title: 01_011_week52

description: Library name: Sample_26

tag: tissue

tag: cell type

tag: treatment arm

tag: date of_birth

value: Chronic glomerulonephritis

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening


title: 01_011_pre

status: Public on Dec 09 2025

type: SRA

city: Cambridge

first: Roy

last: Zhang

address: Cambridge Biomedical Campus, Francis Crick Ave

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Library name: Sample_24

library_source: transcriptomic

data_processing:
Libraries were sequenced on a NovaSeq sequencer (Ilumina) by Genewiz
Sequencing data was demultiplexed to give individual fastq files using Casava (Illumina)
FASTQC was used for quality control
Fastq files were aligned to the human genome (Hg38) using STAR
A table of gene counts was produced using the featureCounts function within Rsubread
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include unnormalised counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA extracted using a pure-link RNA mini kit (Ambion)
0.3 - 0.75µg of RNA was used to produce sequencing libraries using TruSeq Stranded total RNA library prep kit (Illumina) with 14 PCR amplification cycles

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: individual

value: Placebo

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

value: Deceased

tag: donor age

tag: hla-a mismatch

value: Tac, MMF, Pred

tag: study centre

value: Vienna

tag: sample timepoint

value: pre

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: Sex

value: female

tag: batch


title: LG253-NY-152

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

country: USA

institute: Weill Cornell Medicine

description:
Library name: Sample14
mRNA expression in mouse hippocampus

library_source: transcriptomic single cell

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)
RNA-seq

tag: tissue

value: hippocampus

value: Female

tag: age

tag: genotype


title: aortic dissection-6

city: Tianjin

first: chao

last: chang

address: South Taierzhuang Road

country: China

institute: Tianjin University,Tianjin Chest Hospital

data_processing:
Sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2
The read length was 1×50 bp. Clean reads were aligned to the Human genome hg38 using STAR.StringTie
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Assembly: Human genome hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Aortic wall tissue

extract_protocol:
Total RNA was isolated from each sample using the RNAmini kit ( Qiagen, Germany).
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

value: Aortic wall tissue


title: 01_010_week52

description: Library name: Sample_23

tag: cell type

tag: individual

tag: treatment arm

value: Clazakizumab

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

value: Unknown cause

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: CyA, EC-MPS, Pred

value: male


title: 01_011_week12

description: Library name: Sample_25

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)


title: 01_010_week12

description: Library name: Sample_22

tag: tissue

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: igg (%_of_baseline)

tag: Sex

tag: batch


title: aortic dissection-5


title: 01_010_pre

description: Library name: Sample_21

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening


title: aortic dissection-4


title: 01_009_week12

description: Library name: Sample_19

value: FSGN

tag: donor age

tag: hla-a mismatch

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)


title: LG253-NY-72

description:
Library name: Sample11
mRNA expression in mouse hippocampus

tag: tissue

tag: Sex

tag: age

tag: genotype


title: LG253-NY-74

description:
Library name: Sample12
mRNA expression in mouse hippocampus


title: 01_009_week52

description: Library name: Sample_20

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: igg (%_of_baseline)

tag: batch


title: 01_013_pre

description: Library name: Sample_30

tag: donor age

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff


title: 01_009_pre

description: Library name: Sample_18

tag: tissue

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex


title: 01_008_week52

description: Library name: Sample_17

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

value: CyA, EC-MPS

tag: igg (%_of_baseline)

tag: batch


title: LG253-NY-95

description:
Library name: Sample10
mRNA expression in mouse hippocampus

tag: age

tag: genotype


title: aortic dissection-2

tag: tissue


title: 01_005_week52

description: Library name: Sample_14

value: Peripheral blood

tag: cell type

tag: individual

value: Goodpasture syndrome

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Everolimus, EC-MPS, Pred

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff


title: control-6


title: 01_008_pre

description: Library name: Sample_15

value: Peripheral blood mononuclear cells

tag: treatment arm

value: Placebo

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

value: Deceased

tag: donor age

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex


title: aortic dissection-1

tag: tissue


title: LG253-NY-113

description:
Library name: Sample13
mRNA expression in mouse hippocampus

tag: age

tag: genotype


title: LG253-NY-225

description:
Library name: Sample8
mRNA expression in mouse hippocampus


title: 01_004_week52

description: Library name: Sample_11

tag: cell type

tag: individual

value: Pyelonehritis, nephrectomy of left kidney

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: Vienna

tag: igg (%_of_baseline)

tag: batch


title: control-4


title: 01_005_week12

description: Library name: Sample_13

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

value: female


title: LG253-NY-120

description:
Library name: Sample9
mRNA expression in mouse hippocampus

tag: tissue

value: hippocampus

tag: Sex

value: Female

tag: age

tag: genotype


title: aortic dissection-3

value: Aortic wall tissue


title: 01_004_week12

description: Library name: Sample_10

tag: cell type

tag: individual

value: Clazakizumab

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: egfr

tag: dsa (%_of_baseline)


title: APOL3 KO cells + LLOME rep

city: New York

first: Ryan

last: Gaudet

institute: Columbia Unversity

description:
Library name: Sample 8
Column name in gene_counts.txt: APOL3_KO_LLOME_2

data_processing:
Raw paired-end RNA-seq reads were assessed for quality using FastQC.
Reads were aligned to the Homo sapiens GRCh38 primary assembly using STAR (version 2.7.11b) with a two-pass mapping strategy.
Paired-end reads were processed directly from compressed FASTQ files, and alignments were output as BAM files sorted by genomic coordinates.
Gene-level counts were obtained using featureCounts with the same GTF annotation.
Assembly: Homo sapiens GRCh38 primary assembly.
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: HeLa

growth_protocol: HeLa NTC and APOL3-/- cells were cultured in DMEM supplemented with 10% FBS at 37 °C with 5% CO₂ until ~70% confluency.

extract_protocol:
Total RNA was extracted using the Quick-RNA MiniPrep Plus kit (Enzo) according to the manufacturer’s instructions.
Poly(A)-selected mRNA libraries were prepared and sequenced by Genewiz (Azenta Life Sciences) using standard Illumina protocols.

treatment_protocol: Cells were primed or not with IFN-γ (500 U/ml, 18 h), washed, and incubated in fresh DMEM (10% FBS). Selected wells were treated with LLOME (600 μM, 2 h) or DMSO, rinsed, and incubated in recovery media for 8 h.

tag: cell line

value: HeLa

tag: treatment

value: LLOME


title: 01_004_pre

description: Library name: Sample_9

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

value: CyA, EC-MPS, Pred

tag: sample timepoint

value: pre

tag: abmr mmdx

tag: abmr banff

tag: igg (%_of_baseline)

tag: batch


title: LG253-NY-187

description:
Library name: Sample6
mRNA expression in mouse hippocampus

tag: tissue

tag: Sex

tag: age

tag: genotype


title: LG253-NY-218

description:
Library name: Sample7
mRNA expression in mouse hippocampus


title: control-5


title: APOL3 KO cells + LLOME rep 1

description:
Library name: Sample 7
Column name in gene_counts.txt: APOL3_KO_LLOME_1

tag: cell line

tag: treatment


title: LG253-NY-73

description:
Library name: Sample5
mRNA expression in mouse hippocampus


title: control-2


title: 01_003_week52

description: Library name: Sample_8

value: Peripheral blood

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

value: Unknown cause

value: Living

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, EC-MPS, Pred

tag: study centre

tag: egfr

tag: dsa (%_of_baseline)


title: APOL3 KO cells untreated rep 2

description:
Library name: Sample 6
Column name in gene_counts.txt: APOL3_KO_unt_2

value: Untreated


title: LG253-NY-81

description:
Library name: Sample4
mRNA expression in mouse hippocampus

tag: tissue

tag: Sex


title: 01_008_week12

description: Library name: Sample_16

value: Peripheral blood mononuclear cells

value: Placebo

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

value: Deceased

tag: donor age

value: CyA, EC-MPS

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: igg (%_of_baseline)

tag: batch


title: 01_003_week12

description: Library name: Sample_7

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

value: Vienna

value: female


title: control-1

tag: tissue

value: Aortic wall tissue


title: 01_005_pre

description: Library name: Sample_12

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: Goodpasture syndrome

tag: immunosuppression at_screening

value: Everolimus, EC-MPS, Pred

tag: study centre

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex


title: APOL3 KO cells untreated rep 1

description:
Library name: Sample 5
Column name in gene_counts.txt: APOL3_KO_unt_1

tag: cell line

value: HeLa

tag: genotype

tag: treatment


title: 01_003_pre

description: Library name: Sample_6

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: donor type

tag: donor age

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: igg (%_of_baseline)

tag: batch


title: LG253-NY-69

description:
Library name: Sample3
mRNA expression in mouse hippocampus

tag: tissue

value: hippocampus

value: Female

tag: age


title: GFPneg_RNAseq_Rep2

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
RNA-seq data analysis - Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 transcriptome assembly (parameters -l A ‐‐allowDovetail ‐‐validateMappings). All downstream analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using the DESeq2 library (Love et al. 2014).
Riboseq Data analysis - Read 2, the reverse complement read, was used to analyze the RPF data. First, the 12-nt UMI was extracted from the 3' end using umi_tools (Smith et al. 2017). 3’ and 5’ reverse complement adapters (ATTGATGGTGCCTACAGTT and GATCGTCGGACTGTAGAACTCTGAAC) were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt were removed. The reverse complement of each read was obtained using fastx-toolkit (FASTX-Toolkit) and rRNA reads were removed using bowtie (Langmead and Salzberg 2012). The bam file was deduplicated using umi-tools and transcript expression was quantified using Salmon (Smith et al. 2017; Patro et al. 2017) as described above. All further analysis was performed in R. Salmon files were imported using the tximport library (Soneson et al. 2015). Quality control metrics such as periodicity and read size were analyzed using the ribosomeProfilingQC package (Ou and Hoye 2023).
Assembly: GRCh38
Supplementary files format and content: Summary table with raw counts for genes from salmon quantification after applying tx2gene from tximport. Columns indicate samples. Format: comma separated tabular file (.csv)

source_name: undifferentiated hES

growth_protocol: Undifferentiated human embryonic stem (hES) MEL1 INSGFP/W reporter cells (Micallef et al , 2012) were maintained on hES qualified Matrigel in mTeSR+ media. Differentiation to stem cell derived beta like cells (sBCs) was carried out in suspension‐based, bioreactor magnetic stirring system as done previously.

extract_protocol:
RNA-seq: Total RNA was extracted from GFP+ and GFP- sorted samples in trizol using the DirectZol RNA Microprep kit (Zymo Research) following the manufacturer’s instructions with on-column DNaseI treatment.    Ribo-seq: Ribosome footprinting was performed as described previously (Ingolia et al. 2012) with a few modifications. The GFP+ sorted cell pellets were lysed in buffer without cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. The remaining lysate was used as input into the footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN then flash frozen in liquid nitrogen. The lysate was then used as input into immunoprecipitation with RNA immunoprecipitation protocol adapted from (Wessels et al. 2016) using prepared Anti-FLAG M2 Magnetic beads (Sigma). The IP was incubated for two hours at room temperature tumbling end-over-end, followed by post-IP washes with NT2 buffer. The immunoprecipitated RNA was released from the bead complex using TRIzol LS reagent (Invitrogen) and further isolated using chloroform and isopropanol precipitation.
RNA-seq: rRNA was depleted from each total RNA sample following our previously published RNaseH-based method (Baldwin et al. 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche). Libraries were prepared according to the manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for 2x 150bp paired end sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library (University of Colorado Anschutz Genomics and Microarray Core Facility).        Ribo-seq: The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling following the kit instructions. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments 28-29nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit following the manufacturer’s instructions with provided single index adapters. The resulting libraries were pooled and submitted for 2x 150bp paired end sequencing on the Illumina NovaSeq6000 platform to a depth of 60 million paired end reads (Supplemental Table 6) per library (University of Colorado Anschutz Genomics and Microarray Core Facility).

value: undifferentiated hES

value: differentiated beta cells

value: GFP-

tag: library type

value: RNAseq

tag: antibody used


title: 01_002_week52

description: Library name: Sample_5

value: Peripheral blood

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: Postrenal cause, aplasia of right kidney

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, EC-MPS, Pred

tag: study centre

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex

value: male


title: LG253-NY-93

description:
Library name: Sample2
mRNA expression in mouse hippocampus

tag: genotype


title: control-3

tag: tissue


title: 01_002_week12

description: Library name: Sample_4

tag: cell type

value: Peripheral blood mononuclear cells

tag: individual

tag: treatment arm

value: Placebo

tag: date of_birth

tag: donor type

value: Deceased

tag: donor age

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: igg (%_of_baseline)

tag: batch


title: GFPneg_RNAseq_Rep1

tag: cell line

tag: library type

tag: antibody used


title: NTC cells (wildtype) + LLOME rep 1

description:
Library name: Sample 3
Column name in gene_counts.txt: NTC_wt_LLOME_1

value: WT (NTC)

tag: treatment

value: LLOME


title: 01_002_pre

description: Library name: Sample_3

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: Vienna

value: pre

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex


title: NTC cells (wildtype) untreated rep 2

description:
Library name: Sample 2
Column name in gene_counts.txt: NTC_wt_unt_2

value: HeLa

tag: genotype

value: Untreated


title: NTC cells (wildtype) untreated rep 1

description:
Library name: Sample 1
Column name in gene_counts.txt: NTC_wt_unt_1

tag: cell line


title: GFPpos_RNAseq_Rep2

value: undifferentiated hES

tag: cell type

value: GFP+

tag: library type


title: LG253-NY-96

description:
Library name: Sample1
mRNA expression in mouse hippocampus

tag: tissue

value: hippocampus

value: Female

tag: age


title: pre-onset phase EAE2

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

description: Library name: pre-onset phase EAE2

data_processing:
*1. Raw FASTQ reads were quality-checked by FastQC and trimmed to remove adapters and low-quality bases. 2. Clean reads were aligned to the Mus musculus reference genome (GRCm38/NCBIM38) using HISAT2 v2.0.5. 3. Gene-level quantification was performed using HTSeq-count. 4. Expression normalization was performed using FPKM. 5. Differential expression analysis was conducted using DESeq2 with thresholds
Assembly: Mus musculus GRCm38 (NCBIM38), GENCODE vM29 annotation.
Supplementary files format and content: Processed data include gene-level count matrices in tab-delimited text format with rows representing genes and columns representing samples, and normalized expression values (FPKM). Metadata files include sample group (EAE/control), time point (5 dpi / 15 dpi), and sequencing platform (NovaSeq / DNBSEQ-T7).

source_name: Liver

growth_protocol: Female C57BL/6J mice (6–8 weeks old) were obtained from the Laboratory Animal Center of Fourth Military Medical University. Mice were maintained under SPF conditions with a 12 h light/dark cycle, 40–70% humidity, and 20–26 °C ambient temperature, with ad libitum access to food and water.

extract_protocol:
Liver tissue was perfused via the portal vein with cold PBS to remove blood, then dissected and snap-frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen) with on-column DNase I treatment, followed by quality control: A260/A280 1.8–2.1, A260/A230 ≥ 2.0, RIN ≥ 7.0.
Liver transcriptome profiling was conducted at two distinct timepoints during EAE progression. For the first analysis, total RNA was extracted from liver tissues collected at theEAE peak phase (approximately 15 days post-immunization, dpi) and compared with baseline controls (pre-immunization). Libraries were constructed using the Illumina NEBNext® Ultra™ RNA Library Prep Kit following the manufacturer’s protocol. Qualified libraries were pooled and subjected to 150-bp paired-end sequencing on an Illumina NovaSeq 6000 platform. The second transcriptomic study focused on the EAE pre-onset phase (approximately 5 dpi), again comparing livers with baseline controls. RNA extraction was followed by library preparation using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina. Library quality was assessed using an Agilent 2200 system, and sequencing was performed on a DNBSEQ-T7 platform with a 150-bp paired-end configuration.

treatment_protocol: Experimental autoimmune encephalomyelitis (EAE) was induced by immunizing mice with 200 μg MOG35–55 peptide emulsified in CFA containing 500 μg M. tuberculosis, followed by intraperitoneal injection of 200 ng pertussis toxin on days 0 and 2. Neurological scores were assessed daily using a 0–5 scale. Samples were collected at two time points: pre-onset phase (5 days post-immunization) and peak phase (15 days post-immunization). For each time point, both EAE-induced and non-immunized control groups were included, resulting in four experimental groups in total.

value: Liver

value: wild type

tag: treatment

value: MOG35-55 peptide-induced EAE


title: pre-onset phase EAE3

description: Library name: pre-onset phase EAE3


title: 01_001_week12

description: Library name: Sample_2

value: Peripheral blood

tag: individual

tag: treatment arm

value: Clazakizumab

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: IgA nephropathy

tag: donor type

value: Living

tag: donor age

value: CyA, MMF, Pred

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: igg (%_of_baseline)

value: male

tag: batch


title: GFPpos_RNAseq_Rep1

tag: cell line

tag: cell type

value: differentiated beta cells

tag: genotype

tag: library type

value: RNAseq

tag: antibody used


title: RiboSeq_rep2

data_processing:
RNA-seq data analysis - Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 transcriptome assembly (parameters -l A ‐‐allowDovetail ‐‐validateMappings). All downstream analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using the DESeq2 library (Love et al. 2014).
Riboseq Data analysis - Read 2, the reverse complement read, was used to analyze the RPF data. First, the 12-nt UMI was extracted from the 3' end using umi_tools (Smith et al. 2017). 3’ and 5’ reverse complement adapters (ATTGATGGTGCCTACAGTT and GATCGTCGGACTGTAGAACTCTGAAC) were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt were removed. The reverse complement of each read was obtained using fastx-toolkit (FASTX-Toolkit) and rRNA reads were removed using bowtie (Langmead and Salzberg 2012). The bam file was deduplicated using umi-tools and transcript expression was quantified using Salmon (Smith et al. 2017; Patro et al. 2017) as described above. All further analysis was performed in R. Salmon files were imported using the tximport library (Soneson et al. 2015). Quality control metrics such as periodicity and read size were analyzed using the ribosomeProfilingQC package (Ou and Hoye 2023).
Assembly: GRCh38
Supplementary files format and content: Summary table with raw counts for genes from salmon quantification after applying tx2gene from tximport. Columns indicate samples. Format: comma separated tabular file (.csv)
Library strategy: Ribo-seq

value: GFP+, RPL22-FLAG Lentivirus

value: IP-RiboSeq

value: FLAG


title: NCD3

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

institute: Chengdu University of TCM

description:
Library name: sample6
Gene expression data from MDA-MB-233 cells treated with NCD

data_processing:
The clean data obtained from bulk RNA-seq were aligned to the reference genome (GRCh38) using Hisat2, and reads corresponding to each gene were quantified using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium (Gibco, C11875500BT, USA). All mediums were supplemented with 10% fetal calf serum (ExCell, FSP500, China) and 100 units/ml streptomycin and penicillin. All cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA extraction was carried out using the RNA isolator Total RNA Extraction Reagent (Vazyme, R401-01, China) in accordance with the manufacturer's instructions.
Sequencing libraries were prepared using Illumina NovaSeq Reagent Kit

treatment_protocol: MDA-MB-231 cells were treated with 0.1% DMSO or 5 μM NCD for 24 hours.

tag: tissue

value: cell line

value: tumor cells

value: WT

tag: treatment

value: NCD


title: RiboSeq_rep1

value: undifferentiated hES


title: pre-onset phase NC3

description: Library name: pre-onset phase NC3

value: Liver

value: wild type


title: NCD2

description:
Library name: sample5
Gene expression data from MDA-MB-232 cells treated with NCD


title: 01_001_pre

description: Library name: Sample_1

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: individual

tag: treatment arm

value: Clazakizumab

tag: date of_birth

tag: date of_transplant

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: Vienna

value: pre

tag: egfr

tag: dsa (%_of_baseline)

tag: Sex


title: THP-1, 20h, 10 µg/ml RTD-1 LPS exp3

city: Los Angeles

first: Prasad

last: Tongaonkar

state: CA

address: 7504 NRT, 1450 Biggy St

department: Pathology and Laboratory Medicine

institute: USC

data_processing:
Partek Flow 10.0.21.0602
Quality trimming of bases from 3'end, minimum read length of 25 using Partek Flow
Partek Flow was used for mapping Trimmed sequences to hg38-GENCODE GENES release 40 using STAR-2.7.8a
Partek Flow Quantify to Annotation model (Partek E/M) was used to calculate gene counts
Partek Flow was used for normalization using TMM and Add 0.0001
Assembly: hg38
Supplementary files format and content: tab delimited text fie contains gene counts for each sample
Supplementary files format and content: tab delimited text fie contains Normalized values for each sample

growth_protocol: THP-1 cells (ATCC, Manassas, VA) were grown in RPMI + 10% FBS + 1% P/S medium at 37 C and 5% CO2.

extract_protocol:
RNA was extracted using Quick RNA Miniprep kit (Zymo Research)
Libraries were prepared from polyA mRNA selected using oligo dT beads.

treatment_protocol: Cells were resuspended at 3.3 x 105 cells/ml in RPMI + 1% FBS and 1% P/S for 4 h at 37 oC in 5% CO2 and then treated with 1, 3, or 10 μg/ml RTD-1 or 0.01% HOAc (vehicle) control with or without Salmonella enterica LPS and vehicle (PBS) for 20 h.

tag: cell line

tag: cell type

value: monocytic

tag: genotype

value: wildtype

value: 10 µg/ml RTD-1+LPS


title: pre-onset phase NC2

description: Library name: pre-onset phase NC2

tag: tissue

tag: treatment


title: NTC cells (wildtype) + LLOME rep 2

description:
Library name: Sample 4
Column name in gene_counts.txt: NTC_wt_LLOME_2

value: HeLa

value: WT (NTC)

value: LLOME


title: NCD1

description:
Library name: sample4
Gene expression data from MDA-MB-231 cells treated with NCD

value: cell line

value: tumor cells


title: THP-1, 20h, 10 µg/ml RTD-1 LPS exp2


title: RKO, HADH-S_OE

city: hangzhou

first: Yunyi

last: Gao

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: Zhejiang university

data_processing:
Illumina sequencing reads were initially processed using fastp (version 0.23.2) for adaptor removal and quality trimming
The processed reads were aligned to the human reference genome (gencode.v41) using Bwa-mem2 (version 2.2.1) with default parameters.
SAMtools (version 1.9) was applied to eliminate PCR duplications
Peak calling and annotation were performed utilizing MACS2 (version 1.4.2) along with the ChIPseeker package
Assembly: GRCh38
Supplementary files format and content: bw
Supplementary files format and content: tab-delimited text files include RPKM values for each RNA-Seq Sample

source_name: Colon

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated.  Total RNA was isolated from cell lines by Trizol.
ChIP was performed using the EZ-ChIP kit (Merck). Library construction was performed using Universal DNAseq Library Prep Kit (KAITAI-BIO, AT4106). RNA samples were submitted to mRNA library construction.

value: Colon

value: RKO

value: HADH-S overexpression


title: RKO, CTL

value: WT


title: DMSO3

description:
Library name: sample3
Gene expression data from MDA-MB-231 cells treated with DMSO

value: DMSO


title: THP-1, 20h, 10 µg/ml RTD-1 LPS exp1


title: pre-onset phase NC1

description: Library name: pre-onset phase NC1

value: Liver

value: wild type


title: RKO, Input

library_source: genomic

molecule: genomic DNA


title: THP-1, 20h, 3 µg/ml RTD-1 LPS exp3

value: 3 µg/ml RTD-1+LPS


title: 14DPD-3

city: Xi'an

first: Qi

last: Liu

address: No.127, Changle West Road

institute: Air Force Medical University

description: Library name: DPD14-3

data_processing:
RNA-seq
Assembly: Ensembl_release112
Supplementary files format and content: Processed data files.CSV

source_name: gastrocnemius

extract_protocol:
Total RNA was extracted from primary dorsal root ganglion (DRG) neurons using TRIzol® Reagent according to the manufacturer’s instructions with minor modifications.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: gastrocnemius


title: 14DPD-4

description: Library name: DPD14-4


title: DMSO2

description:
Library name: sample2
Gene expression data from MDA-MB-231 cells treated with DMSO


title: RKO, HADH-S, ChIP


title: PCSC+ miR-24-3p

city: Gustavo A. Madero

first: ROSAURA

middle: HERNANDEZ

last: RIVAS

state: Ciudad de México

address: Av. Instituto Politécnico Nacional 2508

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

description:
Library name: Sample 3
PCSC+ transfected with miR-24-3p mimics.

data_processing:
RNA-seq analysis was conducted using the Galaxy platform (Version 24.1.2).
The quality of raw data files was assessed with the FastQC package (Galaxy Version 0.74+galaxy1).
Reads were aligned to the human reference genome (Homo sapiens hg19) using the HISAT2 program (Galaxy Version 2.2.1+galaxy1) with default parameters.
The mapped reads were assembled into transcripts and quantified with the FeatureCounts program (Galaxy Version 2.0.3+galaxy2) using the NCBI RefSeq gene annotation in GTF format.
Differentially Eexpressed Genes (DEGs) were identified using DESeq2 software (Galaxy Version 2.11.40.8+galaxy0).
Assembly: GRCh39
Supplementary files format and content: Tab-delimited text file that include raw counts of each samples.
Supplementary files format and content: Tab-delimited text file that include and r-log normalized counts  of each samples.

growth_protocol: PANC-1 cell line was grown in DMEM high glucose medium (Sigma D-5030), supplemented with Fetal Bovine Serum (FBS, Gibco 10437028) at a final concentration of 10% and in presence of 1X Penicillin/Streptomycin (100x) (Gibco, 10378016) at 37°C under a humidified 5% CO2 atmosphere. Then, PDAC-1 cells (5000/well) were seed in Ultra-low attachment surface 96-well plates (Sigma CLS3474) in serum-free media supplemented with FGF-2 (10 ng/mL) and EGF (20 ng/mL). The spheres were collected after seven days for FACS assays.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) and treated with DNase I from the RNase-Free DNase Set (QIAGEN).
Library preparation and sequencing were performed by Novogene (Hong Kong) using the NovaSeq X Plus Series (PE150), generating 12 G of raw data per sample (Illumina, Inc., San Diego, CA).

treatment_protocol: PCSC+ and PCSC- cells were selected using surface makers (CD24, CD44 and CD133) throught FACS assays.

value: Epithelial

value: Transfection of miR-24-3p mimic


title: pre-onset phase EAE1

description: Library name: pre-onset phase EAE1

value: MOG35-55 peptide-induced EAE


title: THP-1, 20h, 3 µg/ml RTD-1 LPS exp1

value: monocytic

value: wildtype


title: 14DPD-2

description: Library name: DPD14-2


title: PCSC+ Let-7b-5p

description:
Library name: Sample 2
PCSC+ transfected with Let-7b-5p mimics.

value: Transfection of Let-7b-5p mimic


title: 14DPD-1

description: Library name: DPD14-1


title: HD11 cells, chERVs knockdown, AZA 1

city: Yangzhou

first: Xuming

last: Hu

state: Jiangsu

address: No.48 East Wenhui Road

department: College of Animal Science and Technology

institute: Yangzhou University

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: The Excel file includes raw counts for each Sample
Supplementary files format and content: The Excel file includes FPKM values for each Sample

organism: Gallus gallus

growth_protocol: The chicken macrophage cell line HD11 were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) with 5% foetal bovine serum (FBS) at 41°C in 5% CO2 and 95% humidity.

extract_protocol:
Total RNA was extracted from chicken cells or tissues using RNA-easy™ Isolation Reagent (Vazyme, Nanjing, China) according to the ‘manufacturer’s recommendations
The mRNA Library for RNA-seq was preparated by BGI Genomics Co.,Ltd

value: macrophages

value: MARCO knockdown


title: THP-1, 20h, 1 µg/ml RTD-1 LPS exp2

value: 1 µg/ml RTD-1+LPS


title: PCSC+ Control

description:
Library name: Sample 1
PCSC+ Non transfected.

value: Non treated


title: HD11 cells, chERVs wild type, AZA 3

value: MARCO wild type


title: THP-1, 20h, 1 µg/ml RTD-1 LPS exp1


title: HT-1080 cells sgALKBH5

city: Shenzhen

first: YANXI

last: SUN

address: No.66,Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

description:
Library name: SAMPLE4
colname in genes.expression.xls.gz: sgALKBH5_tpm

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).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference_x0002_based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. The TPM formula is shown as follows:Given TPM(i) to be the expression of gene i, N to be reads count of gene i, L to be number of bases on gene i, and sum() to be total number of reads count of all genes after normalization. The TPM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples
Assembly: GRCh38.p14
Supplementary files format and content: xls file include TPM value for each samples

molecule: polyA RNA

growth_protocol: HT-1080 cell lines were cultured in DMEM supplemented with 10% (vol/vol) FBS (Gibco), 100units/mL penicillin, and 100μg/ml streptomycin (Gibco) in 5% CO2 at 37 °C.

extract_protocol:
Cells were collected and total RNA was purified using TRIzol reagent
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments.

value: Fibrosarcoma tumor cell


title: 7DPD-3

description: Library name: DPD7-3


title: HD11 cells, chERVs wild type, AZA 2


title: 7DPD-2

description: Library name: DPD7-2


title: THP-1, 20h, LPS exp3

value: LPS


title: DMSO1

description:
Library name: sample1
Gene expression data from MDA-MB-231 cells treated with DMSO

value: cell line

value: tumor cells

value: WT

value: DMSO


title: HD11 cells, chERVs knockdown, AZA 3


title: HD11 cells, chERVs wild type, AZA 1


title: 7DPD-1

description: Library name: DPD7-1

value: gastrocnemius


title: THP-1, 20h, LPS exp2


title: HT-1080 cells control1

description:
Library name: SAMPLE1
colname in genes.expression.xls.gz: CON1_tpm

value: sgNC


title: HD11 cells, chERVs knockdown, KD3


title: HT-1080 cells sgPKA

description:
Library name: SAMPLE2
colname in genes.expression.xls.gz: sgPKA_tpm

value: sgPKA


title: 5DPD-4

description: Library name: DPD5-4


title: HD11 cells, chERVs knockdown, AZA 2


title: HD11 cells, chERVs knockdown, KD2


title: 5DPD-3

description: Library name: DPD5-3


title: 7DPD-4

description: Library name: DPD7-4


title: THP-1, 20h, 3 µg/ml RTD-1 LPS exp2

value: monocytic

value: 3 µg/ml RTD-1+LPS


title: THP-1, 20h, 1 µg/ml RTD-1 LPS exp3

value: wildtype


title: HD11 cells, chERVs knockdown, KD1

value: macrophages


title: THP-1, 20h, 10 µg/ml RTD-1 exp3

value: 10 µg/ml RTD-1


title: VBT242_rat (10x)

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description:
Library name: VBT242_rat
scRNA-seq Cell lines single-cell RNA-seq

data_processing:
Illumina bcl2fastq 2.20.0.422 and cellranger 7.1.0 were used for demultiplexing
For SMART-Seq2: RNA-seq sequenced reads were mapped to hg19  using hisat2 (2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345  For 10x: cellranger counts v7.1.0 was used to generate all output files (matrix, features, and barcodes). A custom GRCh38 + tdTomato sequence reference was used, and for human + rat samples another custom reference was used with GRCh38 + mRatBN7-2 + tdTomato.
For SMART-Seq2: RNA-seq TPM and counts were calculated using RSEM (v1.3.1) with parameters --estimate-rspd --paired-end -sam
Assembly: hg19, GRCh38 and mRatBN7-1
Supplementary files format and content: Tab-separated values with counts matrix files, qc metrics, and 10x cellranger output filtered bc matrix.

organism:
Homo sapiens
Rattus norvegicus

source_name: Ependymoma Cell lines single-cell

growth_protocol: ZFTA-RELA patient derived xenografts. EP1NS, BT165 and VBT242 cells (500,000 cells in 3 μL PBS per mouse) were injected stereotactically into the cortex of 6-week-old female NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ, The Jackson Laboratory, RRID:IMSR_JAX:005557), which were treated with 0.05 mg/kg buprenorphine and anesthetized with 2% to 3% isoflurane. The skull of the mouse was exposed through a small skin incision, and a small burr hole was made using a 25-gauge needle at the selected stereotactic coordinates: 1.0 mm X, 1 mm Y and -1.5 mm Z. After injection, mice were checked daily for signs of distress, including seizures, weight loss, or tremors. Tumor size was monitored monthly by small animal MRI and BLI starting 4 weeks after injection. Mice were euthanized as they developed neurologic symptoms, including head tilt, seizures, sudden weight loss, loss of balance, and/ or ataxia. All animal studies were performed according to Dana- Farber Cancer Institute Institutional Animal Care and Use Committee (IACUC)–approved protocols (13-053).  ZFTA-RELA patient-derived cell lines. Cells were grown in “complete Neurobasal medium”, which consisted in Neurobasal™-A Medium (ThermoFisher Scientific, 10888022) supplemented with 1X of Antibiotic-Antimycotic 100X (ThermoFisher Scientific, 15240062), 1X GlutaMAXTM (ThermoFisher Scientific, 35050061), 1 mg/mL Heparin solution (StemCell Technologies, 7980), 1X B-27 (Thermo Fisher Scientific, 12587010), 20 ng/ml recombinant Human FGF-basic (Shenandoah Biotech, 100-146) and 20 ng/ml recombinant Human EGF (Shenandoah Biotech, 100-26). For further passaging, floating cells were centrifuged at 300g for 5 min, dissociated with Accutase (Innovative Cell Technologies, Inc., AT104-500) for 5 min at 37 °C, and washed with PBS (Gibco, 10010023).  In vitro co-culture. Primary cultures of rat cortical neurons and astrocytes were prepared from E19 embryos. They were plated at a density of 90.000 cells/cm2 on 12mm diameter coverslips on 24-well plates that were previously coated with poly-L-lysine. The cells were maintained in neurobasal medium supplemented with B27 supplement (50x, 2% v/v) and L-glutamine (0.5 mM). After 7 days, accutase dissociated, cells from patient-derived ZFTA-RELA cell lines were added and co-cultured (1000 cells/well). For timelapse live-cell imaging or immunohistochemistry, coverslips were used 4-14 days in vitro (DIV) after seeding ZFTA-RELA cells. As a control, in vitro monocultures of ZFTA-RELA cells were established from patient-derived ZFTA-RELA cell lines as follows. 12mm diameter coverslips on 24-well plates were coated using poly-L-lysine and maintained in neurobasal medium supplemented with B27 supplement (50x, 2% v/v) and L-glutamine (0.5 mM). After 7 days, accutase dissociated, ZFTA-RELA cells were added and cultured (1000-10000 cells/well). For timelapse live-cell imaging immunohistochemistry, coverslips were used 4-14 days in vitro (DIV) after seeding ZFTA-RELA cells.

extract_protocol:
Sorting of cells grown in cocultures. DIV 08 coverslips of mono- and co-culture were incubated with Trypsin for 5 minutes. Next, 10% FBS was added and cells were washed from coverslips. The samples were stained with a DAPI as a dead cell marker to identify the live cell population. The single cell suspension was sorted with a FACSAria Fusion 2 (BD Biosciences). Tumor cells were identified by their tdTomato expression.  Fresh tumor processing. Live cells were isolated from immediately processed fresh tumor tissue acquired at the time of surgery. Fresh tumor tissue was mechanically dissociated and enzymatically digested using the Brain Tumor Dissociation Kit (Miltenyi Biotec, 130-095-942) and gentleMACS dissociator (Miltenyi Biotec, 130-096-427) for 30 min at 37 °C. Single-cell suspensions were filtered through a 70 µm strainer (Fisher Scientific, 03-421-228), centrifuged at 500g for 5 minutes and resuspended in a solution of 1% bovine serum albumin (BSA) (Biolegend, 644710) in phosphate-buffered saline (PBS) for fluorescence activated cell sorting (FACS).  Frozen tumor processing. Nuclei for snRNA-seq were extracted from snap frozen as well as optimal cutting temperature (OCT)- embedded tumor tissues. Snap frozen tumor tissue was cut on ice while OCT-embedded tissue was cut on a cryostat at -20 °C and washed with PBS. Frozen tumor tissue was suspended in CST and dissociated with sterile surgical scissors for 5 minutes until homogenous. Dissociated tissue was filtered through a 70 µm strainer, 1XST was added to the nuclei solution and once more transferred through a 70 µm strainer. The nuclei solution was centrifuged at 500g for 5 min. Single-nuclei suspensions were re-suspended in PBS supplemented with 1% BSA (Smart-seq2), or 0.05% BSA (10X Genomics). All steps were performed at 4 °C.  Live cell sorting. A single cell suspension of 100 uL (kept in a FACS-tube in PBS/BSA at 4°C) was used for all sorting procedures as unstained control. For stained controls 0,75μL Calcein AM (Life technologies, C34851) and 0.5μL TO-PRO3 Iodide (Life technologies, T3605) were added to resuspended cells in 100μL PBS/1%BSA for 10 min at room temperature (RT). Single-cell sorting was performed on a SH700 sorter (Sony). Single viable tumor cells were selected by positive staining for calcein AM as well as negative staining for TO-PRO3 and sorted into pre chilled (4 °C) 96 well plates containing TCL buffer (Qiagen, 1031576) + 1% β-mercaptoethanol (Thermo Fisher. 21985023).  Sorted plates were centrifuged at 1000 x g for 1 minute at 4 °C and frozen on dry ice followed by transfer to a -80°C freezer for long term storage before whole transcriptome amplification, library preparation and sequencing.  Nuclei sorting. Dissociated frozen tumor tissue derived single-nuclei suspensions were resuspended in PBS + 1% BSA and stained with 2.5mM Vybrant DyeCycle Ruby Stain (Life Technology, V10309). Nuclei sorting was performed on a SH700 SONY sorter. Intact nuclei were sorted into pre chilled (4 °C) 96-well plates containing TCL buffer + 1% β-mercaptoethanol. Sorted plates were centrifuged at 1000 x g for 1 minute at 4 °C and frozen on dry ice followed by transfer to a -80°C freezer for long term storage before whole transcriptome amplification, library preparation and sequencing.
Smart-seq2 whole transcriptome amplification, library preparation and sequencing of single cells/nuclei were performed following a modified Smart-seq2 protocol. RNA was purified with RNAClean XP beads (Beckman Coulter, A66514). Next Oligo-dT primed reverse transcription (RT) was performed using Maxima H Minus reverse transcriptase (Life Technologies, EP0753) and a template-switching oligonucleotide (TSO; Qiagen) followed by PCR amplification (20 cycles for scRNA-seq and 22 cycles for snRNA-seq) using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, 07958935001), and by AMPure XP bead (Beckman Coulter, A63882) purification. Libraries were generated using the Nextera XT Library Prep kit (Illumina, FC-131-1096). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906) on a NextSeq 500 sequencer (Illumina).

value: Ependymoma Cell lines single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: 5DPD-2

description: Library name: DPD5-2


title: HD11 cells, chERVs wild type, C3

value: MARCO wild type


title: THP-1, 20h, 10 µg/ml RTD-1 exp2


title: EP1NS_rat (10x)

description:
Library name: EP1NS_rat
scRNA-seq Cell lines single-cell RNA-seq


title: 5DPD-1

description: Library name: DPD5-1


title: HT-1080 cells control2

description:
Library name: SAMPLE3
colname in genes.expression.xls.gz: CON2_tpm

value: Fibrosarcoma tumor cell


title: cac1Δ::CAC1ACCΔ, glucose depletion, biol rep 3

city: Seoul

first: Yong-Sun

last: Bahn

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

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

description: Library name: CAC1a_m_3

data_processing:
Raw sequencing reads were subjected to quality control and adapter trimming using Cutadapt v2.4 in Python 3.7.4, employing the specified adapter sequence. Subsequent read processing followed previously established protocols
Cleaned reads were aligned to the Cryptococcus neoformans H99 reference genome using Hisat2 v2.2.1, which utilizes the Hisat and Bowtie2 algorithms. Genome annotation files were retrieved from the NCBI FTP repository. Hisat2 was executed with the parameters “-p 30” and “--dta -1,” along with default settings. The resulting alignment files were converted and sorted using Samtools v0.1.19, applying “-Sb -@ 8” for file conversion and “-@ 20” for sorting operations
Gene-level expression matrices were generated and further analyzed using the R package IsoformSwitchAnalyzeR. Data quality was evaluated with DEBrowser, and DEGs were identified using DESeq2 v1.24. DEGs were defined based on a threshold of a >2-fold change and a P-value <0.05, and visualized using the EnhancedVolcano package in R v4.1.0
Assembly: GCA_000149245.3 CNA3
Supplementary files format and content: genecountmatrix.csv: CSV file, comma delimited files.

organism: Cryptococcus neoformans

source_name: yeast cells

growth_protocol: The strains of interest ((wild-type H99, cac1Δ, cac1Δ::CAC1, cac1Δ::CAC1PP2CΔ, cac1Δ::CAC1ACCΔ) were grown in 50 ml liquid YPD for 20 hours at 30°C in triplicates. Following the OD600 measurement, 50 OD equivalent cells for each sample were harvested and washed twice with sterilized purified water. During the second wash, the cell suspension was split into two halves with 25 OD equivalent each into fresh 50 ml conical tubes and pelleted

extract_protocol:
Briefly, 10 ml cultures for five strains (wild-type H99, cac1Δ, cac1Δ::CAC1, cac1Δ::CAC1PP2CΔ, cac1Δ::CAC1ACCΔ) were grown in triplicates in two media conditions, YNB and YNB + 2% glucose. Cells were harvested, snap-frozen, and then lyophilized. The dry cell biomass was weighed and 0.05 g equivalent cells for each sample were used for RNA extraction using the mirVana™ miRNA Isolation Kit (Life Technologies).
The RNA samples were quantified using Qubit and submitted to the Duke Sequencing and Genomic Technologies core facility. The library preparation was performed to select and sequence the PolyA mRNA pool (mRNA-seq). The libraries were then sequenced on Illumina Novaseq X Plus to obtain 150-bp paired-end reads.

treatment_protocol: One set was resuspended in 20 ml of YNB media (minimal media), and the other set was resuspended in 20 ml of YNB media containing 2% glucose. Cells were grown for 4 more hours at 30°C with vigorous shaking. Cells were harvested by centrifugation at 4°C at 3200 rpm for 10 mins and immediately frozen at -80°C

value: yeast cells

value: CAC1 ACC domain knockout

value: minimal media


title: 3DPD-4

description: Library name: DPD3-4

value: gastrocnemius


title: THP-1, 20h, 10 µg/ml RTD-1 exp1


title: THP-1, 20h, 3 µg/ml RTD-1 exp3

value: 3 µg/ml RTD-1


title: HD11 cells, chERVs wild type, C1


title: cac1Δ::CAC1ACCΔ, glucose depletion, biol rep 2

description: Library name: CAC1a_m_2


title: THP-1, 20h, 3 µg/ml RTD-1 exp1

value: monocytic


title: cac1Δ::CAC1ACCΔ, glucose depletion, biol rep 1

description: Library name: CAC1a_m_1


title: 3DPD-2

description: Library name: DPD3-2


title: DNA methylation from IDH mutant medulloblastoma case 5

type: genomic

city: Hamburg

first: Alicia

last: Fürst

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: For subsequent bisulfite conversion, 100-500 ng of DNA were input to the EZ DNA Methylation Kit (Zymo Research). DNA samples were cleaned utilizing the DNA Clean & Concentrator-5 Kit (Zymo Research) and restored by the Infinium HD FFPE DNA Restore Kit (Illumina).

scan_protocol: The iScan system was used in combination with the Infinium HumanMethylation450 or MethylationEPIC BeadChip Kit (Illumina) to detect the methylation status of 450,000 or 850,000 genome-wide CpG sites, respectively.

data_processing: The package minfi v1.43.1 was used to preprocess and normalize Illumina methylation array data (preprocessIllumina function) and calculate β-values in R programming language. The intersection of detected CpGs across all arrays was used for further analyses. SNP-associated CpGs, cross-hybridising probes as well as CpGs located on sex-chromosomes were excluded from analysis.

label: Cy3 and Cy5

source_name: Frozen

label_protocol: Standard Illumina Protocol

extract_protocol: For the generation of DNA methylation array data, the Maxwell® FFPE DNA Kit (Promega) was used for the extraction of genomic DNA from FFPE tissues.

value: Frozen

tag: age at diagnosis [years]

tag: histology

value: desmoplastic MB

tag: idh mutation


title: DNA methylation from IDH mutant medulloblastoma case 6


title: THP-1, 20h, LPS exp1

value: wildtype

value: LPS


title: THP-1, 20h, 3 µg/ml RTD-1 exp2


title: 3DPD-1

description: Library name: DPD3-1


title: cac1Δ::CAC1ACCΔ, glucose repletion, biol rep 3

description: Library name: CAC1a_g_3

value: 2% glucose added minimal media


title: THP-1, 20h, 1 µg/ml RTD-1 exp3

value: 1 µg/ml RTD-1


title: DNA methylation from IDH mutant medulloblastoma case 4

description:
DNA methylation from IDH mutant medulloblastoma
Case4

value: classic MB


title: 1DPD-4

description: Library name: DPD1-4


title: THP-1, 20h, 1 µg/ml RTD-1 exp2


title: DNA methylation from IDH mutant medulloblastoma case 2

description:
DNA methylation from IDH mutant medulloblastoma
Case2

source_name: FFPE

value: FFPE


title: cac1Δ::CAC1ACCΔ, glucose repletion, biol rep 2

description: Library name: CAC1a_g_2


title: BT165_rat (10x)

description:
Library name: BT165_rat
scRNA-seq Cell lines single-cell RNA-seq

value: Ependymoma Cell lines single-cell

value: Primary

value: ZFTA-RELA

value: F

value: scRNA-seq


title: cac1Δ::CAC1ACCΔ, glucose repletion, biol rep 1

description: Library name: CAC1a_g_1

value: yeast cells

value: CAC1 ACC domain knockout


title: DNA methylation from IDH mutant medulloblastoma case 1

description:
DNA methylation from IDH mutant medulloblastoma
Case1


title: 1DPD-3

description: Library name: DPD1-3

value: gastrocnemius


title: cac1Δ::CAC1PP2CΔ, glucose depletion, biol rep 3

description: Library name: CAC1p_m_3

value: CAC1 PP2C domain knockout

value: minimal media


title: 1DPD-2

description: Library name: DPD1-2


title: THP-1, 20h, 1 µg/ml RTD-1 exp1

value: monocytic


title: THP-1, 20h, vehicle exp3

value: wildtype

value: vehicle


title: HD11 cells, chERVs wild type, C2

value: macrophages

value: MARCO wild type


title: cac1Δ::CAC1PP2CΔ, glucose depletion, biol rep 2

description: Library name: CAC1p_m_2


title: 1DPD-1

description: Library name: DPD1-1


title: 3DPD-3

description: Library name: DPD3-3


title: THP-1, 20h, vehicle exp2


title: THP-1, 20h, vehicle exp1


title: Hi-C sequencing Zymospetoria tritici IPO323 wild type replicate 2

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

description: Library name: IPO323_WT2

data_processing:
The sequencing was performed with Illumina NovaSeq X, paired-end 150bp reads. Sample preparation, Hi-C experiment, and sequencing were performed for two independent replicates.
Each Hi-C read-pairs was filtered and trimmed using Trimmomatic v0.3958 with the following settings ILLUMINACLIP:${adapters}:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:5:15 MINLEN:50. We used HiCUP-0.9.259 to evaluate the quality of each Hi-C dataset. Reads were mapped against the reference genome assembly of Z. tritici IPO32326 using bwa-mem260. The construction and analysis of Hi-C interaction matrices were performed using the HiCExplorer suite of tools61. Each replicate interaction matrix was created using hicBuildMatrix, by aligning the paired reads to the reference genome digested in silico with the four restriction enzymes DpnII (GATC), DdeI (CTNAG), HinfI (GANTC), and MseI (TTAA). Contact matrices were individually corrected using the iterative correction and eigenvector decomposition (ICE) method via the hicCorrectMatrix function. The corrected contact matrices from the two biological replicates were combined to generate Hi-C matrices at 1 kb, 3 kb, 10 kb, and 50 kb.
Assembly: IPO323
Supplementary files format and content: Hi-C contact 3kb bins matrix ICE normialized in ginteraction format. The tzo replicates are combined.

organism: Zymoseptoria tritici

source_name: spores

growth_protocol: The reference strain Z. tritici IPO32326 was preserved in 50% glycerol at -80°C. Pre-cultures were prepared with inoculations of ~100uL of glycerol stock spore suspension onto solid YMS medium (4 g/L yeast extract, 4 g/L malt extract, 4 g/L sucrose, and 12 g/L of agar) and grown for 4 days at 18°C. Spores were scraped from plates and re-suspended into PBS buffer (8g/L NaCl, 1.44g/L Na2HPO4, 0.2g/L KCl, 0.24g/L KH2PO4) for sample preparation for epigenomics sequencing as described in Möller et al. 2023

extract_protocol:
Spores were fixed with formaldehyde according to PhaseGenomics instructions (Seattle, Washington, USA). Hi-C experiments were performed with the Phase Genomics Proximo Hi-C Kit (Fungal), which combines four restriction enzymes to ensure homogeneous digestion at AT-rich genomic regions.
The Libraries were obtained from the Phase Genomics Proximo Hi-C Kit (Fungal). The resulting libraries were sequenced at Biomarker Technologies GmbH (BMKgene, Münster, Germany).

value: spores

value: YMA 3dpi


title: CON-4

description: Library name: CK4


title: cac1Δ::CAC1PP2CΔ, glucose depletion, biol rep 1

description: Library name: CAC1p_m_1


title: CON-3

description: Library name: CK3


title: cac1Δ::CAC1PP2CΔ, glucose repletion, biol rep 3

description: Library name: CAC1p_g_3

value: 2% glucose added minimal media


title: Hi-C sequencing Zymospetoria tritici IPO323 wild type replicate 1

description: Library name: IPO323_WT1


title: Olfactory epithelium of zebrafish in the group exposed to alarm substances

city: wuhan

first: Wenjun

last: Chen

address: No. 7 Donghu South Road, Wuchang, Wuhan

department: Chinese Academy of Sciences

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description:
Library name: CAS
10x Genomics

data_processing:
The sequencing data were analyzed using the 10X Cell Ranger pipeline, version 3.1.0. STAR (Spliced Transcripts Alignment to a Reference) was used to map cDNA to the zebrafish genome GRCz11.
Assembly: Grcz11
Supplementary files format and content: Tab-separed values files and matrix files

organism: Danio rerio

source_name: Olfactory epithelium

extract_protocol:
The OE pair from one individual each in the CTR and the CAS group was dissected. The OEs were placed in a Petri dish containing 200 μl of PBS solution, and any excess tissue was removed using tweezers and dissecting needles under a microscope. Next, the OE was transferred and dissociated in a new Petri dish containing 200 μL papain PBS solution with a concentration of 1 U/mL. The cells were then digested at 37 °C with gentle shaking at 80 rpm for 30 min, and purged using a 200 μL pipette every 5 min. After digestion, the cell mixture was filtered through a 40-μm mesh cell strainer (F8200-40um, Solarbio), followed by centrifugation at 700 rpm for 5 min. The resulting pellet was then resuspended in a 30 μL solution of 0.04% BSA/PBS. Cell concentration and viability were determined using a LUNA-FL Fluorescence Cell Counter (Logos Biosystems).
The library construction and sequencing were conducted using Anoroad (Beijing, China). The construction process of the cDNA library included the following steps: (1) gel beads and cells containing poly-T primer sequences connected with cell barcodes and unique molecular identifiers were wrapped in oil droplets to form gel beads in emulsion. (2) The cells were dissolved in this reaction system and reverse-transcribed to obtain a full-length cDNA sequence. (3) After crushing the oil droplets and purifying them, the cDNA library was amplified using polymerase chain reaction (PCR) connected to sequencing primers. (4) The barcode sequencing libraries were quantified using quantitative PCR. After library construction, sequencing libraries were loaded on an Illumina NextSeq 550AR with paired-end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.

value: Olfactory epithelium

value: WT (AB strain CAS)

value: male

value: alarm substance treated

value: CAS exposure


title: CON-2

description: Library name: CK2


title: cac1Δ::CAC1PP2CΔ, glucose repletion, biol rep 2

description: Library name: CAC1p_g_2

value: yeast cells


title: Olfactory epithelium of zebrafish in blank control group

description:
Library name: CTR
10x Genomics

value: WT (AB strain CTR)

value: Whitespace processing

value: blank control group


title: cac1Δ::CAC1PP2CΔ, glucose repletion, biol rep 1

description: Library name: CAC1p_g_1

value: CAC1 PP2C domain knockout


title: CON-1

description: Library name: CK1

value: gastrocnemius


title: Injured tendon, vehicle treated, day 7, biol rep 3

city: London

first: Chavaunne

last: Thorpe

address: Royal College Street

institute: Royal Veterinary College

description:
Library name: VEH9
Column name in miRNAsTable.txt: VEH9

data_processing:
Quality of next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 and multiQC v1.10. Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3, and filtered for a minimum length of 17 nucleotides (nt). Mapping steps were performed with bowtie v1.3.0 and miRDeep2 v2.0.1.2, whereas reads were mapped first against the genomic reference Rnor.6.0 provided by Ensembl allowing for two mismatches and subsequently miRBase v22.1, filtered for miRNAs of Rattus norvegicus only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral and then assigned to various RNA species of interest. Statistical analysis of pre-processed NGS data was done with R v4.0 and the packages pheatmap vNA, pcaMethods v1.82 and genefilter v1.72. Differential expression analysis with edgeR v3.32 used the quasi-likelihood negative binomial generalized log-linear model functions. The independent filtering method of DESeq2 was adapted for use with edgeR to remove low abundant miRNAs and thus optimize the false discovery rate correction.
Assembly: Rnor.6.0
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: tendon

extract_protocol:
EVs were isolated using the qEV single 70nm column (Izon Science, New Zealand) according to the manufacturer’s instructions. Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Germany). 5µL total RNA was used as an input for small RNA sequencing library preparation.
To each RNA sample 1µL of mind spike-in standards (TAmiRNA, Austria) were added prior to small RNA library preparation using the RealSeq Biofluids library preparation kit (RealSeq Biosciences, US). Adapter-ligated libraries are amplified using barcoded Illumina reverse primers in combination with the Illumina forward primer. Library quality control was performed using DNA1000 Chip (Agilent, United States). An equimolar pool consisting of all sequencing libraries was prepared and sequenced on an Illumina Novaseq with 100 bp single-end reads.

value: tendon

value: WT

value: Vehicle


title: cac1Δ::CAC1, glucose depletion, biol rep 3

description: Library name: CAC1c_m_3

value: CAC1 complemenation

value: minimal media


title: Mouse growth plate, rep2

city: Gothenburg

first: Andrei

middle: S

last: Chagin

state: Västra Götaland

address: Guldhedsgatan 10a

department: Institute of Medicine

country: Sweden

institute: University of Gothenburg

description: Library name: P27153_1002

data_processing:
Cellranger (v7.1.0 human and v7.0.1 mouse) was used for alignment
Assembly: GRCh38-2020-A / mm10-2020-A
Supplementary files format and content: Cell Ranger filtered feature matrix

source_name: growth plate

extract_protocol:
The obtained slices were dissected from bone under a stereo microscope, ground into small fragments, transferred to fresh, ice-cold HBSS, and thoroughly pipetted to remove residual blood. Then HBSS was replaced with a digestion solution comprising Collagenase P (3 U/mL, Roche) and TrypLE™ Select Enzyme (1X, Thermo Fisher Scientific, Catalog No: A1217701) in HBSS. The tubes were incubated for 30–40 minutes at 37°C with shaking at 120 rpm. During digestion, the tissue fragments were disrupted every 10 minutes using a 1-mL pipette. The digestion was terminated by the addition of 10 mL of 2% FBS in cold HBSS. The mixture was centrifuged at 300 rpm for 10 minutes at 4°C. The supernatant was carefully removed, and the pellet was resuspended in 100 µL of 2% FBS in 1X PBS. Ice-cold methanol (400 µL) was added dropwise to the suspension, and the sample was placed on ice for 10 minutes. The cells were stored at -80°C for a maximum of six months prior to library preparation.
10X protocol

treatment_protocol: To investigate the mechanisms underlying GH action, human growth plate slices were cultured for 24 hours with or without 40 ng/ml of GH (Norditropin, Novo Nordisk). Following the culture period, the slices were washed with ice-cold PBS, dissected from bone under a stereo microscope, and subjected to single-cell preparation. The explants were incubated at 37°C with 5% carbon dioxide in a culture medium consisting of DMEM/F12 (without phenol red), gentamycin (20 µg/ml), 0.2% bovine serum albumin (BSA), β-glycerophosphate (1 mM), ascorbic acid (5 µg/ml), and 2% fetal bovine serum (FBS)

value: growth plate

value: cartilage

value: primary tissue

tag: batch


title: siMTFP1_2

city: Hefei

first: TC

last: H

address: 130 Changjiang West Road

institute: AAU

description: Library name: Sample 5

data_processing:
The raw data obtained from sequencing were filtered using SOAPnuke (v1.5.6)
The reference genome was aligned using HISAT (v2.2.1)
Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3)
Gene expression quantification was performed using RSEM (v1.3.1)
DESeq2(v1.4.5) was employed for differential gene detection
Assembly: ARS-UCD1.2.v2201
Supplementary files format and content: tab-delimited text files inclued FPKM values for each Sample

organism: Bos taurus

source_name: oocyte

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: oocyte


title: siMTFP1_1

description: Library name: Sample 4


title: NC_3

description: Library name: Sample 3


title: siMTFP1_3

description: Library name: Sample 6


title: Injured tendon, vehicle treated, day 7, biol rep 2

description:
Library name: VEH8
Column name in miRNAsTable.txt: VEH8


title: Injured tendon, vehicle treated, day 7, biol rep 1

description:
Library name: VEH29
Column name in miRNAsTable.txt: VEH29


title: NC_2

description: Library name: Sample 2


title: Mouse growth plate, rep1

description: Library name: P27153_1001


title: cac1Δ::CAC1, glucose depletion, biol rep 2

description: Library name: CAC1c_m_2


title: NC_1

description: Library name: Sample 1


title: Injured tendon, vehicle treated, day 21, biol rep 3

description:
Library name: VEH28
Column name in miRNAsTable.txt: VEH28


title: cac1Δ::CAC1, glucose depletion, biol rep 1

description: Library name: CAC1c_m_1


title: cac1Δ::CAC1, glucose repletion, biol rep 3

description: Library name: CAC1c_g_3

value: 2% glucose added minimal media


title: Injured tendon, vehicle treated, day 21, biol rep 2

description:
Library name: VEH25
Column name in miRNAsTable.txt: VEH25


title: P172_143

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Library name: P172_143

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.39
Read alignment: STAR v2.7
Normalization and analysis: DESeq2
Assembly: GRCm39 (release 104)
Supplementary files format and content: Tab-delimited text files generated by STAR (ReadsPerGene.out.tab), containing raw and strand-specific read counts for each gene.

extract_protocol:
Primary mouse hepatocytes (1 × 106 cells) were plated in 6-well plate for RNA isolation. Medium was removed and cells were rinsed two times with cold PBS. While on ice, 1 mL of TRIzoL reagent was added to each well and plates were scraped. RNA was extracted using an additional 5:1 phenol:chloroform step (Sigma Aldrich, St. Louis, MO). RNA quantity and purity (260/280 ratio) was assessed with a NanoDrop 1000.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions.

treatment_protocol: Hepatocytes were seeded at a density of 1 × 10⁶ cells/well on type I collagen-coated 6-well plates and cultured in WME supplemented with 5% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1% Glutamax, 0.3 mM ascorbic acid, and 100 nM dexamethasone. After a 3-hour attachment period, non-adherent cells were removed and media was replaced with fresh WME containing 1% ITS Premix, antibiotics, Glutamax, ascorbic acid, and dexamethasone with DMSO vehicle or 10 nM TCDD and maintained at 37 °C in a 5% CO₂ incubator for 2, 4, 8, 12, 24, 48, 72, 96 and 120 hours.

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null


title: L3 rep1

city: Kraków

first: Dominika

last: Wloch-Salamon

state: Małopolskie

address: Gronostajowa 7,, 14

country: Poland

institute: Jagiellonian University

description:
Library name: Q_II_3_1
Q3II1

data_processing:
Library construction, sequencing, and the subsequent bioinformatic analysis were carried out by Novogene. Lists of differentially expressed genes (DEGs) were created using the DESeq2 R package
Assembly: Saccharomyces cerevisiae
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Saccharomyces cerevisiae S288C

source_name: population

growth_protocol: Clones were incubated shaking overnight in rich medium at 30°C. The following day, 20 μl of liquid culture (of each clone) was transferred to a 20 ml of YPD medium and incubated shaking at 30 °C for 7 days. Yeast cells were then separated into U and L fractions using Percoll centrifugation (as described previously by Allen at all.  2006) and only L fraction quiescent cells were used. Post-centrifugation, quiescent L cells were collected from the bottom of the tubes and subjected to two sequential washes 8 mL of Tris buffer. After each wash, the supernatant was carefully removed.

extract_protocol:
The optical density (OD) of each sample was measured to ensure an extraction efficiency yielding approximately ≥20 ng/µL, corresponding to ~3 × 10⁸ cells. Total RNA was extracted from the isolated Q cells using the Ribo-Pure™-Yeast Kit (Thermo Fisher Scientific), following the manufacturer's protocol. Each samples had two tech-nical repetition (1/2) that were then stored at –70°C.
Library construction, sequencing, and the subsequent bioinformatic analysis were carried out by Novogene.

tag: strain

tag: cell type

value: quiescent cells

tag: genotype

value: prototroph

tag: treatment

value: 13 days starvation, fractionation, lower fraction

tag: batch


title: L3 rep2

description:
Library name: Q_II_3_2
Q3II2

value: 14 days starvation, fractionation, lower fraction


title: P172_144

description: Library name: P172_144

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name


title: Injured tendon, vehicle treated, day 21, biol rep 1

description:
Library name: VEH15
Column name in miRNAsTable.txt: VEH15

tag: tissue

value: tendon

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: P172_142

description: Library name: P172_142

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

value: type I collagen

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: cac1Δ::CAC1, glucose repletion, biol rep 2

description: Library name: CAC1c_g_2

tag: cell type

value: yeast cells

tag: genotype

value: CAC1 complemenation

tag: treatment

value: 2% glucose added minimal media


title: P172_141

description: Library name: P172_141

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

value: Dimethyl sulfoxide

value: DRE-null


title: cac1Δ::CAC1, glucose repletion, biol rep 1

description: Library name: CAC1c_g_1

tag: cell type

tag: genotype

tag: treatment


title: L2 rep2

description:
Library name: Q_I_5_2
Q5I2

tag: strain

value: quiescent cells

value: prototroph

value: 12 days starvation, fractionation, lower fraction

tag: batch


title: Injured tendon, rapamycin treated, day 21, biol rep 3

description:
Library name: RAP5
Column name in miRNAsTable.txt: RAP5

tag: tissue

value: tendon

value: WT

value: Rapamycin


title: cac1Δ cells, glucose depletion, biol rep 3

description: Library name: CAC1_m_3

value: yeast cells

value: CAC1 whole knockout

value: minimal media


title: L1 rep2

description:
Library name: Q_I_2_2
Q2I2

value: 10 days starvation, fractionation, lower fraction


title: cac1Δ cells, glucose depletion, biol rep 1

description: Library name: CAC1_m_1


title: L1 rep1

description:
Library name: Q_I_2_1
Q2I1

value: 9 days starvation, fractionation, lower fraction


title: Injured tendon, rapamycin treated, day 7, biol rep 2

description:
Library name: RAP19
Column name in miRNAsTable.txt: RAP19


title: P172_140

description: Library name: P172_140

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: cac1Δ cells, glucose repletion, biol rep 3

description: Library name: CAC1_g_3

tag: cell type

value: yeast cells

tag: genotype

value: CAC1 whole knockout

tag: treatment

value: 2% glucose added minimal media


title: U5 ep2

description:
Library name: NQ_III_10_2
NQ10III2

tag: strain

value: quiescent cells

value: prototroph

value: 22 days starvation, fractionation, lower fraction

tag: batch


title: P172_138

description: Library name: P172_138

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

value: Dimethyl sulfoxide

value: DRE-null


title: P172_137

description: Library name: P172_137

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

value: square centimeter

value: type I collagen

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: U5 rep1

description:
Library name: NQ_III_10_1
NQ10III1

tag: strain

tag: cell type

value: quiescent cells

value: prototroph

value: 21 days starvation, fractionation, lower fraction

tag: batch


title: Injured tendon, rapamycin treated, day 21, biol rep 1

description:
Library name: RAP16
Column name in miRNAsTable.txt: RAP16

tag: tissue

value: tendon

value: WT

value: Rapamycin


title: Injured tendon, rapamycin treated, day 7, biol rep 1

description:
Library name: RAP11
Column name in miRNAsTable.txt: RAP11


title: P172_136

description: Library name: P172_136

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

value: hour

value: Dimethyl sulfoxide


title: cac1Δ cells, glucose repletion, biol rep 2

description: Library name: CAC1_g_2

tag: cell type

value: yeast cells

tag: genotype

value: CAC1 whole knockout

tag: treatment

value: 2% glucose added minimal media


title: P172_135

description: Library name: P172_135

tag: tissue

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

value: DRE-null


title: cac1Δ cells, glucose repletion, biol rep 1

description: Library name: CAC1_g_1

tag: cell type

tag: genotype

tag: treatment


title: ACHN Cells, niclosamide 1 µM + Sunitinib 2.5 µM replicate 2

first: Aeryang

last: Jung

address: 222, Banpo-Daero

department: Urology

institute: The Catholic University, Seoul

description:
Library name: Combination_2
SunitinbNiclo-2

data_processing:
Raw reads were quality-checked using FastQC. Adapters and low-quality bases were trimmed with Trimmomatic. Reads were aligned to the human reference genome using TopHat. Aligned reads were quantified using ExDEGA (E-Biogen Inc., Seoul, Republic of Korea). Differential expression and pathway enrichment analyses were performed using ExDEGA and DAVID bioinformatics resources.
Assembly: Human reference genome GRCh38 (hg38).
Supplementary files format and content: Processed data are provided as a CSV file (read_counts_matrix.csv) containing raw read counts per gene (rows = genes, columns = samples).

source_name: ACHN Cells

growth_protocol: ACHN renal cell carcinoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Thermo Fisher Scientific, USA). RNA integrity was confirmed by Bioanalyzer prior to library construction.
RNA libraries were prepared using the NEBNext Ultra Directional RNA-Seq Kit (New England BioLabs, Rowley, MA, USA) according to the manufacturer’s protocol. Libraries were sequenced on the Illumina HiSeq 2500 platform to generate paired-end 100 bp reads.

treatment_protocol: Cells were treated with vehicle control (DMSO), niclosamide (1 µM), sunitinib (2.5 µM), or the combination of niclosamide (1 µM) and sunitinib (2.5 µM) for the indicated durations prior to RNA extraction.

tag: cell line

value: ACHN Cells

value: wild type

value: niclosamide 1 µM + Sunitinib 2.5 µM

tag: batch

value: batch 1


title: ACHN Cells, niclosamide 1 µM + Sunitinib 2.5 µM replicate 1

description:
Library name: Combination_1
SunitinbNiclo-1


title: U4 rep1

description:
Library name: NQ_III_8_1
NQ8III1

tag: strain

value: quiescent cells

value: prototroph

value: 19 days starvation, fractionation, lower fraction


title: P172_134

description: Library name: P172_134

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

value: hour

value: Dimethyl sulfoxide


title: H99 cells, glucose depletion, biolo rep 3

description: Library name: WT_m_3

tag: cell type

value: yeast cells

tag: genotype

value: wild-type

tag: treatment

value: minimal media


title: U3 rep2

description:
Library name: NQ_III_4_2
NQ4III2

tag: strain

value: 18 days starvation, fractionation, lower fraction

tag: batch


title: H99 cells, glucose depletion, biolo rep 2

description: Library name: WT_m_2


title: L2 rep1

description:
Library name: Q_I_5_1
Q5I1

value: quiescent cells

value: 11 days starvation, fractionation, lower fraction


title: cac1Δ cells, glucose depletion, biol rep 2

description: Library name: CAC1_m_2

value: CAC1 whole knockout


title: P172_139

description: Library name: P172_139

tag: tissue

value: Liver

tag: cell type_ontology

tag: tissue ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

value: DRE-null


title: Injured tendon, rapamycin treated, day 7, biol rep 3

description:
Library name: RAP26
Column name in miRNAsTable.txt: RAP26

tag: tissue

value: tendon

tag: genotype

value: WT

tag: treatment

value: Rapamycin


title: ACHN Cells, Sunitinib 2.5 µM replicate 2

description:
Library name: Sunitinib_2
Sunitinb-3

tag: cell line

value: ACHN Cells

value: wild type

value: Sunitinib 2.5 µM

tag: batch

value: batch 1


title: Injured tendon, rapamycin treated, day 21, biol rep 2

description:
Library name: RAP24
Column name in miRNAsTable.txt: RAP24


title: H99 cells, glucose depletion, biolo rep 1

description: Library name: WT_m_1

tag: cell type

value: yeast cells

value: wild-type

value: minimal media


title: P172_133

description: Library name: P172_133

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

value: hour

value: Dimethyl sulfoxide


title: U3 rep1

description:
Library name: NQ_III_4_1
NQ4III1

tag: strain

tag: cell type

value: quiescent cells

tag: genotype

value: prototroph

tag: treatment

value: 17 days starvation, fractionation, lower fraction

tag: batch


title: P172_132

description: Library name: P172_132

tag: tissue

tag: cell type_ontology

tag: tissue ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

value: Williams E medium

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

value: DRE-null


title: ACHN Cells, Sunitinib 2.5 µM replicate 1

description:
Library name: Sunitinib_1
Sunitinb-2

tag: cell line

value: ACHN Cells

tag: genotype

value: wild type

tag: treatment

value: Sunitinib 2.5 µM

tag: batch

value: batch 1


title: U2 rep2

description:
Library name: NQ_III_3_2
NQ3III2

tag: strain

tag: cell type

value: 16 days starvation, fractionation, lower fraction


title: P172_131

description: Library name: P172_131

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration


title: ACHN Cells, niclosamide 1 µM replicate 2

description:
Library name: Niclosamide_2
Niclosamide-2

tag: cell line

tag: genotype

tag: treatment

value: niclosamide 1 µM

tag: batch


title: U4 rep2

description:
Library name: NQ_III_8_2
NQ8III2

tag: strain

tag: cell type

value: quiescent cells

value: prototroph

value: 20 days starvation, fractionation, lower fraction


title: H99 cells, glucose repletion, biol rep 3

description: Library name: WT_g_3

value: yeast cells

value: wild-type

value: 2% glucose added minimal media


title: H99 cells, glucose repletion, biol rep 2

description: Library name: WT_g_2


title: ACHN Cells, niclosamide 1 µM replicate 1

description:
Library name: Niclosamide_1
Niclosamide-1

value: ACHN Cells

value: wild type

value: batch 1


title: H99 cells, glucose repletion, biol rep 1

description: Library name: WT_g_1