title: LN_YRS3

city: Changchun

first: yue

last: lu

state: Jilin Province

address: Xincheng Street

department: College of Horticulture

institute: Jilin Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Reference Genome Information
Supplementary files format and content: excel,expression profiles
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).

organism: Solanum tuberosum

growth_protocol: Seed potatoes were potted after dicing treatment, and two different N treatments were set up. The main source of nitrogen fertilizer was urea (containing N 46%). No nitrogen application: 0kg/667m2, excessive nitrogen application: 25kg/667m2. The dosage of calcium superphosphate (containing P2O5 46%) is 18kg/667m2, the dosage of potassium sulfate (containing K2O 50%) is 36kg/667m2, all fertilizers are applied as base fertilizer at one time, 10 pots are planted in each treatment, and 3 biological plants are set up. Learn to repeat.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: The roots and leaves were collected at the potato seedling stage (Seedling stage, S) and budding stage (A), respectively, quick-frozen in liquid nitrogen, stored at -80 °C and sent to Lianchuan Biotechnology Co., Ltd. for miRNA analysis. Sequencing and degradome analysis and qRT-PCR validation.

value: roots and leaves

tag: tag

value: Urea (containing N 46percent)  25 kg/667m2


title: M28Z-IKO_1

status: Public on Oct 12 2022

type: SRA

city: Beijing

first: Xingying

last: Zhang

address: No. 5, Yard 1, Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: total mRNA

library_source: transcriptomic

data_processing:
RNA-seq:
The library samples were sequenced on the Illumina NovaSeq sequencer with 150 bp paired-end reads.
RNA sequencing reads of CAR-T cells and OT-1 cells were aligned to human reference sequence GRCh38 and mouse reference sequence GRCm39 separately using STAR (2.7.0f).
Read counts and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using RSEM (1.3.2).
ChIP-seq:
The obtained FASTQ files were performed quality control with FastQC (0.11.9). Sequenced reads were aligned to the human reference sequence GRCh38 with BWA (0.7.17) software to obtain the SAM files which were converted to BAM files by SAMtools (1.3.1) software.
Then BAM files were sorted with the SAMtools and were deduplicated with Picard (2.24.0).
Binding sites (peaks) are called using MACS2 (2.2.7.1) relative to a control input library and q-value threshold was set as 0.05.
The deduplicated BAM files were converted to bigwig files using bamCoverage command of deeptools (3.3.0) software and viewed using for IGV (2.7.0) visualization software.
Assembly: GRCh38 (human), GRCm39 (mouse)
Supplementary files format and content: *_readcounts_FPKM.xlsx: Excel files include read counts and FPKM values.
Supplementary files format and content: bigwig format for visualization in IGV.

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was isolated from CAR-T cells and mRNA was enriched with Oligo (dT) and broken randomly, then mRNA was reversed by random hexamers to cDNA.
Terminal of the double-stranded cDNA was added sequencing adaptors and utilized PCR amplification to produce the cDNA library.

tag: tissue

value: blood

tag: cell type

value: Primary T cells

tag: genotype

value: CAR-T IRF4 knockout

tag: treatment

value: co-culture with NCI-H226-luciferase at E:T=0.1:1 for 7 days


title: LN_YRS2

value: Urea (containing N 46percent)  18kg/667m2


title: LN_YRS1

value: Urea (containing N 46percent) 0kg/667m2


title: plate2_A05_S101

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

country: USA

institute: MIT

library_source: transcriptomic single cell

data_processing:
Reads were aligned to hg19 (Gencode v21) using Top Hat and estimated counts and transcripts per million (TPM) matrices generated using RSEM. Any samples with fewer than 5x10E5 or more than 6x10E6 aligned reads or fewer than 10,000 uniquely ex-pressed genes were removed from subsequent analysis.
Assembly: hg19
Supplementary files format and content: Tab-separated gene-by-cell TPM matrix

molecule: polyA RNA

source_name: tonsil

extract_protocol:
Libraries were prepared using a modified SMART-Seq2 protocol as previously reported . In brief, based on FACS analysis (BD FACSAria™), single cells of Tetramer+ (HIV or CMV-specific), and tetramer- cells (bulk/total CD8+ T-cells), were sorted into wells onto 96-well plates with lysis buffer, which contained 1 µl 10 mM dNTP mix, 1 µL 10 µM oligo dT primer, 1.9 µl 1% Triton X-100 (Sigma) plus 0.1 µl 40 U/µl RNase Inhibitor.
The sealed plates were stored frozen at -80°C. Thawed plate is incubated for 3 min at 72°C and placed on ice. Next, SMART-Seq2 Whole Transcriptome Amplification (WTA) was performed: 7 µL of RT mix was added to each well and RT was carried out; then, 14 µL of PCR mix was added to each well and PCR was performed. Thereafter a cDNA cleanup was performed using 0.6x and 0.8x volumes of Agencourt AMPure XP SPRI beads (Beckman Coulter) to eliminate short fragments (less than 500 bp). Libraries were then quantified using a Qubit dsDNA HS Assay Kit (Life Technologies). Library size and quality were measured by Bioanalyzer using a High Sensitivity DNA Analysis Kit (Agilent Technologies). Sequencing libraries were prepared from WTA products using Nextera XT (Illumina). After library construction, a final AMPure XP SPRI clean-up (0.8 volumes) was conducted. Library concentration and size were measured with the KAPA Library Quantification kit (KAPA Biosystems) and a Tape Station (Agilent Technologies), respectively. Library was then constructed using Nextera XT DNA library preparation kit (Illumina FC-131-1096) using index primer. After library construction, sequences were purified using a 0.8X SPRI ratio yielding library sizes with an average distribution of 500-750 pb in length as determined using an Agilent hsD5000 Screen Tape System (Agilent Genomics). Finally, samples were sequenced on a NextSeq500 (30 bp paired-end reads) to an average depth of 5 million reads.

value: T cell

tag: disease state

value: HIV

value: tonsil


title: M28Z-BKO_3

description: total mRNA

value: CAR-T BATF knockout


title: single cell RNA sequence data from CEP83 knockout differentiated hiPSCs at day 7 clone 1 [scRNA_KO1]

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

description: 10x v3.1 chemistry

data_processing:
Digital expression matrices were generated using the Cellranger software version 3.0.2.
All datasets were imported as Seurat objects into R using Seurat version 4.0.5. Cells were filtered using a lower gene number (nGene) cutoff of 500  and an upper cutoff of 6000. Data were then log-normalized and scaled according to the number of unique molecular identifiers (UMIs). All all single cell data samples were merged into one Seurat object. Clustering was performed using highly variable genes on all cells using Seurat’s default settings. UMAP plots were generated using 20 principal components from PCA with highly variable genes.
Assembly: NOT PROVIDED
Supplementary files format and content: Barcodes, features and expression matrix file from Cellranger software

source_name: Intermediate mesoderm cells

extract_protocol:
The differentiated hiPSCs to intermediate mesodermal cells were collected at day 7 of the differentiation from two experiments: The first experiment (WT1 and KO1), and the second experiment (WT2 and KO2) cells. The collected cells were washed with 1x DPBS, dissociated with Accumax, filtered with a 40 µm filter, counted (to achieve 10,000 cells per sample), and checked for viability using Trypan blue staining.
library preparation were performed according to the 10x Genomics single cell protocol (10X Genomics toolkit version v3.1, Pleasanton, CA)

value: CEP83 knockout

tag: time

value: Day 7

value: Intermediate mesoderm cells


title: M28Z_multiround_2

description: total mRNA

value: CAR-T WT

value: three rounds tumor challenge


title: M28Z-BKO_2

description: total mRNA


title: single cell RNA sequence data from wildtype differentiated hiPSCs at day 7 clone 2 [scRNA_WT2]

description: 10x v3.1 chemistry

value: wildtype


title: single cell RNA sequence data from CEP83 knockout differentiated hiPSCs at day 7 clone 2 [scRNA_KO2]

description: 10x v3.1 chemistry


title: plate1_C03_S27


title: HO228_PATOM_PAX300_P22 (biol rep 2)

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files of single-end RNA-Seq reads were aligned with STAR 2.6.0a  to the reference genome GRCh38 with 2-pass mode.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of gene level counts

source_name: Patient-Derived Xenograft

extract_protocol:
mRNA extracted using the Qiagen Rneasy Micro Kit. 200 ng of total RNA according to manufacturers instructions for Illumina TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Patient-Derived Xenograft

value: Pancreatic Ductal Adenocarcinoma

value: PaTOM Media


title: LN_YRA2

value: roots and leaves


title: plate4_B08_S212


title: M28Z-BKO_1

description: total mRNA

value: blood

value: Primary T cells

value: co-culture with NCI-H226-luciferase at E:T=0.1:1 for 7 days


title: LN_YRA1

value: Urea (containing N 46percent) 0kg/667m2


title: single cell RNA sequence data from wildtype differentiated hiPSCs at day 7 clone 1 [scRNA_WT1]

description: 10x v3.1 chemistry


title: plate2_F10_S166

value: T cell

value: HIV


title: hypofunction_3

description: total mRNA


title: LN_YLS3

value: Urea (containing N 46percent)  25 kg/667m2


title: plate2_F11_S167

value: tonsil


title: Subject 5594, Occipital Lobe, Late-onset sporadic AD

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
RNA-Seq data preprocessing was performed using the TrimGalore! Package, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>20).
Trimmed RNA-Seq reads were mapped to the GRCh38.99 human transcriptome using kallisto v0.46.1 with the options -bias, --rf-stranded, and -b 100.
Transcript level summation to the gene level using the R package tximport v1.8.0.
Assembly: GRCh38.99
Supplementary files format and content: Normalized count matrix for all RNA-Seq samples

source_name: Occipital Lobe

extract_protocol:
RNA from brain samples was extracted using the RNeasy Lipid Tissue Mini kit (Qiagen Cat. 74804) according to the manufacturer’s protocol
Libraries were prepared for RNA-Seq using the TruSeq Stranded Total RNA Library prep kit (Illumina, Cat. RS-122-2303) by the Ribo-Zero ribosomal RNA reduction method (Illumina

value: Occipital Lobe

value: Alzheimer's disease

tag: group

value: Late-onset sporadic AD


title: Subject 5569, Occipital Lobe, Late-onset sporadic AD


title: hypofunction_2

description: total mRNA

value: CAR-T WT


title: Subject 5566, Occipital Lobe, Late-onset sporadic AD


title: hypofunction_1

description: total mRNA


title: LN_YLS1


title: activated_3

description: total mRNA

value: co-culture with NCI-H226-luciferase at E:T=2:1 for 24h


title: Lactosis 2

city: Kumamoto

first: Ubonrat

last: Thamrongwaranggoon

address: 2-2-1 Honjo,Chuo-ku,

department: Medical Cell Biology

country: Japan

institute: Institute of Molecular Embryology and Genetics

data_processing:
Resulting reads were aligned to the UCSC hg38 reference genome using STAR.
Normalization, differential analysis, and gene ontology analysis was performed using Strand NGS (Strand Genomics).
Assembly: hg38
Supplementary files format and content: Matrix table include TPM values for each Sample.
Supplementary files format and content: *_fold_change.csv: Comma-separated text files

source_name: Human CCA cell line KKU-213A

growth_protocol: CCA cells were cultured in Low glucose Dulbecco’s modified Eagle’s medium (LG-DMEM) (Wako, Osaka. Japan) supplemented with 10% fetal bovine serum (FBS) (Corning, MA USA) and 1% penicillin/streptomycin (P/S) (Sigma-Aldrich, MO, USA), at 37°C with 5% CO2 incubator equilibrated with 95% air, 5% CO2. The medium was changed every other day.

extract_protocol:
Total RNA from CCA cells was extracted using RNeasy Mini Kit (Qiagen). mRNA was purified using NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB).
cDNA library for sequencing was synthesized using NEB Next Ultra DNA Library Prep Kit for Illumina (NEB) and was sequenced on NextSeq 500 sequencer (Illumina) with 75-bps single-end reads.

treatment_protocol: To generate a lactic acidosis-culture media, complete media LG-DMEM was modified by adding L-lactate and HEPES to get a final concentration of 25 mM L-lactate and 25 mM HEPES. The pH was adjusted to pH 6.7 with hydrochloric acid (HCl). The long term-lactic acidosis (LLA) cells cultured in complete media LG-DMEM were replaced with 25% (v/v) lactic acidosis media for 24 h or for one passage and step wise increased for each sub-passaged until reaching 100% lactic acidosis-cultured media. The acidosis cells were cultured in complete media LG-DMEM pH 6.5 with final concentration of 25 mM HEPES, and lactosis cells were cultured in complete media LG-DMEM pH 7.4 with final concentration of 25 mM L-lactate. To ensure that cells were optimized in the specified condition, cells were cultured in the specified media for at least 5 passages before use.

value: Human mixed (papillary and non-papillary cholangiocarcinoma cell line)

value: Lactosis treated


title: Lactosis 3


title: LN_YLS2

value: Urea (containing N 46percent)  18kg/667m2


title: LN_YRA3

value: roots and leaves


title: Subject 5526, Occipital Lobe, Late-onset sporadic AD


title: Lactosis 1


title: activated_2

description: total mRNA

value: blood


title: Subject 5492, Occipital Lobe, Late-onset sporadic AD


title: LN_YLA2


title: activated_1

description: total mRNA

value: Primary T cells


title: LN_YLA3


title: LN_YLA1


title: LLA 2

value: Lactic acidosis treated


title: Subject 5394, Occipital Lobe, Late-onset sporadic AD


title: LLA 3


title: fresh_3

description: total mRNA


title: LN_DRS3


title: fresh_2

description: total mRNA


title: Acidosis 3

value: Acidosis treated


title: Subject 5376, Occipital Lobe, Late-onset sporadic AD


title: LLA 1


title: Subject 5366, Occipital Lobe, Late-onset sporadic AD


title: LN_DRS2


title: unstimulated_3

description: total mRNA

value: culture for 9 days after resuscitating


title: LN_DRA3


title: Subject 5425, Occipital Lobe, Late-onset sporadic AD


title: Acidosis 2


title: Subject 5303, Occipital Lobe, Late-onset sporadic AD


title: Subject 5275, Occipital Lobe, Late-onset sporadic AD


title: LN_DRA1

value: Urea (containing N 46percent) 0kg/667m2


title: LN_DRS1


title: Subject 5342, Occipital Lobe, Late-onset sporadic AD


title: Control 3

value: Untreated


title: unstimulated_2

description: total mRNA


title: LN_DLS3

value: Urea (containing N 46percent)  25 kg/667m2


title: LN_DRA2


title: Subject 5252, Occipital Lobe, Late-onset sporadic AD

value: Occipital Lobe


title: unstimulated_1

description: total mRNA


title: fresh_1

description: total mRNA


title: Control 1


title: LN_DLS1


title: 4-2_11102016

city: Boston

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: *.tar: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA isolation method was no phenol or chloroform was used. RNA isolation kit was miRcury biofluids (Exiqon).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were not multiplexed. Type of Starting Material was total RNA.

tag: donor

tag: disease status

value: Healthy

tag: time point

value: afternoon

value: Plasma

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)


title: 6-2_11102016


title: Subject 5147, Occipital Lobe, Late-onset sporadic AD

value: Alzheimer's disease

value: Late-onset sporadic AD


title: Control 2

value: Human mixed (papillary and non-papillary cholangiocarcinoma cell line)


title: 3-3_11102016

value: evening


title: Acidosis 1


title: T-ALL patient 18

city: Guangzhou

first: Lenghe

address: No. 106, Zhongshan Second Road

institute: Guangdong Provincial People's Hospital

description: Sample 18

data_processing:
SOAPnuke
HISAT2
Bowtie2
DEGseq
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: excel files include Count values for each sample

source_name: Bone marrow

extract_protocol:
Trizol
OligodT，DNBseq

value: Bone marrow

tag: disease

value: T-ALL

value: myelomoncyte


title: LN_DLA3

value: roots and leaves


title: T-ALL patient 19

description: Sample 19


title: Subject 5065, Occipital Lobe, Late-onset sporadic AD


title: T-ALL patient 20

description: Sample 20


title: LN_DLS2

value: Urea (containing N 46percent)  18kg/667m2


title: T-ALL patient 16

description: Sample 16


title: T-ALL patient 17

description: Sample 17


title: 4-3_11102016


title: Subject 4964, Occipital Lobe, Late-onset sporadic AD


title: 6-3_11102016


title: T-ALL patient 14

description: Sample 14


title: 7-3_11152016


title: T-ALL patient 15

description: Sample 15


title: LN_DLA1

value: Urea (containing N 46percent) 0kg/667m2


title: Subject 4950, Occipital Lobe, Late-onset sporadic AD

value: Occipital Lobe


title: HN_YRS3

value: Urea (containing N 46percent)  25 kg/667m2


title: LN_DLA2


title: T-ALL patient 13

description: Sample 13


title: 6-1_11102016

value: Healthy

value: morning


title: 8-2_11152016

value: afternoon

value: Plasma

value: Entire cardiovascular system


title: T-ALL patient 11

description: Sample 11


title: Subject 5618, Occipital Lobe, Early-onset sporadic AD

value: Alzheimer's disease

value: Early-onset sporadic AD


title: Subject 5197, Occipital Lobe, Late-onset sporadic AD

value: Late-onset sporadic AD


title: Subject 5585, Occipital Lobe, Early-onset sporadic AD


title: T-ALL patient 10

description: Sample 10


title: HN_YRS2


title: T-ALL patient 12

description: Sample 12


title: Subject 5537, Occipital Lobe, Early-onset sporadic AD


title: HN_YRS1


title: 2-3_11102016

value: evening

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: HN_YRA3


title: Subject 5454, Occipital Lobe, Early-onset sporadic AD


title: HN_YRA2


title: Subject 5017, Occipital Lobe, Late-onset sporadic AD


title: 7-2_11152016


title: HN_YRA1


title: T-ALL patient 8

description: Sample 8

value: Bone marrow

value: T-ALL

value: myelomoncyte


title: HN_YLS3

value: roots and leaves


title: 8-1_11152016


title: Subject 5333, Occipital Lobe, Early-onset sporadic AD

value: Occipital Lobe


title: 8-3_11152016


title: Subject 5337, Occipital Lobe, Early-onset sporadic AD


title: HN_YLS2

value: Urea (containing N 46percent)  18kg/667m2


title: T-ALL patient 7

description: Sample 7


title: T-ALL patient 6

description: Sample 6


title: HN_YLA3

value: Urea (containing N 46percent)  25 kg/667m2


title: 2-1_11102016

value: Healthy

value: morning


title: Subject 5273, Occipital Lobe, Early-onset sporadic AD


title: T-ALL patient 4

description: Sample 4


title: HN_YLA2


title: T-ALL patient 5

description: Sample 5


title: 3-1_11102016

value: Plasma


title: Subject 5269, Occipital Lobe, Late-onset sporadic AD


title: 4-1_11102016

value: Entire cardiovascular system


title: Subject 5419, Occipital Lobe, Early-onset sporadic AD

value: Alzheimer's disease


title: T-ALL patient 3

description: Sample 3


title: HN_YLA1

value: Urea (containing N 46percent) 0kg/667m2


title: Subject 5113, Occipital Lobe, Early-onset sporadic AD

value: Early-onset sporadic AD


title: K53-IL-37 treated cells

city: Dublin

first: Pavel

last: Davidovich

address: College Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
CLC Genomics Workbench
Sequencing files were imported into CLC Genomics Workbench and reads of the samples were quality controlled. With a mean Phred score (Q) of 34.02, the data showed a very high average quality.
The human reference genome (GRCh38.p7) was downloaded from NCBI and used as reference sequence. Gene and mRNA tracks extracted from these references were used for counting gene expression values. For mapping purposes of the generated sequencing files, reads were mapped according to their similarity to the reference sequences. The following mapping parameters were applied: mismatch cost: 2; insertion/deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8; global alignment: no; strand specific: Both; maximum number of hits per read: 5.
The applied parameters are described in detail by CLC
Assembly: GRCh38.p7
Supplementary files format and content: Excel files with differential expression analysis

growth_protocol: Primary human neonatal foreskin-derived keratinocytes were maintained in DermaLife K fully supplemented keratinocyte growth medium in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy Mini kit (Qiagen). Concentrations, A260/A280 and A260/A230 ratios of the isolated total RNA were determined by spectral photometry on the NanoDrop ND-1000 instrument. RNA integrity was assessed on the Agilent 2100 Bioanalyzer
300 ng of total RNA were introduced into the reaction for all samples. After purification of the amplified cDNA samples, quality control of each single sample was carried out using the 2100 Bioanalyzer DNA 1000 LabChip. Amplified cDNA samples revealed typical electropherograms showing a broad fragment distribution between 250 bp – 700 bp with a peak around 325 bp for all samples.

treatment_protocol: Primary keratinocytes (10^6/well) were left untreated or stimulated for 2h with 10 nM of active IL-36β and 10 nM of K53-IL-37

value: primary keratinocytes

value: WT


title: Subject 5240, Occipital Lobe, Early-onset sporadic AD


title: 2-2_11102016

value: afternoon

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: HN_YLS1


title: HN_DRS2


title: Active IL-36β treated cells

source_name: Primary human neonatal foreskin-derived keratinocytes


title: T-ALL patient 1

description: Sample 1

value: Bone marrow

value: T-ALL

value: myelomoncyte


title: T-ALL patient 2

description: Sample 2


title: Subject 5107, Occipital Lobe, Early-onset sporadic AD

value: Occipital Lobe


title: Subject 5082, Occipital Lobe, Early-onset sporadic AD


title: HN_DRS1

value: roots and leaves


title: Subject 5020, Occipital Lobe, Early-onset sporadic AD


title: Untreated cells

value: Primary human neonatal foreskin-derived keratinocytes

value: Untreated


title: RNA WT rep2

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

data_processing:
The raw sequences were cleaned using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to human reference genome hg19 by STAR (v2.7.1a) with default parameter. All mapped bam files were converted to bigwig using bedtools (v2.24.0) (Quinlan, 2014). for visualization in IGV. High quality mapped reads were quantified using htseq -count (v0.11.3) (Anders et al., 2015). Differentially expressed genes were analyzed by DEseq2 (Love et al., 2014).
Assembly: hg19
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: mammary gland/breast

growth_protocol: Human breast cancer cell line MDA-MB-231 and HEK293T cells were maintained in Dulbecco’s modified Eagle medium with high glucose (Lifetech), 10% fetal bovine serum (Lifetech), and 1× penicillin/streptomycin (Lifetech). Cells were maintained at 37 °C and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from cultured MBA-MD-231 cells with 10,000,000 cells in each sample.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). RNA-seq paired-end reads were sequenced on the Illumina NovaSeq 6000 platform.

value: mammary gland/breast

value: epithelial, breast cancer cell line

value: wild type


title: Subject 5047, Occipital Lobe, Early-onset sporadic AD

value: Alzheimer's disease


title: RNA WT rep1


title: RNA SUN2KO rep2

value: SUN2 KO


title: PAO1DcolR_media_rep3

city: Vancouver

first: Chrisitna

middle: L

last: Wiesmann

state: British Columbia

address: 1365 - 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: The University of British Columbia

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

organism: Pseudomonas aeruginosa

source_name: Pathogenic Pseudomonas bacteria

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions and stored in RNAprotect Bacteria Reagent (Qiagen) if extraction was not perfomed immediately.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.

tag: background strain

value: grown in M9 minimal media


title: Subject 5184, Occipital Lobe, Early-onset sporadic AD

value: Early-onset sporadic AD


title: RNA LBD rep1

value: LBD


title: Subject 4934, Occipital Lobe, Early-onset sporadic AD


title: HN_DRA3

tag: tag

value: Urea (containing N 46percent)  25 kg/667m2


title: PAO1DcolR_media_rep2


title: SDP_1037, WGBS

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

library_source: genomic

data_processing:
Paired-end FASTQ files were mapped to the human (hg19) genome using bwa-meth (V 0.2.0), with default parameters (Pedersen et al., 2014), then converted to BAM files using SAMtools (V 1.9) (Li et al., 2009).
Duplicated reads were marked by Sambamba (V 0.6.5), with parameters “-l 1 -t 16 --sort-buffer-size 16000 --overflow-list-size 10000000” (Tarasov et al., 2015).
Reads with low mapping quality, duplicated, or not mapped in a proper pair were excluded using SAMtools view with parameters -F 1796 -q 10.
Reads were stripped from non-CpG nucleotides and converted to BETA files using wgbstools (V 0.1.0) (Loyfer and Kaplan).
Assembly: hg19
Supplementary files format and content: beta files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
Supplementary files format and content: bigwig files were generated from beta files using wgbstools beta2bw with default parameteres

molecule: genomic DNA

source_name: Platelets

extract_protocol:
DNA was extracted from three platelet samples using the QIAsymphony liquid handling robot (Qiagen).
Whole-genome bisulfite sequencing libraries were generated with Swift Accel‐NGS Methyl-Seq DNA Library preparation protocol (Swift Biosciences, Ann Arbor, MI). Paired-end sequencing was performed on the Illumina Nextseq 550 System of 300 bp per read at an average depth of 2.54x.

value: Platelets


title: HN_DRS3

tag: tissue


title: Subject 5000, Occipital Lobe, Early-onset sporadic AD


title: HN_DLS2

value: Urea (containing N 46percent)  18kg/667m2


title: SDP_758, WGBS

tag: cell type


title: SDP_1024, WGBS


title: HN_DRA1

value: Urea (containing N 46percent) 0kg/667m2


title: Subject 4988, Occipital Lobe, Early-onset sporadic AD


title: PAO1DcolR_media_rep1

tag: genotype


title: HN_DRA2


title: HN_DLS1


title: RNA SUN2KO rep1


title: HN_DLS3


title: HN_DLA3


title: WTPAO1_media_rep3

value: wild-type

tag: treatment


title: RNA Kashlid rep1

value: Kashlid


title: Subject 4920, Occipital Lobe, Early-onset sporadic AD

value: Occipital Lobe

tag: disease state


title: HN_DLA2

value: roots and leaves


title: RNA LBD rep2


title: HGC-27, Vector, replicate 3

city: Shanghai

first: Yingyan

last: Yu

address: No. 197 Ruijin Second Road

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

description: Sample 6

data_processing:
RNA-seq reads were trimmed by trimmomatic (version 0.32) with the parameters "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 HEADCROP:13 SLIDINGWINDOW:4:15 MINLEN:36"
High-quality reads were mapped to reference genome by HISAT2 (version 2.1.0) with default parameters.
The reads uniquely mapped to exons of genes to quantify the transcript levels of genes by featureCounts (version 2.0.0) with parameters "-p -O -t exon -g gene id".
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file includes mapped reads values for each Sample

growth_protocol: Human gastric cancer cells HGC-27 (Shanghai Outdo Biotech Co. Ltd, Shanghai, China, with authentication by STR technology) were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS; Gibco, Grand Island, NY).

extract_protocol:
The total RNA from HGC-27GC0643 and HGC-27Vector was harvested using Total RNA Extraction Reagent(Vazyme, China) . 2μg of total RNA was used for the construction of sequencing libraries.
Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Agilent Technologies,USA) was used for preliminary RNA quantification. And RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system(NEB,USA) was used for measuring RIN value.NEBNext® Ultra RNA Library Prep Kit for Illumina(NEB,USA) was used for library construction.

value: Human gastric cancer cells

value: Vector control


title: Subject 5709, Occipital Lobe, Non-demented Control

value: Non-demented Control

value: control


title: HGC-27, Vector, replicate 2

description: Sample 5


title: Subject 5114, Occipital Lobe, Non-demented Control


title: Subject 5628, Occipital Lobe, Non-demented Control


title: RNA-seq of adult Xenopus tropicalis midbrain [Xtr_Midbrain_H]

city: Barcelona

first: Federica

last: Mantica

address: Dr. Aiguader 88

country: Spain

institute: CRG

description: Brain from an adult individual

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

organism: Xenopus tropicalis

source_name: Adult brain

extract_protocol:
Trizol
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: genome build

tag: gtf

value: XenTro9 GTF (enriched from Ensembl v101)


title: PAO1DcolR_plant_rep2

value: grown in Arabidopsis rhizosphere


title: Subject 5070, Occipital Lobe, Non-demented Control

tag: group


title: HGC-27, GC0643, replicate 3

description: Sample 3

tag: cell line

value: GC0643 overexpression


title: Subject 4954, Occipital Lobe, Non-demented Control


title: PAO1DcolR_plant_rep1


title: RNA-seq of adult Xenopus tropicalis intestine [Xtr_Intestine_H]

description: Intestine from an adult individual

source_name: Adult intestine

value: Intestine


title: WTPAO1_media_rep2

value: grown in M9 minimal media


title: Subject 5248, Occipital Lobe, Non-demented Control


title: RNA Kashlid rep2

value: mammary gland/breast

value: epithelial, breast cancer cell line


title: WTPAO1_plant_rep3


title: 7-1_11152016

tag: donor

tag: disease status

value: Healthy

value: morning

value: Plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: WTPAO1_media_rep1

value: wild-type


title: HGC-27, GC0643, replicate 1

description: Sample 1

value: Human gastric cancer cells


title: RNA-seq of adult Xenopus tropicalis forebrain [Xtr_Forebrain_H]

description: Forebrain from an adult individual


title: RNA-seq of adult Xenopus tropicalis stomach [Xtr_Stomach_H]

description: Stomach from an adult individual

source_name: Adult stomach

value: Stomach


title: HGC-27, GC0643, replicate 2

description: Sample 2


title: Subject 4942, Occipital Lobe, Non-demented Control

value: Occipital Lobe

value: Non-demented Control

value: control


title: HGC-27, Vector, replicate 1

description: Sample 4

value: Vector control


title: HN_DLA1

value: roots and leaves

value: Urea (containing N 46percent) 0kg/667m2


title: T-ALL patient 9

description: Sample 9

value: Bone marrow

value: T-ALL

value: myelomoncyte


title: RNA-seq of adult Xenopus tropicalis colon [Xtr_Colon_H]

description: Colon from an adult individual

source_name: Adult colon

value: Colon

value: XenTro9 GTF (enriched from Ensembl v101)


title: WTPAO1_plant_rep2

value: grown in Arabidopsis rhizosphere


title: Subject 4870, Occipital Lobe, Non-demented Control


title: ribas_310_on_later_TCR

city: New York

first: Johannes

middle: C

last: Melms

state: New York

address: 650 W 168th Street

institute: Columbia University

description: Single-nuclei RNA sequencing

data_processing:
Library strategy: TCR-seq
Raw sc/snRNA-seq data were analyzed using Cell Ranger (v5.1 for uveal melanoma liver metastasis and cutameous melanoma metastasis datasets, v6.1 for all other datasets). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.1.0). Gene expression matrices were processed individually in R (v4.0.2) using Seurat (v4.0.1).
For cutaneous melanoma metastasis samples, we applied filters to keep only cells with 300-10000 genes, 400-30000 UMIs, and <10% of mitochondrial reads. For uveal melanoma liver metastasis samples, we kept cells with at least 200 genes, 100 UMIs, and <10% of mitochondrial reads. Additionally, we removed cells with gene or UMI counts that were above a sample-specific maximum limit, based on the observed saturation curve between gene and UMI counts for each sample. Please refer to Extended Data Table 4 of the paper for the exact limits. Finally, for all other datasets, we kept cells with at least 300 genes and <20% of mitochondrial reads.
Scrublet was applied to identify and remove doublets with an expected doublet rate of 9.6%.
Genome_build: GRCh38
Supplementary_files_format_and_content: *all_contig_annotations.csv: csv file with all contig annotations from cellranger vdj pipeline
Supplementary_files_format_and_content: *clonotypes.csv: csv file with all clonotypes detected during cellranger vdj pipeline
Supplementary_files_format_and_content: *consensus_annotations.csv: csv file with consensus contig annotations from cellranger vdj pipeline
Supplementary_files_format_and_content: *filtered_contig_annotations.csv: sv file with filtered contig annotations from cellranger vdj pipeline

source_name: Cutaneous Melanoma metastasis

extract_protocol:
Single-cell samples: Samples from surgical resections were dissociated using the human tumor dissociation kit from Miltenyi and viable populations were sorted as indicated. Of each sorting population 12,000-15,000 cells were loaded for droplet-based RNA capture and reverse transcription using 10x Genomics 5’ reagents and a Chromium controller. Single-nuclei samples: Single-nuclei suspension from frozen samples were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications to improve quality and yield while sparing tissue. Salt-tris buffer with Tween-20 (TST) was used for dissociation followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 9,000-15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics reagents and a Chromium controller as indicated.
Single-cell RNA sequencing (scRNA-seq) libraries were generated using Chromium 5’ reagents and T cell enrichment kit according to the manufacturer protocol. SingleSingle-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 3' or 5’ reagents (and T cell enrichment kit) as indicated according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: TCR

tag: kit information

value: Chromium Next GEM Single Cell 5’ v2 reagents

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

value: Pembrolizumab

tag: timepoint

value: On treatment


title: WTPAO1_plant_rep1

tag: background strain

value: wild-type


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 25 clone 3 [WT3_D25]

data_processing:
Provided FASTQ files were aligned using STAR and the mm9 genome.
Reads were then counted using featureCounts34 with -p -t exon -O -g gene_id -s 0.
Raw count values were then transformed to TPM (transcript per million) values.
Assembly: mm9
Supplementary files format and content: TPM

source_name: differentiated organoids

extract_protocol:
Cells were harvested from different time points of differentiation (Day 0,7, and 25). Total RNA was isolated from the cells using RNAasy Mini Kit (QIAGEN, Hilden, Germany, 74104) following the manufacture instructions.
Total RNA was sent to Novogene on dry ice. Novogene performed paired-end RNA-sequencing according to their cmpany guidelines (https://en.novogene.com/next-generation-sequencing-services/gene-regulation/mrna-sequencing-service/). Paired-end Illumina libraries were sequenced on Illumina Novaseq 6000.

tag: genotype

value: wildtype

tag: time

value: Day 25

tag: cell type

value: differentiated organoids


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 25 clone 2 [WT2_D25]


title: PAO1DcolR_plant_rep3

tag: treatment


title: RNA-seq of adult Xenopus tropicalis adipose tissue [Xtr_Adipose_a]

description: Adipose tissue from an adult individual

source_name: Adult adipose

tag: tissue

value: Adipose

tag: genome build

tag: gtf


title: RNA-seq of adult Danio rerio adipose tissue [Dre_Adipose_a]

description: Pooled adipose from adult individuals

organism: Danio rerio

source_name: Adult adipose tissue

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: danRer10 GTF (enriched from Ensembl v80)


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 25 clone 1 [WT1_D25]


title: ribas_310_pre_TCR

description: Single-nuclei RNA sequencing

value: Pre treatment


title: ribas_310_on_TCR

description: Single-nuclei RNA sequencing


title: UMEL_7_3_TCR

description:
Single-nuclei RNA sequencing
UMEL_7_3

data_processing:
Library strategy: TCR-seq
Raw sc/snRNA-seq data were analyzed using Cell Ranger (v5.1 for uveal melanoma liver metastasis and cutameous melanoma metastasis datasets, v6.1 for all other datasets). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.1.0). Gene expression matrices were processed individually in R (v4.0.2) using Seurat (v4.0.1).
For cutaneous melanoma metastasis samples, we applied filters to keep only cells with 300-10000 genes, 400-30000 UMIs, and <10% of mitochondrial reads. For uveal melanoma liver metastasis samples, we kept cells with at least 200 genes, 100 UMIs, and <10% of mitochondrial reads. Additionally, we removed cells with gene or UMI counts that were above a sample-specific maximum limit, based on the observed saturation curve between gene and UMI counts for each sample. Please refer to Extended Data Table 4 of the paper for the exact limits. Finally, for all other datasets, we kept cells with at least 300 genes and <20% of mitochondrial reads.
Scrublet was applied to identify and remove doublets with an expected doublet rate of 9.6%.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression matrix
*all_contig_annotations.csv: csv file with all contig annotations from cellranger vdj pipeline
*clonotypes.csv: csv file with all clonotypes detected during cellranger vdj pipeline
*consensus_annotations.csv: csv file with consensus contig annotations from cellranger vdj pipeline
*filtered_contig_annotations.csv: sv file with filtered contig annotations from cellranger vdj pipeline

source_name: Uvel melanoma (liver metastasis)

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Selumetinib

value: Post treatment


title: Week 70 male brain

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt. The trimmomatic tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides). The quality reads were then mapped to the mouse reference genome GRCm38 using Hisat2 aligner.
Read counting from the alignment data was performed by FeatureCounts. The feature count data was then analyzed by edgeR to determine significance of differential expression of KO compared to WT brain.
Assembly: GRCm39
Supplementary files format and content: comma separated file

organism: Mus musculus

source_name: whole brain

extract_protocol:
Total RNA was isolated from postnatal day 5 and week 70 old male and female mice using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: strain

value: whole brain

tag: age

value: week 70

tag: Sex

value: male


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 25 clone 2 [KO2_D25]

value: CEP83 knockout


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 25 clone 1 [KO1_D25]


title: YMC-331

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: serum:healthy volunteer

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

tag: disease status

value: HV


title: YMC-332

description: miRNA


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 7 clone 3 [WT3_D7]

source_name: Intermediate mesoderm cells

value: Day 7

value: Intermediate mesoderm cells


title: UMEL_7_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_7_2

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: TCR

value: Cellranger v5.1.0

value: On treatment


title: UMEL_7_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_7_1

tag: kit information

tag: cellranger version

tag: cellbender version


title: YMC-330

description: miRNA


title: YMC-329

description: miRNA


title: Postnatal day 5 female brain

value: postnatal day 5

value: female


title: UMEL_6_3_TCR

description:
Single-nuclei RNA sequencing
UMEL_6_3

value: Chromium Next GEM Single Cell 5' v2 reagents

tag: timepoint


title: OT-1-BOE_3

first: Xingying

institute: Institute of Zoology, Chinese Academy of Sciences

description: total mRNA

data_processing:
RNA-seq:
The library samples were sequenced on the Illumina NovaSeq sequencer with 150 bp paired-end reads.
RNA sequencing reads of CAR-T cells and OT-1 cells were aligned to human reference sequence GRCh38 and mouse reference sequence GRCm39 separately using STAR (2.7.0f).
Read counts and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using RSEM (1.3.2).
ChIP-seq:
The obtained FASTQ files were performed quality control with FastQC (0.11.9). Sequenced reads were aligned to the human reference sequence GRCh38 with BWA (0.7.17) software to obtain the SAM files which were converted to BAM files by SAMtools (1.3.1) software.
Then BAM files were sorted with the SAMtools and were deduplicated with Picard (2.24.0).
Binding sites (peaks) are called using MACS2 (2.2.7.1) relative to a control input library and q-value threshold was set as 0.05.
The deduplicated BAM files were converted to bigwig files using bamCoverage command of deeptools (3.3.0) software and viewed using for IGV (2.7.0) visualization software.
Assembly: GRCh38 (human), GRCm39 (mouse)
Supplementary files format and content: *_readcounts_FPKM.xlsx: Excel files include read counts and FPKM values.
Supplementary files format and content: bigwig format for visualization in IGV.

source_name: spleen

extract_protocol:
Total RNA was isolated from CAR-T cells and mRNA was enriched with Oligo (dT) and broken randomly, then mRNA was reversed by random hexamers to cDNA.
Terminal of the double-stranded cDNA was added sequencing adaptors and utilized PCR amplification to produce the cDNA library.

value: spleen

value: Primary T cells

tag: genotype

value: OT-1 BATF overexpression

value: three rounds tumor challenge


title: UMEL_6_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_6_2

value: Selumetinib


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 7 clone 2 [WT2_D7]

value: wildtype

tag: time

tag: cell type


title: bulk RNA-seq from wildtype differentiated hiPSCs at day 7 clone 1 [WT1_D7]


title: YMC-328

description: miRNA

tag: tissue

value: serum


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 25 clone 3 [KO3_D25]

value: CEP83 knockout

value: Day 25

value: differentiated organoids


title: OT-1-BOE_2

description: total mRNA

tag: treatment


title: OT-1-BOE_1

description: total mRNA


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 7 clone 3 [KO3_D7]

value: Day 7

value: Intermediate mesoderm cells


title: UMEL_6_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_6_1

value: frozen

value: TCR

value: Cellranger v5.1.0

value: Pre treatment


title: UMEL_5_3_TCR

description:
Single-nuclei RNA sequencing
UMEL_5_3

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Post treatment


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 7 clone 2 [KO2_D7]


title: YMC-327

description: miRNA

value: HV


title: Week 70 female brain

value: whole brain

value: week 70

value: female


title: Postnatal day 5 male brain

value: postnatal day 5

value: male


title: UMEL_5_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_5_2

value: Selumetinib

value: On treatment


title: OT-1-BKO_3

description: total mRNA

value: spleen

value: Primary T cells

value: OT-1 BATF knockout

value: three rounds tumor challenge


title: bulk RNA-seq from CEP83 knockout differentiated hiPSCs at day 7 clone 1 [KO1_D7]

value: CEP83 knockout

value: Day 7

value: Intermediate mesoderm cells


title: OT-1-BKO_2

description: total mRNA


title: UMEL_5_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_5_1

value: frozen

value: TCR

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Cellranger v5.1.0

value: Pre treatment


title: bulk RNA-seq from wildtype hiPSCs at day 0 clone 3 [WT3_DO]

source_name: undifferentiated hiPSCs

value: wildtype

value: Day 0

value: undifferentiated hiPSCs


title: OT-1-BKO_1

description: total mRNA


title: bulk RNA-seq from wildtype hiPSCs at day 0 clone 2 [WT2_D0]


title: bulk RNA-seq from wildtype hiPSCs at day 0 clone 1 [WT1_D0]


title: OT-1_2

description: total mRNA

value: OT-1 WT


title: bulk RNA-seq from CEP83 knockout hiPSCs at day 0 clone 3 [KO3_D0]


title: bulk RNA-seq from CEP83 knockout hiPSCs at day 0 clone 1 [KO1_D0]


title: bulk RNA-seq from CEP83 knockout hiPSCs at day 0 clone 2 [KO2_D0]


title: UMEL_3_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_3_1

value: Selumetinib


title: UMEL_4_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_4_1


title: UMEL_4_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_4_2

value: On treatment


title: UMEL_3_3_TCR

description:
Single-nuclei RNA sequencing
UMEL_3_3

value: Post treatment


title: UMEL_3_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_3_2


title: Day 10, elongated

city: Lausanne

first: Matthias

last: Lütolf

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

description:
10x Genomics
D6D10_barcodes.tsv.gz
D6D10_features.tsv.gz
D6D10_matrix.mtx.gz
D6D10_metadata.tsv.gz

data_processing:
alignment with cellranger v3.1
Genes expressed in fewer than three cells and in cells with less than 200 features expressed were removed. Cells with unique feature counts between 3000 and 10,000, and less than 10% mitochondrial counts were used for analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Elongated neural tube organoid cultured in Matrigel drop for 10 days

growth_protocol: mESCs were collected by washing with PBS and dissociating with Accutase for 2 min at room temperature. The cell suspension was collected in a centrifuge tube and was centrifuged at 200 g for 5 min. After centrifugation, the cell pellet was resuspended in 1 ml of 10% serum medium and the cells were counted with a hemocytometer. After cell counting, the cells were washed twice with PBS and were resuspended in N2B27 (47.4% Neurobasal medium, 47.4% DMEM/F-12 with 2.50 mM GlutaMAX, 1 mM GlutaMAX supplement, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM β-ME, 1% B27 supplement and 0.5% N-2 supplement) and embedded in Matrigel to a final concentration of 1125 cells/10 μl drop of Matrigel for SBr. 10 μl of the resulting Matrigel embedded cell suspension were deposited in each well of a 24-well plate (Corning). The cells in each well were cultured in 500 μl of Epi medium [N2B27 supplemented with 12 ng/ml basic fibroblast growth factor (bFGF, Thermofisher, PMG0031) and 20 ng/ml activin-A (R&D Systems, 338-AC-010)] for the first 3 days. On D3, the Epi medium of each well was substituted with 1 ml of N2B27. The medium of each well was substituted with 1 ml of N2B27 on D5 and the cells were cultured until D6. For maturation of the neural tube organoid, the organoids were harvested on D6 by washing the Matrigel drops with organoids once with PBS and then treating with 3 mg/ml collagenase IV and 1 mg/ml dispase in HBSS+/+ for 30 min on a shaker to dissolve the Matrigel. After Matrigel was dissolved, the organoids were collected with cut 1000 μl pipette tips coated with 10% serum and centrifuged at 150 g for 5 min. The supernatant was removed and the organoids were suspended in N2B27 medium. The organoids were collected and re-embedded in 10 μl of Matrigel (1 organoid/drop), plated on glass-bottomed 96-well plate and further cultured in 100 μl of N2B27 medium in 5% CO2 and 37°C incubator, and the medium was changed every day.

extract_protocol:
The sample preparation was performed according to the instructions from 10X Genomics Single Cell Protocols (10X Genomics), with some modification. The collected organoids (100 organoids per condition) were washed twice with PBS and trypsinized with TrypLE Express (Gibco, 12605-028) for 7 min in 37°C. The organoids were dissociated into single cells by pipetting up and down with a 1000 μl pipette tip, strained using 40 μm cell strainer and collected in 1.5 μl microcentrifuge tube. Those single cells were centrifuged at 300 g for 5 min and resuspended in 1 ml of PBS with 0.04% BSA after removing the supernatant. The cell concentration was then determined. After the same centrifugation step was repeated, the cells were resuspended in PBS with 0.04% BSA to achieve a final cell concentration of 1 million cells/ml. After the trypsinization, the cells were always placed on ice.
Reverse transcription and library preparation were performed using the Single Cell 3′ Reagent Kit v3 (10X Genomics), following the 10X Genomics protocol.

tag: cell line

value: Sox1::eGFP;Bra::mCherry mESCs

value: Mouse embryonic stem cell (mESCs)


title: 32-10003

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Expression counts determined by spaceranger and reference genome hg38.
The remaining processing and normalization steps described on the paper were not performed on the provided processed data.
Assembly: Hg38
Supplementary files format and content: Compressed file with outputs from spaceranger in a tar.gz file, high resolution image on tiff.

source_name: Kidney

extract_protocol:
Four reference tissues (18-0006, 19-F52, 19-M61, 19-M32) from deceased donor nephrectomies and one  CKD biopsy specimen (20-13437) were obtained from the biopsy biobank cohort of Indiana (BBCI) (PMID:32336487). All remaining samples were provided by the Kidney Precision Medicine Project. All samples were frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to the manufacturer's protocol.
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics

tag: disease

value: Acute Kidney Injury (AKI)

tag: tissue source

value: Biopsy

tag: storage

value: OCT at -80C

tag: gender

value: M

tag: median umis per spot

tag: median genes per spot


title: UMEL_2_3_TCR

description:
Single-nuclei RNA sequencing
UMEL_2_3

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: TCR


title: Day 8, elongated

source_name: Elongated neural tube organoid cultured in Matrigel drop for 8 days


title: OT-1_3

city: Beijing

last: Zhang

address: No. 5, Yard 1, Beichen West Road, Chaoyang District

description: total mRNA

value: spleen

value: Primary T cells

value: three rounds tumor challenge


title: YMC-325

description: miRNA

value: serum

tag: disease status

value: HV


title: YMC-317

description: miRNA


title: YMC-321

description: miRNA


title: YMC-326

description: miRNA


title: 30-10929


title: UMEL_2_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_2_2

tag: kit information

value: Chromium Next GEM Single Cell 5' v2 reagents

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

tag: timepoint


title: OT-1_1

description: total mRNA

tag: tissue

tag: cell type

tag: genotype

value: OT-1 WT


title: YMC-324

description: miRNA


title: YMC-322

description: miRNA


title: Day 6, elongated, batch 2

source_name: Elongated neural tube organoid cultured in Matrigel drop for 6 days

tag: cell line


title: Day 7, elongated

source_name: Elongated neural tube organoid cultured in Matrigel drop for 7 days


title: UMEL_2_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_2_1

tag: treatment

value: Selumetinib

value: Pre treatment


title: YMC-323

description: miRNA


title: YMC-315

description: miRNA


title: YMC-319

description: miRNA


title: YMC-320

description: miRNA


title: YMC-318

description: miRNA


title: YMC-314

description: miRNA


title: 30-10631

tag: disease

tag: tissue source

tag: storage


title: 33-10331

tag: gender

value: F

tag: median umis per spot

tag: median genes per spot


title: UMEL_1_2_TCR

description:
Single-nuclei RNA sequencing
UMEL_1_2

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

value: On treatment


title: UMEL_1_1_TCR

description:
Single-nuclei RNA sequencing
UMEL_1_1

tag: kit information

tag: cellranger version


title: 30-10125

value: Acute Kidney Injury (AKI)

value: Biopsy


title: UM_sn_5_inhib_TCR

description:
Single-nuclei RNA sequencing
UM_sn_5_inhib

source_name: Uveal melanoma (primary)

value: Chromium Single Cell V(D)J Reagents

tag: cellbender version

tag: timepoint


title: 32-10074

value: OCT at -80C

value: M


title: YMC-311

description: miRNA

tag: tissue

tag: disease status


title: 27-10066

value: Diabetic Kidney Disease (DKD)


title: YMC-313

description: miRNA


title: 29-10282


title: UM_sc_5_CD45+_TCR

description:
Single-cell RNA sequencing
UM_sc_5_CD45+

value: fresh

value: TCR


title: YMC-312

description: miRNA

value: serum


title: JGES(K5A)-D7-H3K27ac

first: Li

last: Chen

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
sambamba was used to sort and remove duplicate reads with the following options: [XS] == null and not unmapped and not duplicate.
Alignment BAM files were transformed into read coverage files (bigWig format) using deepTools
Assembly: mm10
Supplementary files format and content: bigwig

source_name: MEF cells after induction

growth_protocol: MEF cells cultured in 10%FBS, infected with WT/N12 Jdp2, Esrrb, Glis1 and WT/K5A Sall4 by retro-virus. Then change medium to iCD3 for induction

extract_protocol:
Around 100,000 living cells were collected for each sample
ChIP-seq library construction was performed using Hyperactive In-Situ ChIP Library Prep Kit for Illumina（pG-Tn5）(Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).

tag: system

tag: time after induction

tag: chip antibody to


title: JGES-D3-H3K27ac

value: JGES


title: 31-10042

tag: disease

tag: tissue source


title: JGES(K5A)-D5-H3K27ac


title: JGES-D0-H3K27ac


title: JGES-D7-H3K27ac


title: JGES-D1-H3K27ac 2


title: YMC-308

description: miRNA

value: HV


title: Mel_sn_5_TCR

description:
Single-nuclei RNA sequencing
Mel_sn_5

source_name: Melanoma metastasis (brain)

value: frozen

value: Cellranger v5.1.0

tag: treatment


title: Mel_sc_5_CD45+_TCR

description:
Single-cell RNA sequencing
Mel_sc_5_CD45+


title: JGES-D5-H3K27ac


title: YMC-309

description: miRNA


title: JGES(K5A)-D3-H3K27ac


title: 28-12265/Medulla

tag: storage

tag: gender

tag: median umis per spot


title: YMC-306

description: miRNA


title: YMC-307

description: miRNA


title: 28-12265/Cortex

tag: median genes per spot


title: JGES(K5A)-D1-H3K27ac 2


title: UM_sc_5_TCR

description:
Single-cell RNA sequencing
UM_sc_5

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type


title: NSCLC_sn_5_TCR

description:
Single-nuclei RNA sequencing
NSCLC_sn_5

source_name: Non-small cell lung cancer metastasis (brain)

tag: kit information

tag: cellranger version

tag: cellbender version


title: JGES(K5A)-D1-Gatad2b 2


title: 29-10404


title: 31-10221


title: YMC-304

description: miRNA

tag: tissue

tag: disease status


title: JGES(K5A)-D0-H3K27ac

tag: system

tag: time after induction


title: UMEL_7_3

description: Single-nuclei RNA sequencing

data_processing:
Raw sc/snRNA-seq data were analyzed using Cell Ranger (v5.1 for uveal melanoma liver metastasis and cutameous melanoma metastasis datasets, v6.1 for all other datasets). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.1.0). Gene expression matrices were processed individually in R (v4.0.2) using Seurat (v4.0.1).
For cutaneous melanoma metastasis samples, we applied filters to keep only cells with 300-10000 genes, 400-30000 UMIs, and <10% of mitochondrial reads. For uveal melanoma liver metastasis samples, we kept cells with at least 200 genes, 100 UMIs, and <10% of mitochondrial reads. Additionally, we removed cells with gene or UMI counts that were above a sample-specific maximum limit, based on the observed saturation curve between gene and UMI counts for each sample. Please refer to Extended Data Table 4 of the paper for the exact limits. Finally, for all other datasets, we kept cells with at least 300 genes and <20% of mitochondrial reads.
Scrublet was applied to identify and remove doublets with an expected doublet rate of 9.6%.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression matrix
*all_contig_annotations.csv: csv file with all contig annotations from cellranger vdj pipeline
*clonotypes.csv: csv file with all clonotypes detected during cellranger vdj pipeline
*consensus_annotations.csv: csv file with consensus contig annotations from cellranger vdj pipeline
*filtered_contig_annotations.csv: sv file with filtered contig annotations from cellranger vdj pipeline

value: Gene Expression

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Cellbender v0.1.0

value: Selumetinib

tag: timepoint

value: Post treatment


title: NSCLC_sn_5_inhib_TCR

description:
Single-nuclei RNA sequencing
NSCLC_sn_5_inhib


title: 29-10280

tag: disease

tag: tissue source

value: Biopsy


title: 29-10012

tag: storage

value: F


title: UMEL_7_1

description: Single-nuclei RNA sequencing

tag: treatment

value: Pre treatment


title: IU-13437

value: OCT at -80C

tag: gender

tag: median umis per spot


title: Trigeminal ganglion, physiological state, n=10

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

data_processing:
use single-cell RNA sequencing ; trim_data use fastp
The cwlref-runner software pipeline provided by BD
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Trigeminal ganglion

extract_protocol:
Five mice were performed euthanasia by 4% isoflurane inhalation and decapitation. Bilateral TGs were carefully harvested (n=10) and then were quickly chopped into small pieces and dissociated using a papain dissociation system (Worthington, Lakewood, NJ, USA, 20 units/ml papain, 0.005% DNase) according to the manufacturer’s instructions. The mixture was incubated at a 37°C water bath for 1 h with constant agitation, and then the cloudy suspension was collected and centrifuged at 300 g for 5 min at room temperature. The supernatant was discarded, and the cell pellets were resuspended in a DNase/papain-inhibitor solution (2.7 ml EBSS, 300 µl papain-inhibitor and 150 µl DNase). The obtained cell suspension was purified by discontinuous density gradient centrifugation (70 g for 6 min), and then the cell pellets were resuspended in DMEM to obtain a single-cell suspension. All solutions were equilibrated with 95% O2 and 5% CO2 throughout the procedure.
scRNA-seq libraries were constructed using the BD Rhapsody™ Single-Cell Analysis System according to the manufacturer’s instructions. Briefly, single cells were captured and lysed with barcoded beads on an array of microwells. The mRNA was enriched by the oligo(dT) beads in the microwell and each mRNA molecule was tagged with a unique molecular identifier (UMI) and cell label. After reverse transcription of the tagged mRNA and amplification, the cDNA libraries were constructed. Libraries were sequenced on the Illumina NovaSeq platform.

value: Trigeminal ganglion

tag: age

value: 5-8 weeks

tag: cell type

value: Neurons, glial cells, immune cells

tag: Sex

value: male


title: 29-10013

value: Diabetic Kidney Disease (DKD)

tag: median genes per spot


title: UMEL_6_3

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

tag: cellranger version


title: Aspartame 4

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using RNA-Seq Alignment version 1.1.1 (Illumina BaseSpace software application). The application uses STAR for alignment to the mouse genome (UCSC mm10) and Salmon was used to generate count tables.
Differential expression analysis of count tables was performed using the default settings of DESeq2 (Benjamini-Hochberg FDR correction).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts generated by DESeq2.

source_name: Amygdala

growth_protocol: 8 week old male mice were purchased from Charles River Laboratory (Wilmington,MA). Animals were kept on a 12 hour light-dark cycle. Food and water were provided ad libitum. Animals were group housed.

extract_protocol:
Mice were anesthetized (Isoflurane, Pivetal, Liberty, MO), decapitated, and the amygdala was collected by microdissection. Samples were snap-frozen in liquid nitrogen.and stored at -80 degrees. Total RNA was extracted from the amygdala from each animal using  a RNeasy mini kit (Qiagen, 74104) according to manufacturer’s directions.
A cDNA library was prepared for each sample using the Illumina TruSeq stranded mRNA library kit. Libraries were barcoded for multiplexing with IDT for Illumina 8 nucleotide i7 and i5 unique dual indexes. Each multiplexed library was sequenced on an Illumina NovaSeq 6000 as a 150 base pair paired-end sequencing run. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). The pooled sample was sequenced, with paired-end, 150 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

treatment_protocol: Mice were provided either plain drinking water or water containing 0.03% aspartame (Sigma Aldrich, # A5139) for 18 weeks.

tag: strain

value: Male

value: 187 Days

tag: tissue

value: Amygdala

tag: agent

value: Aspartame


title: UMEL_7_2

description: Single-nuclei RNA sequencing

source_name: Uvel melanoma (liver metastasis)

value: frozen

value: Gene Expression

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Cellranger v5.1.0

tag: cellbender version

tag: timepoint

value: On treatment


title: Aspartame 3


title: J(N12)GES(K5A)-D1-Gatad2b

tag: system

tag: time after induction

tag: chip antibody to


title: YMC-305

description: miRNA

value: serum

tag: disease status

value: HV


title: YMC-302

description: miRNA


title: YMC-301

description: miRNA


title: YMC-216

description: miRNA

source_name: serum:diabetes mellitus

value: DM


title: YMC-218

description: miRNA


title: UMEL_6_2

description: Single-nuclei RNA sequencing

value: Cellbender v0.1.0

tag: treatment

value: Selumetinib


title: Aspartame 2

tag: Sex

tag: age

value: 189 Days


title: YMC-215

description: miRNA


title: Aspartame 1

value: 188 Days


title: NSCLC_sc_5_TCR

description:
Single-cell RNA sequencing
NSCLC_sc_5

tag: fresh vs frozen

value: fresh

value: TCR

value: Chromium Single Cell V(D)J Reagents


title: YMC-214

description: miRNA


title: UMEL_6_1

description: Single-nuclei RNA sequencing

tag: sequencing chemistry

value: Pre treatment


title: YMC-303

description: miRNA

source_name: serum:healthy volunteer


title: UMEL_5_3

description: Single-nuclei RNA sequencing

tag: library type

value: Post treatment


title: Water 4

value: Male

value: Amygdala

value: water


title: IU-M32

tag: disease

value: Reference

tag: tissue source

value: Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: M

tag: median umis per spot

tag: median genes per spot


title: IU-M61


title: UMEL_5_2

description: Single-nuclei RNA sequencing

value: frozen

value: Gene Expression

tag: kit information

value: Chromium Next GEM Single Cell 5' v2 reagents

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

tag: timepoint

value: On treatment


title: Water 3

tag: strain

value: 187 Days

tag: tissue

tag: agent


title: UMEL_5_1

description: Single-nuclei RNA sequencing

value: Cellbender v0.1.0

tag: treatment

value: Selumetinib


title: IU-F59

value: F


title: UMEL_4_1

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: Pre treatment


title: Water 2

tag: Sex

value: Male

tag: age

value: 189 Days


title: IU-F52

tag: disease


title: UMEL_3_3

description: Single-nuclei RNA sequencing

tag: sequencing chemistry

tag: library type

value: Post treatment


title: UMEL_4_2

description: Single-nuclei RNA sequencing


title: YMC-212

description: miRNA

value: serum

tag: disease status

value: DM


title: YMC-209

description: miRNA


title: Water 1

value: Amygdala

value: water


title: YMC-211

description: miRNA


title: deltaEed EPC. rep3

city: Yokohama

first: Osamu

last: Masui

address: 1-7-22 Suehirocho, Tsurumi

department: IMS

institute: RIKEN

data_processing:
Allele specific RNA-seq analysis was performed as described previously (Sakata et al., 2017) by constructing the B6-ChrXTMSM specific reference. After trimming away any portion of the SMARTer adaptor sequences and the first two bases of read 1 (an error-prone stretch caused by random hexamer priming during library preparation), paired-end reads were mapped to the custom reference as single-end reads. For each gene, the number of B6 (maternal) and MsM (paternal) allele-specific reads were counted and ratios of expression from paternal alleles were calculated. We considered genes with more than 10 allele-specific reads as informative. In initial analysis, we noticed that Tmsb4x and Tsix showed aberrant data due to a error-prone variant and incompleteness of strand specificity, respectively. Therefore, those two genes were omitted from further analysis.
The numbers of maternal and paternal allele-specific reads for each gene were counted using custom scripts.
Gene expression was quantified in a non-allelic manner using Cufflinks v2.2.1 cuffdiff with option '--library-type ff-firststrand --multi-read-correct'.
Assembly: mm9
Supplementary files format and content: Excel file includes patRatio (the ratio of the number of paternal reads to the number of total allele specific reads), asReads (the total number of allele-specific reads), and FPKM values for each sample.

source_name: Ectoplacental cone

growth_protocol: To obtain control Eed and ∆Eed EPC embryos, in vitro fertilised eggs were cultured in KSOM medium until blastocyst stage.

extract_protocol:
Dissected ectoplacental cones of E7.5 embryos either from Eed control (Eedfl/fl) and ∆Eed (Eeddl/dl) were used for total RNA extraction using All-prep DNA/RNA micro kit (Qiagen).
RNA-seq libraries were prepared with the SMARTer Stranded Total RNA-seq Kit v2 using 10 ng total RNA and sequenced by the NovaSeq 6000 as 100 bp paired-end.

treatment_protocol: To induce CreERT2-dependent Eed inactivation, in vitro cultured blastocysts were treated with 4-hydroxytamoxifen for 10 hours.

value: Ectoplacental cone

tag: developmental stage

tag: genotype

value: Eed^dl/dl

value: 4-hydroxytamoxifen at E3.5


title: P_c_pre_24_CTRL

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads (~36.8 M/sample) were aligned to human genome (Ensembl GRCh38, release 98) using STAR v2.7.2b resulting in ~28 M/sample uniquely aligned reads.
2) Gene read coverages (~23.7 M/sample) were computed with featureCounts v1.6.2 using same human genome annotation.
3) Differential expression analysis was performed using edgeR v3.28.1 with "y ~ 0 + group" design (group represents the combinations of "Disease", "EPS treatment" and "Hormone treatment" together) while filtering low count reads using built-in function filterByExpr (n = 19,231 genes) and blocking for "Patient ID"s with voomLmFit function.
Assembly: hg38
Supplementary files format and content: counts.tsv.gz: Text file in tab separated format with gene coverages in units of read counts
Supplementary files format and content: logCPM_filtered_batchCorrected.tsv.gz: Text file in tab separated format with gene coverages in units of log2 counts per million (CPM). The logCPM values are batch corrected for "Patient IDs". See "data processing step 3" for details.

source_name: myotubes obtained from vastus lateralis

growth_protocol: Myotubes were grown in α-MEM with 10% v/v fetal bovine serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B, and later differentiated for 6 days in α-MEM with 2% v/v horse serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA universal kit (Qiagen)
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: Treaments were applied following differentation: i) non-treated control (no treatment and no EPS); ii) TGFβ1 (5 ng/ml); iii) AMH (30 ng/ml); iv) EPS; v) EPS+TGFβ1 (5 ng/ml) and vi) EPS+AMH (30 ng/ml).  In conditions where EPS and hormone treatment were combined, the treatment (TGFB1, AMH) was applied for 16 hours then cells were washed with PBS before fresh serum free media was added and the 6 hours of EPS was applied.

tag: group

tag: participant id

value: PCOS

tag: eps treatment

value: noEPS

tag: hormone treatment

tag: cell type

value: myotubes

tag: gender

value: female

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: UMEL_3_2

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: frozen

value: Gene Expression

tag: kit information

value: Chromium Next GEM Single Cell 5' v2 reagents

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: treatment

value: Selumetinib

tag: timepoint

value: On treatment


title: YMC-213

description: miRNA

tag: tissue

value: serum

tag: disease status

value: DM


title: YMC-205

description: miRNA


title: YMC-207

description: miRNA


title: YMC-206

description: miRNA


title: UMEL_3_1

description: Single-nuclei RNA sequencing

tag: sequencing chemistry

tag: library type

value: Pre treatment


title: Control Eed EPC. rep3

value: Ectoplacental cone

tag: developmental stage

tag: genotype

value: Eed^fl/fl


title: deltaEed EPC. rep1

value: Eed^dl/dl

value: 4-hydroxytamoxifen at E3.5


title: deltaEed EPC. rep2


title: YMC-204

description: miRNA


title: P_c_pre_26_CTRL

tag: group

tag: participant id

tag: disease

value: PCOS

tag: eps treatment

value: noEPS

tag: hormone treatment

tag: cell type

tag: gender

tag: age

tag: height (m)


title: P_c_pre_10_CTRL

value: myotubes

value: female

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: UMEL_2_3

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

value: Gene Expression

tag: kit information

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint

value: Post treatment


title: YMC-203

description: miRNA

tag: tissue

tag: disease status


title: Control Eed EPC. rep2

tag: developmental stage

tag: genotype


title: P_c_EPS_B5_27

tag: group

tag: participant id

tag: disease

tag: eps treatment

value: EPS

tag: hormone treatment

value: tgfb

tag: cell type

tag: gender

tag: age


title: UMEL_2_2

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

value: Chromium Next GEM Single Cell 5' v2 reagents

value: Cellranger v5.1.0

value: Cellbender v0.1.0

value: Selumetinib

value: On treatment


title: UMEL_2_1

description: Single-nuclei RNA sequencing

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint

value: Pre treatment


title: shLuciferase-JGES-D7-2 [RNA-Seq]

data_processing:
raw counts was generated by RSEM (v. 1.2.28)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen).
Libraries were prepared using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme, NR601-01/02,) with 1 µg RNA per sample following the manufacturer’s instruction

treatment_protocol: knockdown Chd4 or Gatad2b by shRNA

tag: system

value: JGES

tag: knockdown

value: Luciferase

tag: time after induction


title: P_c_pre_11_CTRL

tag: group

tag: participant id

tag: disease

value: PCOS

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: P_c_EPS_B5_26

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: age


title: P_c_EPS_B5_24


title: shLuciferase-JGES-D7-1 [RNA-Seq]


title: P_c_EPS_B5_11


title: shLuciferase-JGES-D5-2 [RNA-Seq]


title: YMC-202

description: miRNA

tag: tissue

value: serum

tag: disease status

value: DM


title: Control Eed EPC. rep1

value: Ectoplacental cone

tag: developmental stage

tag: genotype

value: Eed^fl/fl

tag: treatment

value: 4-hydroxytamoxifen at E3.5


title: UMEL_1_1

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: Gene Expression

tag: kit information

tag: cellranger version

tag: cellbender version

tag: timepoint


title: P_c_EPS_B5_10

tag: group

tag: participant id

tag: disease

tag: eps treatment

value: EPS

value: tgfb

value: myotubes

value: female

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: P_c_EPS_A30_27

tag: hormone treatment

value: amh

tag: cell type

tag: gender

tag: age


title: KCC-049

description: miRNA

source_name: serum:urothelial cancer

tag: tissue

tag: disease status

value: UC


title: shLuciferase-JGES-D5-1 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: ribas_310_on_later

description: Single-nuclei RNA sequencing

source_name: Cutaneous Melanoma metastasis

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

value: Chromium Next GEM Single Cell 5' v2 reagents

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: treatment

value: Pembrolizumab

tag: timepoint

value: On treatment


title: KCC-051

description: miRNA

value: serum


title: KCC-048

description: miRNA


title: ribas_310_on

description: Single-nuclei RNA sequencing


title: UMEL_1_2

description: Single-nuclei RNA sequencing

value: Selumetinib


title: KCC-046

description: miRNA


title: KCC-047

description: miRNA


title: shLuciferase-JGES-D3-1 [RNA-Seq]

value: JGES

value: Luciferase


title: P_c_pre_27_CTRL

tag: group

tag: participant id

tag: disease

value: PCOS

tag: eps treatment

value: noEPS

tag: hormone treatment

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: ribas_310_pre

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

value: Gene Expression

value: Pre treatment


title: P_c_EPS_A30_24

value: EPS

tag: cell type

value: myotubes

tag: gender

value: female

tag: age


title: shLuciferase-JGES-D3-2 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: shLuciferase-JGES-D1-2 [RNA-Seq]


title: P_c_EPS_A30_11

tag: group

tag: participant id

value: amh


title: shLuciferase-JGES-D1-1 [RNA-Seq]


title: KCC-045

description: miRNA

tag: tissue

tag: disease status

value: UC


title: KCC-044

description: miRNA


title: UM_sn_5p_inhib

description: Single-nuclei RNA sequencing

tag: library type

tag: kit information

value: Chromium Single Cell V(D)J Reagents

tag: cellranger version

value: Cellranger v6.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: treatment

tag: timepoint


title: UM_sc_5p_CD45+

description: Single-cell RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry


title: Mel_sn_5p_v2

description: Single-nuclei RNA sequencing

value: Chromium Next GEM Single Cell 5' v2 reagents


title: shLuciferase-JGES-D0-1 [RNA-Seq]


title: P_c_EPS_A30_26

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: P_c_EPS_26

tag: group

tag: participant id

tag: age


title: shLuciferase-JGES-D0-2 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: P_c_EPS_27


title: KCC-041

description: miRNA

tag: tissue

value: serum

tag: disease status


title: UM_sc_5p

description: Single-cell RNA sequencing

tag: fresh vs frozen

value: fresh

tag: sequencing chemistry

tag: library type

tag: kit information

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint


title: shGatad2b_JGES_D7_1 [RNA-Seq]

value: JGES


title: P_c_EPS_24

tag: disease

value: PCOS

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: YMC-102

description: miRNA

tag: tissue

tag: disease status


title: YMC-101

description: miRNA


title: Mel_sn_5p

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information


title: Mel_sn_3p

description: Single-nuclei RNA sequencing

value: Chromium Single Cell 3' Reagent Kits

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint


title: P_c_EPS_11

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: age


title: YMC-099

description: miRNA

tag: tissue


title: P_c_EPS_A30_10

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: shGatad2b_JGES_D5_2 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: Mel_sc_5p_CD45+

description: Single-cell RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint


title: Mel_sc_5p_CD45-

description: Single-cell RNA sequencing


title: P_c_EPS_10

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: age


title: shGatad2b_JGES_D5_1 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: P_c_B5_27

value: noEPS

value: tgfb

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: YMC-098

description: miRNA

tag: tissue

tag: disease status


title: NSCLC_sn_5p_inhib

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: Gene Expression

tag: kit information

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint


title: shGatad2b_JGES_D7_2 [RNA-Seq]

tag: system

tag: knockdown


title: P_c_B5_24

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

value: myotubes

tag: gender

tag: age

tag: height (m)


title: P_c_B5_26

value: female

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: shGatad2b_JGES_D3_1 [RNA-Seq]

tag: time after induction


title: shGatad2b_JGES_D1_2 [RNA-Seq]


title: P_c_B5_11


title: YMC-094

description: miRNA

tag: tissue

tag: disease status


title: YMC-096

description: miRNA


title: NSCLC_sn_3p_inhib

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

tag: cellranger version

tag: cellbender version

tag: treatment

tag: timepoint


title: NSCLC_sn_3p

description: Single-nuclei RNA sequencing


title: shGatad2b_JGES_D1_1 [RNA-Seq]

tag: system

tag: knockdown


title: P_c_B5_10

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: age

tag: height (m)

tag: weight (kg)


title: YMC-093

description: miRNA

tag: tissue

tag: disease status


title: YMC-092

description: miRNA


title: YMC-097

description: miRNA


title: NSCLC_sn_5p_v2

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

tag: cellranger version

tag: cellbender version


title: shGatad2b_JGES_D0_2 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: YMC-090

description: miRNA


title: YMC-091

description: miRNA


title: P_c_A30_27

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

value: amh

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: YMC-201

description: miRNA

tag: tissue

tag: disease status

value: DM


title: shGatad2b_JGES_D3_2 [RNA-Seq]


title: NSCLC_sn_5p

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

value: Chromium Single Cell V(D)J Reagents

tag: treatment

tag: timepoint


title: NSCLC_sc_5p

description: Single-cell RNA sequencing

tag: kit information

tag: cellranger version

value: Cellranger v6.1.0

tag: cellbender version


title: shGatad2b_JGES_D0_1 [RNA-Seq]

tag: system

tag: knockdown

tag: time after induction


title: P_c_A30_26

tag: group

tag: participant id

tag: disease

tag: eps treatment

tag: hormone treatment

tag: cell type

tag: gender

tag: age

tag: height (m)

tag: weight (kg)


title: YMC-089

description: miRNA

tag: tissue

tag: disease status

value: UC


title: shChd4-JGES-D7-2 [RNA-Seq]


title: T8

city: Nanjing

first: shouyu

last: wang

address: 22 Hankou Road

institute: Nanjing university medical school

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 whole genome using Hisat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Expression_FPKM_Transcript.txt: Tab-delimited text file includes RPKM values for each Sample (FPKM >= 0.5).

source_name: Stomach

extract_protocol:
Total RNA extracted using RNeasy Plus Mini Kit with QIAshredder columns (Qiagen) following manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gastric cancer tissue

tag: donor


title: P_c_A30_24

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: YMC221

description: miRNA

value: serum


title: YMC220

description: miRNA


title: shChd4-JGES-D5-2 [RNA-Seq]

city: Guangzhou

tag: system

tag: knockdown

tag: time after induction


title: P_c_A30_10

tag: group

tag: participant id

tag: disease


title: T7


title: N8

value: Matched adjacent tissue


title: P_c_A30_11

tag: eps treatment

tag: hormone treatment

tag: cell type


title: shChd4-JGES-D5-1 [RNA-Seq]

value: JGES


title: C_c_pre_7_CTRL

value: CTRL

tag: gender

tag: age

tag: height (m)


title: T6

tag: tissue


title: N7

tag: donor


title: C_c_pre_6_CTRL

tag: weight (kg)

tag: body mass index (kg/m2)


title: N6


title: shChd4-JGES-D3-2 [RNA-Seq]


title: shChd4-JGES-D1-2 [RNA-Seq]


title: shChd4-JGES-D3-1 [RNA-Seq]


title: T1


title: YMC210

description: miRNA

tag: disease status


title: YMC-088

description: miRNA


title: shChd4-JGES-D1-1 [RNA-Seq]

tag: system


title: YMC-087

description: miRNA


title: YMC208

description: miRNA


title: C_c_pre_5_CTRL

tag: body fat (%)

tag: lean mass (%)


title: N1


title: shChd4-JGES-D7-1 [RNA-Seq]

tag: knockdown

tag: time after induction


title: C_c_pre_3_CTRL

tag: group

tag: participant id

tag: disease


title: shChd4-JGES-D0-2 [RNA-Seq]


title: YMC-086

description: miRNA


title: YMC219

description: miRNA


title: C_c_pre_2_CTRL

tag: eps treatment

tag: hormone treatment

tag: cell type


title: UMEL_1_3

description: Single-nuclei RNA sequencing

tag: fresh vs frozen

tag: sequencing chemistry

tag: library type

tag: kit information

value: Chromium Single Cell 3' Reagent Kits

tag: cellranger version

value: Cellranger v5.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: treatment

value: Selumetinib

tag: timepoint

value: Post treatment