title: ATAC-seq, Liver, Female, WT, Rep 1

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description: Library name: ATAC-seq_Midn-T_Female_Rep1

data_processing:
Raw sequencing reads were quality-checked and aligned to the Mus musculus reference genome (GRCm39/mm39) using STAR aligner (version 2.7 or later) with default parameters for stranded paired-end RNA-seq. Aligned reads were assigned to genes using HTSeq (reverse-stranded mode) based on Ensembl gene annotation (Mus_musculus.GRCm39.110.chr.gtf). Gene-level count matrices were generated for downstream analysis. Differential gene expression analysis was performed using DESeq2 in R.  ATAC-seq reads were aligned to the Mus musculus GRCm39 (mm39) reference genome using STAR. Duplicate reads were removed prior to peak calling. Peaks were identified using MACS2, and peaks from all samples were merged to generate a unified peak set. Peak-level read counts were obtained using featureCounts on a 500 bp window centered at each peak midpoint. Differential accessibility analysis between WT and Midn-T samples was performed using edgeR
Assembly: Mus musculus GRCm39 (mm39), Ensembl release 110.
Supplementary files format and content: Genome-wide signal coverage tracks derived from RNA-seq and ATAC-seq data are provided in bigWig (.bw) format. Differentially expressed genes and differentially accessible peaks are provided as tab-delimited text files.

source_name: Liver

growth_protocol: All animal procedures were approved by the City of Hope Institutional Animal Care and Use Committee (IACUC). Mice were housed and maintained in accordance with the approved protocol.

extract_protocol:
Total RNA was isolated from mouse liver tissue using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Briefly, tissues were homogenized in Buffer RLT containing β-mercaptoethanol, followed by centrifugation to remove debris. RNA was purified using silica membrane spin columns, washed, and eluted in RNase-free water. RNA quality and integrity were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer.  For ATAC-seq, nuclei were isolated from frozen liver tissue using the Singulator™ 200 system (S2 Genomics) according to the manufacturer’s protocol.
For RNA-seq, ribosomal RNA (rRNA) was depleted from 25–1,000 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (Roche). The remaining RNA was fragmented and converted to cDNA using random priming. Second-strand synthesis incorporated dUTPs. Sequencing adapters were ligated, and libraries were PCR-amplified and quality-checked using an Agilent Bioanalyzer.  For ATAC-seq, 50,000 nuclei per sample were subjected to transposition using Tn5 transposase (Active Motif ATAC-Seq Kit). Adapter-ligated DNA fragments were PCR-amplified using indexed primers. Library size distribution was assessed using an Agilent TapeStation, and libraries were quantified by qPCR.  All libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: Liver-specific Midn depletion was achieved by crossing Midn-XTR mice with Albumin-Cre transgenic mice. No additional treatments were applied. Liver tissues were collected from mice aged 11–14 weeks.

value: Liver

value: Midn TR


title: P3 cortex-layer 2-repeat#3

status: Public on Aug 14 2026

type: SRA

city: Baltimore

first: Alex

middle: L.

last: Kolodkin

state: MD

address: 600 N. Wolfe St.

department: Neuroscience

country: USA

institute: Johns Hopkins School of Medicine

description: Library name: VNec-P3_15_3

library_source: transcriptomic

data_processing:
HISAT2 index
.sam to .bam conversion, sorting and indexing of .bam files
stringtie & featurecounts
Assembly: GRCm39
Supplementary files format and content: .txt, TPMs for each gene

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Rneasy mini kit
SMART-Seq mRNA LP kit

tag: tissue

value: cerebral cortex

tag: cell type

value: layer 2 CPN

tag: genotype

value: wt

tag: treatment

value: postnatal day 3


title: P3 cortex-layer 3-repeat#1

description: Library name: VNec-P3_14_1

value: layer 3 CPN


title: SZ_11

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description:
nuclear mRNA
snRNAseq

data_processing:
10x Genomics Cell Ranger v3.1.
Genome_build: hg38 pre-mRNA transcriptome supplied with Cell Ranger v3.1.
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix.

organism: Homo sapiens

source_name: frozen postmortem dorsolateral prefrontal cortex brain

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols.
Libraries were prepared according to 10x Genomics manufacturer protocols.

value: dorsolateral prefrontal cortex

tag: diagnosis

value: Schizophrenia

tag: Sex

value: Male

tag: ethnicity

value: European


title: ATAC-seq, Liver, Male, Midn-T, Rep 2

description: Library name: ATAC-seq_WT_Female_Rep1

library_source: genomic

molecule: genomic DNA

value: Female

value: Midn XTR


title: P3 cortex-layer 2-repeat#1

description: Library name: VNec-P3_15_1


title: SZ_12

description:
nuclear mRNA
snRNAseq


title: ATAC-seq, Liver, Male, Midn-T, Rep 3

description: Library name: ATAC-seq_WT_Female_Rep2


title: P3 cortex-layer 3-repeat#2

description: Library name: VNec-P3_14_2


title: SZ_10

description:
nuclear mRNA
snRNAseq


title: ATAC-seq, Liver, Female, WT, Rep 2

description: Library name: ATAC-seq_Midn-T_Female_Rep2


title: ATAC-seq, Liver, Male, Midn-T, Rep 1

description: Library name: ATAC-seq_Midn-T_Male_Rep2


title: Pistia stratiotes, Stolon region, replicate 1

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

description:
Library name: Pistia_Stolon_1
RNA-seq of Pistia Stolon region, biological replicate 1

data_processing:
Salmon v1.10.0
Reads were pseudo-aligned and quantified using Salmon v1.10.0 with --validateMappings against a gentrome index built from the species-specific reference transcriptome and genome as decoys.
TPM values were extracted from Salmon quant.sf output files and assembled into gene x sample matrices.
Genes were filtered to remove those where max organ-averaged TPM was not at least 2.0 in at least one organ.
Assembly: Spirodela polyrhiza: Sp_polyrhiza_9509-REF-OXFORD-3.0 (lemna.org); Pistia stratiotes: chromosome-level assembly, Qian et al. 2022 (Molecular Ecology Resources 22:2732-2743, doi:10.1111/1755-0998.13653)
Supplementary files format and content: CSV files containing TPM (Transcripts Per Million) values for each gene across all samples per species

molecule: polyA RNA

organism: Pistia stratiotes

source_name: Stolon

growth_protocol: Duckweed and Pistia were grown at 22 °C under fluorescent lighting as per Ware et al. 2023.

extract_protocol:
Duckweed samples (Spirodela): Samples were recovered from RNAlater by sieving through 70uM cell strainers, blotted from underneath with tissue paper to remove excess RNAlater, and snap frozen. Samples were ground on liquid nitrogen in 1.5ml Eppendorf tubes with plastic pestles. RNA was extracted using a RNeasy UCP Micro Kit (Qiagen) as per manufacturer's instructions.
Pistia: RNA extractions were performed using a RNeasy kit (Qiagen) as per manufacturer's instructions with an additional RPE wash.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies). Library preparation and sequencing were performed by Novogene. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. After adenylation of 3' ends, adaptors with hairpin loop structure were ligated. Library fragments of 370-420 bp were purified with AMPure XP system (Beckman Coulter). PCR was performed with Phusion High-Fidelity DNA polymerase. Clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Libraries were sequenced on an Illumina NovaSeq platform generating 150 bp paired-end reads.

value: Stolon


title: Pistia stratiotes, Stem region, replicate 2

description:
Library name: Pistia_Stem_2
RNA-seq of Pistia Stem region, biological replicate 2

source_name: Stem

value: Stem


title: ATAC-seq, Liver, Male, WT, Rep 3

description: Library name: ATAC-seq_Midn-T_Male_Rep1


title: Pistia stratiotes, Stolon region, replicate 4

description:
Library name: Pistia_Stolon_4
RNA-seq of Pistia Stolon region, biological replicate 4


title: Pistia stratiotes, Stolon region, replicate 3

description:
Library name: Pistia_Stolon_3
RNA-seq of Pistia Stolon region, biological replicate 3


title: Pistia stratiotes, Stem region, replicate 4

description:
Library name: Pistia_Stem_4
RNA-seq of Pistia Stem region, biological replicate 4


title: Pistia stratiotes, Stolon region, replicate 2

description:
Library name: Pistia_Stolon_2
RNA-seq of Pistia Stolon region, biological replicate 2


title: SZ_08

description:
nuclear mRNA
snRNAseq


title: Pistia stratiotes, Stem region, replicate 3

description:
Library name: Pistia_Stem_3
RNA-seq of Pistia Stem region, biological replicate 3


title: SZ_07

description:
nuclear mRNA
snRNAseq


title: SZ_06

description:
nuclear mRNA
snRNAseq


title: ATAC-seq, Liver, Male, WT, Rep 1

description: Library name: ATAC-seq_WT_Male_Rep1


title: Pistia stratiotes, Basal region, replicate 2

description:
Library name: Pistia_Basal_2
RNA-seq of Pistia Basal region, biological replicate 2

source_name: Basal

value: Basal


title: Pistia stratiotes, Basal region, replicate 4

description:
Library name: Pistia_Basal_4
RNA-seq of Pistia Basal region, biological replicate 4


title: RNA-seq, Liver, Female, Midn-T, Rep 3

description: Library name: RNA-seq_Midn-T_Female_Rep3


title: Pistia stratiotes, Stem region, replicate 1

description:
Library name: Pistia_Stem_1
RNA-seq of Pistia Stem region, biological replicate 1


title: SZ_05

description:
nuclear mRNA
snRNAseq


title: SZ_09

description:
nuclear mRNA
snRNAseq


title: RNA-seq, Liver, Female, Midn-T, Rep 2

description: Library name: RNA-seq_Midn-T_Female_Rep2


title: ATAC-seq, Liver, Male, WT, Rep 2

description: Library name: ATAC-seq_WT_Male_Rep2


title: Pistia stratiotes, Basal region, replicate 3

description:
Library name: Pistia_Basal_3
RNA-seq of Pistia Basal region, biological replicate 3


title: Pistia stratiotes, Basal region, replicate 1

description:
Library name: Pistia_Basal_1
RNA-seq of Pistia Basal region, biological replicate 1


title: Pistia stratiotes, Petiole region, replicate 1

description:
Library name: Pistia_Petiole_1
RNA-seq of Pistia Petiole region, biological replicate 1

source_name: Petiole

value: Petiole


title: RNA-seq, Liver, Female, WT, Rep 3

description: Library name: RNA-seq_WT_Female_Rep3

value: Liver


title: Pistia stratiotes, Petiole region, replicate 2

description:
Library name: Pistia_Petiole_2
RNA-seq of Pistia Petiole region, biological replicate 2


title: Pistia stratiotes, Apical region, replicate 1

description:
Library name: Pistia_Apical_1
RNA-seq of Pistia Apical region, biological replicate 1

source_name: Apical

value: Apical


title: Pistia stratiotes, Petiole region, replicate 4

description:
Library name: Pistia_Petiole_4
RNA-seq of Pistia Petiole region, biological replicate 4


title: SZ_04

description:
nuclear mRNA
snRNAseq


title: SZ_01

description:
nuclear mRNA
snRNAseq


title: RNA-seq, Liver, Female, Midn-T, Rep 1

description: Library name: RNA-seq_Midn-T_Female_Rep1

value: Midn TR


title: SZ_03

description:
nuclear mRNA
snRNAseq


title: Pistia stratiotes, Petiole region, replicate 3

description:
Library name: Pistia_Petiole_3
RNA-seq of Pistia Petiole region, biological replicate 3


title: sgMETTL13_RNA_rep2

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

description: Library name: sgMETTL13_RNA_rep2

data_processing:
Total RNA samples: Sequencing reads were preprocessed using BBmap (v. 36.59; parameters: k = 13, ktrim = n, useshortkmers = t, mink = 5, qtrim = t, trimq = 10, minlength = 20). Processed reads were aligned to the human reference genome (hg38) using HISAT (v.2.0.4; in addition to default parameters, “–no-mixed” and “–no-discordant” were applied. Uniquely aligned reads were quantified using the featureCounts function from the RSubread R/Bioconductor package (v.2.6.4; in addition to default parameters, “strandSpecific=2”) against the RefSeq annotation GCF_000001405.40, filtered to include only protein-coding genes.
Ribosome profiling: Sequencing reads were preprocessed using cutadapt (v. 1.18; parameters: --nextseq-trim=20 --minimum-length 20 -a TCTCCTTGCATAATCACCAACC --discard-untrimmed). UMI were extracted using umi_tools extract (v. 1.1.2 ; parameters: --bc-pattern='^(?P<umi_1>.{4}).+(?P<umi_2>.{4})\$'). Remaining 'T' was removed using cutadapt (parameters: -g ^T). In addition, BBmap [REF] was used to remove reads matching ribosomal RNA sequences obtained from the SILVA ribosomal RNA database. The remaining reads were aligned to the hg38 genome assembly using Bowtie (v.1.2.2; parameters: -a -m 1 --best --strata -n 2 -l 20). Reads that uniquely aligned or failed to align to the genome were subsequently aligned to RefSeq transcript sequences (GCF_000001405.40) using Bowtie (parameters: -a --best –strata -n 2 -l 20). Umi_tools dedup was used to remove duplicated sequences. To extract the genuine ribosome footprints, only reads with lengths between 25 and 34 nucleotides (inclusive) were retained for further analysis. P-site positions were determined using Ribowaltz. P-sites counts were then summarised at the gene-level across coding sequences defined by RefSeq annotations GCF_000001405.40. When multiple transcript isoforms were present, one isoform was selected at random for quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

growth_protocol: T3M4 cells were serum straved for 18hours and then stimulated with 10%FBS for 2 hours

extract_protocol:
Cells were washed three times with PBS and harvested by flash-freezing the plate in liquid nitrogen and scrapping the cells with polysome lysis buffer (50mM Tris pH7.5, 100mM KoAc, 15mM Mg(oAc)2, 5% Glycerol and 1%triton). Lysate were centrifuged (8 min at 20,000g) and supernatants were collected for RNA and Riboseq.
For RNA-seq, total RNA was used to prepare stranded poly(A) mRNA libraries. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5′-phosphorylated, with a protruding 'A' at the 3′ end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3′ end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing quality control. The library was amplified with phi29 to make DNA nanoballs (DNBs), each containing more than 300 copies of one molecule. The DNBs were loaded onto a patterned nanoarray, and paired-end 150 bp reads were generated by sequencing-by-synthesis. Libraries were sequenced by BGI and adapter sequences used were: adapter3 = AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA; adapter5 = AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG.  For ribosome profiling, active ribosome-protected mRNA fragments (RPFs) were isolated using the ALL-IN-ONE RiboLace Gel Free kit (Immagina BioTechnology). Briefly, lysate collected was subjected to nuclease digestion to generate RPFs. Magnetic beads functionalized with a biotinylated puromycin analog (3P, RiboLace Smart Probe) were used to selectively pull down active ribosome complexes via affinity purification, and RPF-containing RNA was extracted from the captured ribosomes. For library construction, the purified RPFs were 5′-phosphorylated, followed by ligation of the LaceSeq Linker MC+ to the 3′-phosphate end of the RPFs. The ligated products were then circularized, followed by reverse transcription using a primer annealing to the linker sequence to generate single-stranded cDNA. The cDNA was PCR amplified in two sequential rounds (PCR1 and PCR2), with Illumina-compatible Unique Dual Indexes (iUDIs) added during PCR2. Library quality was assessed using an Agilent 2100 Bioanalyzer with the High Sensitivity DNA Kit. Libraries were sequenced by TB-Seq, Inc. on an Illumina NovaSeq platform, single-end, 1x150 cycles. The 3′ adapter sequence used was: TCTCCTTGCATAATCACCAACC (LaceSeq 3′ linker).

tag: cell line


title: Pistia stratiotes, Apical region, replicate 3

description:
Library name: Pistia_Apical_3
RNA-seq of Pistia Apical region, biological replicate 3


title: RNA-seq, Liver, Female, WT, Rep 2

description: Library name: RNA-seq_WT_Female_Rep2


title: Pistia stratiotes, Apical region, replicate 2

description:
Library name: Pistia_Apical_2
RNA-seq of Pistia Apical region, biological replicate 2


title: RNA-seq, Liver, Female, WT, Rep 1

description: Library name: RNA-seq_WT_Female_Rep1


title: sgControl_RNA_rep1

description: Library name: sgControl_RNA_rep1

value: sgControl


title: CT_16

description:
nuclear mRNA
snRNAseq

value: Control


title: sgMETTL13_RNA_rep1

description: Library name: sgMETTL13_RNA_rep1


title: RNA-seq, Liver, Male, Midn-T, Rep 2

description: Library name: RNA-seq_Midn-T_Male_Rep2


title: shDKC1_atac_rep2

city: Beijing

first: Xiaoyang

last: Liu

address: 5th Yiheyuan road

country: China

institute: Peking University

description:
Library name: shDKC1_atac_rep2
ATAC-Seq of HeLa DKC1 KD cells with DMSO treatment,replicate2

data_processing:
Adapter sequences were removed from the raw reads via Cutadapt (v4.4) to obtain clean reads. Subsequently, these clean reads were aligned to the reference genome and mitochondrial genome (hg38 GENCODE v42) using Bowtie2 (v2.5.1), with the parameter -x 2000 set to accommodate the longer fragment lengths of ATAC - Seq data. To ensure data quality, reads aligned to the mitochondrial genome, located in blacklist regions, and arising from PCR duplicates were filtered out by combining ENCODE scripts and Picard (v3.1.1). Next, the BAM files were converted to tagAlign format, and positional correction was performed based on the characteristics of the Tn5 transposase: reads on the positive strand were shifted forward by 4 bp, while those on the negative strand were shifted backward by 5 bp to compensate for the 9 - bp base offset. Peak calling was implemented using MACS2 (v2.2.7.1) run through ENCODE's official script encode_task_macs2_atac.py, with parameters set as -p 0.01 --shift -75 --extsize 150 to accurately simulate Tn5 insertion sites. Additionally, the encode_task_overlap.py script was adopted to take the intersection of identified peaks, further filtering for high - confidence peak regions. For the annotation phase, functional annotation of the peaks was conducted using the ChIPseeker (v1.34.1) package in the R (v4.2.3) environment, laying a solid foundation for subsequent analyses.
Assembly: hg38
Supplementary files format and content: bed file of ATAC peaks

source_name: HeLa

extract_protocol:
The protocol for isolating fresh DNA was carried out in accordance with the manufacturer's instructions provided in the Hyperactive ATAC - Seq Library Prep Kit for Illumina (Vazyme).
Fresh DNA was isolated from HeLa cells in this study. Prior to library construction, trypan blue staining was performed to verify the cell viability, and subsequent library preparation was required to be completed promptly. The cells were divided into four groups as follows: the Control group treated with DMSO for 48 hours, the Nira group treated with 5 µM Nira for 48 hours, the shDKC1 group consisting of a DKC1 stably depleted cell line, and the Combined group where the DKC1 stably depleted cell line was treated with 5 µM Nira for 48 hours. The protocol for isolating fresh DNA was carried out in accordance with the manufacturer's instructions provided in the Hyperactive ATAC - Seq Library Prep Kit for Illumina (Vazyme). During the library amplification step, 11 PCR cycles were set for amplification, and the amplified products were purified using ATAC DNA Clean Beads.

value: HeLa

value: Human Cervical Carcinoma Cells

value: DKC1 KD

value: DMSO


title: sgControl_RNA_rep2

description: Library name: sgControl_RNA_rep2


title: RNA-seq, Liver, Male, Midn-T, Rep 1

description: Library name: RNA-seq_Midn-T_Male_Rep1

value: Male


title: CT_14

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

value: European


title: Nira_atac_rep1

description:
Library name: Nira_atac_rep1
ATAC-Seq of HeLa control cells with Nira treatment,replicate1

value: control

value: Nira


title: CT_12

description:
nuclear mRNA
snRNAseq


title: Ctrl_atac_rep2

description:
Library name: Ctrl_atac_rep2
ATAC-Seq of HeLa control cells with DMSO treatment,replicate2


title: RNA-seq, Liver, Male, WT, Rep 3

description: Library name: RNA-seq_WT_Male_Rep3

value: Midn XTR


title: CT_13

description:
nuclear mRNA
snRNAseq


title: CT_11

description:
nuclear mRNA
snRNAseq


title: shDKC1_atac_rep1

description:
Library name: shDKC1_atac_rep1
ATAC-Seq of HeLa DKC1 KD cells with DMSO treatment,replicate1


title: Ctrl_atac_rep1

description:
Library name: Ctrl_atac_rep1
ATAC-Seq of HeLa control cells with DMSO treatment,replicate1


title: Nira_atac_rep2

description:
Library name: Nira_atac_rep2
ATAC-Seq of HeLa control cells with Nira treatment,replicate2


title: 5007, ADT, circulating CD4+ T cells and monocytes

city: Herston

first: Cameron

middle: Gerard

last: Williams

state: QLD

address: 300 Herston Road

department: Infection and Inflammation

country: Australia

institute: QIMR Berghofer

description:
Library name: 5007_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

library_source: other

data_processing:
Raw FASTQ files were processed using ‘cellranger count’ pipeline from Cell Ranger version 3.0.2 (10X Genomics) with 10X human genome release 3.0 as a reference.
Assembly: GRCh38
Supplementary files format and content: cellranger count output containing GEX data
Supplementary files format and content: cellranger count output containing ADT data
Library strategy: CITE-seq

molecule: protein

source_name: blood

extract_protocol:
Cryopreserved human PBMCs were thawed and stained for surface markers by incubation with the following antibodies: CD4 PE (clone SK3, BD Biosciences) and CD14 APC (clone HCD14, Biolegend). Viable CD4+ T cells (7AAD-CD4+CD14-) and CD14+ monocytes (7AAD-CD14+) from each sample were isolated by fluorescent-activated cell sorting into cold 1% BSA/PBS buffer. CD4+ T cells and CD14+ monocytes were then pooled at a 2:1 ratio, respectively, and stained with TotalSeq™-A anti-human antibodies for 30 minutes at 4°C.
Cells were suspended at a concentration of 1 x 106 cells/mL and loaded onto a Chromium controller (10X Genomics) for generation of gel bead-in-emulsions. Sequencing libraries for both gene expression and antibody derived tags (ADTs) were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI) before sequencing on a MGISEQ-2000 instrument (BGI).

treatment_protocol: TBI and BMT followed by no treatment or IL-6R blockade via Tocilizumab.

value: blood

value: CD4+ T cells and monocytes

value: F

tag: age

tag: cmv reactivation/day_of_onset

value: N

tag: cmv serotype

value: D-R-

tag: conditioning

value: Flu/Mel

tag: disease state

value: no GvHD

tag: gvhd grade

value: placebo


title: 3021, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 3021_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: D+R+

value: CyTBI

value: TCZ


title: CT_09

description:
nuclear mRNA
snRNAseq

value: Control

value: Male


title: Dsg2 F536C knock-in 6

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Library name: KI6

data_processing:
Illumina DRAGEN Bio-IT Platform v4.0.3
The original Fastq data underwent secondary analysis using the DRAGEN RNA Pipeline for sequence alignment and gene expression quantification.
Reads were aligned to the Mus musculus GRCm39/mm39 reference genome (Genome Reference Consortium Mouse Build 39, GCA_000001635.9) downloaded from the UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/), using the soft-masked assembly sequence file mm39.fa.gz and the matching mm39 gene annotation files.
Assembly: Mus musculus GRCm39/mm39 reference genome (Genome Reference Consortium Mouse Build 39, GCA_000001635.9)
Supplementary files format and content: Tab-delimited text file containing raw gene counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM (Transcripts Per Million) values for each sample

source_name: right ventricular

extract_protocol:
Total RNA was isolated from RV with the TRIzol reagent and was further purified and concentrated by using the TriRNA Pure kit . The quality and quantity of total RNA were analyzed by using a LabChip GX
Total RNA was used for library preparation using the Illumina Stranded mRNA Prep kit. Poly(A)+ mRNA was first enriched using poly-T beads, followed by RNA fragmentation and first- and second-strand cDNA synthesis. End repair, adapter ligation, and PCR amplification were performed to generate indexed libraries. Libraries were then purified using magnetic beads and assessed for quality and quantity. All procedures were carried out according to the manufacturer’s protocol provided by Illumina.

value: right ventricular


title: RNA-seq, Liver, Male, WT, Rep 2

description: Library name: RNA-seq_WT_Male_Rep2

value: Liver


title: 1153, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1153_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual


title: WT_AVI4_A

status: Public on Aug 15 2026

type: RNA

city: Barcelona

first: Lluís

last: Hernández

state: Barcelona

address: Rossello 153

department: Area 5

country: Spain

institute: IDIBAPS

description: Sample from Aviano

hyb_protocol: The ss-cDNA was fragmented and labeled and hybridized onto the  Affymetrix Human Clariom D, for 16hr at 45ºC and 60rpm, using Affymetrix Hybridization 645 oven. Afterwards, arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

data_processing: The data was analyzed with Transcriptome Expression Console Software (TAC v4.0.2) using (log2)  SST-RMA algorithm normalization.

label: biotin

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition A

label_protocol: Starting from 10ng of purified total RNA , a reverse transcription reaction was initiated at the Poly-A tail as well as throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA. Complementary RNA (cRNA) amplification was achieved using low-cycle PCR followed by linear amplification using T7 in vitro transcription (IVT) technology. The cRNA was then converted to biotinylated sense-strand DNA hybridization targets for unbiased coverage of the transcriptomeand scanned using the Affymetrix GeneChip Scanner 3000 System.

growth_protocol: RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin+IL-2 (1.54 ng/ml)+CpG-ODN2006 (0.38 ug/ml)

extract_protocol: miRNAeasy kit (Qiagen)

treatment_protocol: see samples/summary for the different protocols

value: Primary CLL cells

value: Condition A


title: 1149, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1149_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: blood

value: D-R+

value: GvHD

value: grade IV (d22)


title: RNA-seq, Liver, Male, WT, Rep 1

description: Library name: RNA-seq_WT_Male_Rep1

value: Midn XTR


title: CT_07

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

value: European


title: 1137, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1137_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: CD4+ T cells and monocytes

value: M

value: N

value: no GvHD

value: placebo


title: Dsg2 F536C knock-in 4

description: Library name: KI4


title: CT_10

description:
nuclear mRNA
snRNAseq

value: Control

value: Male


title: THP-1, FLAG-FULL-3+DOX-REP3

city: Tian Jin

first: meng

last: yang

state: Tianjin

address: Nanjing Road No.288

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

description: Library name: FLAG-FULL-3+DOX

data_processing:
Subsequent analysis followed established computational pipelines detailed in the CUT&Tag Data Processing and Analysis Protocol (Zheng et al., 2020; Protocol.io). Differential peaks analysis was performed using Diff Bind (v3.10.1) with statistically significant peaks identified at p < 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiment in combination with the Hyperactive TM In-Situ ChIP Library Prep Kit for Illumina from Vazyme (TD902-01).
The extracted DNA fragments were extracted and subjected to high-throughput sequencing.

value: AML cell


title: THP-1, FLAG-T3-3+DOX-REP3

description: Library name: FLAG-T3-3+DOX


title: 1085, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1085_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: Flu/Mel


title: CT_08

description:
nuclear mRNA
snRNAseq

value: Female


title: WT_AVI3_C

description: Sample from Aviano

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition C

value: Primary CLL cells

value: Condition C


title: Dsg2 F536C knock-in 3

description: Library name: KI3

value: right ventricular


title: 1035, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1035_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: blood

value: F

value: D+R-

value: TCZ


title: CT_05

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

value: European


title: CT_06

description:
nuclear mRNA
snRNAseq


title: 1021, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1021_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: CD4+ T cells and monocytes

value: N

value: D-R-


title: SZ_02

description:
nuclear mRNA
snRNAseq

value: Schizophrenia


title: CT_04

description:
nuclear mRNA
snRNAseq

value: Control

value: Male


title: THP-1, FLAG-T6-3+DOX-REP3

description: Library name: FLAG-T6-3+DOX

value: AML cell


title: Dsg2 F536C knock-in 5

description: Library name: KI5


title: 1017, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1017_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: M

value: D+R+

value: Flu/Mel

value: no GvHD


title: CT_03

description:
nuclear mRNA
snRNAseq

value: Female


title: wild type-6

description: Library name: WT6

value: right ventricular


title: 1024, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1024_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: blood

value: GvHD

value: grade III (d28)

value: placebo


title: 1071, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1071_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: CD4+ T cells and monocytes

value: D+R-

value: CyTBI

value: TCZ


title: 5007, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 5007_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: F

value: N

value: D-R-


title: CT_15

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

value: Control

value: Male

value: European


title: 3021, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 3021_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: D+R+

value: no GvHD


title: Pistia stratiotes, Apical region, replicate 4

description:
Library name: Pistia_Apical_4
RNA-seq of Pistia Apical region, biological replicate 4

value: Apical


title: 1153, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1153_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood


title: 1018, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1018_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: M

value: Flu/Mel

value: GvHD

value: grade III (d24)


title: 1006, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1006_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: CD4+ T cells and monocytes


title: Dsg2 F536C knock-in 1

description: Library name: KI1

value: right ventricular


title: 1149, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1149_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: F

value: D-R+

value: CyTBI

value: grade IV (d22)

value: placebo


title: Dsg2 F536C knock-in 2

description: Library name: KI2


title: Combine_atac_rep1

description:
Library name: Combine_atac_rep1
ATAC-Seq of HeLa DKC1 KD cells with Nira treatment,replicate1

value: HeLa

value: Human Cervical Carcinoma Cells

value: DKC1 KD

value: Nira


title: RNA-seq, Liver, Male, Midn-T, Rep 3

description: Library name: RNA-seq_Midn-T_Male_Rep3

value: Liver

value: Male

value: Midn TR


title: 5017, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 5017_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood

value: M

value: N

value: grade III (d32)


title: CT_02

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

value: Control

value: European


title: 1137, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1137_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: CD4+ T cells and monocytes

value: D+R+

value: CyTBI

value: no GvHD


title: wild type-5

description: Library name: WT5

value: right ventricular


title: PBMC_1-1, GEX

city: Seoul

first: Byungjin

last: Hwang

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description: count matrix for all samples included

library_source: transcriptomic single cell

data_processing:
Each set of replicate raw data was processed using CellRanger v7.1.0 multi, producing separate outputs.
Sample demultiplexing
Genes and cells were filtered by QC criteria (total count, n_gene per cells, mitochondrial contnts)
Doublets removed
Assembly: GRCh38
Supplementary files format and content: The GEX h5ad file contains all sample demultiplexed information and filtered cells.
Supplementary files format and content: The VDJ h5ad file contains all VDJ contig information and filtered cell indice.

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Histopaque gradient. Single cells were then encapsulated in GEMs using the 10X Controller.
Libraries were generated using 10X Chromium VDJ & 5’ library and Gel Bead according to the user guide. To produce hashtag antibody libraries, TSC additive primer were spiked in at the step of cDNA amplification small size-selected amplified cDNA sample were used as template.

value: Blood

value: PBMC

value: Mixed (non-rejection, acute rejection)


title: wild type-2

description: Library name: WT2


title: 1085, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1085_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: D-R+

value: Flu/Mel

value: placebo


title: Case_165, Dedifferentiated chondrosarcoma

type: genomic

city: Bern

first: Jon

last: Brugger

address: Private Address

country: Switzerland

institute: Private

description: Sample ID: 206644420023_R05C01

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using mepylome version 0.10.0 and python 3.13
[processed value definition]  Beta values, calculated with mepylome using the Illumina method

label: Cy5 and Cy3

source_name: KRYO

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

value: Dedifferentiated chondrosarcoma

tag: grade

value: high-grade

tag: origin

value: NL

value: WT

value: Rib

tag: gender

value: male

tag: follow-up

tag: status

value: DoD

value: KRYO


title: Case_156, Chondrosarcoma

description: Sample ID: 207130360153_R02C01

value: Chondrosarcoma

value: Diaphragma

value: dead of unknown cause

tag: tissue


title: wild type-1

description: Library name: WT1

value: right ventricular


title: 1071, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1071_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood

tag: cell type

value: CD4+ T cells and monocytes

value: M

value: N

value: D+R-

value: CyTBI

value: no GvHD

tag: treatment

value: TCZ


title: Case_157, Chondrosarcoma

description: Sample ID: 207130360153_R03C01

tag: subdiagnosis

value: Metastasis

value: high-grade

value: NL

value: WT

value: Spine


title: wild type-4

description: Library name: WT4


title: Combine_atac_rep2

description:
Library name: Combine_atac_rep2
ATAC-Seq of HeLa DKC1 KD cells with Nira treatment,replicate2

value: HeLa

value: Human Cervical Carcinoma Cells

tag: genotype

value: DKC1 KD

value: Nira


title: SCD_Day_HIP

city: Hong Kong

first: Jin Young

last: KIM

address: 83 Tat Chee Ave, Kowloon Tong

department: Biomedical Sciences

institute: City University of Hong Kong

description:
Library name: SD-6-Hip
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
The hippocampus and hypothalamus were harvested and snap-freezed in liquid nitrogen. Nuclei isolation was processed with a Chromium Nuclei Isolation Kit (PN-1000494, 10X Genomics) following the manufacturer’s instructions. The isolated nuclei were immediately processed for single nucleus-specific barcoding by a droplet-based technique with targeted cell recovery at 10,000 nuclei per sample.
Single nucleus-specific barcoding was performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (4 rxns PN-1000130, 10X Genomics), Gel Bead Kit v3.1 (4 rxns PN-1000129, 10X Genomics), and 10X Genomics Controller following the manufacturer’s instruction. Then, cDNA amplification and library construction steps were followed using the Library Construction Kit (4 rxns, PN-1000196, 10X Genomics) for RNA sequencing.

treatment_protocol: NSC or SCD conditions

value: Hippocampus

value: Neural cells

value: sleep cycle disturbance


title: 2002, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 2002_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood

value: CD4+ T cells and monocytes

tag: Sex

value: M

value: N

value: D-R-

value: Flu/Mel

value: GvHD

value: grade III (d52)

value: placebo


title: 5017, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 5017_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

tag: age

value: D-R+

value: CyTBI

value: grade III (d32)


title: 1024, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1024_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

tag: cmv reactivation/day_of_onset

value: D+R+

value: grade III (d28)


title: Case_154, Chondrosarcoma

description: Sample ID: 207130360143_R02C01

value: Chondrosarcoma

value: high-grade

value: NL

value: WT

value: Scapula

value: male

value: alive

value: KRYO


title: Case_153, Chondrosarcoma

description: Sample ID: 207130360137_R08C01


title: wild type-3

description: Library name: WT3

value: right ventricular


title: HEK293T, RNA, antimir mix transfection, rep2

city: Zurich

first: Jonathan

last: Hall

address: Vladimir-Prelog-Weg 1-5/10

institute: ETH Zurich

description: Library name: RNA_antimir_mix_Rep2

data_processing:
De-multiplexed RNA-Seq reads were aligned to the GRCh38 genome including transcript annotations using STAR v2.7.10b. RNA-Seq reads were counted per gene using HTSeq 2.0.9. with intersection-strict mode and ignoring non-unique alignments.
Assembly: hg38/GRCh38
Supplementary files format and content: Table with gene read counts for 6 RNA-Seq samples obtained after antimir transfection: All_geneCounts_mRNASeq_antimir_samples.out.gz

growth_protocol: HEK293T cells were seeded 6–8 h prior to transfection in 12-well plates (150,000 cells/well).

extract_protocol:
For total RNA isolation, frozen cell pellet was dissolved in 1 ml TRI Reagent® (Sigma: T9424-200) and incubated for 5 minutes at room temperature. Thereafter, RNA isolation was proceed using Direct-zol RNA MiniPrep kit (Cat. No. R2050, Zymo research) according to manufacturer protocol including DNase treatment on column. RNA was eluted in 50ul of elution buffer and submitted to Genomic facility DBSSE, Basel for library preparation and sequencing. The quantity of RNA was measured with RNA BR Qubit Kit (Invitrgen) and their integrity was monitored on TapeStation RNA SS kit (Agilent).
200ng Total RNA was used for library preparation using TruSeq Stranded mRNA Library Prep kit (illumina, Cat# 20020595) according to kit manual where RNA fragmentation was done for 8 minutes at 94°C. Final PCR was done for 15 cycles. After library preparation, samples were pooled to equal molarity. The pool was sequenced Single-End 76 bases (in addition: 8 bases for index 1 and 8 bases for index 2) on NextSeq 500 using the NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005).

treatment_protocol: Transfections were performed using Lipofectamine 2000 (Invitrogen, #11668027) with final oligonucleotide concentrations up to 50 nM, following the manufacturer’s instructions. Complexes were formed by incubating reagents for ~25 min before adding to cells. Incubation proceeded for up to 48 h.

tag: cell line

value: transfection with mix of anti-mirs for miR-17 family (anti-miR106a, anti-miR17, anti-miR20a, anti-miR93)


title: CT_01

description:
nuclear mRNA
snRNAseq

value: dorsolateral prefrontal cortex

tag: diagnosis

value: Control

value: Male

tag: ethnicity

value: European


title: SCD_Day_HY

description:
Library name: SD-6-Y
10X Genomics

source_name: Hypothalamus

value: Hypothalamus

value: Neural cells

value: sleep cycle disturbance


title: 1021, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1021_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood

value: CD4+ T cells and monocytes

value: F

value: N

tag: cmv serotype

value: D-R-

tag: conditioning

value: Flu/Mel

tag: disease state

value: no GvHD

tag: gvhd grade

value: placebo


title: 1143, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1143_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: M

value: CyTBI

value: GvHD

value: grade IV (d45)


title: Dsg2 F536C knock-in 7

description: Library name: KI7

value: right ventricular


title: 2002, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 2002_d21_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: grade III (d52)


title: HEK293T, RNA, mock transfection, rep3

description: Library name: RNA_antimir_mock_Rep3

value: mock transfection


title: 1035, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1035_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: D+R-

value: TCZ


title: NSC_Day_HY

description:
Library name: NS-6-Y
10X Genomics

value: Hypothalamus

value: Neural cells

value: normal sleep cycle


title: HEK293T, RNA, mock transfection, rep2

description: Library name: RNA_antimir_mock_Rep2


title: 1017, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1017_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: blood

value: CD4+ T cells and monocytes

value: N

value: D+R+


title: 1018, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1018_d21_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: Flu/Mel

value: grade III (d24)

value: placebo


title: 1006, GEX, circulating CD4+ T cells and monocytes

description:
Library name: 1006_d30_GEX
Gene expression of circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual.

value: M

value: no GvHD


title: SCD_Night_HIP

description:
Library name: SD-18-Hip
10X Genomics

value: Hippocampus

value: sleep cycle disturbance


title: Case_155, Chondrosarcoma

description: Sample ID: 207130360143_R06C01

value: Chondrosarcoma

tag: grade

value: high-grade

tag: origin

value: NL

value: WT

value: Rib

tag: gender

value: male

value: dead of unknown cause

value: KRYO


title: HEK293T, RNA, ASmut2 transfected, rep3

description:
Library name: RNA_ASmut2_Rep3
ASmut2_3

data_processing:
For RNA-Seq: RNA-Seq reads were aligned to the GRCh38 genome including transcript annotations with STAR v2.7.10b. RNA-Seq reads were counted per gene using HTSeq 2.0.9. with intersection-strict mode and ignoring non-unique alignments.
For smallRNA-Seq: Only unique reads which contained the 3' adapter sequence (AACTGTAGGCACCATCAA) were considered. The 3' adapter sequence and all nucleotides downstream of this sequence were removed from the reads, and only reads >= 15 nucleotides were retained. The occurences of reads were counted for all 48 samples.
Assembly: hg38/GRCh38
Supplementary files format and content: Table with gene read counts for all 48 RNA-Seq samples: All_geneCounts_mRNASeq_samples.out.gz
Supplementary files format and content: Table with processed smallRNA-Seq read counts for all 48 samples: AllReads15nt_smallRNASeq_samples.tab.gz

extract_protocol:
HEK293T cells were washed with ice-cold PBS and lysed in TRIzol reagent (Invitrogen, #15596-018). RNA was extracted per the manufacturer’s protocol.
For RNA-Seq: Libraries were prepared from 200 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2103). Libraries were pooled to equal molarity and quantified using the QuantiFluor ONE dsDNA System (Promega, #E4871). Final pools were diluted to 1.4 pM and sequenced on a NextSeq 500 (Illumina) using the High Output 75-cycle kit (#FC-4041005) in single-end 76 bp format with dual 8 bp indexes.
For smallRNA-Seq: 200ng total RNA were used to perform Library preparation using the QIAseq miRNA Library Kit (96) (Qiagen, Cat# 331505) and the QIAseq miRNA 48 Index IL, 96 (Qiagen, Cat# 331595). 15 cycles of PCR were performed. Samples were pooled to equal molarity by series of 48. Each pool was quantified by fluorometry (PicoGreen measurement) in order to be adjusted to equal molarity and the pool was quantified and adjusted to 1.4pM for being used for clustering on the NextSeq 500 instrument (Illumina). In order to take advantage of the UMIs sequences (meant at correcting the data for PCR bias), samples were sequenced single-reads 76 bases using the NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005).

value: ASmut2 transfection


title: HEK293T, RNA, antimir mix transfection, rep1

description: Library name: RNA_antimir_mix_Rep1

value: transfection with mix of anti-mirs for miR-17 family (i.e. anti-miR106a, anti-miR17, anti-miR20a, anti-miR93)


title: Case_148, Chondrosarcoma

description: Sample ID: 206644420109_R02C01

value: Spine

value: female

tag: follow-up

tag: status

tag: tissue


title: Epithelium, stage I66, rep f

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description: Library name: I66f

data_processing:
Single cell libraries were sequenced on Novaseq and raw data was processed through Cell Ranger v7.0.0 for basecalling, aligning to Xenopus_tropicalis.UCB_Xtro_10.0, filtering barcodes and UMIs, and generating gene-by-cell count matrices.
Assembly: Xenopus_tropicalis.UCB_Xtro_10.0
Supplementary files format and content: Cell Ranger output files matrix.tsv.gz, features.tsv.gz and barcodes.tsv.gz

organism: Xenopus tropicalis

source_name: Intestinal epithelium

extract_protocol:
To isolate intestinal epithelial cells, 4–5 small intestines from each developmental stage were dissected, pooled, and flushed with 0.7x PBS using a 30-gauge needle. The tissue was then cut open longitudinally and washed twice with 0.7x PBS. The intestines were cut into 2–3 mm segments and incubated in 2 mL of 1 U/mL Dispase II (Roche) for 8 minutes. Following dispase digestion, the solution was treated with 0.7x PBS-EDTA (10mM) and incubated on ice for 30 minutes with periodic twirling. The resulting cell suspension was vortexed and passed through a 70 µm filter. The remaining tissue was washed with 10 mL of 0.7x PBS and vortexed again. The supernatants were combined, centrifuged at 300 x g for 5 minutes, and resuspended in 0.7x PBS to obtain a filtrate enriched in epithelial cells.
Libraries were generated according to the Chromium X Single Cell 3’ v3 protocol (10X Genomics).

value: Intestinal epithelium

tag: Stage

tag: biological replicate


title: Case_150, Chondrosarcoma

description: Sample ID: 206644420120_R03C01

value: Pelvis

tag: age

value: alive


title: Epithelium, stage I66, rep g

description: Library name: I66g


title: Case_151, Chondrosarcoma

description: Sample ID: 207130360090_R07C01


title: Vegetative + 40nM bEST

city: Atherton

first: Constantine

last: Bartolutti

state: California

address: 69 Santiago Avenue

institute: Stanford University

description:
Library name: Sample4
bEST_40

data_processing:
used clip linker to clip the linker from the sequencing reads
used align_rRNA to campture unaligned reads to subtract any additional rRNA sequencing
Used Star align on untrimmed reads to SK1 reference genome - outputs bam files and optionally outputs unique alignment reads
Used samtools index to index the bam files outputted from star align
feature counts command used to assemble raw counts numbers for all files
Assembly: GCA_000766265.2
Supplementary files format and content: .csv files contain RPKM values

organism: Saccharomyces cerevisiae

source_name: vegetative

growth_protocol: Vegetative: Strains were grown with YPD at 30 degrees with shaking.

extract_protocol:
Cells were harvested via pelleting liquid culture at 6000 RCF then aspirating media before snap freezing in liquid nitrogen. Cells were thawed on ice and resuspended in 625ul TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). An equal volume of citrate-buffered acid phenol (pH 4.3, P4682, Sigma-Aldrich) was added to cells, and they were incubated at 65C for 1 hour in a Thermomixer C (Eppendorf) shaking at 1400 RPM. After microcentrifugation (20,000 g for 10 min) the aqueous phase was transferred to a second tube with 600ul acid phenol. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and transferred to a third tube with 600ul chloroform. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and RNA was precipitated in 100% isopropanol with 350 mM sodium acetate (pH 5.2) overnight at –20C. Pellets were washed with 80% ethanol and resuspended in DEPC water
RNA-seq libraries were generated with the NEXTflex Rapid Directional mRNA-Seq Bundle with poly(A) beads (NOVA-5138, Bioo Scientific) according to manufacturer’s instructions. 10 mg of total RNA was used as input for all libraries. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp. Libraries were quantified using the Agilent 4200 TapeStation (Agilent Technologies, Inc). Samples were submitted for 50 bp single-end sequencing by the Vincent J. Coates Genomics Sequencing Laboratory with a HiSeq 4000.

treatment_protocol: Vegetative cells were harvested in exponential growth phase (OD600=0.6).

tag: strain

tag: genotype

tag: cell type

value: vegetative


title: NSC_Day_HIP

description:
Library name: NS-6-Hip
10X Genomics

value: Hippocampus

value: Neural cells

tag: treatment

value: normal sleep cycle


title: SCD_Night_HY

description:
Library name: SD-18-Y
10X Genomics

value: Hypothalamus

value: sleep cycle disturbance


title: HEK293T, RNA, antimir mix transfection, rep3

description: Library name: RNA_antimir_mix_Rep3

tag: cell line

value: transfection with mix of anti-mirs for miR-17 family (anti-miR106a, anti-miR17, anti-miR20a, anti-miR93)


title: NSC_Night_HIP

description:
Library name: NS-18-Hip
10X Genomics


title: Epithelium, stage I66, rep d

description: Library name: I66d


title: Case_152, Chondrosarcoma

description: Sample ID: 207130360137_R07C01

value: Chondrosarcoma

value: high-grade

value: NL

value: WT

value: Scapula

value: male


title: HEK293T, RNA, miR106b transfected, rep3

description:
Library name: RNA_miR106b_Rep3
106b_3

value: miR106b transfection


title: Case_147, Chondrosarcoma

description: Sample ID: 206644410047_R02C01

value: KRYO


title: Epithelium, stage I66, rep e

description: Library name: I66e

value: Intestinal epithelium


title: HEK293T, RNA, mock transfection, rep1

description: Library name: RNA_antimir_mock_Rep1

value: mock transfection


title: 1143, ADT, circulating CD4+ T cells and monocytes

description:
Library name: 1143_d30_ADT
Antibody-derived transcripts from circulating CD4+ T cells and monocytes. Each sample number corresponds to a different individual

value: blood

value: CD4+ T cells and monocytes

tag: Sex

value: M

tag: cmv reactivation/day_of_onset

value: N

tag: cmv serotype

value: D-R-

tag: conditioning

value: CyTBI

value: GvHD

value: grade IV (d45)

value: placebo


title: Vegetative + 20nM bEST

description:
Library name: Sample3
bEST_20

value: vegetative


title: HEK293T, RNA, Smut transfected, rep3

description:
Library name: RNA_Smut_Rep3
Smut_3

value: Smut transfection


title: HEK293T, RNA, ASmut3 transfected, rep3

description:
Library name: RNA_ASmut3_Rep3
ASmut3_3

value: ASmut3 transfection


title: Epithelium, stage I561, rep d

description: Library name: I61d


title: Case_140, Chondrosarcoma

description: Sample ID: 207130360143_R04C01

value: Chondrosarcoma

tag: grade

value: high-grade

tag: origin

value: NL

value: WT

value: Scapula

value: male

value: alive


title: Case_149, Chondrosarcoma

description: Sample ID: 206644420109_R07C01

value: Rib

tag: gender

value: female

tag: follow-up

value: KRYO


title: Case_146, Chondrosarcoma

description: Sample ID: 206644410004_R01C01

value: Femur

tag: status

tag: tissue


title: Case_145, Chondrosarcoma

description: Sample ID: 206639830042_R07C01

value: Sternum


title: Case_139, Chondrosarcoma

description: Sample ID: 207130360143_R03C01

value: Pelvis


title: HEK293T, RNA, miR106a transfected, rep3

description:
Library name: RNA_miR106a_Rep3
106a_3

value: miR106a transfection


title: HEK293T, RNA, ASmut3 transfected, rep2

description:
Library name: RNA_ASmut3_Rep2
ASmut3_2


title: Case_138, Chondrosarcoma

description: Sample ID: 207130360090_R08C01


title: Vegetative + 40nM EtOH (volume matched)

description:
Library name: Sample2
EtOH_40

value: vegetative


title: OB2

city: GUANGZHOU

first: ZHU

last: TIANXIN

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital

description: circRNA expression from eWAT of OB2 mouse

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA V2 array at 65°C for 17 hours.

scan_protocol: The arrays were scanned using the Agilent Scanner G2505C.

data_processing: Raw data were extracted by Agilent Feature Extraction software, followed by quantile normalization and subsequent analyses using the R software limma package.

source_name: eWAT, OB2

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit).

extract_protocol: Total RNA was digested with Rnase R to remove linear RNAs and enrich circular RNAs.

treatment_protocol: eWAT was extracted from 16 week obese mice and littermate control mice, and RNA was extracted

tag: tissure

value: adipose


title: OB3

description: circRNA expression from eWAT of OB3 mouse

source_name: eWAT, OB3


title: Epithelium, stage I56, rep p

description: Library name: I56p

value: Intestinal epithelium

tag: Stage

tag: biological replicate


title: HEK293T, RNA, Smut transfected, rep2

description:
Library name: RNA_Smut_Rep2
Smut_2

value: Smut transfection


title: Case_137, Chondrosarcoma

description: Sample ID: 207130360090_R04C01

value: Chondrosarcoma

value: high-grade

tag: age


title: Vegetative + 20nM EtOH (volume matched)

description:
Library name: Sample1
EtOH_20

tag: strain

tag: genotype

value: WT

tag: cell type


title: Epithelium, stage I66, rep c

description: Library name: I66c


title: HEK293T, RNA, ASmut2 transfected, rep2

description:
Library name: RNA_ASmut2_Rep2
ASmut2_2

tag: cell line

tag: treatment

value: ASmut2 transfection


title: Case_141, Chondrosarcoma

description: Sample ID: 207130360143_R07C01

value: NL

value: male


title: Epithelium, stage I56, rep pilot

description: Library name: I56pilot


title: Ctrl3

description: circRNA expression from eWAT of Ctrl3 mouse

source_name: eWAT, Ctrl3


title: Case_136, Chondrosarcoma

description: Sample ID: 206644420120_R04C01

value: alive


title: HEK293T, RNA, let7a transfected, 50nM, rep3

description:
Library name: RNA_let7a_50_Rep3
let7_6

value: let7a 50nM transfection


title: HEK293T, RNA, ASmut1 transfected, rep3

description:
Library name: RNA_ASmut1_Rep3
ASmut1_3

value: ASmut1 transfection


title: Epithelium, stage I61, rep c

description: Library name: I61c


title: Case_135, Chondrosarcoma

description: Sample ID: 206639830042_R04C01

value: KRYO


title: HEK293T, RNA, miR106a transfected, rep2

description:
Library name: RNA_miR106a_Rep2
106a_2


title: Case_134, Chondrosarcoma

description: Sample ID: 206639830020_R07C01

value: Spine


title: Ctrl2

description: circRNA expression from eWAT of Ctrl2 mouse

source_name: eWAT, Ctrl2


title: Epithelium, stage I61, rep b

description: Library name: I61b


title: Epithelium, stage I61, rep a

description: Library name: I61a


title: OB1

description: circRNA expression from eWAT of OB1 mouse

source_name: eWAT, OB1


title: Epithelium, stage I56, rep a

description: Library name: I56a


title: HEK293T, RNA, ASmut1 transfected, rep2

description:
Library name: RNA_ASmut1_Rep2
ASmut1_2


title: NSC_Night_HY

description:
Library name: NS-18-Y
10X Genomics

value: Hypothalamus

value: Neural cells

value: normal sleep cycle


title: CK parallel sample 2

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

description: Library name: F2

data_processing:
Raw sequencing reads were processed following Illumina’s standard pipeline.
Assembly: Filtered reads were aligned to the E. coli reference genome (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000005845.2/) using Bowtie2 (v2.4.2)
Supplementary files format and content: csv file include TPM values for each sample
Supplementary files format and content: csv file include FPKM values for each sample

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Strains were grown in TSB medium at 37  °C with shaking at 180 rpm in the dark.

extract_protocol:
Total RNA was extracted from E. coli samples using the cetyltrimethylammonium bromide method.
RNA-seq libraries were prepared using the Illumina® Stranded mRNA Prep Kit (Illumina, USA).

treatment_protocol: In the co-culture system, E. coli and S. aureus were grown to stationary phase in TSB medium and mixed equally. This mixture was then inoculated at 1% into 500 μL of TSB medium, with three different treatments: (1) no additive, (2) 0.5 mg/L AgNPs, and (3) 0.5 mg/L Ag+. Each condition had 24 replicates. Monocultures of E. coli and S. aureus were also cultivated separately under each of the three conditions, with 9 replicates for each treatment. All cultures were kept in 96-well deep plates at 37 °C with shaking at 160 rpm. Every 24 h, 1% of the culture was transferred to fresh medium under the same conditions until a dominant species emerged in the co-culture system, over a total period of 9 days.

value: bacterial cell

value: wt

value: CK parallel sample


title: Case_129, Chondrosarcoma

description: Sample ID: 206644410004_R07C01

value: Chondrosarcoma

value: Thorax


title: HEK293T, RNA, ASmut2 transfected, rep1

description:
Library name: RNA_ASmut2_Rep1
ASmut2_1


title: 8hr sporulation media input 2

description: Library name: EUAB004_30_S30

data_processing:
ChIP-seq reads were aligned to the SK1 genome using Bowtie2 version 2.3.4.1
The output SAM files were converted to BAM format and sorted using samtools version 1.7.
Peaks were called using MACS2 version 2.2.9.1 with a significance cut-off q-value <= 0.01.
Peaks were annotated using ChIPseeker version 1.44.0. This was done by finding overlap between summits (called by MACS2) and promoters (defined here as 600bp upstream of each gene). Only peaks with a fold enrichment of ChIP/input >=4 were used for this analysis.
Assembly: ASM205788v1
Supplementary files format and content: score (-log10(q-value))

organism: Saccharomyces cerevisiae SK1

growth_protocol: Vegetative: Strains were grown with YPD at 30 degrees with shaking. Meiotic: Strains were grown in YPD at 30 degrees until saturation before back dilution and growth in BYTA. Strains were grown at 30 degrees in BYTA until saturation before washing with water and resuspention in sporulation media. Premeiotic starvation: Strains were grown with YPD at 30 degees with shaking until saturation. Strains were back diluted in BYTA media.

extract_protocol:
Cells were fixed using fresh 1% formaldehyde (Sigma Aldrich 252549) with periodic inversion at room temperature for 15 minutes. The crosslinking reactions were quenched using 125mM glycine (Fisher BP381-1) with light shaking for 5 minutes. Cells were pelleted at 4°C, then washed using ice cold PBS and pelleted again. Supernatant was discarded and cell pellets were resuspended in cold FA lysis buffer (50 mM Hepes pH 7.5 (Fisher BP310-1), 150 mM NaCl, 1 mM EDTA, 1% Triton (Sigma Aldrich T9284), 0.1% sodium deoxycholate (Sigma Aldrich D6750)) with 0.1% SDS and protease inhibitors (Roche cOmplete protease inhibitor cocktail, PMSF, Pepstatin A). SDS was added fresh to every buffer from a 20% stock solution. Samples were centrifuged, supernatant was discarded, and pellets were flash frozen in liquid nitrogen. For the BYTA ChIP collection, a BYTA culture was started at an OD600 of 0.2 and grown at 30°C. Approximately 90 OD600 units of cells were harvested at 6 hour and 21 hour timepoints. Cells were treated as above. For the meiotic ChIP collection, SPO cultures were set up at on OD600 of 1.9 at 30°C. Approximately 170 OD600 units of cells were harvested at 5 hour 30 minutes, 6 hour 45 minutes, and 8 hour timepoints. Approximately 500uL Zirconia beads (Biospec 11079105z) were added to cell pellets, and cells were resuspended in cold FA lysis buffer with 0.1% SDS and protease inhibitors and lysed by Beadbeater (Mini-Beadbeater-96, Biospec Products). Lysates were collected by centrifuging at 500xg for 1 min. All centrifugation steps were carried out at 4°C. Cell debris was pelleted at 2000xg for 3 min. Supernatants were retrieved and centrifuged at 20,000xg for 15 minutes to pellet chromatin. Chromatin pellets were resuspended in cold FA lysis buffer with 0.1% SDS and protease inhibitors and moved to 15 mL sonication tubes containing 300 uL sonication beads (Diagenode C01020031). Samples were sonicated in a Bioruptor Pico (Diagenode) for 30 seconds on / 30 seconds off for 8 cycles to generate fragments around 150–400 bp. Samples were centrifuged at 20,000xg for 1 min and supernatant was saved for use in the immunoprecipitation (IP).
Sequencing libraries were generated using the NEXTFLEX Rapid DNA-Seq kit 2.0 according to manufacturer’s instructions (Revvity NOVA 5188-02). SPRIselect beads were used to select for fragments between 200-700 bp (Beckman Coulter B23318). Libraries were quantified using a Qubit fluorometer (Invitrogen), and library size was checked using the Agilent 4200 TapeStation (Agilent Technologies, Inc). Samples were submitted for 150 bp paired-end sequencing on the NovaSeq X at the Vincent J. Coates Genomics Sequencing Laboratory (QB3 Genomics, UC Berkeley, Berkeley, CA, RRID:SCR_022170).

treatment_protocol: Vegetative cells were harvested in exponential growth phase (OD600=0.6). Premeiotic cells were harvested at times indicated, with 0hr being the time that the cells were transfered from YPD to BYTA media. Meiotic cells were harvested at times indicated, with 0 hr being the time that the cells were transferred into sporulation media.

value: WT

value: meiotic


title: HEK293T, RNA, ASmut1 transfected, rep1

description:
Library name: RNA_ASmut1_Rep1
ASmut1_1


title: HEK293T, RNA, let7a transfected, 50nM, rep2

description:
Library name: RNA_let7a_50_Rep2
let7_5


title: Epithelium, stage I56, rep b

description: Library name: I56b

value: Intestinal epithelium


title: HEK293T, RNA, miR106b transfected, rep2

description:
Library name: RNA_miR106b_Rep2
106b_2

value: miR106b transfection


title: 8hr sporulation media input 1

description: Library name: EUAB004_27_S27


title: coculture with S.aureus and AgNPs treatment parallel sample 2

description: Library name: E2


title: HEK293T, RNA, Smut transfected, rep1

description:
Library name: RNA_Smut_Rep1
Smut_1

value: Smut transfection


title: Case_124, Chondrosarcoma

description: Sample ID: 206644420120_R02C01

value: high-grade

value: NL

value: male

value: alive


title: CK parallel sample 3

description: Library name: F3


title: coculture with S.aureus parallel sample 3

description: Library name: C3

value: coculture with S.aureus parallel sample


title: Case_123, Chondrosarcoma

description: Sample ID: 206644420023_R06C01

value: Sternum

value: KRYO


title: Case_133, Chondrosarcoma

description: Sample ID: 206639830020_R05C01

value: Skin


title: CK parallel sample 1

description: Library name: F1

value: bacterial cell

value: wt


title: 6hr 45min sporulation media ChIP 1

description: Library name: EUAB004_40_S40


title: HEK293T, RNA, ASmut3 transfected, rep1

description:
Library name: RNA_ASmut3_Rep1
ASmut3_1

value: ASmut3 transfection


title: Ctrl1

description: circRNA expression from eWAT of Ctrl1 mouse

source_name: eWAT, Ctrl1

value: adipose


title: 6hr 45min sporulation media ChIP 2

description: Library name: EUAB004_43_S43

value: WT


title: Case_127, Chondrosarcoma

description: Sample ID: 207130360153_R06C01

value: Chondrosarcoma

value: Thorax


title: 8hr sporulation media ChIP 2

description: Library name: EUAB004_44_S44

value: meiotic


title: Case_126, Chondrosarcoma

description: Sample ID: 207130360143_R05C01

value: Rib


title: coculture with S.aureus and AgNPs treatment parallel sample 3

description: Library name: E3


title: coculture with S.aureus and AgNPs treatment parallel sample 1

description: Library name: E1


title: coculture with S.aureus parallel sample 2

description: Library name: C2


title: 8hr sporulation media ChIP 1

description: Library name: EUAB004_41_S41


title: HEK293T, RNA, miR106a transfected, rep1

description:
Library name: RNA_miR106a_Rep1
106a_1

value: miR106a transfection


title: Case_125, Chondrosarcoma

description: Sample ID: 206644420120_R06C01

value: high-grade

value: NL

value: female


title: coculture with S.aureus parallel sample 1

description: Library name: C1

value: coculture with S.aureus parallel sample


title: HEK293T, RNA, let7a transfected, 50nM, rep1

description:
Library name: RNA_let7a_50_Rep1
let7_4

value: let7a 50nM transfection


title: Case_121, Chondrosarcoma

description: Sample ID: 206644410047_R08C01

value: alive

value: KRYO


title: HEK293T, RNA, ASmut3_let7a transfected, rep3

description:
Library name: RNA_ASmut3+let7a_Rep3
ASmut3_let7_3

value: ASmut3+let7a co-transfection


title: Case_122, Chondrosarcoma

description: Sample ID: 206644420023_R01C01


title: Case_120, Chondrosarcoma

description: Sample ID: 206644410047_R05C01


title: HEK293T, RNA, ASmut2+let7a transfected, rep3

description:
Library name: RNA_ASmut2+let7a_Rep3
ASmut2_let7_3

value: ASmut2+let7a co-transfection


title: coculture with S.aureus and Ag+ treatment parallel sample 2

description: Library name: B2

value: bacterial cell

value: wt


title: HEK293T, RNA, miR106b transfected, rep1

description:
Library name: RNA_miR106b_Rep1
106b_1

value: miR106b transfection


title: 5.5hr sporulation media ChIP 2

description: Library name: EUAB004_42_S42

value: WT


title: Case_119, Chondrosarcoma

description: Sample ID: 206644410004_R02C01

value: Chondrosarcoma

value: Tibia

value: male


title: 5.5hr sporulation media ChIP 1

description: Library name: EUAB004_39_S39

value: meiotic


title: 5.5hr sporulation media input 2

description: Library name: EUAB004_28_S28


title: HEK293T, RNA, ASmut1+let7a transfected, rep3

description:
Library name: RNA_ASmut1+let7a_Rep3
ASmut1_let7_3

value: ASmut1+let7a co-transfection


title: coculture with S.aureus and Ag+ treatment parallel sample 1

description: Library name: B1


title: 5.5hr sporulation media input 1

description: Library name: EUAB004_25_S25


title: 6hr 45min sporulation media input 1

description: Library name: EUAB004_26_S26


title: Case_118, Chondrosarcoma

description: Sample ID: 206639830020_R03C01

value: high-grade

value: NL

value: Sternum


title: 21hr BYTA ChIP 1

description: Library name: EUAB004_36_S36

value: premeiotic starvation


title: AgMPs parallel sample 1

description: Library name: A1

value: AgMPs parallel sample


title: HEK293T, RNA, miR106a+let7a transfected, rep3

description:
Library name: RNA_miR106a+let7a_Rep3
106a_let7_3

value: miR106a+let7a co-transfection


title: 6hr 45min sporulation media input 2

description: Library name: EUAB004_29_S29


title: 21hr BYTA ChIP 2

description: Library name: EUAB004_38_S38


title: coculture with S.aureus and Ag+ treatment parallel sample 3

description: Library name: B3


title: Case_117, Chondrosarcoma

description: Sample ID: 206897320048_R04C01

source_name: FFPE

value: low-grade

value: BSL

value: Rib

value: alive

value: FFPE


title: Case_112, Chondrosarcoma

description: Sample ID: 206184840116_R04C01

value: MUT

value: Skull

value: female


title: Case_116, ACT

description: Sample ID: 206897310046_R08C01

value: ACT

value: FAILED

value: Humerus


title: Case_111, Chondrosarcoma

description: Sample ID: 205809360171_R01C01

value: Chondrosarcoma


title: HEK293T, RNA, miR106b+let7a transfected, rep3

description:
Library name: RNA_miR106b+let7a_Rep3
106b_let7_3

value: miR106b+let7a co-transfected


title: HEK293T, RNA, mock transfected, rep3

description:
Library name: RNA_mock_Rep3
mock_3

value: mock transfection


title: AgMPs parallel sample 2

description: Library name: A2

value: bacterial cell

value: wt


title: Spirodela polyrhiza, Tract region, replicate 3

description:
Library name: Spirodela_Tract_3
RNA-seq of Spirodela Tract region, biological replicate 3

data_processing:
Salmon v1.10.0
Reads were pseudo-aligned and quantified using Salmon v1.10.0 with --validateMappings against a gentrome index built from the species-specific reference transcriptome and genome as decoys.
TPM values were extracted from Salmon quant.sf output files and assembled into gene x sample matrices.
Genes were filtered to remove those where max organ-averaged TPM was not at least 2.0 in at least one organ.
Assembly: Spirodela polyrhiza: Sp_polyrhiza_9509-REF-OXFORD-3.0 (lemna.org); Pistia stratiotes: chromosome-level assembly, Qian et al. 2022 (Molecular Ecology Resources 22:2732-2743, doi:10.1111/1755-0998.13653)
Supplementary files format and content: CSV files containing TPM (Transcripts Per Million) values for each gene across all samples per species

organism: Spirodela polyrhiza

source_name: Tract

extract_protocol:
Duckweed samples (Spirodela): Samples were recovered from RNAlater by sieving through 70uM cell strainers, blotted from underneath with tissue paper to remove excess RNAlater, and snap frozen. Samples were ground on liquid nitrogen in 1.5ml Eppendorf tubes with plastic pestles. RNA was extracted using a RNeasy UCP Micro Kit (Qiagen) as per manufacturer's instructions.
Pistia: RNA extractions were performed using a RNeasy kit (Qiagen) as per manufacturer's instructions with an additional RPE wash.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies). Library preparation and sequencing were performed by Novogene. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. After adenylation of 3' ends, adaptors with hairpin loop structure were ligated. Library fragments of 370-420 bp were purified with AMPure XP system (Beckman Coulter). PCR was performed with Phusion High-Fidelity DNA polymerase. Clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Libraries were sequenced on an Illumina NovaSeq platform generating 150 bp paired-end reads.

value: Tract

tag: strain/clone


title: 6hr BYTA ChIP 1

description: Library name: EUAB004_35_S35

value: WT

value: premeiotic starvation


title: HEK293T, RNA, ASmut3+let7a transfected, rep2

description:
Library name: RNA_ASmut3+let7a_Rep2
ASmut3_let7_2

value: ASmut3+let7a co-transfection


title: Spirodela polyrhiza, Tract region, replicate 1

description:
Library name: Spirodela_Tract_1
RNA-seq of Spirodela Tract region, biological replicate 1


title: Case_110, Chondrosarcoma

description: Sample ID: 203808720128_R03C01

value: low-grade

value: BSL

value: NP (unsufficient materials left)

value: alive


title: Spirodela polyrhiza, Tract region, replicate 2

description:
Library name: Spirodela_Tract_2
RNA-seq of Spirodela Tract region, biological replicate 2


title: HEK293T, RNA, ASmut2+let7a transfected, rep2

description:
Library name: RNA_ASmut2+let7a_Rep2
ASmut2_let7_2

value: ASmut2+let7a co-transfection


title: Case_109, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360153_R04C01

value: Dedifferentiated chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Femur

value: male

value: KRYO


title: 6hr BYTA input 2

description: Library name: EUAB004_23_S23


title: HEK293T, RNA, neg control transfected, rep3

description:
Library name: RNA_neg_Rep3
neg_3

value: neg control transfection


title: Spirodela polyrhiza, Node region, replicate 4

description:
Library name: Spirodela_Node_4
RNA-seq of Spirodela Node region, biological replicate 4

source_name: Node

value: Node


title: AgMPs parallel sample 3

description: Library name: A3

value: bacterial cell

value: wt

value: AgMPs parallel sample


title: HEK293T, RNA, Smut+let7a transfected, rep3

description:
Library name: RNA_Smut+let7a_Rep3
Smut_let7_3

value: Smut+let7a co-transfection


title: HEK293T, RNA, ASmut1+let7a transfected, rep2

description:
Library name: RNA_ASmut1+let7a_Rep2
ASmut1_let7_2

value: ASmut1+let7a co-transfection


title: 21hr BYTA input 2

description: Library name: EUAB004_24_S24

value: WT

value: premeiotic starvation


title: Spirodela polyrhiza, Tract region, replicate 4

description:
Library name: Spirodela_Tract_4
RNA-seq of Spirodela Tract region, biological replicate 4

value: Tract


title: Case_113, Chondrosarcoma

description: Sample ID: 206639830042_R06C01

value: Chondrosarcoma

value: Head & Neck

value: female

value: alive


title: HEK293T, RNA, let7a transfected, 10nM, rep3

description:
Library name: RNA_let7a_Rep3
let7_3

value: let7a 10nM transfection


title: 6hr BYTA input 1

description: Library name: EUAB004_21_S21


title: 6hr BYTA ChIP 2

description: Library name: EUAB004_37_S37


title: 21hr BYTA input 1

description: Library name: EUAB004_22_S22


title: HEK293T, RNA, Smut+let7a transfected, rep2

description:
Library name: RNA_Smut+let7a_Rep2
Smut_let7_2


title: Case_105, ACT

description: Sample ID: 206644420109_R05C01

value: ACT

value: low-grade

value: NL

value: MUT

value: Humerus


title: vegetative + DTT ChIP 2

description: Library name: EUAB004_34_S34

value: vegetative + DTT


title: Case_103, ACT

description: Sample ID: 206644420100_R05C01

value: Tibia

value: KRYO


title: Case_104, ACT

description: Sample ID: 206644420100_R07C01

value: Femur


title: Spirodela polyrhiza, Node region, replicate 1

description:
Library name: Spirodela_Node_1
RNA-seq of Spirodela Node region, biological replicate 1

value: Node


title: Spirodela polyrhiza, Node region, replicate 2

description:
Library name: Spirodela_Node_2
RNA-seq of Spirodela Node region, biological replicate 2


title: HEK293T, RNA, miR106b+let7a transfected, rep2

description:
Library name: RNA_miR106b+let7a_Rep2
106b_let7_2

value: miR106b+let7a co-transfected


title: vegetative + DTT input 2

description: Library name: EUAB004_20_S20

value: WT


title: HEK293T, RNA, let7a transfected, 10nM, rep2

description:
Library name: RNA_let7a_Rep2
let7_2


title: Case_102, ACT

description: Sample ID: 206644410047_R03C01


title: T26_0184

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

description: failed QC

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC version 2 array using standard Illumina protocols

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended Illumina scanner protocols

data_processing: SeSAMe pipline (v1.24.0)

label: Cy3 and Cy5

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: vegetative +DTT input 1

description: Library name: EUAB004_18_S18


title: Case_101, ACT

description: Sample ID: 206644410004_R05C01


title: T26_0065

description: failed QC


title: HEK293T, RNA, mock transfected, rep2

description:
Library name: RNA_mock_Rep2
mock_2

value: mock transfection


title: Case_100, ACT

description: Sample ID: 206644410004_R03C01

value: female


title: T26_0201

description: failed QC


title: vegetative ChIP 1

description: Library name: EUAB004_31_S31

value: vegetative


title: HEK293T, RNA, neg control transfected, rep2

description:
Library name: RNA_neg_Rep2
neg_2

value: neg control transfection


title: Spirodela polyrhiza, Node region, replicate 3

description:
Library name: Spirodela_Node_3
RNA-seq of Spirodela Node region, biological replicate 3


title: HEK293T, RNA, miR106a+let7a transfected, rep2

description:
Library name: RNA_miR106a+let7a_Rep2
106a_let7_2

value: miR106a+let7a co-transfection


title: T26_0225

description: failed QC


title: HEK293T, RNA, ASmut1+let7a transfected, rep1

description:
Library name: RNA_ASmut1+let7a_Rep1
ASmut1_let7_1

value: ASmut1+let7a co-transfection


title: vegetative +DTT ChIP 1

description: Library name: EUAB004_32_S32


title: vegetative input 1

description: Library name: EUAB004_17_S17


title: Case_106, ACT

description: Sample ID: 206644420109_R06C01

value: ACT

value: low-grade

value: NL

value: alive


title: vegetative ChIP 2

description: Library name: EUAB004_33_S33


title: Case_169, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170089_R05C01

value: Dedifferentiated chondrosarcoma

value: high-grade

value: SWE

value: Sternum

value: male

value: FFPE


title: T26_0282

description: failed QC

value: meningioma


title: T26_0285

description: failed QC


title: Case_168, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170072_R07C01

value: WT

value: Femur


title: vegetative input 2

description: Library name: EUAB004_19_S19

value: vegetative


title: HEK293T, RNA, miR106b+let7a transfected, rep1

description:
Library name: RNA_miR106b+let7a_Rep1
106b_let7_1

value: miR106b+let7a co-transfected


title: hac1 +aTC BYTA 6hr rep2

description:
Library name: Sample35
hac1_aTc_6hr_BYTA_2

data_processing:
Used Star align on untrimmed reads to SK1 reference genome - outputs bam files and optionally outputs unique alignment reads
Used samtools index to index the bam files outputted from star align
feature counts command used to assemble raw counts numbers for all files
Assembly: GCA_000766265.2
Supplementary files format and content: .csv files contain RPKM values

extract_protocol:
Cells were harvested via pelleting liquid culture at 6000 RCF then aspirating media before snap freezing in liquid nitrogen. Cells were thawed on ice and resuspended in 625ul TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). An equal volume of citrate-buffered acid phenol (pH 4.3, P4682, Sigma-Aldrich) was added to cells, and they were incubated at 65C for 1 hour in a Thermomixer C (Eppendorf) shaking at 1400 RPM. After microcentrifugation (20,000 g for 10 min) the aqueous phase was transferred to a second tube with 600ul acid phenol. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and transferred to a third tube with 600ul chloroform. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and RNA was precipitated in 100% isopropanol with 350 mM sodium acetate (pH 5.2) overnight at –20C. Pellets were washed with 80% ethanol and resuspended in DEPC water
RNA-seq libraries for three biological replicates were generated with the NEXTflex Rapid Directional mRNA-Seq Bundle with poly(A) beads (NOVA-5138, Bioo Scientific) according to manufacturer’s instructions. 10 mg of total RNA was used as input for all libraries. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp. Libraries were quantified using the Agilent 4200 TapeStation (Agilent Technologies, Inc). Samples were submitted for 100 bp single-end sequencing by the Vincent J. Coates Genomics Sequencing Laboratory with a NovaSeq X.

value: hac1 delete

value: premeiotic starvation


title: Case_167, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170072_R05C01

value: Thorax


title: HEK293T, RNA, ASmut2+let7a transfected, rep1

description:
Library name: RNA_ASmut2+let7a_Rep1
ASmut2_let7_1

value: ASmut2+let7a co-transfection


title: HEK293T, RNA, miR106a+let7a transfected, rep1

description:
Library name: RNA_miR106a+let7a_Rep1
106a_let7_1

value: miR106a+let7a co-transfection


title: HEK293T, RNA, ASmut3+let7a transfected, rep1

description:
Library name: RNA_ASmut3+let7a_Rep1
ASmut3_let7_1

value: ASmut3+let7a co-transfection


title: hac1 +aTC BYTA 21hr rep1

description:
Library name: Sample34
hac1_aTc_21hr_BYTA_1


title: hac1 +aTC BYTA 6hr rep1

description:
Library name: Sample33
hac1_aTc_6hr_BYTA_1


title: Case_87, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360153_R08C01

value: Dedifferentiated chondrosarcoma

value: NL

value: MUT

value: Humerus

value: dead of unknown cause

value: KRYO


title: HEK293T, RNA, Smut+let7a transfected, rep1

description:
Library name: RNA_Smut+let7a_Rep1
Smut_let7_1

value: Smut+let7a co-transfection


title: Case_97, ACT

description: Sample ID: 206639830002_R05C01

value: ACT

value: low-grade

value: female

value: alive


title: hac1 +aTC BYTA 21hr rep2

description:
Library name: Sample36
hac1_aTc_21hr_BYTA_2

value: hac1 delete


title: Case_99, ACT

description: Sample ID: 206639830020_R02C01


title: Case_96, ACT

description: Sample ID: 206639830002_R02C01

value: Femur


title: Case_85, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360090_R06C01

value: high-grade

value: Pelvis

value: male


title: Case_86, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360153_R07C01


title: HEK293T, RNA, neg control transfected, rep1

description:
Library name: RNA_neg_Rep1
neg_1

value: neg control transfection


title: Case_164, Chondrosarcoma

description: Sample ID: 208404170089_R07C01

value: Chondrosarcoma

value: GX

value: SWE

value: WT

value: FFPE


title: hac1 BYTA 6hr rep2

description:
Library name: Sample31
hac1_EtOH_6hr_BYTA_2

value: premeiotic starvation


title: Case_98, ACT

description: Sample ID: 206639830020_R01C01

value: NL

value: MUT

value: Humerus

value: KRYO


title: Case_84, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360090_R02C01

value: Dedifferentiated chondrosarcoma

value: dead of unknown cause


title: Case_166, Dedifferentiated chondrosarcoma

description: Sample ID: 207961470091_R08C01

value: Rib

value: female


title: Case_95, ACT

description: Sample ID: 206639830002_R01C01

value: ACT

value: low-grade

value: alive


title: hac1 BYTA 21hr rep1

description:
Library name: Sample30
hac1_EtOH_21hr_BYTA_1

value: hac1 delete


title: Case_82, Dedifferentiated chondrosarcoma

description: Sample ID: 206644420120_R08C01

value: high-grade

value: Scapula

value: DoD


title: Case_81, Dedifferentiated chondrosarcoma

description: Sample ID: 206644420109_R03C01

value: Femur

value: male


title: Case_163, Chondrosarcoma

description: Sample ID: 208404170105_R07C01

value: Chondrosarcoma

value: SWE

value: IDH1 WT (IDH2 Failed)

value: Thorax

value: FFPE


title: Case_162, Chondrosarcoma

description: Sample ID: 208404170089_R06C01

value: WT

value: Spine


title: hac1 BYTA 21hr rep2

description:
Library name: Sample32
hac1_EtOH_21hr_BYTA_2

value: premeiotic starvation


title: HEK293T, smallRNA, ASmut1 transfected, rep3

description:
Library name: smallRNA_ASmut1_Rep3
ASmut1_3

value: ASmut1 transfection


title: HEK293T, RNA, let7a transfected, 10nM, rep1

description:
Library name: RNA_let7a_Rep1
let7_1

value: let7a 10nM transfection


title: HEK293T, smallRNA, ASmut2 transfected, rep3

description:
Library name: smallRNA_ASmut2_Rep3
ASmut2_3

value: ASmut2 transfection


title: Case_160, Chondrosarcoma

description: Sample ID: 208404170087_R04C01

value: Rib

value: female


title: WT BYTA 21hr rep2

description:
Library name: Sample28
WT_21hr_BYTA_2


title: HEK293T, smallRNA, Smut transfected, rep3

description:
Library name: smallRNA_Smut_Rep3
Smut_3

value: Smut transfection


title: Case_83, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360090_R01C01

value: Dedifferentiated chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Pelvis

value: alive

value: KRYO


title: Case_159, Chondrosarcoma

description: Sample ID: 208404170087_R03C01

value: Chondrosarcoma

value: SWE

value: IDH1 WT (IDH2 Failed)

value: Femur

value: male

value: FFPE


title: hac1 BYTA 6hr rep1

description:
Library name: Sample29
hac1_EtOH_6hr_BYTA_1

value: hac1 delete

value: premeiotic starvation


title: HEK293T, smallRNA, ASmut3 transfected, rep3

description:
Library name: smallRNA_ASmut3_Rep3
ASmut3_3

value: ASmut3 transfection


title: WT BYTA 6hr rep2

description:
Library name: Sample27
WT_6hr_BYTA_2

value: WT


title: Case_161, Chondrosarcoma

description: Sample ID: 208404170089_R03C01

value: Thorax

value: female


title: Case_158, Chondrosarcoma

description: Sample ID: 208404170072_R08C01

value: high-grade


title: Case_79, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410006_R01C01

value: Dedifferentiated chondrosarcoma

value: BSL

value: MUT


title: WT BYTA 21hr rep1

description:
Library name: Sample26
WT_21hr_BYTA_1


title: HEK293T, smallRNA, miR106b transfected, rep3

description:
Library name: smallRNA_miR106b_Rep3
106b_3

value: miR106b transfection


title: Case_78, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410005_R07C01


title: Case_80, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410006_R02C01

value: IDH1 WT (IDH2 failed)

value: alive


title: hac1 9.5hr sporulation media rep2

description:
Library name: Sample24
hac1_9_5hr_2

value: meiotic


title: WT BYTA 6hr rep1

description:
Library name: Sample25
WT_6hr_BYTA_1


title: hac1 8hr sporulation media rep2

description:
Library name: Sample23
hac1_8hr_2


title: Case_142, Chondrosarcoma

description: Sample ID: 207961470049_R03C01

value: Chondrosarcoma

value: SWE

value: Spine

value: KRYO


title: Case_77, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410005_R03C01

value: NP (unsufficient materials left)

value: Femur

value: FFPE


title: Case_76, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410005_R02C01

value: FAILED

value: Pelvis


title: HEK293T, smallRNA, miR106a transfected, rep3

description:
Library name: smallRNA_miR106a_Rep3
106a_3

value: miR106a transfection


title: HEK293T, RNA, mock transfected, rep1

description:
Library name: RNA_mock_Rep1
mock_1

value: mock transfection


title: Case_132, Chondrosarcoma

description: Sample ID: 208404170077_R05C01

value: low-grade

value: WT


title: HEK293T, smallRNA, ASmut2 transfected, rep2

description:
Library name: smallRNA_ASmut2_Rep2
ASmut2_2

value: ASmut2 transfection


title: HEK293T, smallRNA, ASmut3 transfected, rep2

description:
Library name: smallRNA_ASmut3_Rep2
ASmut3_2

value: ASmut3 transfection


title: hac1 5.5hr sporulation media rep2

description:
Library name: Sample21
hac1_5_5hr_2

value: hac1 delete


title: Case_143, Chondrosarcoma

description: Sample ID: 208404170090_R05C01

value: high-grade

value: IDH1 WT (IDH2 Failed)

value: female


title: hac1 6hr 45 minute sporulation media rep2

description:
Library name: Sample22
hac1_6hr_45min_2

value: meiotic


title: Case_75, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410004_R08C01

value: Dedifferentiated chondrosarcoma

value: BSL

value: male

value: DoD


title: Case_131, Chondrosarcoma

description: Sample ID: 208404170042_R06C01

value: Chondrosarcoma

value: SWE

value: KRYO


title: HEK293T, smallRNA, let7a transfected, 50nM, rep3

description:
Library name: smallRNA_let7a_50_Rep3
let7_6

value: let7a 50nM transfection


title: Case_144, Chondrosarcoma

description: Sample ID: 208404170105_R06C01

value: Humerus

value: FFPE


title: hac1 9.5hr sporulation media rep1

description:
Library name: Sample20
hac1_9_5hr_1


title: HEK293T, smallRNA, ASmut1 transfected, rep2

description:
Library name: smallRNA_ASmut1_Rep2
ASmut1_2

value: ASmut1 transfection


title: Case_130, Chondrosarcoma

description: Sample ID: 208404170087_R06C01

value: WT

value: Foot


title: hac1 8hr sporulation media rep1

description:
Library name: Sample19
hac1_8hr_1

value: hac1 delete


title: Case_128, Chondrosarcoma

description: Sample ID: 208404170109_R03C01

value: high-grade

value: Thorax


title: HEK293T, smallRNA, Smut transfected, rep2

description:
Library name: smallRNA_Smut_Rep2
Smut_2

value: Smut transfection


title: Case_71, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360153_R05C01

value: Dedifferentiated chondrosarcoma

value: NL

value: MUT

value: Shoulder

value: alive


title: HEK293T, smallRNA, miR106b transfected, rep2

description:
Library name: smallRNA_miR106b_Rep2
106b_2

value: miR106b transfection


title: Case_69, Dedifferentiated chondrosarcoma

description: Sample ID: 206644420120_R07C01

value: Femur

value: male

value: dead of unknown cause

value: KRYO


title: hac1 6hr 45 minute sporulation media rep1

description:
Library name: Sample18
hac1_6hr_45min_1

value: meiotic


title: Case_115, Chondrosarcoma

description: Sample ID: 208404170072_R04C01

value: Chondrosarcoma

value: SWE

value: WT

value: Head & Neck

value: female

value: FFPE


title: Case_68, Dedifferentiated chondrosarcoma

description: Sample ID: 206639830020_R04C01

value: Dedifferentiated chondrosarcoma

value: high-grade


title: HEK293T, smallRNA, miR106a transfected, rep2

description:
Library name: smallRNA_miR106a_Rep2
106a_2

value: miR106a transfection


title: Case_67, Dedifferentiated chondrosarcoma

description: Sample ID: 201904410005_R06C01

value: BSL

value: MUT

value: Pelvis

value: DoD


title: Case_108, Chondrosarcoma

description: Sample ID: 208404170105_R05C01

value: GX

value: male


title: HEK293T, smallRNA, let7a transfected, 50nM, rep2

description:
Library name: smallRNA_let7a_50_Rep2
let7_5

value: let7a 50nM transfection


title: WT 8hr sporulation media rep2

description:
Library name: Sample15
WT_8hr_2

value: meiotic


title: Case_55, Chondrosarcoma

description: Sample ID: 207130360143_R01C01

value: Chondrosarcoma

value: NL

value: Femur

value: KRYO


title: HEK293T, smallRNA, Smut transfected, rep1

description:
Library name: smallRNA_Smut_Rep1
Smut_1

value: Smut transfection


title: Case_53, Chondrosarcoma

description: Sample ID: 206644420120_R05C01

value: Tibia

value: dead of unknown cause


title: Case_94, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170105_R08C01

value: Dedifferentiated chondrosarcoma

value: high-grade

value: SWE

value: IDH1 WT (IDH2 Failed)

value: FFPE


title: Case_107, Chondrosarcoma

description: Sample ID: 207961480091_R06C01

value: low-grade

value: WT

value: Rib


title: HEK293T, smallRNA, ASmut1 transfected, rep1

description:
Library name: smallRNA_ASmut1_Rep1
ASmut1_1

value: ASmut1 transfection


title: WT 5.5hr sporulation media rep2

description:
Library name: Sample13
WT_5_5hr_2

value: meiotic


title: WT 6hr 45 minute sporulation media rep2

description:
Library name: Sample14
WT_6hr_45min_2


title: Case_93, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170105_R01C01

value: MUT

value: female


title: Case_51, Chondrosarcoma

description: Sample ID: 206644420100_R02C01

value: Chondrosarcoma

value: NL

value: Humerus

value: male

value: alive


title: WT 9.5hr sporulation media rep1

description:
Library name: Sample12
WT_9_5hr_1


title: Case_91, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170089_R04C01

value: Dedifferentiated chondrosarcoma

value: Femur


title: WT 8hr sporulation media rep1

description:
Library name: Sample11
WT_8hr_1


title: HEK293T, smallRNA, ASmut2+let7a transfected, rep3

description:
Library name: smallRNA_ASmut2+let7a_Rep3
ASmut2_let7_3

value: ASmut2+let7a co-transfection


title: Case_47, Chondrosarcoma

description: Sample ID: 206639830002_R06C01

value: high-grade

value: Pelvis

value: KRYO


title: HEK293T, smallRNA, ASmut3_let7a transfected, rep3

description:
Library name: smallRNA_ASmut3+let7a_Rep3
ASmut3_let7_3

value: ASmut3+let7a co-transfection


title: Case_74, Chondrosarcoma

description: Sample ID: 208404170109_R04C01

value: GX

value: SWE

value: WT

value: FFPE


title: Case_70, Dedifferentiated chondrosarcoma

description: Sample ID: 207130360090_R03C01

value: MUT

value: Lung


title: Case_114, Chondrosarcoma

description: Sample ID: 208404170087_R07C01

value: Chondrosarcoma

value: Skull

value: female