title: BMDM progeniors, WT, day3, biol rep3

description: Library name: WT3_day3


title: 114N

status: Public on Dec 30 2024

type: genomic

city: Seoul

first: Dawon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Yonsei University

hyb_protocol: Bisulphite converted DNA was hybridized to Illumina EPIC BeadChip according to manufacturer's protocol.

scan_protocol: Standard Illumina iScan scanning protocol.

data_processing:
Normalized Average Beta using Functional Normalization Method in Bioconductor minfi R package.
totalliver_funnorm_beta850_2022NT.txt: Normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal liver 114

label_protocol: Illumina Protocol.

extract_protocol: Genomic DNA was extracted using MagListo™ 5M Genomic DNA Extraction Kit (Bioneer) according to manufacturer's protocol.

tag: gender

value: Male

tag: diagnosis

value: Hepatocellular carcinoma (HCC)

tag: tissue

value: normal liver tissue adjacent to the tumor (NAT)

tag: patient


title: BMDM progeniors, WT, day3, biol rep1

type: SRA

city: Bethesda

first: Sakshi

last: Chauhan

state: Maryland

address: Building 6A, Room 2A11,6 Center Drive

country: USA

institute: NICHD

description: Library name: WT1_day3

library_source: transcriptomic

data_processing:
CCBR pipeliner and SARTools
Sequence reads were trimmed for adaptor sequence using cutadapt.
Trimmed sequence reads were mapped to mm10 using STAR aligner.
Assembly: mm10
Supplementary files format and content: tab delimited text file inclues raw count for each sample

molecule: total RNA

organism: Mus musculus

source_name: BMDM progenitors

extract_protocol:
RNA was purified using Zymogen quick RNA miniprep kit.
NEBNext® rRNA Depletion Kit was used to deplete rRNA. RNA library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.

tag: cell type

value: BMDM progenitors

tag: genotype

value: WT


title: BMDM progeniors, cKO, day3, biol rep1

description: Library name: KO1_day3


title: BMDM progeniors, WT, day3, biol rep2

description: Library name: WT2_day3


title: 112N

source_name: Normal liver 112


title: 110N

source_name: Normal liver 110

value: Female


title: BMDMs, cKO (IgG control_2)

description: Library name: KO_IgG_2

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequences using Cutadapt.
Sequence reads were aligned to mm10 reference genome using Bowtie.
Peaks were called using Homer.
bigwig files were generated using deeptools bamcoverage.
Assembly: mm10
Supplementary files format and content: bigwigfiles and bed files (except for IgG control)
Library strategy: CUT&Run

growth_protocol: Cells were cultured in the DMEM media supplemented with 10% FBS, 1X antibiotic and 20 % L929 conditioned media for 6-8 days.

extract_protocol:
Cells were bound to concanavalin A-coated magnetic beads and subsequently permeablized with digitonin.
CUT&RUN seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. Libraries were size selected at ~350 bp in length using SPRIselect beads. Libraries were vaildated using the Agilent High Sensitivity DNA kit.

value: BMDM


title: BMDM progeniors, cKO, day5, biol rep3

description: Library name: KO3_day5


title: 109N

source_name: Normal liver 109


title: BMDMs, cKO, biol rep2(H3K36me3)

description: Library name: KO2_H3K36me3


title: BMDMs, cKO, biol rep1(H3K36me3)

description: Library name: KO1_H3K36me3


title: 108N

source_name: Normal liver 108


title: BMDMs, WT (IgG contol_2)

description: Library name: WT_IgG_2


title: 118N

source_name: Normal liver 118


title: BMDMs, WT, biol rep2(H3K36me3)

description: Library name: WT2_H3K36me3


title: 116N

source_name: Normal liver 116


title: 107N

source_name: Normal liver 107


title: Transcriptome of Paraescarpia echinospica: plume [ONT]

city: shandong

first: Nannan

last: Zhang

address: Hengyun Mountain Road

country: China

institute: BGI Research, Qingdao, Shandong

description: Library name: Transcriptome of Paraescarpia echinospica: plume

data_processing:
Initially, the original fastq data underwent filtration based on short fragments and low-quality reads (less than 500bp in length and a Qscore < 6) to obtain a cleaned dataset. The complete sequences were then aligned to the reference genome using the minimap2 software. Subsequently, clustering was performed based on comparison information, and consensus sequences were generated using the pinfish software. To avoid redundancy, multiple copies of the same transcript were not included in a single consensus sequence. Subsequently, the consensus sequences were merged and aligned with the reference genome through minimap2, and the comparison results were de-redundant.
Assembly: HKBU_Pec_v1
Supplementary files format and content: tsv includes gene information and count information

organism: Paraescarpia echinospica

source_name: plume

extract_protocol:
Total RNA was extracted from the plume using the RNeasy Mini Kit (Qiagen) and following the manufacturer’s protocol. The RNA concentration was measured using the NanoDrop (Thermo Fisher Scientific) and the RNA integrity was assessed using the RNA Nano 6000 Assay Kit and Agilent 2,100 Bioanalyzer (Agilent Technologies).
The following experimental process was carried out according to the standard protocol provided by Oxford Nanopore Technologies (ONT), including sample quality detection, library construction and library quality detection. The final library was sequenced on the Nanopore PromethION platform.

value: plume

tag: age

value: adult

value: all cells


title: 113N

source_name: Normal liver 113


title: BMDMs, WT, biol rep1(H3K36me3)

description: Library name: WT1_H3K36me3


title: BMDMs, cKO, biol rep2(H3K27ac)

description: Library name: KO2_H3K27ac


title: Entero_brain_2

first: Jeung Hee

last: An

address: 47 Kkachisan-ro 24-gil, Gangseo-gu

institute: Gangseo University

description: Library name: Entero_brain_2

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: brain

growth_protocol: The animals were housed under standardized conditions, maintaining a temperature of 21–22 °C, a 12-h light/dark cycle, and 70% humidity, with ad libitum access to chow and water.

extract_protocol:
Total RNA was extracted from the cells with the use of a TruSeq Stranded mRNA Kit (Illumina) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Daejeon University (approval number: DJUARB2022-026). Six-week-old male C57BL/6 mice were sourced from Raon Bio Inc. (Gyeonggi-do, Korea) and maintained under controlled conditions with free access to food and water. After a one-week acclimation period, mice were assigned to five treatment groups (n = 8/group): (1) normal, (2) MPTP-intoxicated at 20 mg/kg (Sigma-Aldrich, St. Louis, MA, USA), (3) MPTP + levodopa at 2 mg/kg (Sigma-Aldrich), and (4) MPTP + low-dose En. faecium FBL1 (109 log CFU·mL-1·day-1), and (5) MPTP + high-dose En. faecium FBL1 (10¹⁰ log CFU·mL-1·day-1). The normal group was fed a standard diet for 28 days, while the MPTP group received MPTP for the first seven days, followed by a standard diet for 28 days. Groups 3–5 underwent MPTP treatment for seven days, after which they were treated with levodopa or En. faecium FBL1 for 28 days (Fig. 3a). Upon completion of the treatment period, the mice were sacrificed and their brain and muscle tissues were collected for molecular analyses.

value: brain

tag: time

value: 6 week

tag: Sex

value: male

tag: treatment

value: 1 weeks of stabilization, MPTP treatment for 1 week followed by oral injection of Enterococcus faecium for 4 weeks.


title: Entero_brain_3

description: Library name: Entero_brain_3


title: 104N

source_name: Normal liver 104


title: BMDMs, WT (IgG contol_1)

description: Library name: WT_IgG _1

source_name: WT_IgG _1


title: 103N

source_name: Normal liver 103


title: BMDMs, cKO, biol rep1(H3K27ac)

description: Library name: KO1_H3K27ac


title: Entero_brain_1

description: Library name: Entero_brain_1


title: BMDMs, WT, biol rep1(H3K27ac)

description: Library name: WT1_H3K27ac


title: 102N

source_name: Normal liver 102


title: BMDMs, biol rep2 (CUT & RUN)

description: Library name: H3.3_HA2


title: BMDMs, WT, biol rep2(H3K27ac)

description: Library name: WT2_H3K27ac


title: 119N

source_name: Normal liver 119


title: 21T

description: cancer

label: Cy5 and Cy21

source_name: HCC 21

value: Hepatocellular carcinoma


title: BMDMs, KO, biol rep2

description: Library name: KO2

data_processing:
Paired reads were aligned to mouse reference genome mm10 using Bowtie2-2.5.1
Peak calling was performed by using Genrich with default settings.
Assembly: mm10
Supplementary files format and content: bigwig files and narrowPeak files

source_name: BMDM

extract_protocol:
Crude nuclei were preapred by lysing cells in NP40 containing lysis buffer.
Transposition reaction was performed using Illumina Tagment DNA enzyme .Transposed DNA was collected using DNA Clean & Concentrator™-5 purification columns.


title: TC1_sgNAT10_IP(acRIPseq)

city: Suzhou

first: Wancheng

last: Liu

state: jiangsu

address: 100 Chongwen Road, Industrial Park

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Library name: Tcell_sgNAT10_IP(acRIPseq)
TC1_sgNAT10(acRIP_seq)_diff_peak.txt
KO-IP

data_processing:
Fastqc software used for quality control.
Sequenced reads were trimmed by trim_galore software for adaptor sequence with parameters -q 25 --phred33 --length 36 -e 0.1 --stringency 5 --paired, then mapped to mm10 whole genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts software.
Assembly: mm10
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: mouse fibrosarcoma TC1 cells

extract_protocol:
Total RNA was extracted and purified from WT and sgNAT10 TC1 cells using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TC1 wild type (WT) and sgNAT10 cells or sgMyc were analyzed by RNA-seq, acRIP-seq, and Ribo-seq

tag: cell line

value: mouse fibrosarcoma TC1 cells


title: TC1_WT_Input(acRIPseq)

description:
Library name: Tcell_WT_Input(acRIPseq)
TC1_sgNAT10(acRIP_seq)_diff_peak.txt
WT-Input

value: wild type


title: TC1_sgNAT10_Input(acRIPseq)

description:
Library name: Tcell_sgNAT10_Input(acRIPseq)
TC1_sgNAT10(acRIP_seq)_diff_peak.txt
KO-Input


title: 101N

source_name: Normal liver 101

value: Male


title: 100N

source_name: Normal liver 100

value: Hepatocellular carcinoma (HCC)


title: Brain, KO LPS x2, replicate 2

first: Seunghee

last: Hong

state: Seoul

address: 50, Yonsei-ro, Seodaemun-gu

department: Biochemistry

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoaded processing, counting, and aggregating were done using Cell Ranger v6.1.2 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Breifly, raw BCL files from illumina sequencing instrument were demultiplexed to generate FASTQ files using 'cellranger mkfastq'. Then, these files were analyzed using 'cellranger count.' The reference genome mm10-2020-A were used for measuring gene expression with UMI and cell barcode, determining cell clusters, and conducting DEG analysis. The final dataset was built by aggregating multiple independent samples using 'cellranger aggr.'
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files

molecule: polyA RNA

source_name: Brain

extract_protocol:
Mice were transcardially perfused with ice-cold PBS and the brain tissues were freshly collected. The brain tissues were then enzymatically dissociated using Adult Brain Dissociation Kit (Miltenyi Biotec) to obtain brain single cell suspensions.
Libraries were prepared using Chromium controller according to the 10x chromium Next GEM Single Cell 3' v3.1 protocol (CG000315). Briefly, the cell suspension was mixed with master mix and loaded with Single Cell 3'V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and were subjected to repair process. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies).

value: Brain

value: LPS x2


title: TC1_WT_IP(acRIPseq)

description:
Library name: Tcell_WT_IP(acRIPseq)
TC1_sgNAT10(acRIP_seq)_diff_peak.txt
WT-IP


title: BMDMs, biol rep1 (CUT & RUN)

description: Library name: H3.3_HA1


title: 105N

source_name: Normal liver 105

value: normal liver tissue adjacent to the tumor (NAT)


title: Brain, KO PBS, replicate 2

description: 10x Genomics

value: PBS


title: BMDMs, cKO (IgG control_1)

description: Library name: KO_IgG_1

value: BMDM


title: BMDMs, KO, biol rep1

description: Library name: KO1


title: 99N

source_name: Normal liver 99

value: Female


title: IgG control

description: Library name: HA_control


title: BMDMs, WT, biol rep2

description: Library name: WT2

value: WT


title: 98N

source_name: Normal liver 98


title: Brain, WT LPS x2, replicate 2

description: 10x Genomics


title: TC1_sgNAT10_1(Riboseq)

description:
Library name: Tcell_sgNAT10_1(Riboseq)
TC1_sgNAT10(Ribo_seq).fpkm.txt
TC1_sgNAT10_1


title: 97N

source_name: Normal liver 97


title: BMDMs, WT, biol rep1

description: Library name: WT1


title: TC1_WT2(Riboseq)

description:
Library name: Tcell_WT2(Riboseq)
TC1_sgNAT10(Ribo_seq).fpkm.txt
TC1_WT2


title: Brain, WT LPS x1, replicate 2

description: 10x Genomics

value: LPS x1


title: TC1_sgNAT10_2(Riboseq)

description:
Library name: Tcell_sgNAT10_2(Riboseq)
TC1_sgNAT10(Ribo_seq).fpkm.txt
TC1_sgNAT10_2


title: Spl_D7_75ng#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Spleen

extract_protocol:
Whole tissue was homogenized in Trizol and RNA was extracted with phenol/chloroform extraction, followed by purification with an RNeasy Kit (Quiagen). RNA was diluted in TCL buffer before library construction.
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

value: Spleen

tag: time point

value: ob/ob

value: Leptin pump


title: 96N

source_name: Normal liver 96


title: Brain, WT PBS, replicate 2

description: 10x Genomics


title: Brain, KO LPS x2, replicate 1

description: 10x Genomics


title: 94N

source_name: Normal liver 94


title: 92N

source_name: Normal liver 92


title: Spl_D1_75ng#1


title: Brain, KO PBS, replicate 1

description: 10x Genomics


title: Spl_D1_75ng#2


title: TC1_cell_sgMYC_3(mRNAseq)

description:
Library name: Tcell_sgMYC3
TC1_sgMyc_mRNAseq_fpkm.txt
K3

value: sgMYC


title: 93N

source_name: Normal liver 93


title: TC1_cell_sgMYC_2(mRNAseq)

description:
Library name: Tcell_sgMYC2
TC1_sgMyc_mRNAseq_fpkm.txt
K2


title: Brain, WT LPS x2, replicate 1

description: 10x Genomics


title: Brain, WT LPS x1, replicate 1

description: 10x Genomics


title: 91N

source_name: Normal liver 91


title: Spl_D0_75ng#2


title: TC1_cell_sgMYC_1(mRNAseq)

description:
Library name: Tcell_sgMYC1
TC1_sgMyc_mRNAseq_fpkm.txt
K1


title: Spl_D0_75ng#3


title: Spl_D0_75ng#1


title: luc7a2 luc7b and luc7rl triple knockout replicate 3

city: Cambridge

first: Connor

middle: J

last: Kenny

address: 31 Ames Street

department: Biology

institute: MIT

description: Library name: tA2B1RL1-3

data_processing:
Aligned with star v2.7.3a.
Analyzed with rmats- v.4.1.1.
Assembly: hg38 and TAIR10
Supplementary files format and content: rmats tables with corrected dPSI estimates.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol:
Cell line: HEK293T RMCE cell lines were cultured in Advanced DMEM supplemented with 5% FBS, 25 mM HEPES and Glutamax. For each experiment, cells were plated 24 hours in advance in 24-well plates.
Seedlings: Seeds of Wildtype Col0, luc7 single mutants (luc7a-1, luc7a-2, luc7b-1 and luc7rl-1), luc7 double mutants (luc7a-1 luc7b-1, luc7a-2 luc7b-1, luc7a-1 luc7rl-1 and luc7b-1 luc7rl-1) and a luc7 triple mutant (luc7a-2 luc7b-1 luc7rl-1) were surface sterilized with chlorine-gas and then grown on half-strength Murashige Skoog (MS) plates containing 0.8% phytoagar in continuous light at 22°C for 10 days.

extract_protocol:
Cell line: RNA was extracted 24 hours after transfection using the Qiagen RNeasy Mini kit (cat. no. 74104) according to the manufacturer’s instructions with the optional on-column DNase digestion (cat. No 79254). Seedlings: Seedlings were collected and flash frozen in liquid nitrogen. Total RNA was isolated using RNeasy® Plant Mini Kit (Qiagen, cat. nos. 74904) according to the manufacturer’s instructions.
Cell line: Illumina-compatible libraries were prepared by MIT BioMicroCenter using NEB II Ultra Directional RNA with poly(A) selection and sequenced on NovaSeq 6000 with 2 x 150 bp reads. Seedlings: mRNA stranded library preparation and sequencing (PE150) was done by Novogene (Cambridge, United Kingdom) using an Illumina Novaseq6000 system.

value: seedling

value: luc7a2 luc7b and luc7rl triple knockout


title: TC1_cell_WT3(mRNAseq)

description:
Library name: Tcell_WT(3)
TC1_sgMyc_mRNAseq_fpkm.txt
W3

value: mouse fibrosarcoma TC1 cells

value: wild type


title: Brain, WT PBS, replicate 1

description: 10x Genomics


title: 88N

source_name: Normal liver 88

value: Male

value: Hepatocellular carcinoma (HCC)


title: Spl_D7_Sal#3

value: Saline pump


title: TC1_cell_WT1(mRNAseq)

description:
Library name: Tcell_WT(1)
TC1_sgMyc_mRNAseq_fpkm.txt
W1


title: TC1_cell_WT2(mRNAseq)

description:
Library name: Tcell_WT(2)
TC1_sgMyc_mRNAseq_fpkm.txt
W2


title: 89N

source_name: Normal liver 89

value: normal liver tissue adjacent to the tumor (NAT)


title: 87N

source_name: Normal liver 87


title: luc7a2 luc7b and luc7rl triple knockout replicate 2

description: Library name: tA2B1RL1-2


title: TC1_WT1(Riboseq)

description:
Library name: Tcell_WT1(Riboseq)
TC1_sgNAT10(Ribo_seq).fpkm.txt
TC1_WT1

source_name: mouse fibrosarcoma TC1 cells


title: Spl_D7_75ng#1


title: Spl_D7_Sal#2


title: 86N

source_name: Normal liver 86


title: luc7a2 luc7b and luc7rl triple knockout replicate 1

description: Library name: tA2B1RL1-1


title: TC1_sgNAT10_1(mRNAseq)

description:
Library name: Tcell_sgNAT10_1
TC1_sgNAT10_mRNAseq.fpkm.txt
TC1_sgNAT10_1


title: Spl_D1_Sal#3


title: luc7rl knockout replicate 3

description: Library name: RL-3

value: luc7rl knockout


title: Spl_D1_Sal#2


title: 85N

source_name: Normal liver 85


title: TC1_WT2(mRNAseq)

description:
Library name: Tcell_WT2
TC1_sgNAT10_mRNAseq.fpkm.txt
TC1_WT_2


title: Spl_D1_Sal#1


title: luc7rl knockout replicate 2

description: Library name: RL-2


title: Spl_D0_Sal#3


title: luc7rl knockout replicate 1

description: Library name: RL-1


title: 83N

source_name: Normal liver 83


title: TC1_WT1(mRNAseq)

description:
Library name: Tcell_WT1
TC1_sgNAT10_mRNAseq.fpkm.txt
TC1_WT_1


title: luc7b and luc7rl double knockout replicate 3

description: Library name: dB1RL1-3

value: luc7b and luc7rl double knockout


title: 82N

source_name: Normal liver 82


title: 81N

source_name: Normal liver 81


title: WT_3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)
Assembly: mm10
Supplementary files format and content: csv of raw read counts

source_name: testis

growth_protocol: In this study, all mice were housed in the pathogen-free barrier facility, under controlled conditions with a 12 h light/dark cycle and free access to food and drinking water.

extract_protocol:
To extract total RNA from decapsulated testis we used the RNeasy Mini kit from Qiagen (cat. Nr. 74104) by following the manufacturer instructions.
Illumina stranded mRNA

treatment_protocol: no treatment was performed

value: testis

value: wild-type (C57Bl/6J)


title: Spl_D0_Sal#1

source_name: Spleen


title: Spl_D0_Sal#2


title: luc7b and luc7rl double knockout replicate 1

description: Library name: dB1RL1-1


title: Lung_D7_Lep#3

source_name: Lung

value: Lung


title: 80N

source_name: Normal liver 80


title: WT_1


title: WT_4


title: luc7a2 and luc7b double knockout replicate 3

description: Library name: dA2B1-3

value: luc7a2 and luc7b double knockout


title: luc7b and luc7rl double knockout replicate 2

description: Library name: dB1RL1-2


title: TC1_sgNAT10_2(mRNAseq)

description:
Library name: Tcell_sgNAT10_2
TC1_sgNAT10_mRNAseq.fpkm.txt
TC1_sgNAT10_2


title: WT_2


title: Lung_D7_Lep#1

value: ob/ob


title: 84N

source_name: Normal liver 84


title: 79N

source_name: Normal liver 79


title: Irp2_KO_3

value: global knockout for the gene Ireb2


title: luc7a2 and luc7b double knockout replicate 2

description: Library name: dA2B1-2


title: 77N

source_name: Normal liver 77


title: Lung_D1_Lep#3

value: Leptin pump


title: Irp2_KO_2


title: luc7a2 and luc7b double knockout replicate 1

description: Library name: dA2B1-1

source_name: seedling

value: seedling


title: 76N

source_name: Normal liver 76


title: Lung_D1_Lep#2


title: 74N

source_name: Normal liver 74


title: Irp2_KO_1


title: luc7a1 and luc7rl double knockout replicate 3

description: Library name: dA1RL1-3

value: luc7a1 and luc7rl double knockout


title: Lung_D1_Lep#1


title: 73N

source_name: Normal liver 73

value: Female


title: luc7a1 and luc7rl double knockout replicate 2

description: Library name: dA1RL1-2


title: Irp1_KO_7

value: global knockout for the gene Aco1


title: Irp1_KO_2


title: 72N

source_name: Normal liver 72

value: Male


title: luc7a1 and luc7b double knockout replicate 3

description: Library name: dA1B1-3

value: luc7a1 and luc7b double knockout


title: luc7a1 and luc7rl double knockout replicate 1

description: Library name: dA1RL1-1


title: 71N

source_name: Normal liver 71

value: Hepatocellular carcinoma (HCC)


title: Irp1_KO_1


title: Lung_D0_Lep#2


title: Lung_D0_Lep#1


title: 70N

source_name: Normal liver 70

value: normal liver tissue adjacent to the tumor (NAT)


title: Lung_D7_Sal#3

value: Saline pump


title: luc7a1 and luc7b double knockout replicate 1

description: Library name: dA1B1-1


title: Rh-43

city: jiangsu

first: tianle

last: ma

institute: nanjing university of chinese medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 .
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each sample

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: liver

tag: strain

value: Liverparenchymal cells


title: luc7a1 and luc7b double knockout replicate 2

description: Library name: dA1B1-2


title: 69N

source_name: Normal liver 69


title: Lung_D7_Sal#2


title: luc7b knockout replicate 3

description: Library name: B1-3

value: luc7b knockout


title: Rh-41


title: Lung_D7_Sal#1

value: Lung


title: luc7b knockout replicate 2

description: Library name: B1-2


title: Lung_D0_Lep#3


title: 66N

source_name: Normal liver 66


title: Lung_D1_Sal#3


title: luc7b knockout replicate 1

description: Library name: B1-1


title: Lung_D1_Sal#2


title: Irp1_KO_6

source_name: testis

value: testis


title: Mod-12


title: Mod-14


title: Lung_D1_Sal#1

value: ob/ob


title: luc7a knockout strain 2 replicate 2

description: Library name: A2-2

value: luc7a knockout


title: Con-4


title: Mod-11


title: luc7a knockout strain 2 replicate 3

description: Library name: A2-3


title: 63N

source_name: Normal liver 63


title: Rh-42


title: 62N

source_name: Normal liver 62


title: luc7a knockout strain 2 replicate 1

description: Library name: A2-1


title: 67N

source_name: Normal liver 67


title: Lung_D0_Sal#3

source_name: Lung


title: 61N

source_name: Normal liver 61


title: luc7a knockout strain 1 replicate 3

description: Library name: A1-3


title: Lung_D0_Sal#1


title: Con-2


title: Con-3


title: luc7a knockout strain 1 replicate 2

description: Library name: A1-2


title: 65N

source_name: Normal liver 65


title: luc7a knockout strain 1 replicate 1

description: Library name: A1-1

source_name: seedling


title: 59N

source_name: Normal liver 59


title: HFD, replicate 1,ST

city: Beijing

first: Lijuan

last: Zhou

state: State

address: No.5 North Line Pavilion, Xicheng District, Beijing

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen tissue was embedded by OCT, and frozen sections 10µm thick were cut using a cryotome
Spataltranscriptome sequencing lbrares were prepared wih 10xGenomics Visium Spatal Gene Expression Sides & Reagent kit according to manufacturer's construction

value: hematopoietic stem cell

value: Immune cell

value: HFD


title: Hypothalamus, PND56, rep3

city: Nicosia

first: Leonidas

middle: A

last: Phylactou

state: Not US or Canada

address: 6 Iroon Avenue, Ayios Dometios

department: Molecular Genetics, Function & Therapy Department

country: Cyprus

institute: The Cyprus Institute of Neurology and Genetics

data_processing:
Adapter Trimming using TrimGalore
Alignment against miRBase hairpin and mature miR refernce bases using Bowtie
Alignment against host reference genome mm10 using Bowtie
Differential expression analysis using DEseq2 in R
Post-processing and visualisation in R
Assembly: mm10
Supplementary files format and content: Count_Matrix_Hyp.csv, Column1: miR ID, Columns2-15: Sample Names

source_name: Hypothalamus

extract_protocol:
Total RNA containing microRNAs was isolated from hypothalamic tissues using the mirVana miRNA isolation Kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. RNA concentration was evaluated by NanoDrop One spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA).
Samples were proceeded using the QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. To evaluate library quality and size, each library was analyzed by High Sensitivity D1000 ScreenTape on an Agilent TapeStation 2200 (Agilent Technologies, Waldbronn, Germany). Libraries were quantify using the Qubit™ dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, CA, USA).

value: Hypothalamus

value: PND56 (week8)


title: control seedling replicate 3

description: Library name: Col0-3

value: seedling

value: control


title: Hypothalamus, PND56, rep2


title: NCD, replicate 1,ST

description: 10X Genomics

value: NCD


title: 58N

source_name: Normal liver 58

value: Male

value: Hepatocellular carcinoma (HCC)

value: normal liver tissue adjacent to the tumor (NAT)


title: Hypothalamus, PND56, rep1


title: 64N

source_name: Normal liver 64

value: Female


title: Hypothalamus, PND35, rep3

value: PND35 (week5)


title: control seedling replicate 2

description: Library name: Col0-2


title: Lung_D0_Sal#2

value: Lung

value: Saline pump


title: 57N

source_name: Normal liver 57


title: 56N

source_name: Normal liver 56


title: JQF, replicate 1,ScRNA-seq

description: 10X Genomics

data_processing:
Preprocessing of the Raw Gene Expression Matrix was performed using the Cell Ranger pipeline (version 6.0.1) with the mouse reference genome (mm10). Subsequently, the Seurat R package (version 4.0.3) was utilized for analysis. Following the assessment of varying data quality, low-quality cells were filtered out based on sample-specific criteria, while the remaining high-quality cells were subjected to further analysis. The SCTransform function was employed for normalization and scaling of the samples. High-quality cells were integrated into the matrix, and cell clustering was performed based on shared features. The final step involved the visualization and analysis of all clustered cells using the UMAP (Uniform Manifold Approximation and Projection) algorithm, enabling scRNA-seq visualization and exploration
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Following hepatic perfusion, mouse liver tissues from the NCD group (n=1), HFD group (n=2), and JQF group (n=1) were collected for scRNA-seq analysis.In brief, the liver samples were cut into small pieces following the manufacturer's protocol and digested with a digestion solution. A 20uL aliquot of the digestion suspension was stained with Trypan Blue for microscopic examination. The centrifuge tubes were sealed with sealing film and the samples were incubated on a 37ºC shaker for 1 hour for digestion. After digestion, the suspension was sequentially transferred through 100μm and 40μm filters into centrifuge tubes. The tubes were centrifuged at 300g for 5 minutes, and the supernatant was discarded. Red blood cell lysis buffer was added to gently disperse the cells, followed by a 3-minute incubation. Then, a sufficient amount of wash buffer was added to stop the red blood cell lysis. The tubes were centrifuged at 300g for 5 minutes, and the supernatant was discarded. The cells were resuspended and mixed well with an appropriate amount of wash buffer. A 20uL aliquot was taken for AO/PI counting and Trypan Blue microscopic examination. Based on the quality control results, suitable procedures were chosen to remove impurities and dead cells.
The Chromium instrument and the Single Cell 3’ Reagent kit V3.1 (Dual Index) was used to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol (10X Genomics). Briefly, sample partitioning and molecular barcoding were done on the Chromium Controller (10x Genomics), where we loaded cellular suspensions together with the Single-cell 3’ Gel Beads on a Single-cell 3’ chip, in which gel beads in emulsion (GEM) generation took place. RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell reagent kit V3.1 (10X Genomics). Sequencing was performed with Illumina (NovaSeq 6000) according to the manufacturer’s instructions.

value: liver

value: TCM formula (JQF)


title: Hypothalamus, PND35, rep2


title: control seedling replicate 1

description: Library name: Col0-1


title: 55N

source_name: Normal liver 55


title: Hypothalamus, PND35, rep1


title: Microglia young DRN

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

data_processing:
Basecalls performed using  using RTA workflow version 1.18.64
Sequenced reads were trimmed for adaptor sequence,  low-complexity or low-quality sequence using trimmomatic v0.39 and fastp v0.20.1, then mapped to hg19 whole genome using STAR v2.7.4a with parameters --twopassMode Basic --outSAMstrandField intronMotif
Raw counts of sequencing reads for genes were perfomred using featureCounts method in Rsubread V2.01.
Read counts normalization, Reads Per Kilobase of exon per Megabase of library size (RPKM), and detection of differentailly expressed genes were processed using edgeR v3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads per gene for each Sample

source_name: microglia

growth_protocol: Microglia at differentiation day 25 and DRNs at day 21, were mixed with mouse astrocytes at ratio (MG: DRN: AS= 5:10:1) and were cultured in coculture media (Advanced F12, 1×N2, 1×Glutamax, 2-mercaptoethanol (1.7 ul/50ml), IL-34(100 ng/ml), M-CSF (25 ng/ml), TGF-β1(50 ng/ml), BDNF (20 ng/ml; R&D) and GDNF 20 ng/ml; R&D) for 10 days.

extract_protocol: Total RNA isolation with Trizol kit

treatment_protocol: Incubation of microgli and DRNs for 10 days

value: microglia

tag: cell derivation

value: iPSC-derived microglia

value: cocultured with fibroblast-direct reprogrammed neurons (DRNs)

tag: neuron type

value: directly reprogrammed from young fibroblasts


title: HFD, replicate 1,ScRNA-seq

description: 10X Genomics

value: hematopoietic stem cell

value: Immune cell

value: HFD


title: 53N

source_name: Normal liver 53


title: HFD, replicate 2,ScRNA-seq

description: 10X Genomics


title: 60N

source_name: Normal liver 60


title: Hypothalamus, PND14, rep3

value: Hypothalamus

value: PND14 (week 2)


title: NCD, replicate 1,ScRNA-seq

description: 10X Genomics

value: NCD


title: 52N

source_name: Normal liver 52

value: Male

value: Hepatocellular carcinoma (HCC)

value: normal liver tissue adjacent to the tumor (NAT)


title: 51N

source_name: Normal liver 51


title: 49N

source_name: Normal liver 49


title: Hypothalamus, PND56, rep5

value: PND56 (week8)


title: Hypothalamus, PND14, rep1


title: 48N

source_name: Normal liver 48


title: Tumor Treg_WT

city: Zhejiang

first: Sang Nee

last: Tan

address: Hangzhou

department: School of Medicine

institute: Westlake University

description: Library name: Sample 4

data_processing:
Single-cell sequencing data pre-processing were performed using the BD Rhapsody™ Sequence Analysis Pipeline (version 2.1, BD Biosciences Inc) with GRCm39 as the mouse reference genome.
The filtered Cell-by-Feature data tables of the four samples were conducted in Seurat (version 5.0.2) R package and subjected to the following quality control (QC): First, selecting the cells with detected genes no less than 200 and genes expressed in at least 3 cells. Then, Low-quality cells with less than 500 UMIs and 300 expressed genes or more than 7500 expressed genes were filtered out, as well as with more than 20 % mitochondrial gene expression.
The cells with ratio of log10 (nUMI) and log10 (nGene) less than 0.8, and the potential doublets which were calculated by DoubletFinder (version 2.0.4) with 7.5% doublet formation rate, were also removed.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Tumors

growth_protocol: Hepa1-6 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat-inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. Cell cultures were maintained at 37 °C with 5% CO2.  Hepa1-6 tumor cells were subcutaneously injected into Foxp3YFP-cre mice and Foxp3YFP-cre Tbx21fl/fl mice.

extract_protocol:
Tumors were subjected to tumor-infiltrating lymphocytes (TIL) isolation. CD4+ T cells were isolated by using Mouse CD4 (L3T4) MicroBeads (Miltenyi Biotec) according to the manufacturer’s protocol. Intra-tumoral Treg cells (CD4+ YFP+) were sorted from the isolated CD4+ T cells by using BD FACSAria Cell Sorter. Conventional CD4+ T cells (CD4+YFP-) and Treg cells (CD4+YFP+) sorted from Hepa1-6 tumors and tumor-free LN of Foxp3YFP-cre mice respectively were included for comparison. Cells were pooled from multiple mice per sample.
BD Rhapsody 8-lanes cartridges (664887 BD Biosciences) were loaded with 80,000 cells to capture 50,000-60,000 cells per sample. Single cells were isolated with the BD Rhapsody HT Xpress Single-Cell Analysis System using the BD RhapsodyTM Enhanced Cartridge Reagent Kit (633773 BD Biosciences) and BD Rhapsody cDNA Kit (633733 BD Biosciences) according to the manufacturer’s recommendations (BD Biosciences). cDNA libraries were prepared using the Whole Transcriptome Analysis Amplification Kit (633801 BD Biosciences) following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) Preparation Protocol (BD Biosciences). All the libraries were sequenced in a paired-end mode (PE150) on DNBseq-T7 (GenePlus).

treatment_protocol: The tumor-bearing Foxp3YFP-cre mice were sacrificed on day 23.

value: Tumors

value: Treg cells

value: Foxp3YFP-cre mice

value: Hepa1-6 tumor inoculation


title: 47N

data_processing:
Normalized Average Beta using Functional Normalization Method in Bioconductor minfi R package.
totalliver_funnorm_beta850_2022NT.txt: Normalized Average Beta

source_name: Normal liver 47

extract_protocol: Genomic DNA was extracted using MagListo™ 5M Genomic DNA Extraction Kit (Bioneer) according to manufacturer's protocol.

value: Female


title: Hypothalamus, PND56, rep4


title: 46N

source_name: Normal liver 46


title: 45N

source_name: Normal liver 45


title: Hypothalamus, PND35, rep5

source_name: Hypothalamus

value: PND35 (week5)


title: Hypothalamus, PND14, rep5


title: Tumor CD4+ Tconv_WT

description: Library name: Sample 2

value: CD4+ Tconv


title: Microglia old DRN

value: microglia

value: iPSC-derived microglia

value: cocultured with fibroblast-direct reprogrammed neurons (DRNs)

value: directly reprogrammed from old fibroblasts


title: Tumor Treg_Tbx21 KO

description: Library name: Sample 3


title: 43N

source_name: Normal liver 43


title: LN Treg_WT

description: Library name: Sample 1

source_name: Lymph nodes

value: Lymph nodes

value: Not applicable


title: Hypothalamus, PND35, rep4

value: Hypothalamus


title: Hypothalamus, PND14, rep4

value: PND14 (week 2)


title: Experiment 3, Barcode: Adnp Mutant and Wild-type Mice at E16.5 - Dorsal Telencephalon

city: Ottawa

first: José Alex

last: Lourenço Fernandes

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics

library_source: other

data_processing:
Output files were filtered and analyzed using Scanpy version 1.9.1 in Python (Python Core Team n.d.). Genes detected in less than 3 cells were removed from the analysis. Contaminant or low-quality cells (less than 5000 genes detected, less than 20 000 reads/counts detected or more than 0.05% of mitochondrial genes detected) were also excluded. Differential gene expression analyses were performed using or Scanpy (Wilcoxon signed-rank test), or MAST version 1.24.0. In order to avoid batch effects, pairwise comparisons were made between cKO samples and littermate control samples that had been processed together in the same batch. Littermate Chd4 cHet samples were used as paired controls for E16.5 Chd4 cKOs, and littermate Adnp cHet samples were compared with E18.5 Adnp cKOs. GO terms analysis was performed using ShinyGO. Gene scoring was generated using Scanpy (scanpy.tl.score_genes). Ensembl BioMart92 was first used to obtain mouse orthologues of human SFARI genes, or “definitive” SysNDD genes. Orthologues could not be obtained for 7 SFARI genes and 14 SysNDD genes. Statistical analysis of the gene score results was performed using Scipy.stats.
Contaminating cells were intentionally removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: Brain

extract_protocol:
Embryos were harvested and the dorsal telencephalon was microdissected. Cells were dissociated with papain (Worthington) in the presence of DNAse I, washed, and then barcoded. Briefly, 250 000 dissociated cells per replicate were incubated with ‘anchor’ and ‘co-anchor’ lipid-modified oligonucleotides generously provided by the Gartner lab.
Each replicate was then co-incubated with barcode oligonucleotides for 10 minutes and then washed 3 times with PBS. Replicates were then pooled in equivalent ratios, and approximately 20 000 pooled cells were combined in individual Chromium™ runs (3’ Library & Gel Bead Kit v2, PN-120237, 10X Genomics). Expression library FASTQs were processed using CellRanger (10X Genomics). The deMULTIplex workflow was used to remove doublets and exclude cells lacking barcodes.

value: Brain

tag: tissue region

value: Dorsal Telencephalon

value: Adnp Mutant and Wild-type


title: 40N

source_name: Normal liver 40

value: Male

value: Hepatocellular carcinoma (HCC)

value: normal liver tissue adjacent to the tumor (NAT)


title: Experiment 3, run 1: Adnp Mutant and Wild-type Mice at E16.5 - Dorsal Telencephalon

description: 10x Genomics


title: 39N

source_name: Normal liver 39


title: Experiment 2, Barcode: Adnp Mutant and Wild-type Mice at E13.5 - Dorsal Telencephalon

description: 10x Genomics


title: lung of control mice

type: RNA

city: Changsha

first: Xudong

last: Xiang

address: NO.139 Middle Renmin Road

institute: Central South University

description: lncRNA and mRNA expression

hyb_protocol: 1.Add 500 uL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2.Equilibrate water bath to 60°C. 3.For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube.  4.Mix well but gently on a vortex mixer. 5.Incubate at 60°C for exactly 30 minutes to fragment RNA.  6.Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.               7.Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8.Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9.Place sample on ice and load onto the array as soon as possible.  10.Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11.Slowly dispense the volume of hybridization sample onto the gasket well in a 'drag and dispense manner.                                         12.Slowly place an array ?active side? down onto the SureHyb gasket slide, so that the Agilent-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13.Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14.Hand-tighten the clamp onto the chamber. 15.Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16.Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17.Hybridize at 65°C for 17 hours.

scan_protocol: 1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Extract data using Agilent Feature Extraction Software

source_name: lung of control mice

label_protocol: 1.Add 84 uL of nuclease-free water to your cRNA sample, for a total volume of 100 uL. 2.Add 350 uL of Buffer RLT and mix well by pipetting. 3.Add 250 uL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge. 4.Transfer the 700 uL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube. 5.Transfer the RNeasy column to a new collection tube and add 500 uL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube. 6.Add another 500 uL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube. 7.Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report uLabeling Efficiency-QC?) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. 8.Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9. Take 1.5 ul of each sample to determine the yield and specific activity by using the NanoDrop ND-2000

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

treatment_protocol: 100ug house dust mite, 100ug ovalbumin and 15ug lipopolysaccharide were used to establish the Th17-mediated neutrophil-predominant asthma model, 25ug ovalbumin was used to establish the Th2-mediated eosinophil-predominant asthma model, the control  group received saline instead.

value: lung

value: female

tag: sample group

value: control mice


title: Hypothalamus, PND14, rep2


title: lung of Th2-mediated eosinophil-predominant asthma mice

description: lncRNA and mRNA expression

tag: gender


title: Experiment 2, run 1: Adnp Mutant and Wild-type Mice at E13.5 - Dorsal Telencephalon

description: 10x Genomics


title: 38N

source_name: Normal liver 38

value: Female

tag: diagnosis


title: lung of Th17-mediated neutrophil-predominant asthma mice

description: lncRNA and mRNA expression

tag: tissue


title: Experiment 1, Barcode: Adnp and Chd4 Mutant Mice at E18.5 - Neocortical and Hippocampal

description: 10x Genomics

value: Neocortical and Hippocampal

value: Adnp and Chd4 Mutant


title: 37N

source_name: Normal liver 37

tag: patient


title: 35N

source_name: Normal liver 35


title: 44N

source_name: Normal liver 44


title: 30N

source_name: Normal liver 30


title: 31N

source_name: Normal liver 31


title: ARF-2_S23

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
FASTQC passed reads were quantified in mapping-based mode using Salmon v1.4.0 using a decoy-aware transcriptome index generated using GENCODE mouse reference assembly (GRCm39, M26 release)
Transcript abundance estimates were coallated  for gene-level quantification using the tximport function in DESeq2
Differential gene expression analysis was performed using un-normalized gene level counts as input for DESeq2
Assembly: GRCm39, M26 release
Supplementary files format and content: DESeq2_normalized_counts.txt (contains normalized gene-level counts from DESeq2 and Gene Symbol)

source_name: DRG/nerve root neurosphere cells (DNSC)

extract_protocol:
Qiagen RNeasy Plus Mini (QiaShredder, on-column DNase treatement)
KAPA mRNA Hyperprep Kit (Roche), 100ng input total RNA, 13 cycles PCR amplification

value: DRG/nerve root neurosphere cells (DNSC)

tag: cell type

value: isolated and cultured from murine embryo at day 13.5

value: Cre-GFP-encoding adenovirus


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 2

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Samples were analyzed using the UTAP pipeline (PMID: 30909881)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm10 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –alignSoftClipAtReferenceEnds No).
Read count extraction (UMI counts) was performed after marking duplicates using HTSeq-count in union mode.
Assembly: mm10
Supplementary files format and content: C2_countsUmiCorrectedMatrix.txt;
Supplementary files format and content: read count matrix

source_name: Mammary gland

growth_protocol: NMuMG-C2 dual reporter cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, 100 unit/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine and 1X MEM non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was produced using the RNeasy mini kit (Qiagen). 50ng of total RNA was used for the construction of sequencing libraries.
Library preparation protocol was bulk-adapted from MARS-seq

treatment_protocol: Cell were plated at 50% confluency in 24-wells plate with DMEM+ 10% FBS and cultured for 24h. Following 24h cells were added with the indicated treatment: BMP4 (31.25ng/ml, R&D), Control- no added ligand, TGFb1 (1.92ng/ml, R&D), or BMP4+ TGFb1 and cultured for additional 6h.

value: Mammary gland

value: Epithel

tag: genotype

value: Double reporter cells with BMP RE mCherry and TGFb RE mCitrine


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 4


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 3


title: 36N

first: Dawon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: Yonsei University

source_name: Normal liver 36


title: 28N

source_name: Normal liver 28


title: ARF-1_S22


title: 41N

source_name: Normal liver 41


title: Experiment 1, run 1: Adnp and Chd4 Mutant Mice at E18.5 - Neocortical and Hippocampal

description: 10x Genomics

value: Brain


title: C2 cells, TGFb1 added, 6h, biol rep 3


title: CRE-2_S17


title: CRE-3_S18


title: ARF-3_S24


title: 29N

source_name: Normal liver 29


title: 27N

source_name: Normal liver 27


title: C2 cells, TGFb1 added, 6h, biol rep 2


title: C2 cells, TGFb1 added, 6h, biol rep 4


title: 26N

source_name: Normal liver 26


title: CRE-1_S16


title: GFP-3_S15

value: GFP-encoding adenovirus


title: C2 cells, control- no ligand added, 6h, biol rep 4

value: No treatment


title: GFP-2_S14


title: 25N

source_name: Normal liver 25

value: Male

value: Hepatocellular carcinoma (HCC)


title: 24N

source_name: Normal liver 24

value: normal liver tissue adjacent to the tumor (NAT)


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 1


title: C2 cells, control- no ligand added, 6h, biol rep 3


title: 23N

source_name: Normal liver 23


title: C2 cells, control- no ligand added, 6h, biol rep 2


title: GFP-1_S13


title: Brown adipose tissues,AWBSCR16KO3

city: Shanghai

first: Shengjie

last: Zhang

address: No. 573, Xujiahui Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, A base added, and ligated to Illumina sequencing adapters.
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co.

value: brown adipose tissue

value: WBSCR16 KO


title: 21N

city: Seoul

source_name: Normal liver 21


title: C2 cells, control- no ligand added, 6h, biol rep 1


title: Brown adipose tissues,AWBSCR16KO2


title: 16N

source_name: Normal liver 16


title: Brown adipose tissues,AWBSCR16KO1


title: 18N

source_name: Normal liver 18

value: Female


title: 17N

source_name: Normal liver 17


title: Brown adipose tissues,Floxed3

value: Floxed


title: 15N

source_name: Normal liver 15


title: C2 cells, BMP4 added, 6h, biol rep 2


title: C2 cells, BMP4 added, 6h, biol rep 3


title: 14N

source_name: Normal liver 14


title: C2 cells, BMP4 added, 6h, biol rep 1

source_name: Mammary gland


title: Brown adipose tissues, Floxed1


title: 13N

source_name: Normal liver 13


title: KO_3 (ASYAP5SA)

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

institute: Université de Montréal

data_processing:
Gene expression was obtained using the RNA-seq quantitation pipeline in SeqMonk NGS visualization and analysis tool (v1.48.1, Babraham Institute)
Gene expression was normalized into reads per kilobase of transcripts per million mapped reads (RPKM) values and log2 tranformed using SeqMonk
DeSeq2 version 1.22.2  was then used to detect differential expression. Thresholds used for P-value and fold change were 0.05 and ±1.5 or ±2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Adrenal gland

extract_protocol:
Whole adrenal glands conserved at -80 were defrozen and total RNA was extracted using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.
BAM files were generated from the IRIC sequencing platform using STAR

value: Adrenal gland

value: Rosa26YAP5SA/+; AScre/+


title: Prdm16_Vcam1_DKO_rep1

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

institute: UCLA

description: 10x Genomics

data_processing:
FASTQ files were generated using CellRanger mkfastq (v.6.1.1) and samples were analyzed using CellRanger count (v6.1.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The V-SVZ of the lateral walls of the lateral ventricles from one-month old (P31-33) mice were dissected according to published protocols (Mirzadeh et al., 2010). Single cell suspensions were prepared as described in (Brewer and Torricelli, 2007). Briefly, a 2 mg/ml papain solution was pre-activated at 37℃ for 20 min. The V-SVZ samples were then digested in the papain solution at 30℃ for 30 min with a shaking speed of 60 rpm in a shaker. The tissue sample is then mechanically dissociated by trituration with a Pasteur pipette 10~15 times per round for three rounds, washed, and centrifuged with an OptiPrep density gradient to remove myelin and cellular debris. After centrifugation, the dense white layer and all layers above were carefully aspirated. The lower layers were pelleted at 200g for 3min, resuspended in 1 ml PBS with 0.04% bovine serum albumin (0.04% BSA-PBS), filtered through 40 μm strainers, and resuspended in 0.04% BSA-PBS at 700-1,200 cells/µl for single cell capture.
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10X Genomics), Chromium Next GEM Chip G Single Cell Kit (10X Genomics), and Single Index Kit T Set A (10X Genomics) according to the manufacturer’s instructions. Cells were loaded to target 10K cells to form GEMs and barcode individual cells. GEMs were then cleaned, and cDNA libraries were created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System and D1000 ScreenTape (both from Agilent) and Qubit 2.0 (Invitrogen) for concentration and size distribution.

value: brain


title: 12N

source_name: Normal liver 12


title: Prdm16_cKO_rep3

description: 10x Genomics

value: hGFAP-Cre+/-; Prdm16flox/flox


title: KO_1 (ASYAP5SA)


title: KO_2 (ASYAP5SA)


title: Prdm16_cKO_rep2

description: 10x Genomics


title: C2 cells, BMP4 added, 6h, biol rep 4

value: Mammary gland


title: 10N

source_name: Normal liver 10


title: 11N

source_name: Normal liver 11


title: CONT_3 (ASYAP5SA)


title: Prdm16_cKO_rep1

description: 10x Genomics


title: Control_rep3

description: 10x Genomics

value: Prdmflox/flox


title: Brown adipose tissues,Floxed2


title: 8N

source_name: Normal liver 8


title: Control_rep2

description: 10x Genomics


title: scRNA-Seq of Paraescarpia echinospica: plume4

city: shandong

first: Nannan

address: Hengyun Mountain Road

institute: BGI Research, Qingdao, Shandong

description: MGI

data_processing:
The scRNA-Seq data was processed using PISA and FastQC for quality control, and then mapped to the reference genome of P. echinospica. Cell clustering was performed using Seurat based on a graph-based approach, with cell filtration based on gene counts and mitochondrial UMIs. Differential gene expression analysis was conducted using the 'findallmarker' function in Seurat
Assembly: HKBU_Pec_v1
Supplementary files format and content: RDS includes values files and matrix files

source_name: plume

extract_protocol:
The dissected plume of P. echinospica was transferred onto petri dishes and washed with ice-cold artificial seawater. The seawater was prepared according to previous reports[23]. Then the plume was transferred on new petri dishes and minced by scalpel. The minced plume was collected into cell dissociation buffer containing 10mg/ml Bacillus licheniformis protease (Sigma-Aldrich) and 0.5mM EDTA, the reaction was lasted for 30 minutes at 8℃. After the reaction, the suspension was filtered through 30μm cell strainer and spanned down at 500g for 5 min at 4℃. The supernatant was carefully removed, then the pellets were washed by ice-cold artificial sea water. After that, the pellets were resuspended in 1x PBS containing 0.04% bovine serum albumin. The cell concentration was counted with Trypan Blue for subsequent DNBelab C Series Single-Cell library construction.
The DNBelab C Series Single-Cell Library Prep Set (MGI) was utilized as previously described [24]. In brief, single cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, cDNA amplification and purification. Indexed sequencing libraries were constructed according to the manufacturer’s protocol. The sequencing libraries were quantified by Qubit™ ssDNA Assay Kit (Thermo Fisher Scientific).

value: plume

tag: age

value: adult

value: hemocytes


title: scRNA-Seq of Paraescarpia echinospica: plume5

description: MGI


title: scRNA-Seq of Paraescarpia echinospica: plume7

description: MGI


title: 6N

source_name: Normal liver 6


title: Control_rep1

description: 10x Genomics


title: scRNA-Seq of Paraescarpia echinospica: plume3

description: MGI


title: KO_3 (ASL1L2)

data_processing:
Gene expression was obtained using the RNA-seq quantitation pipeline in SeqMonk NGS visualization and analysis tool (v1.48.1, Babraham Institute)
Gene expression was normalized into reads per kilobase of transcripts per million mapped reads (RPKM) values and log2 tranformed using SeqMonk
DeSeq2 version 1.22.2  was then used to detect differential expression. Thresholds used for P-value and fold change were 0.05 and ±1.5 or ±2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
Whole adrenal glands conserved at -80 were defrozen and total RNA was extracted using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.
BAM files were generated from the IRIC sequencing platform using STAR
Illumina Nextseq500- 0.5 Flowcell High Output


title: KO_2 (ASL1L2)


title: scRNA-Seq of Paraescarpia echinospica: plume2

description: MGI


title: cre+lkb1

city: Tianjin

first: Yu

address: 890 Jingu Road, Jinnan District

institute: Tianjin haihe hospital

description: one sample from the lung of Nkx2.1 Cre;Lkb1f/f mice

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: murine lung tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: 5 week

value: lung

value: Nkx2.1 Cre;Lkb1f/f


title: C2 cells, TGFb1 added, 6h, biol rep 1

value: Epithel

value: Double reporter cells with BMP RE mCherry and TGFb RE mCitrine


title: lkb1

description: one sample from the lung of Lkb1f/f mice


title: 5N

source_name: Normal liver 5

value: Hepatocellular carcinoma (HCC)

value: normal liver tissue adjacent to the tumor (NAT)


title: CONT_3 (ASL1L2)

value: Male


title: scRNA-Seq of Paraescarpia echinospica: plume6

description: MGI


title: 4N

source_name: Normal liver 4

value: Female


title: CONT_2 (ASYAP5SA)

value: Adrenal gland


title: Shh-Ai9+ NP cells

city: 市辖区

first: zaiqi

last: xie

state: 徐汇区

address: 上海市徐汇区岳阳路320号

institute: chinese academy of science

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
MT% < 20%;  Cell Gene Number < 10000; Cell Gene Number > 200.
PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: Shh-Cre;Ai9+ single NP cells

growth_protocol: Mice intervertebral disc cells were extracted from 4-weeks-old Shh-Cre; Rosa26tdTomato mice and cut into pieces of ~1 cm3 using ophthalmological scissors. Then, intervertebral disc tissues were digested for 5 minutes with 0.25% trypsin at 37°C. Digestions was terminated with αMEM + 10% fetal bovine serum (FBS). Cells were washed twice by centrifugation at 800g for 5 min with ice-cold DPBS (Corning, 21-031-CMR); Subsequently, 0.2% Type II Collagenase was used to digest intervertebral disc tissues for 2 hr. Digestion was again terminated with αMEM + 10% FBS. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec，C3702) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Shh-Ai9+ NPs were sorted using BD FACS AriaIII(405).

extract_protocol:
Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

tag: strain background

value: Nucleus pulposus

value: post natal day 28


title: 9N

source_name: Normal liver 9


title: CONT_1 (ASYAP5SA)

tag: Sex


title: 3N

source_name: Normal liver 3


title: CONT_2 (ASL1L2)


title: donkey epididymis corpus

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

description: Library name: Samples3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Assembly: 10mm
Supplementary files format and content: Tab-separated values files and matrix files

organism: Equus asinus

source_name: epididymis corpus

extract_protocol:
The testis and epididymis (divided into caput, corpus and cauda) were washed in PBS immediately after dissociation. These samples were stored in MACS Tissue Storage Solution within 48 h . Before dissociation, the testis and epididymis tissues were cut into small pieces and transferred to 0.2% collagenase IV and DNase I digestion solution, followed by incubation at 37°C for 15 min. After digestion and mechanical striking into single cells, the cell suspension was filtered through a cell strainer and converted to barcoded scRNA-seq libraries in accordance with the manufacturer's protocol.
DNBelab C series high-throughput single-cell RNA library preparation kit is based on droplet microfluidic technology and independently designed using MGI C4 droplet generation device, through efficient mRNA capture magnetic beads and droplet recognition microbeads and single-cell RNA library preparation kit The single-cell (nuclear) suspension can be quickly prepared into a dedicated library corresponding to the sequencing platform. The DNBelab C library contains cDNA Library and Oligo library, which are derived from MRNA-capturing magnetic beads and droplet recognition microbeads, respectively.

value: epididymis corpus

value: single

value: somatic cells


title: P-hep-orgs

city: Guangdong

first: Wu

last: Haibin

state: 广州

address: No. 382 Waihuan East Rd., Guangzhou University City, Panyu District, Guangzhou, Guangdong, P.R.China

institute: South China University of technology

data_processing:
The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by DNBSEQ-T7（BGISEQ）sequencing platform on a 150 bp paired-end run.
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we used STARsolo (version 2.7.10a) along with human genome GRCh38 (ensemble annotation version 104).
The raw digital gene expression matrix was filtered, normalized, and clustered using R and R package Seurat v4.0.
Cells with counts fewer than 1000, mitochondrial content more than 40% were removed. Genes detected in less than three cells were removed.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output files.

growth_protocol: In order to generate HB-orgs, HB spheres were dissociated into single cells with TrypLE (Gibco) and seeded in ultra-low attachment 6-well plates at a cell density of 2 × 105 cells/ml and cultured in HB-expansion medium that consisted of IMDM medium, 10% FBS, 1% ITSE (Gibco), 1% NEAA, 1% GlutaMax I, 0.3 mM 1-thioglycerol, 10 mM Nicotinamide (Sigma), 5 μM CHIR99021, 10 μM SB431542, 10 μM Forskolin (both from MedChemExpress), 20 ng/ml BMP4, 20 ng/ml FGF4, 20 ng/ml EGF (all cytokines from Peprotech) and 10 μM Y-27632 (MedChemExpress) for one day (the primary HB-expansion (pre-expansion) medium was consisted of HB-expansion medium supplemented with 20 ng/ml HGF (Peprotech) and 10 μM Y-27632). The cells reaggregated to form into spheres. 24 hours after seeding, the culture medium supplemented with dispersing 5% growth factor reduced Matrigel (Corning) using 1,000 mL tips, and the medium was changed daily for 5-6 days and  the typical morphology of HB-orgs would emerged within 5 days. For passaging organoids, HB-orgs were dissociated into single cells with TrypLE and split at 1:4-6 every 5-6 days, and 5% ice-cold growth factor reduced Matrigel was added when seeding cells. Ordinarily, the representative morphology of HB-orgs was formed at passage 2. In order to obtain P-hep-orgs in vitro, HB-orgs were directly transferred to hepatocyte culture medium (HCM) supplemented with SingleQuots (Lonza) minus EGF, supplemented with 1% B27 (Gibco), 100 nM dexamethasone, 20 ng/ml FGF4, 20 ng/ml HGF and 40 ng/ml Oncostatin M (Peprotech). To induce polarized Hep-orgs, 5% ice-cold growth factor reduced Matrigel was added into the medium when HB-orgs were transferring. The medium was changed every other day for at least 6 days for the polarized hep-orgs to maturate.

extract_protocol:
H9 derived HB-orgs at passage 6 and P6-HB-orgs derived P-hep-orgs differentiated at day 8 were dissociated into single cells by TrypLE.
Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR.

value: H9 differentiated hepatic organoids


title: donkey epididymis caput

description: Library name: Samples2

source_name: epididymis caput

value: epididymis caput


title: 2N

source_name: Normal liver 2


title: 1N

source_name: Normal liver 1

value: not collected


title: donkey testis

description: Library name: Samples1

source_name: testis

value: testis

value: germ cells


title: HB-orgs

value: H9 differentiated hepatoblast organoids


title: scRNA-Seq of Paraescarpia echinospica: plume1

description: MGI

value: plume

value: adult

value: hemocytes


title: KO_1 (ASL1L2)

source_name: Adrenal gland

value: Male


title: wild type, mature leaf, replicate 4

status: Public on Dec 29 2024

city: BERN

first: Michael

middle: T

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

description: Library name: WT9_wild_type

data_processing:
HISAT2 mapping (usegalaxy.eu)
htseq-count (usegalaxy.eu)
DESeq2 ®
Assembly: Kalanchoe laxiflora_OBG_diploid_v1
Supplementary files format and content: rawcounts_TPM_all.csv

organism: Kalanchoe laxiflora

source_name: mature leaf (7th leaf pair)

extract_protocol:
Qiagen Rneasy Plant Minikit with on-column DNAseI digest
Revelo mRNA-Seq for MagicPrep NGS kit B (15 cycles PCR)

value: mature leaf (7th leaf pair)

value: wild type


title: wild type, mature leaf, replicate 1

description: Library name: WT6_wild_type


title: KlaxMUTE1 overexpression, mature leaf, replicate 2

description: Library name: OE5_KlaxMUTE1_overexpression

value: KlaxMUTE1 overexpression


title: KlaxMUTE1 overexpression, mature leaf, replicate 3

description: Library name: OE6_KlaxMUTE1_overexpression


title: wild type, mature leaf, replicate 3

description: Library name: WT8_wild_type


title: CONT_1 (ASL1L2)

value: Adrenal gland


title: Patient urine 412

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1057

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files was performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags were extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 was performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads were collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample were generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference was performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Assembly: GRCh38
Supplementary files format and content: 1 combined tab-delimited text file includes raw count values for each Sample.

source_name: urine

growth_protocol: No growth

extract_protocol:
RNA was extracted from 200 µL of human plasma or synovial fluid using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204) or 250 µL to 1 mL human urine using Norgen Biotek's Urine Cell-Free Circulating RNA Purification Mini Kit following manufacturer instructions (Cat #56900).
miRNA libraries for miRNA-seq were prepared using Qiagen's QIAseq miRNA Library Kit optimized for biofluid samples (Cat # 331505). Individual libraries were quantified using a fluorometric high-sensitivity dsDNA assay and assessed using Bioanalyzer high sensitivity assay.

treatment_protocol: No treatment

value: MALE

tag: bmi

tag: procedure

value: PRIMARY LEFT KNEE REPLACEMENT

value: urine

tag: leap id


title: wild type, mature leaf, replicate 2

description: Library name: WT7_wild_type


title: Patient urine 409

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U929


title: Patient urine 410

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U998

value: FEMALE

value: PRIMARY RIGHT KNEE REPLACEMENT


title: KlaxMUTE1 overexpression, mature leaf, replicate 1

description: Library name: OE4_KlaxMUTE1_overexpression


title: Patient urine 413

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1068

value: PRIMARY BILATERAL KNEE REPLACEMENT


title: Patient urine 411

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1033


title: Patient urine 408

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U927


title: Patient urine 407

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U904


title: Patient urine 414

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1140


title: MDAMB436_olaparib

city: Boston

first: Antoine

last: Simoneau

address: 201 Brookline

institute: Tango Therapeutics

description:
Library name: SAMPLE 7
MDAMB436 cells were passaged for 10 doublings in the presence of 10 nM olaparib. MDAMB436_DMSO_2 was used as control

data_processing:
In-house customized pipeline for mapping and counting for sgRNAs
Assembly: GrCh38
Supplementary files format and content: Tab-delimited text files include guide count and clone count values for each sample
Supplementary files format and content: gene_symbol: gene name
Supplementary files format and content: gene_sgrna_id: gRNA identifier of each gene (1-4 or 1-6)
Supplementary files format and content: umi_barcode: unique molecular identifier barcode sequence
Supplementary files format and content: sample_counts: number of counts for a specific guide and barcode
Library strategy: CRISPR Screen

source_name: Cell line

growth_protocol: Cells were grown in the presence of DMSO, TNG348 or olaparib for 10 population doublings in 1:1 RPMI1640:MEBM + 3% FBS (UWB1.289), RPMI1640 + 10% FBS (MDAMB436, HCC1395) or DMEM +10% FBS (COV362)

extract_protocol:
Genomic DNA was extracted with DNeasy Blood & Tissue Kit (Qiagen, 69506) for UWB1.289 and MDAMB436 and with ReliaPrep large volume HT gDNA isolation system for COV362 and HCC1395 (Promega, A2751)
sgRNA sequences with primers forward: F: 5′- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNCTTGTGGAAAGGACGAAACACCG-3′, reverse: R: 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′ and purified with Kapa Pure Beads (Roche, KK8802)

treatment_protocol: UWB1.289 were treated with 200 nM TNG348, 1uM olaparib or equivalent concentration of DMSO. MDAMB436 cells were treated with 100 nM TNG348, 10 nM olaparib or equivalent concentration of DMSO. COV362 and HCC1395 were treated with 500 nM TNG348 or equivalent concentrations of DMSO.

value: Cell line

tag: cell line

value: Breast cancer cell line

tag: treatment

value: 10 nM olaparib


title: HCC1395_DMSO

description:
Library name: SAMPLE 10
HCC1395 cells were passaged for 10 doublings in the presence of DMSO

value: DMSO


title: UWB1.289_DMSO

description:
Library name: SAMPLE 1
UWB1.289 cells were passaged for 10 doublings in the presence of DMSO

value: Ovarian cancer cell line


title: UWB1.289_TNG348

description:
Library name: SAMPLE 2
UWB1.289 cells were passaged for 10 doublings in the presence of 200 nM TNG348


title: MDAMB436_DMSO_1

description:
Library name: SAMPLE 4
MDAMB436 cells were passaged for 10 doublings in the presence of DMSO


title: UWB1.289_olaparib

description:
Library name: SAMPLE 3
UWB1.289 cells were passaged for 10 doublings in the presence of 1 uM olaparib

value: 1 uM olaparib


title: HCC1395_TNG348

description:
Library name: SAMPLE 11
HCC1395 cells were passaged for 10 doublings in the presence of 500 nM TNG348


title: MDAMB436_TNG348

description:
Library name: SAMPLE 5
MDAMB436 cells were passaged for 10 doublings in the presence of 100 nM TNG348. MDAMB436_DMSO_1 was used as control


title: COV362_TNG348

description:
Library name: SAMPLE 9
COV362 cells were passaged for 10 doublings in the presence of 500 nM TNG348


title: MDAMB436_DMSO_2

description:
Library name: SAMPLE 6
MDAMB436 cells were passaged for 10 doublings in the presence of DMSO


title: COV362_DMSO

description:
Library name: SAMPLE 8
COV362 cells were passaged for 10 doublings in the presence of DMSO


title: Patient urine 406

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U903


title: Patient urine 404

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U854


title: Patient urine 405

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U875


title: Patient urine 401

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U748


title: Patient urine 402

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U754


title: Patient urine 403

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U784


title: Patient urine 399

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U425


title: Patient urine 400

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U675


title: Patient urine 398

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U419


title: Patient urine 396

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U370


title: Patient urine 395

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U324


title: Patient urine 394

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U305


title: Patient urine 393

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U280


title: Patient urine 391

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U100


title: Patient urine 392

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U138


title: Patient urine 390

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U44


title: Patient urine 388

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1310


title: Patient urine 382

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1266


title: Patient urine 386

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1286


title: Patient urine 380

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1254


title: Patient urine 385

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1281


title: Patient urine 375

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1227


title: Patient urine 381

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1260


title: Patient urine 376

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1231


title: Patient urine 379

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1251


title: Patient urine 389

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U25


title: Patient urine 378

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1244


title: Patient urine 384

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1279


title: Patient urine 387

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1304


title: Patient urine 374

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1226


title: Patient urine 383

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1271


title: Patient urine 370

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1209


title: Patient urine 369

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1208


title: Patient urine 373

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1223


title: Patient urine 397

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U411


title: Patient urine 372

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1217


title: Patient urine 368

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1206


title: Patient urine 367

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1204


title: Patient urine 366

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1195


title: Patient urine 365

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1194


title: Patient urine 364

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1191


title: Patient urine 377

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1233


title: Patient urine 359

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1174


title: Patient urine 360

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1182


title: Patient urine 358

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1173


title: Patient urine 361

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1185


title: Patient urine 363

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1189


title: Patient urine 362

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1186


title: Patient urine 352

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1157


title: Patient urine 371

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1215


title: Patient urine 355

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1170


title: Patient urine 353

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1158


title: Patient urine 350

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1147


title: Patient urine 354

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1165


title: Patient urine 357

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1172


title: Patient urine 347

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1143


title: Patient urine 356

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1171


title: Patient urine 349

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1146


title: Patient urine 345

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1128


title: Patient urine 344

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1122


title: Patient urine 342

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1117


title: Patient urine 346

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1132


title: Patient urine 343

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1119


title: Patient urine 348

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1145


title: Patient urine 340

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1106


title: Patient urine 337

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1102


title: Patient urine 341

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1108


title: Patient urine 338

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1103


title: Patient urine 336

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1101


title: Patient urine 335

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1096


title: Patient urine 351

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1155


title: Patient urine 330

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1077


title: Patient urine 334

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1092


title: Patient urine 329

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1066


title: Patient urine 331

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1082


title: Patient urine 327

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1064


title: Patient urine 321

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1029


title: Patient urine 333

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1090


title: Patient urine 319

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1015


title: Patient urine 328

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1065


title: Patient urine 316

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U988


title: Patient urine 323

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1046


title: Patient urine 324

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1054


title: Patient urine 315

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U985


title: Patient urine 318

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1011


title: Patient urine 322

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1044


title: Patient urine 339

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1105


title: Patient urine 317

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1001


title: Patient urine 320

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1019


title: Patient urine 314

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U984


title: Patient urine 312

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U970


title: Patient urine 310

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U964


title: Patient urine 309

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U961


title: Patient urine 308

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U957


title: Patient urine 326

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1060


title: Patient urine 325

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1058


title: Patient urine 313

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U982


title: Patient urine 307

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U948


title: Patient urine 332

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U1089


title: Patient urine 306

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U944


title: Patient urine 305

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U897


title: Patient urine 304

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U891


title: Patient urine 303

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U887


title: Patient urine 302

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U876


title: Patient urine 298

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U850


title: Patient urine 301

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U874


title: Patient urine 299

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U860


title: Patient urine 297

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U841


title: Patient urine 300

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U867


title: Patient urine 294

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U817


title: Patient urine 293

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U810


title: Patient urine 296

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U836


title: Patient urine 290

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U720


title: Patient urine 291

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U767


title: Patient urine 289

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U667


title: Patient urine 311

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U966


title: Patient urine 288

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U640


title: Patient urine 285

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U491


title: Patient urine 286

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U537


title: Patient urine 284

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U473


title: Patient urine 282

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U327


title: Patient urine 283

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U391


title: Patient urine 281

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U277


title: Patient urine 279

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U145


title: Patient urine 280

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U257


title: Patient urine 278

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U139


title: Patient urine 277

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U86


title: Patient urine 275

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U943


title: Patient urine 295

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U826


title: Patient urine 276

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U946


title: Patient urine 292

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U777


title: Patient urine 272

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U899


title: Patient urine 271

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U885


title: Patient urine 266

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U852


title: Patient urine 287

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U551


title: Patient urine 268

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U866


title: Patient urine 269

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U868


title: Patient urine 265

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U851


title: Patient urine 270

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U869


title: Patient urine 264

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U843


title: Patient urine 267

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U862


title: Patient urine 260

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U827


title: Patient urine 258

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U821


title: Patient urine 257

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U820


title: Patient urine 261

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U828


title: Patient urine 255

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U804


title: Patient urine 259

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U822


title: Patient urine 253

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U800


title: Patient urine 256

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U809


title: Patient urine 252

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U799


title: Patient urine 251

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U791


title: Patient urine 274

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U913


title: Patient urine 273

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U900


title: Patient urine 250

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U789


title: Patient urine 249

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U786


title: Patient urine 254

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U803


title: Patient urine 248

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U782


title: Patient urine 247

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U780


title: Patient urine 246

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U778


title: Patient urine 263

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U837


title: Patient urine 262

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U832


title: Patient urine 245

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U776


title: Patient urine 244

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U775


title: Patient urine 242

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U772


title: Patient urine 243

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U774


title: Patient urine 240

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U768


title: Patient urine 236

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U751


title: Patient urine 237

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U756


title: Patient urine 241

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U770


title: Patient urine 239

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U765


title: Patient urine 235

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U745


title: Patient urine 234

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U735


title: Patient urine 233

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U733


title: Patient urine 232

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U714


title: Patient urine 231

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U697


title: Patient urine 229

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U683


title: Patient urine 228

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U677


title: Patient urine 227

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U676


title: Patient urine 226

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U617


title: Patient urine 221

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U545


title: Patient urine 224

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U609


title: Patient urine 223

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U582


title: Patient urine 225

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U616


title: Patient urine 222

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U569


title: Patient urine 216

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U462


title: Patient urine 220

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U507


title: Patient urine 238

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U757


title: Patient urine 213

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U431


title: Patient urine 218

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U478


title: Patient urine 211

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U357


title: Patient urine 209

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U331


title: Patient urine 217

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U464


title: Patient urine 212

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U412


title: Patient urine 207

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U326


title: Patient urine 215

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U455


title: Patient urine 206

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U310


title: Patient urine 230

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U687


title: Patient urine 214

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U447


title: Patient urine 210

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U336


title: Patient urine 205

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U292


title: Patient urine 202

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U216


title: Patient urine 203

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U245


title: Patient urine 208

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U328


title: Patient urine 201

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U195


title: Patient urine 204

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U286


title: Patient urine 199

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U164


title: Patient urine 200

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U188


title: Patient urine 219

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U500


title: Patient urine 198

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U153


title: Patient urine 195

description:
2023_Match414_3biofluids_miRNA_counts.tsv
U29