV1 CD4 T cells were isolated at day 17 post-leukemia challenge.


title: HV1 day 9 post-leukemia challenge CD4+ T-cells, ATAC

description: Single cell ATAC sequencing

value: CD45.1+ mice injected with CD45.2+ HV1 CD4 T cells followed by injection with LM138 leukemia cells the next day. HV1 CD4 T cells were isolated at day 9 post-leukemia challenge.


title: X38, Lesional skin


title: HV1 CD4+ and CD8+ T-cells, GEX

description: GEX (3' RNA) library: Read 1 file contains cell barcodes and UMIs; read 2 file contains transcripts.

value: Mixed treatments corresponding to hashtags:(1) Naïve HV1, (2) leukemia challenged , (3) leukemia challenged and nilotinib + Isotype treated, (4) leukemia challenged and nilotinib + aPDL1 treated, (5) leukemia challenged and nilotinib + aIL10R treated

value: scRNA-seq


title: HV1 naïve CD4+ T-cells, ATAC

description: Single cell ATAC sequencing

value: Control - naïve CD45.2+ CD4 T cells from a leukemia-specific TCR transgenic mouse (HV1 CD4 T cells)


title: HV1 day 13 post-leukemia challenge CD4+ T-cells, ATAC

description: Single cell ATAC sequencing

value: CD45.1+ mice injected with CD45.2+ HV1 CD4 T cells followed by injection with LM138 leukemia cells the next day. HV1 CD4 T cells were isolated at day 13 post-leukemia challenge.


title: X37, non-lesional skin

value: non-lesional skin

value: Psoriasis


title: X36, Lesional skin

value: Lesional skin

value: male


title: X35, Lesional skin


title: Hippo_VH6

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Hippocampus

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice were infused with angiotensin II (0.7mg/kg/d) or saline (0.9%) via an osmotic minipump for 2 weeks. Some mice received hydralazine (50mg/kg) in their drinking water. After 2 weeks, the mice were  culled and the brain was dissected and collected.

value: Hippocampus

value: WT

value: Vehicle + hydralazine

tag: Sex

value: Male

tag: disease state

value: Control


title: X33, non-lesional skin

tag: timepoint

value: BL


title: X44, Lesional skin

tag: condition


title: Hippo_VH4


title: X32, Lesional skin

tag: gender

value: female


title: Hippo_VH3


title: X31, Lesional skin

tag: subjectid


title: Hippo_VH2


title: X30, Lesional skin


title: Hippo_VH1


title: X39, Lesional skin


title: Hippo_V6

value: Vehicle


title: X29, non-lesional skin


title: Hippo_V5


title: Hippo_V4


title: X27, Lesional skin


title: X28, Lesional skin


title: X26, Lesional skin


title: Hippo_V3


title: X25, non-lesional skin


title: Hippo_V1


title: X23, Lesional skin


title: X22, Lesional skin


title: Hippo_V2


title: Hippo_VH5


title: Hippo_AH6

value: Angiotensin II + hydralazine

value: Hypertension


title: X34, Lesional skin


title: X24, Lesional skin


title: X21, non-lesional skin


title: Hippo_AH5


title: X20, Lesional skin


title: Hippo_AH3


title: Hippo_AH4


title: Hippo_AH2


title: X18, Lesional skin


title: X17, non-lesional skin


title: Hippo_AH1


title: Hippo_A6

value: Angiotensin II


title: Hippo_A5


title: X15, Lesional skin


title: Hippo_A4


title: X14, Lesional skin


title: Hippo_A3


title: X11, Lesional skin


title: Hippo_A2


title: X9, non-lesional skin


title: Hippo_A1


title: X10, Lesional skin


title: VH6

source_name: Brain hemisphere

value: Brain hemisphere


title: VH4


title: X8, Lesional skin


title: X7, Lesional skin


title: X19, Lesional skin


title: VH3


title: VH5


title: VH2


title: X5, non-lesional skin


title: X6, Lesional skin


title: VH1


title: V6


title: X4, Lesional skin


title: X3, Lesional skin


title: X16, Lesional skin


title: V5


title: X2, Lesional skin


title: X1, non-lesional skin


title: V3


title: X13, non-lesional skin


title: V2


title: V1


title: AH6


title: MTX,replicate 1,bulk RNA-seq

city: 广州

first: zhanying

last: wu

state: 广东

address: 803, Building 2, Jinxiyuan, Zengbian, Xinzao Town, Panyu District, Guangzhou, China

institute: GZHMU

data_processing:
For scRNA-seq, Fastp (v0.20.1) was used to trim primer sequence and low quality bases  of raw  reads  and  collect the basic  statistics. Seekoul Tools pipeline was used to process the cleaned reads and generated the transcript expression matrix. For bulk RNA-seq, clean reads were processed using RSEM v1.2.25.
Assembly: GRCh38
Supplementary files format and content: tab-delimited file includes TPM values for each sample

extract_protocol:
For scRNA-seq, Peripheral blood mononuclear cells (PBMCs) were collected through density gradient centrifugation according to the Histopaque-1077 procedure (Sigma-Aldrich Co. LLC). For bulk RNA-seq, total RNA of NK-92 cell line was extracted using the RNeasy micro-RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.
For scRNA-seq, Single-cell RNA-seq libraries were generated using the SeekOne® MM Single Cell 3’ library preparation kit (SeekGene Catalog No. SO01V3.1). For bulk RNA-seq, RNA libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell line

value: Juvenile idiopathic arthritis (JIA)

value: MTX


title: AH4


title: AH5


title: Control,replicate 2,bulk RNA-seq


title: 220125A-LFS2_1,scRNA-seq

source_name: PBMCs

value: PBMCs

value: post-MTX treatment


title: AH1


title: Control,replicate 1, bulk RNA-seq


title: AH3


title: AH2


title: 220125A-LFS1, scRNA-seq

value: pre-MTX treatment


title: A6


title: HBMEC_replicate_5

first: Andrew

middle: A

last: Sproul

address: 650 West 168th Street

institute: Columbia Univeristy

data_processing:
Illumina bcl2fastq 2.17 software
Possible adapter sequences and mucleotides rewmoed by using Trimmomatic v.0.36
Trimmed reads were mapped to Homo sapiens reference genome with STAR aligner v.2.5.2b
Hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited files contain raw counts for each sample
Supplementary files format and content: comma-seperated values contain FPKM values for each sample

source_name: Brain

extract_protocol:
RNAs were harvested using QIAGEN mini RNA easy kit. 2 ul RNA was used for construction of RNA sequence
RNA libraries built woth NEBNext Ultra II RNA Library Prep Kit.

value: Brain

value: HBMEC


title: A5

value: WT


title: A4

value: Male


title: V4

value: Control


title: CDG-12105,scRNAseq

city: New York City

first: Rameen

last: Shah

address: 1425 Madison Avenue

institute: Mount Sinai

data_processing:
10x Genomics Cell Ranger v6.0.1 was used  to analyze the data.
Assembly: hg38
Supplementary files format and content: h5 files containing count matrices

extract_protocol:
At day 92, 4 human corical brain organoids per cell line (CDG-0458, CDG-1017, CDG-11740, CTRL-8856.3, CTRL-1363.1, CTRL-8399) were dissociated into a single cell suspension using the Miltenyi Biotec Neurosphere Dissociation Kit (P) and resuspended  in 1x PBS + 0.04% BSA
The cDNA master mix was prepared according to the manufacture’s instruction for Chromium Single Cell 3’ Library and Gel Bead Kit (10x Genomics). Per sample the aim was to recover 10,000 cells and as such the cDNA master mix was added to the cells so that we have 500,000 cell per ml.  Subsequently, these cells, Gel Beads, and partitioning oil were added to the Chromium Single Cell G chip. The filled chip was loaded into the Chromium X Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled Gel Beads-In-Emulsion (GEMs).  The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contained a pool of uniquely barcoded molecules, and a portion of this cDNA was taken for library construction. To create gene expression libraries, standard Illumina sequencing primers and unique sample index (Dual Index Kit TT-Set A; 10x Genomics) were added to each cDNA pool. All cDNA pools and resulting libraries were quantified using Qubit High Sensitivity assays (Thermo Fisher Scientific) and Agilent Bioanalyzer High Sensitivity chips (Agilent). The libraries were subsequently sequenced at 50,000 fragment reads per cell by using the Illumina’s standard protocol and the Illumina NovaSeq™ 6000 S4 flow cell

value: CDG

value: Neuronal

value: F


title: A3


title: A2


title: MTX,replicate 3, bulk RNA-seq


title: CDG-12016,scRNAseq


title: HBMEC_replicate_4


title: MTX, replicate 2, bulk RNA-seq


title: A1


title: CTRL-1363.1,scRNAseq


title: Paraspinal tumor, Shp2i-1595

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: 10X Genomics 3v3.1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Tab-delimited barcodes, features, matrix in gzip format

source_name: Paraspinal tumor

extract_protocol:
Mice were anesthetized with isoflurane, perfused with ice cold phosphate-buffered saline (PBS) lacking calcium and magnesium. Paraspinal tumors were collected within 5 minutes of death and stored in L-15 medium until tissue was cut into 1-mm3 pieces and placed into dissociation medium in 50 mL tubes containing 20 mL L-15 medium, 10 mg collagenase type I, and 50 mg Dispase II in a 37°C incubator for 2 hours, with 170 rpm shaking. The dissociation process was stopped by adding 30 mL DMEM containing 10% FBS. Samples were centrifuged at 800g for 5 minutes at 4°C. Supernatants were removed and cell pellets were resuspended into 50 mL of 1× PBS containing 0.1% BSA. Suspensions were sequentially filtered with 70 μm, 40 μm, and 20 μm cell strainers and centrifuged at 600g for 5 minutes at 4°C. Pellets were resuspended into 100 μL of 1× PBS/0.1% BSA. Trypan blue–negative viable cells were counted to determine the cell concentration for droplet-based scRNA-seq.
Library was performed according to the manufacturer's instructions (single cell 3v3.1 protocol, 10x Genomics)

treatment_protocol: Nf flox/flox;DhhCre mice were treated for 30 days with 1.5 mg/kg/day of the MEK inhibitor PD-032590, 10mg/kg/day of the SHP2 inhibitor RMC-4550, or vehicle control.

value: Paraspinal tumor

value: Nf flox/flox;DhhCre

value: SHP2 inhibitor


title: Control,replicate 3, bulk RNA-seq


title: CTRL-8856.3,scRNAseq


title: Paraspinal tumor, Shp2i-1594

description: 10X Genomics 3v3.1


title: MDA-MB231 cells, SG3_3

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
Dataset2 (raw counts)
counts_raw.tsv

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (hg38) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: hg38
Supplementary files format and content: tab delimited text files

growth_protocol: MDA-MB231 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37celsius.

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen).
see manufacturer's web site at https://www.novogene.com/us-en/services/research-services/transcriptome-sequencing/?keyword=novogene%20rna%20seq&campaign=10977825508&gclid=Cj0KCQjwlZixBhCoARIsAIC745DHh6VSpKhxxuBgJLLwMbSTmWCm9H4SeN4xZj8t1pZyDbH4cJ1DNXsaArZNEALw_wcB&gad_source=1

value: breast cancer

value: KIF20A knockdown


title: MDA-MB231 cells, SG3_2

description:
Dataset2 (raw counts)
counts_raw.tsv


title: Paraspinal tumor, Shp2i-1573

description: 10X Genomics 3v3.1


title: MDA-MB231 cells, SG3_1

description:
Dataset2 (raw counts)
counts_raw.tsv


title: Paraspinal tumor, PD-1519

description: 10X Genomics 3v3.1

value: MEK inhibitor


title: Paraspinal tumor, PD-1540

description: 10X Genomics 3v3.1


title: CTRL-8399,scRNAseq


title: Paraspinal tumor, PD-1536

description: 10X Genomics 3v3.1


title: MDA-MB231 cells, SG1_2

description:
Dataset2 (raw counts)
counts_raw.tsv


title: MDA-MB231 cells, SG1_3

description:
Dataset2 (raw counts)
counts_raw.tsv


title: Paraspinal tumor, Nacitveh-1593

description: 10X Genomics 3v3.1

value: Vehicle


title: Paraspinal tumor, Nacitveh-NF90

description: 10X Genomics 3v3.1


title: MDA-MB231 cells, CTRL1

description:
Dataset2 (raw counts)
counts_raw.tsv


title: MDA-MB231 cells, CTRL3

description:
Dataset2 (raw counts)
counts_raw.tsv


title: MDA-MB231 cells, KIF20AOE2

description:
Dataset1 (FPKM)
geneMatrixFPM_KIF20A.txt

value: KIF20A overexpression


title: Paraspinal tumor, mcelveh-NF92

description: 10X Genomics 3v3.1


title: Paraspinal tumor, control-1622

description: 10X Genomics 3v3.1


title: CDG-11740,scRNAseq


title: MDA-MB231 cells, SG1_1

description:
Dataset2 (raw counts)
counts_raw.tsv


title: Paraspinal tumor, PD-1538

description: 10X Genomics 3v3.1


title: MDA-MB231 cells, CTRL2

description:
Dataset2 (raw counts)
counts_raw.tsv


title: MDA-MB231 cells, KIF20AOE3


title: Paraspinal tumor, control-1711

description: 10X Genomics 3v3.1


title: Ms_Microglia_Media_rep4

city: Durham

first: Kristina

last: Sakers

state: NC

address: 307 Research Dr

institute: Duke University

data_processing:
FastQC v0.11.7
Adapters were trimmed using Trimmomatic v0.39
Trimmed reads were aligned with Bowtie2 (v2.3.5.1)
Reads were counted using featureCounts from Subread (v1.6.3)
Differential expression was performed in R (v4.0.0) using edgeR (v3.30.3)
Assembly: mm10
Supplementary files format and content: FPKM for all samples is included

source_name: Forebrain

growth_protocol: P7-P9 mouse pups were transcardially perfused with Medium A to clear. Brains were collected in ice-cold HBSS. Forebrains without olfactory bulbs were digested in papain ~7.5 Units/mL + DNase (1,000 Units/mL) at 37°C for 45 min. Every 15 min., tissue was triturated in digestion buffer. After digestion, sample was passed through 30 µm cell strainer and washed with HBSS to get a single cell suspension. Suspension was centrifuged at 500 g at room temperature for 10 min. to pellet cells. Supernatant was removed and cell pellet was resuspended in 5 mL of MACS buffer. Cells were centrifuged at 500 g at room temperature for 7 min. to pellet cells. Cells were resuspended in MACS buffer to a concentration of ~ 1x105 cells/µL. 30 uL of CD11b microbeads were added to the cells and mixed by pipetting up and down. Cells with beads were incubated on ice for 15 min. Beads were washed off cells by adding 15 mL of MACS buffer and centrifuged at 500 g for 5 min. at room temperature. Supernatant was removed and cells were resuspended in 1 mL MACS buffer. Suspension was then passed through a 30 µm cell strainer into a rinsed LS MACS column in the MACS separator. LS Columns with bound cells were washed 3 times with 3 mL of MACS buffer each wash. Cells were collected by removing LS columns from the MACS separator and plunging 5 mL of MACS buffer through column into a 15 mL conical tube. Cells were then pelleted by centrifugation at 500 g for 5 min. at room temperature. Cell pellet was resuspended in microglia growth media equilibrated in 10% CO2 and plated at 40,000-80,000 cells per well of a 96-well tissue culture plate. Cells were allowed to settle in 10% CO2 incubator at 37°C for 10 min. before treatments were added.

extract_protocol:
RNA was extracted using Trizol reagent following manufacturer’s instructions. In brief, Trizol samples were thawed and RNA was extracted by phenol-chloroform separation. RNA was precipitated using Glycoblue reagent as a co-precipitant following manufacturer’s recommendations. Following phenol-chloroform extraction, RNA samples were then processed using the Zymo RNA Clean and Cocentrator kit with DNase treatment following manufacturer’s instructions. RNA yield was measured using Qubit High-sensitivity RNA assay kit following manufacturer's instructions.
2x100bp libraries were made using 100ng total RNA using an Illumina TruSeq stranded mRNA kit.

treatment_protocol: Cells were treated with recombinant proteins at a final concentration of 500 nM. Cells treated with LPS received final concentration of 50 ng/mL. Cells treated with OxPAPC received a final concentration of 15ug/mL and cells receiving protease inhibitors received a final concentration of 1X per manufacturer’s instructions. Control cells received equal volume of additional microglia growth media at this time. Microglia were cultured for 6 hours after treatment was added at 37°C + 10% CO2. After incubation, cells were spun at 500 g for 2 min. Supernatant was removed and cells were collected in Trizol reagent and stored at -80°C until ready for RNA extraction.

value: Forebrain

value: Microglia

value: Wild-type

value: Media


title: MDA-MB231 cells, KIF20AOE1


title: Ms_Microglia_LPS_rep4

value: LPS


title: MDA-MB231 cells, EV3

value: WT


title: Ms_Microglia_Hevin_rep4

value: Hevin


title: MDA-MB231 cells, EV2


title: MDA-MB231 cells, EV1


title: Ms_Microglia_LPS_rep3


title: BLEO/M-03

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
PE150 high throughout data
MT_vs_B.deseq2.annot
Sample 9 (BLEO/Melatonin)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome (UCSC GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: human prostate

growth_protocol: Human primary prostate stromal cell line (PSC27) was routinely cultured in PSCC media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) at 50 ug/ml and/or Melatonin at 200mM.

extract_protocol:
Cells from both culture conditions were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Cells were allowed to stay in culture with appropriate media change until 7-10 days later when they were exposed to Melatonin at 200mM for 2-3 days, then lysed or immediately collected for lysis.

value: human prostate

value: Wild type

value: Bleomycin/Melatonin


title: Ms_Microglia_Hevin_rep3


title: BLEO/M-01

description:
PE150 high throughout data
MT_vs_B.deseq2.annot
Sample 7 (BLEO/Melatonin)

value: Human primary prostate stromal cell line


title: BLEO/M-02

description:
PE150 high throughout data
MT_vs_B.deseq2.annot
Sample 8 (BLEO/Melatonin)


title: Ms_Microglia_Media_rep2


title: Ms_Microglia_Hevin_rep2


title: Ms_Microglia_Media_rep1


title: ND33947, HD, DMSO replicate 1

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and coefficients for conditions, sex, age, and BMI were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.1.
Assembly: Ensemble release 76
Supplementary files format and content: Tab delimited .txt file contains CPM for each sample

source_name: cell culture

extract_protocol:
Trizol extraction and total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 10ng of total RNA. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were treated from PID14 to PID30 with Raphin1 or DMSO.

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons

value: HTT CAG expansion

value: DMSO


title: ND33947, HD, DMSO replicate 2


title: Ms_Microglia_LPS_rep1


title: ND33947, HD, Raphin1 replicate 2


title: Ms_Microglia_Hevin_rep1


title: ND33947, HD, Raphin1 replicate 3


title: GM04198, HD, DMSO replicate 2


title: HSC-BC-reprecate4

city: minato-ku

first: Tsuyoshi

last: Fukushima

state: tokyo

address: siroganedai 4-6-1

department: Cell therapy

institute: Institute of Medical Science

description: random DNA barcode

data_processing:
Cell barcodes, features and counts were extracted by Cell Ranger
Random DNA barcodes were extracted using python codes.
Assembly: mm10
Supplementary files format and content: matrix files
Supplementary files format and content: txt files

molecule: other

source_name: bone marrow

extract_protocol:
Exstraction was performed acording to the manifacter's instruction (single cell 3' v2 protocol, 10x Genomics)
Library was performed acording to the manifacter's instruction (single cell 3' v2 protocol, 10x Genomics)

value: bone marrow

value: HSC


title: HSC-BC-reprecate3

description: random DNA barcode


title: HSC-BC-reprecate2

description: random DNA barcode


title: ND33947, HD, Raphin1 replicate 1


title: HSC-BC-reprecate1

description: random DNA barcode


title: GM04198, HD, DMSO replicate 1


title: GM04198, HD, DMSO replicate 3


title: HSC-scRNAseq-reprecate4

description: 10x Genomics


title: Ms_Microglia_Media_rep3

value: Forebrain


title: HSC-scRNAseq-reprecate3

description: 10x Genomics


title: GM04198, HD, Raphin1 replicate 2


title: GM04198, HD, Raphin1 replicate 3


title: HSC-scRNAseq-reprecate2

description: 10x Genomics


title: GM04198, HD, Raphin1 replicate 1


title: HSC-scRNAseq-reprecate1

description: 10x Genomics


title: GM04196, HD, DMSO replicate 3


title: Ms_Microglia_LPS_rep2

value: Microglia


title: Post-treatment replicate2, scRNA

first: Lu

last: Chen

address: No.197, Ruijin Road II

department: Department of Urology

institute: Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital

description:
Singleron
RT_85

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.12.0 (Singleron Biotechnologies) with default parameters.
Assembly: GRCm38 (mm10)
Supplementary files format and content:
*_matrix.tar Files: the unique lineage DNA barcode information. In this study, DNA barcoding technology was used for cell lineage tracing. We engineered mouse renal adenocarcinoma cells to express unique lineage DNA barcodes as labels, allowing us to track individual tumor cell lineages after treatment with anti-PD-1 therapy.
*_auto_matrix.tar Files: single-cell RNA sequencing information of the transcriptome in individual cells.

source_name: tumor

extract_protocol:
The fresh tissues were stored in the Primary Tissue Storage Solution (bioGenous) on ice after the surgery within 30 mins. The specimens were washed with PBS (HyClone) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture [Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300×g, 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS. GFP+ RENCA cells were isolated using FACS. Finally, the samples were stained with Trypan Blue and the cell viability was evaluated microscopically.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: tumor

value: RENCA tumor cell line

value: subcutaneous graft tumor

value: Balb/c

value: anti-PD-1 antibody


title: Post-treatment replicate1, scRNA

description:
Singleron
RT_83

value: WT


title: Pre-treatment replicate3, scRNA

description:
Singleron
PT_88

value: IgG control


title: Pre-treatment replicate2, scRNA

description:
Singleron
PT_86


title: GM04196, HD, DMSO replicate 2


title: GM04196, HD, DMSO replicate 1


title: GM04196, HD, Raphin1 replicate 1


title: GM04194, HD, DMSO replicate 1


title: GM04196, HD, Raphin1 replicate 2


title: NK, KO, RNA, rep3

city: Hangzhou

first: Xinhua

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

data_processing:
ChIP-seq and ATAC-seq analysis
The raw sequencing data were preprocessed by using fastp, an ultra-fast all-in-one fastq preprocessing software, to remove adapters and low-quality reads. The remaining reads were aligned to GRCm38/mm10 reference genome through Bowtie2 for the Ezh2 ChIP-seq and ATAC-seq data. A synthetic genome composed of GRCm38/mm10 and D. melanogaster (dm6) reference genome was used as the reference for the ChIP-seq data of H3K4me3, H3K27me3, H3K27ac that contained D. melanogaster as spike-in genome. Peak calling was conducted via the Model-based Analysis of ChIP-seq (MACS) version2 with the threshold of q value < 0.05 and broad model for H3K27me3 and Ezh2 and narrow model for H3K27ac and H3K4me3 ChIP-seq and ATAC-seq data. ChIPseeker R package was used for the peak annotation with the 3000bp up- and down-stream centered transcriptional start site (TSS) defined as promoter.
Differential peak analysis
Significantly differential peaks of histone modification ChIP-seq and ATAC-seq between wild-type and Ezh2 knock-out samples were identified through MAnorm. In brief, the mapping signal of every sequencing data were normalized according to their sequencing depth and the scale factor calculated based on the read count of spike-in genome per million sequencing reads. The peak signal was defined as significantly different between two groups with the threshold of q value < 0.05 and the absolute log2(signal ratio) > 1.
Hi-C analysis
Preprocessing, including the mapping of each of the pair-end read, removal of artificial fragment and formation of interaction matrix in hic format was all conducted through juicer, a one-click system for analyzing Hi-C data. Compartment and topological association domain (TAD) analysis were performed by homer at the resolution of 100kb and 10kb, respectively. Visualization of overall or regional interaction frequency accompanied with the genomic features, such as gene density, signal of specific factors or histone modifications, were performed by JuicerBox or FAN-C.
Assembly: mm10
Supplementary files format and content: bigwig, ChIP-seq and ATAC-seq signal
Supplementary files format and content: hic, interaction matrix

source_name: Bone marrow

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes and crosslinked chromatin was sheared by sonication to obtain 150-500 base-pair fragments. For ATAC-seq, cells were lysed to isolate the nuclei and the isolated nuclei were then incubated with Tn5 transposase and tagmentation buffer. For Hi-C, cells were cross-linked, lysed, and nuclei were digested with DpnII. For RNA-seq, total RNA was harvested using Trizol reagent.
Nucleic acid libraries were prepared using illumina Novaseq 6000.

value: Bone marrow

value: Ezh2 KO

value: Induced NK cell


title: NK, KO, RNA, rep2


title: Pre-treatment replicate1, scRNA

description:
Singleron
PT_84


title: GM04194, HD, DMSO replicate 2

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons


title: NK, KO, RNA, rep1


title: NK, WT, RNA, rep3


title: ND33947, HD, DMSO replicate 3

value: HTT CAG expansion

value: DMSO


title: GM04196, HD, Raphin1 replicate 3


title: NK, WT, RNA, rep2


title: GM04194, HD, Raphin1 replicate 3


title: GM04194, HD, Raphin1 replicate 1


title: NK, WT, RNA, rep1


title: GM04194, HD, DMSO replicate 3


title: GM02171, Healthy Control, DMSO replicate 2

value: Healthy control


title: NK, KO, Hi-C, rep1


title: NK, KO, Hi-C, rep2


title: GM02171, Healthy Control, DMSO replicate 3


title: GM02171, Healthy Control, DMSO replicate 1


title: NK, WT, Hi-C, rep2


title: NK, WT, Hi-C, rep1


title: AG08379, Healthy Control, DMSO replicate 3


title: AG08379, Healthy Control, DMSO replicate 1


title: NK, KO, ATAC


title: NK, WT, ATAC


title: NK, KO, Input

tag: chip antibody

value: Input


title: AG08379, Healthy Control, DMSO replicate 2


title: NK, WT, Input


title: GM04194, HD, Raphin1 replicate 2


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  8

city: Helsinki

first: Philipp

last: Sergeev

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

description: 10x Genomics

data_processing:
Data processing and analysis were performed using 10x Genomics Cell Ranger v3.1 pipelines. Cell Ranger includes several pipelines of which the “cellranger mkfastq” was used to produce FASTQ (raw sequence data) files and “cellranger count” to perform alignment, filtering and UMI counting. mkfastq was run using the Illumina bcl2fastq v2.2.0 and alignment was done against human genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Viably frozen myeloma patient bone marrow mononuclear cells were thawed in +37°C water bath. Cells were washed with 25% conditioned medium (CM; RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml) and 25% conditioned medium from the HS-5 human bone marrow stromal cell line), centrifuged 5 min at 300g RT and supernatant discarded. Cells were resuspended in 25% CM and filtered through a cell strainer to remove any remaining cell debris and large clumps. Cell viability was masured by staining the cells with Trypan blue dye and Countess II cell counter. Cells were centrifuged 5 min at 300g RT and supernatant discarded. These cell were placed in the density of 1M cells / ml PBS with 0.04% BSA. The cells were stained with CD138-APC antibody (clone MI15, BD Biosciences) and 7-AAD viability dye (BD Biosciences) and incubated for 15 min in the dark at RT. Cells were washed with PBS with 0.04% BSA and centrifuged 5 min at 300g RT . Cells were resuspended to plain RPMI at 5 million cells/ml, placed on ice and keptprotected from light. FACS was performed for the  viable CD138 positive (CD138+) and CD138 negative (CD138-) cells using  BD Influx Cell Sorter (BD Biosciences). After CD138+ and  CD138- cells were sorted, the cells were centrifuged 10 min at 300g +4°C and supernatant reuced to 20  µl if there were less than 200,000 CD138+/CD138- cells and to 30 µl  if there were more than 200,000 cells. The CD138+ cells were mixed with CD138- cells in a ratio of 1:1 with a maximum of 800,000 cells per sample. If there were fewer than 400,000 CD138+ cells, then all CD138+ cells were mixed with 400,000 CD138− cells
Library preparation was performed on the mixed CD138+ and CD138- cells using the Chromium Single Cell 3′ Gene Expression v3 reagent kit (10x Genomics). The gel beads in emulsion (GEM) generation, cDNA amplification and library preparation were performed according to the manufacturer’s instructions.

value: Mononuclear cells


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  7

description: 10x Genomics


title: NK, KO, H3K27ac ChIP


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  6

description: 10x Genomics


title: NK, WT, H3K4me3 ChIP


title: NK, KO, H3K27me3 ChIP


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  5

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  3

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  4

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  1

description: 10x Genomics


title: NK, WT, H3K27ac ChIP


title: NK, WT, H3K27me3 ChIP


title: Multiple myeloma BM sample, melflufen high sensitivity, rep  2

description: 10x Genomics


title: NK, WT, Ezh2 Input


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  7

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  8

description: 10x Genomics


title: BMDM, WT, IL-4 24h

first: Xingguang

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

growth_protocol: BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml).

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit (MagBeads) (Cat#T102096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

treatment_protocol: WT and Phlpp1 deficient BMDMs were stimulated with IL-4 (20ng/ml) for 12 hours or 24 hours

value: bone marrow

value: Mouse primary bone marrow-derived macrophages

value: IL-4(20ng/ml) for 24h


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  6

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  5

description: 10x Genomics


title: BMDM, WT, IL-4 12h

value: IL-4(20ng/ml) for 12h


title: BMDM, KO, IL-4 12h


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  4

description: 10x Genomics


title: NK, KO, H3K4me3 ChIP


title: AMs, WT-3, day 7

source_name: broncho-alveolar lavage fluid

treatment_protocol: Wild-type (WT) and Phlpp1-deficient mice were exposed to bleomycin for 7 days. Alveolar macrophages of broncho-alveolar lavage fluid (BALF) from mice that were intratracheally instilled with saline or bleomycin were obtained.

value: broncho-alveolar lavage fluid

value: alveolar macrophages


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  1

description: 10x Genomics


title: AMs, WT-2, day 7

growth_protocol: Wild-type (WT) and Phlpp1-deficient mice were exposed to bleomycin for 7 days.

value: WT


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  8

description: 10x Genomics

value: Bone marrow


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  7

description: 10x Genomics


title: NK, WT, Ezh2 ChIP


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  3

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  6

description: 10x Genomics


title: AMs, KO-3, day 7


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  5

description: 10x Genomics


title: BMDM, WT, 4h

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastx v0.0.13, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.05
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Broncho-alveolar lavage fluid

extract_protocol:
Cells were trypsinized with 0.25% trypsin-EDTA and resuspended in 1X PBS (calcium and magnesium-free).
For the ATAC-seq library preparation, 5×104 viable cells were used and collected. The cell pellets were resuspended in cold lysis buffer (1 M Tris-HCl, pH 7.4, 5 M NaCl, 1 M MgCl2, IGEPALCA-630) and incubated on ice for 5 min. Then, the cells were collected and resuspended with 50 μl transposition mixtures according to ATAC Kit instructions (Vazyme, #TD501). Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme, #N411) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme #TD202). Amplification products were further purified with VAHTS DNA Clean Beads.
Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme, #N411) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme #TD202).

treatment_protocol: WT and Phlpp1 deficient BMDMs were stimulated with IL-4 (20ng/ml) for 4 hours

value: Broncho-alveolar lavage fluid

value: Alveolar macrophage


title: AMs, KO-1, day 7


title: AMs, KO-2, day 7


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  3

description: 10x Genomics


title: AMs, WT-1, day 7


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  4

description: 10x Genomics


title: BMDM, KO, IL-4 24h


title: PpardECKO, lung, LPS

city: Shatin

first: XiaoYu

last: TIAN

state: Hong Kong

address: Rm208, LKIBSB, Area 39, Chinese University of Hong Kong

country: Hong Kong

institute: Chinese University of Hong Kong

description: 10X Genomics

data_processing:
The raw sequencing data were processed with Cell Ranger count (10x Genomics, version 6.1.1) to perform alignment, filtering, barcode counting, UMI counting, and gene annotation.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated value files and matrix files

source_name: lung

extract_protocol:
Mouse lung tissues were harvested and single cell suspensions were prepared for flow cytometry sorting. Viable CD45−CD326−CD144+CD31+ ECs were sorted into collection buffer (DMEM/F12 supplemented with 10% FBS) using BD Aria Fusion Cell Sorter.
ScRNA-seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

value: lung

value: Endothelial cells

value: PpardEC KO

value: LPS


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  2

description: 10x Genomics


title: Multiple myeloma BM sample, melflufen low sensitivity, rep  1

description: 10x Genomics


title: BMDM, KO, 4h

value: PHLPP1 cKO


title: PpardECKO, lung, ctl

description: 10X Genomics

value: Vehicle


title: PpardECWT, lung, ctl

description: 10X Genomics

value: PpardEC WT


title: MSCs treated with GTC_2

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: fpkm(.txt)

source_name: mesenchymal stem cells

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: mesenchymal stem cells

value: incubating with 120 ug/mL GTC for 14 days


title: PpardECWT, lung, LPS

description: 10X Genomics


title: MSCs treated with GTC_1


title: Multiple myeloma BM sample, melflufen intermediate sensitivity, rep  2

description: 10x Genomics

value: Mononuclear cells


title: BA1

city: Guangzhou

first: Jia

state: Guangdong

address: The Third Affiliated Hospital of Sun Yat sen University, No. 600 Tianhe Road, Tianhe District, Guangzhou

department: Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research

institute: Third Affiliated Hospital of Sun Yat-sen University

description: ACLF with Baicalein treatment

data_processing:
CLC Genomics Workbench V 11.0.1
Sequence reads were trimmed for adaptor sequencelow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequnce reads were mapped to GrCM3/mm10 using CLC genomic berchwork parameters-mismat cost 2inserton cost- 3 deleton ost-3 ength faction: 0.3 similanty faction:0.3
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKlI values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasv miri lus kit (Ciagen). 1 3 u of total RNA was used for the construcfion of seauencina libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Sea Library Prep Kit folowino manufa cturer's protocols

value: liver

value: ACLF with Baicalein treatment


title: MSCs treated with control_3 (GTC control)

value: incubating with control for 14 days