title: Mouse kidney, PT-2385, 4

city: Adelaide

first: Alison

middle: Elizabeth

last: Roennfeldt

state: SA

address: Adelaide Health and Medical Sciences Building

country: Australia

institute: The University of Adelaide

description: Library name: Kidney_PT4

data_processing:
FastQC was used to check for overrepresentaed adapters
Adapters trimmed using AdapterRemoval
Assembly: Trimmed reads aligned to GRCm39/mm39 using STAR and transcriptome read counts were quantified using featureCounts
Supplementary files format and content: Tab delimited txt files contain the raw counts for each sample

source_name: Kidney

growth_protocol: 21 day old female CBAF1 female mice were maintained in 12-hour light / 12-hour dark conditions for the duration of the expeirment

extract_protocol:
Ovary: RNA extracted using the Monarch Total RNA miniprep kit. Kidney: RNA extracted using trizol. 1.8 - 5 ug total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep kit as per the manufacturers protocol.

treatment_protocol: Mice were injected i.p. in saline with 7.5 mg/kg PT-2385 or vehicle DMSO 12-hourly for 4 days. Within this 4 day period, mice were treated i.p. with 5 IU PMSG, then 13 h 5 IU hCG. Tissue collected at the 13 h hCG timepoint.

value: Kidney

value: 7.5 mg/kg PT-2385 in saline 12-hourly for 4 days, including 48 h 5 IU PMSG then 13 h 5 IU hCG


title: palbo 5

status: Public on Feb 15 2026

type: SRA

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Library name: 38314 P5

library_source: transcriptomic

data_processing:
Sequencing reads were mapped separately to Human (GRCh38) and Mouse (GRCm37) genomes using STAR aligner (version 2.7.11a)
R-package XenofilteR was then used to separate mouse reads from human sequence reads. Gene based counting was performed on the human reads using the featureCount function from Rsubread package
Gene count data was used assess inter-sample relationships using hierarchal clustering and PCA.Differential expression analysis was performed using DESeq2 v1.48.2 (Love, Huber, and Anders 2014). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by Rsubread package.

molecule: total RNA

organism: Homo sapiens

source_name: Xenographt tumor

growth_protocol: 2.5*10^6 cells were injected subcoutaneusly in the mice. When tumor reach 100 mm^3, mice were randomized in 4 experimental group: vehicle, rsl3, palbociclib and Palbociclib+rsl3.

extract_protocol:
RNA was extracted performing the lysis of the tissue with the use of Trizol and Chloroform. Then we extracted the RNA using the Qiagen Rneasy Mini Kit
NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module

tag: tissue

value: Xenographt tumor

tag: cell line

tag: cell type

value: prostate cancer

tag: sample group

value: palbo


title: PANC2.03 cells, Scr_n1 (control)

city: Manhattan

first: Mohamad

last: Assi

state: NY

address: 550 1st Ave

department: Radiation Oncology

country: USA

institute: NYU Medical Center

data_processing:
Raw data of FASTQ format were firstly processed through fastp to generate clean data.
Paired-ends were there mapped to the reference genome using TopHat v2.0.9 software
Cuffdiff (v2.1.1) was used to calculate FPKM of coding genes in each sample
ClusterProfiler software was used for enrichment analysis
Assembly: hg38
Supplementary files format and content: Text file contains FPKM values for each sample

source_name: Cell line

growth_protocol: DMEM 10% FBS, 1% Pen/Strep.

extract_protocol:
RNAqueous Kit (AM1912, Ambion)
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)

value: Cell line

value: Pancreatic cancer cells

tag: genotype

value: WT

tag: treatment

value: siRNA-transfected


title: palbo 3

description: Library name: 38097 P3


title: Mouse kidney, PT-2385, 3

description: Library name: Kidney_PT3

molecule: polyA RNA

organism: Mus musculus


title: palbo 4

description: Library name: 38317 P4


title: C. scindens supplemented with riboflavin at 12 hours - rep C

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

description:
Library name: C09
JNorth009_C09_386_260123_S28_L001

data_processing:
Raw sequencing reads were processed using Trimmomatic v0.38. Adapter sequences and low-quality bases were removed using the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:50. Reads were trimmed based on when the average quality of the bases dropped below a Phred score of 15 and reads lower than 50 bases after trimming were discarded.
Trimmed reads were aligned with the Clostridium scindens reference genome using Bowtie2 v2.4.1. Alignment output files were written into SAM format.
Alignments were sorted based on chromosomal coordinates using samtools v1.17.
Duplicate reads were identified and marked using the MarkDuplicates function in picard v3.0.0, with the alignment sort order set to “coordinate,” then retained for downstream analysis.
Gene-level read counts were aligned to an annotated reference genome using the featureCounts tool from the subread v2.0.8 package. Reads were aligned to genomic features type gene using gene identification as meta-features. A count table was exported as a text file for downstream analysis. Differential gene expression analysis was conducted using the R package DESeq2 v1.46.0
Assembly: NCBI RefSeq Assembly: GCF_004295125.1
Supplementary files format and content: .txt file. Includes summarized read counts generated by featurecounts using subread

organism: [Clostridium] scindens

source_name: Strain

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was depleted from the extracted RNA using the Hybridized Probe, rRNA Depletion, and Probe Removal reaction mixtures from the Illumina Stranded Total RNA Prep (Illumina Inc., San Diego, CA, USA). rRNA-depleted samples were purified using a 2.0x sbeadex SAB bead cleanup (Biosearch Technologies, Hoddesdon, UK) with a single 80% ethanol wash. Following cDNA library construction and indexing, the cDNA libraries were quantified using the Qubit™ 1X dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Thermo Fisher, Carlsbad, CA, USA) and the fragment sizes were assessed using a 4150 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).

value: Strain

value: Bacteria


title: PATU8902 spheroids, YS6A_n2

growth_protocol: DMEM 10% FBS, 1% Pen/Strep with 3% Matrigel for 3 days in ultralow attachment plates

value: YAP1S6A overexpression

value: Transduced and 3D-cultured in Matrigel


title: Mouse kidney, PT-2385, 2

description: Library name: Kidney_PT2


title: rsl3 6

description: Library name: 38083 V+R6


title: palbo 1

description: Library name: 38318 P1


title: PATU8902 spheroids, YS6A_n1


title: Mouse kidney, PT-2385, 1

description: Library name: Kidney_PT1


title: palbo 2

description: Library name: 38315 P2


title: rsl3 5

description: Library name: 38086 V+R5


title: rsl3 3

description: Library name: 38302 V+R3


title: rsl3 4

description: Library name: 38218 V+R4


title: Mouse kidney, vehicle control, 4

description: Library name: Kidney_DMSO4

value: 5% DMSO in saline 12-hourly for 4 days, including 48 h 5 IU PMSG then 13 h 5 IU hCG


title: PATU8902 spheroids, EV_n2 (control)


title: rsl3 2

description: Library name: 38216 V+R2


title: Mouse kidney, vehicle control, 3

description: Library name: Kidney_DMSO3


title: rsl3 1

description: Library name: 38082 V+R1


title: vehicle 6

description: Library name: 38095 V6

value: vehicle


title: Mouse kidney, vehicle control, 2

description: Library name: Kidney_DMSO2


title: PATU8902 spheroids, EV_n1 (control)


title: vehicle 5

description: Library name: 38213 V5


title: PATU8902 spheroids, sgNF2_n3

value: NF2 Knockout

value: CRISPR-transduced and 3D-cultured in Matrigel


title: Mouse kidney, vehicle control, 1

description: Library name: Kidney_DMSO1

value: Kidney


title: vehicle 4

description: Library name: 38291 V4


title: vehicle 3

description: Library name: 38301 V3


title: PATU8902 spheroids, sgNF2_n2


title: Mouse ovary, PT-2385, 4

description: Library name: Ovary_PT4

source_name: Ovary

value: Ovary

value: 7.5 mg/kg PT-2385 in saline 12-hourly for 4 days, including 48 h 5 IU PMSG then 13 h 5 IU hCG


title: vehicle 2

description: Library name: 38303 V2

value: Xenographt tumor

value: prostate cancer


title: vehicle 1

description: Library name: 38214 V1


title: PATU8902 spheroids, sgNF2_n1

value: Cell line


title: Mouse ovary, PT-2385, 3

description: Library name: Ovary_PT3


title: SENESCENT SK-MEL103 TREATED WITH ETOPOSIDE REPLICATE 4

description: Library name: SK-MEL ETO 4

data_processing:
Reads were processed using cutadapt v4.7 (Martin 2011) to remove Illumina adapters, trim, and filter on quality with the settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, -n 1, -m 31, --nextseq-trim 20, --max-n 0
Reads were quantified using Salmon v1.9.0 against GRCh38 Ensembl 110 cDNA and ncRNA transcripts with the settings: --softclip --softclipOverhangs --allowDovetail --seqBias --gcBias
Within R v4.4.2, gene count data was used assess inter-sample relationships using hierarchal clustering and PCA.Differential expression analysis was performed using DESeq2 v1.40.2 (Love, Huber, and Anders 2014). Independent hypothesis weighting was conducted to optimise the power of p value filtering using IHW v1.28.0 (Ignatiadis et al. 2016) and log2 fold-change shrinkage was performed using ashr v2.2-63 (Stephens 2017). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: Gzipped quant.sf files produced by Salmon v1.9.0

source_name: skin

growth_protocol: Cells were treated for 6 days with DMSO, Etoposide (0.25 uM) or Tozasertib (0.5 uM) and then RNA was extracted. At day 3 media was changed and drugs were added again.

extract_protocol:
RNA was extracted following the Qiagen Rneasy Mini Kit
NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module

value: skin

value: MELANOMA CELLS


title: H69GV_HLA_Positive

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: H69GV_p

library_source: genomic

data_processing:
ChIP-sequencing reads were aligned to the human genome build hg19 using the Burrows-Wheeler Aligner (BWA) version 0.7.1764. Non-uniquely mapped and redundant reads were discarded. MACS v2.1.1.2014061665 was used for ChIP-seq peak calling with a q-value (FDR) threshold of 0.01. ChIP-seq data quality was evaluated by a variety of measures, including total peak number, FrIP (fraction of reads in peak) score, number of high-confidence peaks (enriched >10-fold over background), and percent of peak overlap with DNAse hypersensitivity (DHS) peaks78,79 derived from the ENCODE project. ChIP-seq peaks were assessed for overlap with gene features and CpG islands using annotatr6680. IGV v2.8.26781 was used to visualize normalized ChIP-seq read counts at specific genomic loci
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Tumor - Lung

growth_protocol: Human SCLC cell lines H69, H69EZ-G, H69EZ-GV were cultured in RPMI-1640 ATCC modification (Thermo Fisher Scientific) containing 10% FBS (Gemini Bio-products), 1X penicillin/streptomycin (Thermo Fisher Scientific), and prophylactic Plasmocin (2.5 ug/mL; Invivogen). H69EZ-G and H69EZ-GV were sorted based on HLA+ or HLA- expression (HLA-ABC)

extract_protocol:
To perform ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine. Cells were then re-suspended in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, 1× protease inhibitor cocktail). Chromatin was sheared to 300 to 500 bp using the Covaris E220 ultrasonicator. Fragmented chromatin was diluted in lysis buffer to 1 mL and coupled with 40 μl protein A and protein G beads (Invitrogen) pre-incubated with anti-H3K27Ac (Abcam) antibody at 4 degrees Celsius overnight. Five percent of the sample was not exposed to antibody and was used as a control input.
The beads were then washed six times (twice in 3 buffers) using low-Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 150 mM NaCl), High-Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 500 mM NaCl), and LiCl Wash Buffer (10 mM Tris pH 7.5, 250 mM LiCl, 1% NP-40, 1% Na-Doc, 1 mM EDTA) and rinsed with TE buffer (pH 8.0) once. The samples were then de-cross-linked, treated with RNase and proteinase K, and DNA was extracted (Qiagen). DNA sequencing libraries were prepared from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit (TakaraBio). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

treatment_protocol: For H69EZ-G and H69EZ-GV derivation, H69 cells were treated with EZH2 inhibitor (GSK126, 5mM; Cayman Chemical Company) for 6 days. On day 3, EZH2 inhibitor was replenished, and H69EZ-GVcells were additionally treated with Vorinostat (1 mM; Selleckchem).  After 3 days, treated or control cells were thoroughly washed twice in PBS (Thermo Fisher Scientific) and all cells recultured in cell culture medium without drug. Cultures were routinely passaged as necessary and were examined daily for the emergence of adherent populations.

value: Tumor - Lung

value: NonNE-SCLC


title: PATU8902 spheroids, sgLUC_n3 (control)

value: Pancreatic cancer cells

value: WT


title: Mouse ovary, PT-2385, 2

description: Library name: Ovary_PT2


title: SENESCENT SK-MEL103 TREATED WITH TOZASERTIB REPLICATE 4

description: Library name: SK-MEL TOZA 4


title: NON SENESCENT SK-MEL103 REPLICATE 4

description: Library name: SK-MEL DMSO 4


title: PATU8902 spheroids, sgLUC_n2 (control)


title: H69GV_HLA_Negative

description: Library name: H69GV_n


title: Mouse ovary, PT-2385, 1

description: Library name: Ovary_PT1


title: SENESCENT SK-MEL103 TREATED WITH ETOPOSIDE REPLICATE 3

description: Library name: SK-MEL ETO 3


title: PATU8902 spheroids, EV_n3 (control)

value: Transduced and 3D-cultured in Matrigel


title: H69EZ_HLA_Positive

description: Library name: H69EZ_p


title: Mouse ovary, vehicle control, 4

description: Library name: Ovary_DMSO4

value: 5% DMSO in saline 12-hourly for 4 days, including 48 h 5 IU PMSG then 13 h 5 IU hCG


title: NON SENESCENT SK-MEL103 REPLICATE 3

description: Library name: SK-MEL DMSO 3


title: HEK-IP-IV-rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

data_processing:
Trim adapter: Adapter sequence of “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” was first trimmed from the 3’ end of poly-A RNA R2
Deduplicate using bbmap clumpify.sh
Trim UMI: Reads R2 from samples generated with superscript III were trimmed 6 nt on the 5’ end and 5 nt on the 3’ end, whereas reads from samples generated with superscript IV was trimmed 7nt on the 5’ end and 5nt on the 3’ end as superscript IV tends to elongate for one more nucleotide.
Reads after adapter trimming, deduplication and UMI trimming were mapped to hg38 using hisat2 with options of “--known-splicesite-infile --rna-strandness F --no-softclip”.
Assembly: hg38

source_name: HEK 293T

growth_protocol: HEK 293T, HeLa and LN229 cell lines were grown and maintained in DMEM supplemented with 10% FBS and 1% pen-strep antibiotics under 37 °C with 5% CO2.  Only cells within passage number of 10 were used for all experiments.

extract_protocol:
RNAs were extracted from cells using Trizol reagent and polyA RNA were extracted using Dynabeads® mRNA DIRECT™ Kit for two rounds. Messenger RNAs were extracted with an additional ribosome RNA removal step using the RiboMinus™ Eukaryote Kit v2.
The libraries were prepared using a customized protocol

treatment_protocol: For interferon stimulation, interferon-α was added to LN229 cell lines at 500 U/mL when cells were at least 80% confluency and incubated for 24 h before collecting cells for RNA isolation.

value: HEK 293T

value: cancer cells


title: H69EZ_HLA_Negative

description: Library name: H69EZ_n


title: Mouse ovary, vehicle control, 3

description: Library name: Ovary_DMSO3


title: PATU8902 spheroids, sgLUC_n1 (control)

value: CRISPR-transduced and 3D-cultured in Matrigel


title: SENESCENT SK-MEL103 TREATED WITH TOZASERTIB REPLICATE 2

description: Library name: SK-MEL TOZA 2


title: HEK-IP-III-rep2


title: Mouse ovary, vehicle control, 2

description: Library name: Ovary_DMSO2


title: HEK-IP-IV-rep1


title: SENESCENT SK-MEL103 TREATED WITH ETOPOSIDE REPLICATE 2

description: Library name: SK-MEL ETO 2


title: Mouse ovary, vehicle control, 1

description: Library name: Ovary_DMSO1


title: IMR90 RAS siSF3B1_16 Rep 3 [iRas_5_SF3B1_16]

data_processing:
Primary analysis was performed using RTA 1.18.54 and Secondary analysis using CASAVA- 2.17
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to hg19 genome using STAR aligner (version2.6.0c )
Gene based counting was performed using the STAR (version 2.6.0c ).
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.24.0 )
Assembly: hg19
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by  STAR aligner.

extract_protocol: Total RNA was extracted using Trizol and the Rneasy isolation kit (Qiagen).

treatment_protocol: IMR90 Control cells and IMR90 RAS cells were transfected with siRNAs 6 days after induction of HRASG12V and RNA was collected 48 hours after transfection.

value: fetal lung fibroblasts

tag: time

value: 48 hours


title: H69_Parental

description: Library name: H69_Parental

value: NE-SCLC


title: HEK-IP-III-rep1


title: SENESCENT SK-MEL103 TREATED WITH TOZASERTIB REPLICATE 1

description: Library name: SK-MEL TOZA 1


title: V65_dMir290e_r3

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to the mm10 reference index with default parameters by Hisat2, and the resulting aligned reads file was converted to a sorted, indexed BAM file using Samtools.
Created a positional gene reference GTF from RefSeq (mm10). Quantified coverage of all genes using Htseq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files that contain gene name and TPM for each sample

growth_protocol: mESC V6.5 cells are male cells derived from a C57BL/6(F) x 129/sv(M) cross. All cell lines were cultured in 2i + LIF medium.

extract_protocol:
RNA samples were isolated using AllPrep DNA/RNA Mini Kit (QIAGEN 80204). RNA libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HRM) (Roche KK8651). Briefly, rRNA were depleted by hybridization of complementary DNA oligonucleotides and treatment with RNase and DNase. RNA samples were fragmented, and double strand cDNA were generated by two steps of cDNA synthesis.
Illumina TruSeq DNA UD Indexes (IDT 20040870) were used to make libraries. Libraries were amplified using KAPA HiFi HotStart ReadyMix (2X) and Library Amplification Primer Mix (10X), followed by Qubit dsDNA quantification (Invitrogen Q32853), and 2100 BioAnalyzer D1000 kit (Agilent 50671504) and Illumina MiSeq Nano v2 QC.

treatment_protocol: Enhancer deleted line V6.5_dMir290e are gifts provided by Dr. Young at the Whitehead Institute.

value: emborynic stem cells

value: Enhancer Deletion


title: IMR90 RAS siSF3B1_16 Rep 1 [iRas_1_SF3B1_16]


title: IMR90 RAS siSF3B1_16 Rep 2 [iRas_3_SF3B1_16]


title: HeLa-IP-IV-rep2

source_name: HeLa

value: HeLa


title: V65_dMir290e_r2


title: HeLa-IP-III-rep2


title: SENESCENT SK-MEL103 TREATED WITH ETOPOSIDE REPLICATE 1

description: Library name: SK-MEL ETO 1

value: skin


title: V65_dMir290e_r1


title: NON SENESCENT SK-MEL103 REPLICATE 1

description: Library name: SK-MEL DMSO 1

value: MELANOMA CELLS


title: IMR90 RAS siSF3B1_13 Rep 2 [iRas_4_SF3B1_13]


title: IMR90 RAS siSF3B1_13 Rep 3 [iRas_5_SF3B1_13]


title: V65_r3


title: IMR904OHT-siRBM39-08-4

description: Library name: IMR904OHT-siRBM39-08_4_S48

data_processing:
Lowly expressed genes were filtered by excluding those with total log10 counts ≤ 3.5.
Counts were then normalised using the TMM method (edgeR) and transformed to log2CPM using voom (limma), which adjusts for the mean–variance relationship in RNA-seq data.
The final expression matrix is in log2CPM units.
Assembly: hg19
Supplementary files format and content: filtered and normalised expression matrix.
Supplementary files format and content: raw counts obtained directly from VAST-TOOLS;
Supplementary files format and content: alternative splicing inclusion tables obtained directly from VAST-TOOLS;

source_name: Lung

growth_protocol: Cells were induced with 4OHT (or DMSO, control) for 6 days in complete DMEM medium before transfection, then kept for another 2 days in low serum condition (0.5% FBS DMEM)

extract_protocol:
RNeasy Kits for RNA Purification (Qiagen)
Library construction was done using the Watchmaker Genomics mRNA Capture kit followed by the Watchmaker Genomics RNA Library Prep Kit according to manufacturers instructions. Libraries were indexed using IDT xGen Unique Dual Index Primers and pooled together for sequencing.

treatment_protocol: siRNA against SF3B1 or RBM39 (or non-targeting, control)

value: Lung

value: Fibroblasts

value: ER:RAS G12V

value: 4OHT siRBM39-08


title: HeLa-input-IV-rep2

value: WT


title: HeLa-input-III-rep2


title: IMR904OHT-siRBM39-08-3

description: Library name: IMR904OHT-siRBM39-08_3_S47


title: HeLa-IP-IV-rep1


title: IMR90 RAS siNT2 Rep 3 [iRas_5_siNT2]


title: V65_r1


title: IMR904OHT-siRBM39-08-2

description: Library name: IMR904OHT-siRBM39-08_2_S46


title: IMR90 RAS siNT2 Rep 2 [iRas_4_siNT2]


title: mite, untreated, rep1,snATAC

city: Wuxi

first: YUBAO

last: CUI

state: Jiangsu

address: No. 299 at Qingyang Road

country: China

institute: The Affiliated Wuxi People's Hospital of Nanjing Medical University

description:
Library name: mite3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the D. farinae genome (NCBI_ASM2080927v1) with CellRanger, and a cell by gene matrix was generated by UMI counting. Subsequent analysis in Seurat (v4.1.0) included filtering low quality cells (>200 genes, <25% mitochondrial reads), normalization, scaling, PCA based dimensionality reduction, and clustering (top 20 PCs) visualized via UMAP/t SNE. Cluster specific markers were identified (FindAllMarkers) requiring >10% expression, adjusted P ≤ 0.01, and log₂FC ≥ 0.26.
Assembly: GenBank No. JAMLFS000000000.1
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Dermatophagoides farinae

source_name: whole organism

extract_protocol:
Whole mites were cut into small fragments (∼0.1 cm) and suspended in a mixture of lysis buffer and PBS. After two washes with PBS, ice cold lysis buffer was added for 2 min on ice. Tissue was homogenized using a Dounce homogenizer, gently pipetted, and incubated on ice for 6 min. Lysis was stopped with chilled 4% BSA, followed by gentle trituration. Following centrifugation (300 g, 5 min, 4 °C), the pellet was resuspended in lysis buffer with 4% BSA, incubated on ice, and cleared of debris using a Debris Removal Solution. After another centrifugation, nuclei were resuspended in nuclear resuspension buffer (PBS with 2% BSA and 0.1% RNase inhibitor), pooled from three replicates, filtered through a 20 μm strainer, and counted.
Single nucleus RNA seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Kit (v3) and sequenced on an Illumina NovaSeq 6000 platform, yielding >20,000 paired end reads per nucleus.

value: whole organism


title: IMR904OHT-siRBM39-08-1

description: Library name: IMR904OHT-siRBM39-08_1_S45


title: HeLa-IP-III-rep1


title: HeLa-input-IV-rep1


title: NON SENESCENT SK-MEL103 REPLICATE 2

description: Library name: SK-MEL DMSO 2


title: IMR90 RAS siNT2 Rep 1 [iRas_3_siNT2]


title: HeLa-input-III-rep1


title: Mite, untreated, rep3,snRNA

description:
Library name: Mite_3
10x Genomics


title: IMR90DMSO-siRBM39-08-4

description: Library name: IMR90DMSO-siRBM39-08_4_S44

value: DMSO siRBM39-08


title: Mite, untreated, rep2,snRNA

description:
Library name: Mite_2
10x Genomics


title: RNA-seq, mRNA, untreated, patient 1

city: New Haven

first: Paulina

last: Podszywalow-Bartnicka

state: CT

address: 333 Cedar Street

department: Department of Molecular Biophysics and Biochemistry

institute: Yale University

description: Library name: CML_untr1

data_processing:
Fastp was used to filter raw reads for quality and trim; STAR was used to align reads to the reference genome; FeatureCounts was used to determine number of reads per gene in each sample in the STAR output bam file.
Assembly: GRCh38.p14
Supplementary files format and content: The ‘CML_featurecounts.txt’ is a file containing featureCounts output numbers of reads assigned to genes (Geneid) for each STAR output bam file.

source_name: CML CD34

growth_protocol: Primary CD34+ cells were enriched from CML patient samples using magnetic beads with anti-CD34 antibodies and separated on columns, following the manufacturer’s protocol (Miltenyi).

extract_protocol:
Trizol (TRI Reagent) is used to isolate total RNA from whole cells.
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Samples are then fragmented using heat and magnesium. 1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated and the library is amplified.  Strands marked with dUTPs are not amplified allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using KAPA Biosystems kit (# KK4854) and insert size distribution determined with Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: Imatinib was pre-diluted in growth media and added to the cell culture at 1uM.

value: CML CD34

value: patient 1

value: untreated


title: IMR90 RAS siNT1 Rep 2 [iRas_4_siNT1]

value: fetal lung fibroblasts

value: 48 hours


title: Oligo-IP-rep2

library_source: other

molecule: other

organism: synthetic construct

source_name: synthetic oligo

value: synthetic oligo


title: IMR90DMSO-siRBM39-08-2

description: Library name: IMR90DMSO-siRBM39-08_2_S42


title: Mite, untreated, rep1,snRNA

description:
Library name: Mite_1
10x Genomics


title: IMR90DMSO-siRBM39-08-3

description: Library name: IMR90DMSO-siRBM39-08_3_S43


title: IMR90 RAS siNT1 Rep 3 [iRas_5_siNT1]


title: IMR90 RAS siNT1 Rep 1 [iRas_3_siNT1]


title: D_1

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description:
Library name: Sample 4
4T1 cells were collected from Control group for 24 h

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 6000 platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: reference sequence used for mice
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: 4T1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing. The mRNA libraries were constructed and sequenced. In brief, mRNA was purified with poly-T oligo beads and fragmented. First-strand cDNA was synthesized by random hexamer primers, and followed by second-strand synthesis. cDNA products were end-repaired and A-tailed before size selection and adapter ligation. The AMPure XP system was preferentially selected cDNA fragments between 150 and 200 bp in length. Individual sequence libraries were amplified by PCR. Libraries were pooled, and 150 basepair paired-end reads were sequenced.
the mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4T1 cells (5 × 105) were seeded in a six-well plate and incubated for 24 h, and then CS-HA-DAP( 1.17mg·mL-1) were added to the wells and then incubated in an incubator overnight.

value: breast

value: cancer cell

tag: batch


title: Genomic DNA from conjunctival control C9

type: genomic

city: Madurai

first: Daipayan

last: Banerjee

state: Tamil Nadu

address: 1, Anna Nagar,

department: Proteomics Department

country: India

institute: Aravind Medical Research Foundation

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium Methylation EPICv2.0 BeadChip

scan_protocol: Arrays were scanned using Illumina iScan system and standard Illumina iScan setting

data_processing: ChAMP package in R programme

label: Cy3 and Cy5

source_name: Conjunctival

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA isolated from Dneasy Blood & Tissue Kit (Qiagen, Cat#69504)

tag: Sex

value: Male

tag: disease

value: Catarct

value: Conjunctival


title: Oligo-IP-rep1


title: Genomic DNA from conjunctival control C4

value: Female


title: IMR90 Control siSF3B1_16 Rep 2 [EV_2_SF3B1_16]

value: Control


title: IMR90 Control siSF3B1_16 Rep 3 [EV_3_SF3B1_16]


title: IMR90DMSO-siRBM39-08-1

description: Library name: IMR90DMSO-siRBM39-08_1_S41

value: Lung

value: Fibroblasts

value: ER:RAS G12V


title: Genomic DNA from conjunctival control C3


title: IMR904OHT-siRBM39-06-3

description: Library name: IMR904OHT-siRBM39-06_3_S39

value: 4OHT siRBM39-06


title: Oligo-input-rep2


title: IMR90 Control siSF3B1_13 Rep 3 [EV_4_SF3B1_13]


title: Genomic DNA from conjunctival control C7


title: IMR904OHT-siRBM39-06-4

description: Library name: IMR904OHT-siRBM39-06_4_S40


title: IMR904OHT-siRBM39-06-1

description: Library name: IMR904OHT-siRBM39-06_1_S37


title: HEK-sictrl-IP-IV-rep1

description: Library name: Library-60

data_processing:
Only R2 reads were used except for the sictrl and siDKC1 samples as described below.
Trim adapter: Adapter sequence of “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” was first trimmed from the 3’ end of poly-A RNA R2
Deduplicate using bbmap clumpify.sh
Trim UMI: Reads R2 from samples generated with superscript III were trimmed 6 nt on the 5’ end and 5 nt on the 3’ end, whereas reads from samples generated with superscript IV was trimmed 7nt on the 5’ end and 5nt on the 3’ end as superscript IV tends to elongate for one more nucleotide.
For the sictrl and siDKC1 samples, paired end sequencing were used. However, reads R1 and R2 were first merged, then decomplexed based on the internal barcodes. The resulting files are therefore uploaded as one file for each sample and labeled as "single-end" even though they were merged paired-end reads. The internal barcodes and UMI (8 nt in total on the 5' end and 5 nt in total on the 3' end) need to be trimmed after reads de-duplication.
Reads after adapter trimming, deduplication and UMI trimming were mapped to hg38 using hisat2 with options of “--known-splicesite-infile --rna-strandness F --no-softclip”.
Assembly: hg38
Supplementary files format and content: The .xlsx files contain information of candidate modification sites identified in different cell lines and under different conditions and the change of enrichment levels under the control and DKC1 knockdown conditions.

growth_protocol: HEK 293T, HeLa and LN229 cell lines were grown and maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C with 5% CO2. The day before transfection, 2 × 10⁶ HEK293T cells were seeded onto each 15 cm cell culture plate.

extract_protocol:
RNAs were extracted from cells using Trizol reagent and polyA RNA were extracted using Dynabeads® mRNA DIRECT™ Kit for two rounds. Messenger RNAs were extracted with an additional ribosome RNA removal step using the RiboMinus™ Eukaryote Kit v2.
Libraries were constructed using a customized protocol. For the experiments of DKC1 knockdown, internally barcoded RNA adapters, wo that the four input samples (2 sictrl reps and 2 siDKC1 reps) and the four pull-down samples can be pooled together right after the RNA ligation.  For IVT RNA, the RNA was mixed with rice mRNA in 1:1 ratio and then proceeded with library construction using ELAP-seq.

treatment_protocol: For interferon stimulation, interferon-α was added to LN229 cell lines at 500 U/mL when cells were at least 80% confluency and incubated for 24 h before collecting cells for RNA isolation. For siRNA knockdown experiments, transfection was performed using RNAiMax transfection reagent following manufacturer's instructions. For one 15 cm plate, 20 μL of 20 μM siDKC1 (Qiagen, Hs_DKC1_6 FlexiTube siRNA) or siCtrl (Sigma Aldrich, catalog # sic001) was used. Cells were harvested 72–96 hours post-transfection.

value: HEK 293T

value: cancer cells

value: WT


title: Sample33_INA6_RNAseq_sgELL2_withIL6_rep3

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

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

department: IRDA

country: Japan

institute: Kumamoto University

description: Library name: Sample33

data_processing:
Sequence reads in FASTQ were processed for alignment with STAR(2.7.10b) with basic two-pass mode.
Sequence reads with primary alignment were selected with samtools (1.19.2).
Sequence reads were analyzed for PSI using PSI-Sigma (2.3) with supporting read threshold >= 10 and GRCh38 Ensembl version 108 as reference.
Assembly: GRCh38, Ensembl version 108
Supplementary files format and content: output values from PSI-sigma

growth_protocol: Multiple myeloma cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 mM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Strand-specific mRNA library construction were performed at BGI Genomics (Shenzhen, China) or Novogene (Bejing, China).

treatment_protocol: Multiple myeloma cells were treated with or without IL-6. For knockdown experiments, multiple myeloma cells expressing Cas9 were transduced with sgRNA by lentivirus. The infected cells were selected with puromycin for 2 days.

value: multiple myeloma cell line

value: sgELL2, with IL-6


title: IMR90 Control siSF3B1_16 Rep 1 [EV_1_SF3B1_16]

value: fetal lung fibroblasts

value: 48 hours


title: Genomic DNA from conjunctival control C1


title: Sample31_INA6_RNAseq_sgELL2_withIL6_rep1

description: Library name: Sample31


title: IMR90DMSO-siRBM39-06-4

description: Library name: IMR90DMSO-siRBM39-06_4_S36

value: DMSO siRBM39-06


title: IMR904OHT-siRBM39-06-2

description: Library name: IMR904OHT-siRBM39-06_2_S38


title: Genomic DNA from pterygium P18

source_name: Pterygium

value: Male

value: Pterygium


title: IMR90 Control siSF3B1_13 Rep 1 [EV_2_SF3B1_13]


title: Sample32_INA6_RNAseq_sgELL2_withIL6_rep2

description: Library name: Sample32


title: IMR90DMSO-siRBM39-06-3

description: Library name: IMR90DMSO-siRBM39-06_3_S35


title: Sample29_INA6_RNAseq_sgPOU2AF1_withIL6_rep2

description: Library name: Sample29

value: sgPOU2AF1, with IL-6


title: Genomic DNA from conjunctival control C2

value: Female

value: Catarct

value: Conjunctival


title: IMR90DMSO-siRBM39-06-2

description: Library name: IMR90DMSO-siRBM39-06_2_S34

value: Lung

value: Fibroblasts


title: IMR90 Control siSF3B1_13 Rep 2 [EV_3_SF3B1_13]

value: Control


title: Sample28_INA6_RNAseq_sgPOU2AF1_withIL6_rep1

description: Library name: Sample28


title: Sample30_INA6_RNAseq_sgPOU2AF1_withIL6_rep3

description: Library name: Sample30


title: IMR90DMSO-siRBM39-06-1

description: Library name: IMR90DMSO-siRBM39-06_1_S33

value: ER:RAS G12V


title: IMR90 Control siNT2 Rep 3 [EV_4_siNT2]


title: Genomic DNA from pterygium P16


title: IMR90 Control siNT2 Rep 2 [EV_3_siNT2]


title: Genomic DNA from pterygium P12


title: Sample27_INA6_RNAseq_sgEGFP_withIL6_rep3

description: Library name: Sample27

value: sgEGFP, with IL-6


title: IMR904OHT-siSF3B1-16-4

description: Library name: IMR904OHT-siSF3B1-16_4_S32

value: 4OHT siSF3B1-16


title: IMR90 Control siNT2 Rep 1 [EV_2_siNT2]


title: Sample26_INA6_RNAseq_sgEGFP_withIL6_rep2

description: Library name: Sample26

value: multiple myeloma cell line


title: Genomic DNA from pterygium P13


title: IMR90 Control siNT1 Rep 3 [EV_4_siNT1]


title: Genomic DNA from pterygium P9


title: IMR904OHT-siSF3B1-16-3

description: Library name: IMR904OHT-siSF3B1-16_3_S31


title: Sample25_INA6_RNAseq_sgEGFP_withIL6_rep1

description: Library name: Sample25


title: IMR90 Control siNT1 Rep 2 [EV_2_siNT1]


title: Genomic DNA from pterygium P8


title: IMR904OHT-siSF3B1-16-2

description: Library name: IMR904OHT-siSF3B1-16_2_S30


title: Sample24_MM1S_RNAseq_sgELL2_withIL6_rep3

description: Library name: Sample24

value: sgELL2, with IL-6 for 24 h


title: Sample23_MM1S_RNAseq_sgELL2_withIL6_rep2

description: Library name: Sample23


title: IMR90 Control siNT1 Rep 1 [EV_1_siNT1]

value: fetal lung fibroblasts


title: Genomic DNA from pterygium P4


title: IMR904OHT-siSF3B1-16-1

description: Library name: IMR904OHT-siSF3B1-16_1_S29


title: iRas_pos_4

data_processing:
Primary analysis RTA 1.18.64 and Secondary analysis CASAVA- 1.8.4
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to hg19 genome using Tophat 2.0.11
Gene based counting was performed using the Rsubread package.
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.18.1 )
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file include raw counts for each Sample generated by  Rsubread.

source_name: IMR90 ER:RAS

growth_protocol: IMR90 ER:RAS  and IMR90 cells (senescent and growing) were grown in DMEM 10% FBS. Quiescent IMR90 cells were grown in DMEM 0.5% FBS from day 3 to day 8. Media was exchanged every 3 days.

treatment_protocol: To induce RAS activation, IMR90 ER:RAS cells were treated with 4OHT (100nM, continuously). To induce senescence in IMR90 cells, cells were treated with doxorubicin (0.5uM for 24h), etoposide (50uM for 48h), palbociclib (1uM, continuously), irradiation (10Gy).

tag: day after beginning of experiment

tag: cell state

value: senescent


title: IMR90DMSO-siSF3B1-16-4

description: Library name: IMR90DMSO-siSF3B1-16_4_S28

value: DMSO siSF3B1-16


title: Genomic DNA from pterygium P3


title: Sample22_MM1S_RNAseq_sgELL2_withIL6_rep1

description: Library name: Sample22


title: Genomic DNA from pterygium P2

value: Male


title: IMR90DMSO-siSF3B1-16-3

description: Library name: IMR90DMSO-siSF3B1-16_3_S27


title: Sample21_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_withIL6_rep3

description: Library name: Sample21

value: sgEGFP, with IL-6 for 24 h


title: iRas_pos_2


title: iRas_pos_3


title: IMR90DMSO-siSF3B1-16-2

description: Library name: IMR90DMSO-siSF3B1-16_2_S26


title: iRas_pos_1


title: Sample20_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_withIL6_rep2

description: Library name: Sample20


title: HY19636 tumor, D14

city: San Francisco

first: Nicholas

middle: F

last: Kuhn

state: CA

address: 513 Parnassus Ave, HSW518

department: Pathology

institute: University of California, San Francisco

description:
Library name: CAF KO Osmr Tgfbr2 Il1r1
10x Genomics FLEX

data_processing:
Sequencing output was processed using cellranger-7.2.0 and the mouse transcriptome probe set v1.0.1_mm10-2020-A with added custom Egfp probes from above. Samples were demultiplexed using the provided Probe Barcodes.
Assembly: Mouse mm10
Supplementary files format and content: Cell ranger output: sample_raw_feature_bc_matrix.h5

source_name: tumor s.c.

extract_protocol:
Mice were euthanized and tumor mass was carefully excised from the subcutaneous region without collecting the adjacent skin and surrounding adipose tissue. On ice, samples were finely minced with scissors and then placed in a 2 ml tube containing 1.5 ml of digestion medium (2 mg/ml collagenase XI (Millipore Sigma, C7657), 0.5 mg/ml hyaluronidase (Worthington, LS005477), 0.1 mg/ml DNase (Roche, 10104159001) in DMEM (Gibco, 11995065) supplemented with 10% FBS (Foundation C, Gemini Bio, 900-308), 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, and 50 µM beta-mercaptoethanol (Gibco, 21985-023). The tube was placed horizontally in a bacterial shaker for 45 min at 37ºC and 225 rpm. The tumor samples were then filtered through a 40 µm filter. Samples were then washed with 10 ml cold PBS. Prior to sorting of cells on on a BD FACSAria II cell sorter (BD Biosciences), cells were stained with Zombie-NIR (BioLegend, 1:200) and  Calcein blue AM (Thermo Fisher Scientific, C1429, 10 µM working concentration). Samples were additionally stained with anti-mouse CD45-BUV395 (clone 30-F11, BD Biosciences, 1:500), anti-Thy1.2/CD90.2-BV786 (clone 53-2.1, BD Biosciences, 1:500, for Thy1 detection), and anti-E-Cadherin/CD324-PE-Cy7 (clone DECMA-1, BioLegend, 1:200). Four live cell (Zombie-NIR-negative, Calcein blue AM-positive) populations were sorted: (1) CD45+ (immune cells), (2) CD45- EGFP+ Thy1+ (fibroblasts), (3) CD45- EGFP- E-Cadherin- (miscellaneous), (4) CD45- EGFP- E-Cadherin+ (tumor cells). The four populations from each sample were then pooled in a 15 ml Falcon tube and pelleted for 7 minutes at 500 g.
Cells were processed using the Chromium Fixed RNA Profiling (Gene Expression Flex) pipeline. In brief, each sample was first fixed using the Single Cell Fixed RNA Sample Preparation Kit (10x Genomics, PN-1000414) following the manufacturer’s instructions. Samples were fixed for 18 h at 4 °C and, after addition of quenching buffer and storage buffer, stored at -80 °C until further processing. After thawing of samples, samples were processed using the Chromium Fixed RNA Kit, Mouse Transcriptome (10x Genomics, PN-1000496) following the manufacturer’s instructions to generate a fixed RNA gene expression library. For multiplexing, each sample (4 replicates * 4 AAV groups = 16 total) was hybridized with a separate Probe Barcode library including added custom probes (Egfp, 8casd09, GGTAGTGGTCGGCGAGCTGCACGCTGCCGTCCTCGATGTTGTGGCGGATC; and Egfp, 8casd10, AGGGTGTCGCCCTCGAACTTCACCTCGGCGCGGGTCTTGTAGTTGCCGTC). Approximately 2.5e5 total cells were encapsulated and sequenced on two lanes of a NovaSeq X flow cell (1.25 B reads/lane) to reach about 10.000 reads/cell.

value: tumor s.c.

value: HY19636 (pancreatic cancer)

value: AAV

value: day 14


title: IMR90DMSO-siSF3B1-16-1

description: Library name: IMR90DMSO-siSF3B1-16_1_S25

value: Lung


title: Puberulic Acid 5

city: Bunkyoku

first: Yuta

last: Sekiguchi

state: Tokyo

address: 1-5-45, Yushima

institute: Institute of Science Tokyo

description: Library name: SAMPLE20

data_processing:
Raw reads were trimmed and filtered using fastp (v0.22.0) with the options: -q 20 -u 30 -n 10 -l 30 -w 8. Quality control was performed before and after trimming using FastQC (v0.12.1), and consolidated quality reports were generated using MultiQC (v1.28).
Transcript-level quantification was performed using Salmon (v1.10.3). The transcriptome index was built using GENCODE Mouse Release M33 (GRCm39), with the files gencode.vM33.transcripts.fa and gencode.vM33.annotation.gtf
Gene-level count matrices were generated using the tximport package with the option countsFromAbundance = "lengthScaledTPM" to incorporate transcript length normalization, which improves compatibility with DESeq2's statistical model.
Assembly: GENCODE M33 (GRCm39)
Supplementary files format and content: Tab-dilineated text file includes raw counts.

source_name: Kidney

growth_protocol: Mice were purchased at 7 weeks of age and acclimated for one week before being used for experiments. Eight-week-old male C57BL/6J mice were used in all experiments. Mice were randomly assigned to four groups (n = 6–10 per group): (1) control (PBS), (2) Choleste-Help normal batch (1,000 mg/day), (3) Choleste-Help toxic batch (1,000 mg/day), and (4) puberulic acid (1 mg/day).

extract_protocol:
Total RNA was extracted by initially homogenizing kidney tissues in Sepasol-RNA I Super G (Nacalai Tesque, Japan), followed by purification using the Direct-zol RNA Miniprep Plus Kit (Zymo Research, R2070) according to the manufacturer’s protocol. RNA integrity was assessed using an Agilent Bioanalyzer, and all samples had RIN values greater than 7.5.
RNA-seq library preparation and sequencing were outsourced to ReRexa Inc. Libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: Each group received the designated compound either by oral gavage or intraperitoneal injection once daily from Day 0 to Day 5 (a total of six administrations). After a one-day withdrawal period on Day 6, organs were harvested on Day 7.

value: Kidney

value: Puberulic Acid for 6 Days


title: Sample19_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_withIL6_rep1

description: Library name: Sample19


title: iRas_neg_4

value: DMSO

value: growing


title: Puberulic Acid 4

description: Library name: SAMPLE19


title: IMR904OHT-siSF3B1-13-4

description: Library name: IMR904OHT-siSF3B1-13_4_S24

value: Fibroblasts

value: ER:RAS G12V

value: 4OHT siSF3B1-13


title: iRas_neg_3


title: Sample18_MM1S_RNAseq_sgPOU2AF1_withIL6_rep3

description: Library name: Sample18

value: multiple myeloma cell line

value: sgPOU2AF1, with IL-6 for 24 h


title: IMR904OHT-siSF3B1-13-3

description: Library name: IMR904OHT-siSF3B1-13_3_S23


title: Sample17_MM1S_RNAseq_sgPOU2AF1_withIL6_rep2

description: Library name: Sample17


title: iRas_neg_2


title: Puberulic Acid 3

description: Library name: SAMPLE18


title: Puberulic Acid 2

description: Library name: SAMPLE17


title: IMR904OHT-siSF3B1-13-2

description: Library name: IMR904OHT-siSF3B1-13_2_S22


title: Sample16_MM1S_RNAseq_sgPOU2AF1_withIL6_rep1

description: Library name: Sample16


title: iRas_neg_1


title: IMR904OHT-siSF3B1-13-1

description: Library name: IMR904OHT-siSF3B1-13_1_S21


title: IMR90_Irrad_4

value: irradiation

value: senescent


title: Sample15_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_withIL6_rep3

description: Library name: Sample15

value: sgEGFP, with IL-6 for 24 h


title: IMR90DMSO-siSF3B1-13-4

description: Library name: IMR90DMSO-siSF3B1-13_4_S20

value: DMSO siSF3B1-13


title: Puberulic Acid 1

description: Library name: SAMPLE16


title: Sample14_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_withIL6_rep2

description: Library name: Sample14


title: Choleste-Help Toxic Lot 5

description: Library name: SAMPLE15

value: Choleste-Help Toxic Lot for 6 Days


title: Sample13_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_withIL6_rep1

description: Library name: Sample13


title: IMR90_Irrad_3


title: IMR90_Irrad_2


title: Choleste-Help Toxic Lot 3

description: Library name: SAMPLE13


title: IMR90 RAS siSF3B1_13 Rep 1 [iRas_2_SF3B1_13]

value: fetal lung fibroblasts

value: 48 hours


title: V65_r2

value: emborynic stem cells


title: IMR90DMSO-siSF3B1-13-2

description: Library name: IMR90DMSO-siSF3B1-13_2_S18

value: Lung


title: Sample12_INA6_RNAseq_withIL6_24h_rep3

description: Library name: Sample12

value: with IL-6 for 24 h


title: IMR90DMSO-siSF3B1-13-3

description: Library name: IMR90DMSO-siSF3B1-13_3_S19


title: Choleste-Help Toxic Lot 4

description: Library name: SAMPLE14

value: Kidney


title: Choleste-Help Toxic Lot 2

description: Library name: SAMPLE12


title: IMR90_Irrad_1


title: IMR90DMSO-siSF3B1-13-1

description: Library name: IMR90DMSO-siSF3B1-13_1_S17


title: IMR90_Palbo_4

value: palbociclib


title: Sample11_INA6_RNAseq_withIL6_24h_rep2

description: Library name: Sample11


title: Choleste-Help Toxic Lot 1

description: Library name: SAMPLE11


title: IMR904OHT-siNT2-4

description: Library name: IMR904OHT-siNT2_4_S16

value: Fibroblasts

value: 4OHT siNT1


title: Sample10_INA6_RNAseq_withIL6_24h_rep1

description: Library name: Sample10


title: IMR90_Palbo_3


title: Choleste-Help Normal Lot 5

description: Library name: SAMPLE10

value: Choleste-Help Normal Lot for 6 Days


title: Sample9_INA6_RNAseq_withoutIL6_24h_rep3

description: Library name: Sample9

value: multiple myeloma cell line

value: without IL-6 for 24 h


title: IMR90_Palbo_2


title: Choleste-Help Normal Lot 4

description: Library name: SAMPLE9


title: Sample8_INA6_RNAseq_withoutIL6_24h_rep2

description: Library name: Sample8


title: IMR904OHT-siNT2-3

description: Library name: IMR904OHT-siNT2_3_S15

value: ER:RAS G12V


title: IMR904OHT-siNT2-2

description: Library name: IMR904OHT-siNT2_2_S14


title: PATU8902 spheroids, Input_n1

data_processing:
Data quality control was performed using FastQC
Mapping onto human genome and peak calling were performed using BWA and MACS, respectively
functional analysis of peak-associated genes and pathway analysis were performed with GOSeq/topGO, Bioconductor and KOBAS
Assembly: hg38
Supplementary files format and content: Data are submitted as bigwig files for each sample

source_name: Cell line

extract_protocol:
SimpleChIP® Enzymatic Chromatin IP Kit (9003S, Cell signaling Tech)
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Cell line

value: Pancreatic cancer cells


title: Choleste-Help Normal Lot 3

description: Library name: SAMPLE8


title: Sample7_INA6_RNAseq_withoutIL6_24h_rep1

description: Library name: Sample7


title: IMR90_Palbo_1

value: senescent


title: IMR904OHT-siNT2-1

description: Library name: IMR904OHT-siNT2_1_S13


title: IMR90_Eto_4

value: etoposide


title: IMR90DMSO-siNT2-4

description: Library name: IMR90DMSO-siNT2_4_S12

value: DMSO siNT2


title: Sample6_MM1S_RNAseq_withIL6_24h_rep3

description: Library name: Sample6


title: IMR90_Eto_3


title: Choleste-Help Normal Lot 1

description: Library name: SAMPLE6


title: Choleste-Help Normal Lot 2

description: Library name: SAMPLE7


title: IMR90DMSO-siNT2-3

description: Library name: IMR90DMSO-siNT2_3_S11


title: Sample5_MM1S_RNAseq_withIL6_24h_rep2

description: Library name: Sample5


title: IMR90_Eto_2


title: Control 5

description: Library name: SAMPLE5

value: PBS for 6 Days


title: IMR90DMSO-siNT2-2

description: Library name: IMR90DMSO-siNT2_2_S10


title: IMR90_Eto_1


title: Control 4

description: Library name: SAMPLE4


title: IMR90DMSO-siNT2-1

description: Library name: IMR90DMSO-siNT2_1_S9


title: Sample3_MM1S_RNAseq_withoutIL6_24h_rep3

description: Library name: Sample3


title: Sample18_MM1S_RNAseq_withoutIL6_24h_rep2

description: Library name: Sample18

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore.
Trimmed sequence reads were mapped to hg19 using STAR 2.7.8a.
Read count extraction and normalization were performed using RSEM v1.3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM for each sample.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: matrix column_name


title: Oligo-input-rep1

value: synthetic oligo


title: Sample4_MM1S_RNAseq_withIL6_24h_rep1

description: Library name: Sample4


title: C. scindens supplemented with riboflavin at 11 hours - rep C

description:
Library name: C06
JNorth009_C06_386_260123_S25_L001

data_processing:
Raw sequencing reads were processed using Trimmomatic v0.38. Adapter sequences and low-quality bases were removed using the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:50. Reads were trimmed based on when the average quality of the bases dropped below a Phred score of 15 and reads lower than 50 bases after trimming were discarded.
Trimmed reads were aligned with the Clostridium scindens reference genome using Bowtie2 v2.4.1. Alignment output files were written into SAM format.
Alignments were sorted based on chromosomal coordinates using samtools v1.17.
Duplicate reads were identified and marked using the MarkDuplicates function in picard v3.0.0, with the alignment sort order set to “coordinate,” then retained for downstream analysis.
Gene-level read counts were aligned to an annotated reference genome using the featureCounts tool from the subread v2.0.8 package. Reads were aligned to genomic features type gene using gene identification as meta-features. A count table was exported as a text file for downstream analysis. Differential gene expression analysis was conducted using the R package DESeq2 v1.46.0
Assembly: NCBI RefSeq Assembly: GCF_004295125.1
Supplementary files format and content: .txt file. Includes summarized read counts generated by featurecounts using subread

source_name: Strain

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was depleted from the extracted RNA using the Hybridized Probe, rRNA Depletion, and Probe Removal reaction mixtures from the Illumina Stranded Total RNA Prep (Illumina Inc., San Diego, CA, USA). rRNA-depleted samples were purified using a 2.0x sbeadex SAB bead cleanup (Biosearch Technologies, Hoddesdon, UK) with a single 80% ethanol wash. Following cDNA library construction and indexing, the cDNA libraries were quantified using the Qubit™ 1X dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Thermo Fisher, Carlsbad, CA, USA) and the fragment sizes were assessed using a 4150 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).

value: Strain

value: Bacteria


title: Control3

city: xinxing

first: xiaojing

last: xia

address: hualandadao

institute: HENAN INSTITUTE OF SCIENCE AND TECHNOLOGY

description:
Library name: C3
c3_FPKM
c3_SRPBM

data_processing:
The transcrptome was assembled using the String Tle based on the reads mapped to the reference genome .The assembled transcripts were annotated using the gffcompare program . The unknowntranscripts were used to screen for putative IncRNAs. Four computational approaches include CPC2/CNCIPfam/CPAT were combined to sort non-protein codingRNA candidates from putative protetn-coding RNAs In the unknown transcripts Putative proleln- coding RNAs were fitered out using aminimum length and exon number threshold . Transcripts with lengths more than 200 nt and have more than two exons were selected as IncRNA candidates and further screened using CPC2ICNCIPfam/CPAT that have the power to distinguish the protein-coding genes trom the non- coding genes. As well as the different types of IncRNAs Include lIncRNA IntronidncRNA, antl-sense IncRNA, sense IncRNA were selected using cuffcompare
Assembly: GRCm38_release79
Supplementary files format and content: .xls Gene Expression Matrix

source_name: Peritoneal cavity

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitcred on 1.5% agarose gels.RNA concentration and purity was mesured using the advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing
A total amount of 1.5 ug RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, IMadison, WI, USA) Sequencing libraries were generated using NEBNext Uitra TlM Directional RNA Library Prep Kit for Iluminaß (NEB, USA) following manufacturer's recommendations and index codes were added to attrbute sequences to each sample. Briely, Fragmenlation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Butfer (5X) , First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonucleaseipolymerase activitles. Atter adenylalion of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragmenls were punified with AlAPure XP Beads (Beckman Coulter, Beverty, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-igated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelty DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purtied (Al, (Pure XP system) and library quality was assessed on the Agilent Bloanalyzer 2100 and qPCR

value: Peritoneal cavity

value: Marcrophages


title: Sample13_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_rep1

description: Library name: Sample13

value: sgEGFP


title: C. scindens supplemented with riboflavin at 11 hours - rep A

description:
Library name: C04
JNorth009_C04_386_260123_S23_L001


title: ss3_23_056s_K08_accepted_hits_sorted_deduplicated.bam

status: Public on Feb 16 2026

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

description:
Library name: Single cell sample 163
Smart-seq3

data_processing:
Samples were de-multiplexed yielding single-cell fastq files that were quality-trimmed using Trim Galore and UMI were extracted using the UMI-tools package.
Reads were then mapped to the danio rerio reference genome GRCz11 using STAR and duplicates were removed using UMI-tools dedup based on identified UMI’s
Per cell and gene raw-count expression matrices were prepared using the featureCounts package
Counts data was processed and analyzed using Seurat and pagoda2 packages in R-software
Assembly: GRCz11
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

organism: Danio rerio

source_name: meninges

extract_protocol:
3 brains per group were dissected and put in a buffer containing 0.5% Trypsin, 1mM EDTA, and 10U DNaseI (Promega) for 10 min at 30°C and shaken at 600rpm every 3 minutes until the BLECs were detached from the brain. Brains were removed, and the cells were centrifuged at 2000 rpm for 5 min. The pellet was washed and resuspended in PBS containing 3 % FCS and then filtered through a 40 µm nylon cell strainer. Cells were FACS-sorted into 384-well plates containing lysis buffer.
RNA libraries were prepared using the Smart-Seq3 protocol at SICOF Huddinge, Sweden.

value: meninges

value: BLEC

tag: group

value: control


title: IgG-Seq Sample IgG15B

city: Jacksonville

first: John

last: Gubatan

state: FL

address: Mayo Clinic Mangurian Building 5220, 4500 San Pablo Rd

institute: Mayo Clinic Florida

description:
Library name: IgG15B
Novogene
IGGSEQ.rds

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

source_name: Stool

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.

treatment_protocol: Patients with established inflammatory bowel disease (ulcerative colitis or Crohn’s disease) were screened and invited to participate in vitamin D prospective study at Stanford University (IRB 60958) and the University of Copenhagen (IRB 2021-1696). Patients who met inclusion criteria (adult patients (18 years or older) with inflammatory bowel disease (ulcerative colitis or Crohn's disease), low serum vitamin D (25(OH)D ≤ 25 ng/mL, not on vitamin D supplementation at time of recruitment, no prior bowel resections, no antibiotic use in past 3 months) were enrolled. Patients who had prior bowel surgeries (colectomy, small bowel resections), renal dysfunction, history of hypercalcemia, history of HIV (human immunodeficiency virus), history of IgA deficiency, history of common variable immunodeficiency (CVID), or current or recent C. diff infection were excluded from study. All patients provided consent in accordance with Institutional Review Board guidance for each institution as noted above. At the time of enrollment (week 0), patients had blood and stool samples collected. Patients were then treated with 50,000 units of oral vitamin D (ergocalciferol) once per week for 12 weeks. Blood and stool samples were collected at the end of study (week 12). C-reactive protein and fecal calprotectin were measured from week 0 and week 12 blood and stool samples, respectively. Disease activity scores (partial Mayo score for ulcerative colitis, Harvey Bradshaw Index for Crohn’s disease), quality of life scores (short inflammatory bowel disease questionnaire/SIBDQ) were collected at week 0 and week 12.

value: Stool

value: Post-vitamin D


title: hapo_newborn_cordblood_A0431

first: Jami

middle: L

last: Josefson

address: 225 E Chicago Avenue

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

value: Male

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: IgG-Seq Sample IgG37A

description:
Library name: IgG37A
Novogene
IGGSEQ.rds

value: Pre-vitamin D


title: H3K27ac-CKO-2 Cut&tag

city: Chongqing

first: Yuanyuan

last: Liu

address: No. 1 Medical College Road, Yuzhong District, Chongqing, China

institute: Chongqing Medical Journal

description: Library name: Sample-13

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: BigWig files.
Library strategy: CUT&Tag

source_name: Bone Marrow

extract_protocol:
About 25,000-30,000 HSCs were isolated by FACS and the ATAC-seq was performed following the protocol of Corces et al. About 25,000-30,000 HSCs were isolated by FACS and the CUT&Tag assay was performed.
ATAC-seq: HSCs were lysed and the DNA fragments were broken using the TruePrepTM DNA Library Prep Kit V2 (Vazyme). DNA fragment amplification was performed using KAPA HiFi HotStart Ready Mix (KAPA Biosystems, USA). The Agencourt AMPure XP kit was used to purify cDNA (Beckman Coulter, USA).  Sequencing was performed on the Illumina NovaSeq 6000. CUT&Tag assay: HSCs were harvested and combined with ConA beads (NovoNGS® ConA Beads) and antibodies (H3K27ac, H3K9ac, H3K4me3, IgG and Smarca4), followed by the formation of transposomes using ChiTag Transposome. Transposition fragmentation was performed using constant temperature. DNA extraction was performed using WAHTS DNA Clean Beads (Vazyme). DNA amplification was performed using CUT&Tag 2.0 High-Sensitivity Kit (NovoNGS). Sequencing was performed on the Illumina NovaSeq 6000.

value: Bone Marrow

value: Primary cell

value: Hematopoietic stem cell

value: CKO


title: Whole Stool 16S Sample S33B

description:
Library name: S33B
Novogene

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged VD16Seq2.rds Phyloseq object
Library strategy: 16S rRNA-seq

organism: human feces metagenome

tag: patient id


title: Sample2_MM1S_RNAseq_withoutIL6_24h_rep2

description: Library name: Sample2

value: multiple myeloma cell line

value: without IL-6 for 24 h


title: IMR90_Doxo_4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

institute: MRC London Institute of Medical Sciences

extract_protocol: Total RNA was extracted using Trizol and the Rneasy isolation kit (Qiagen).

value: doxorubicin

value: senescent


title: IMR90_Doxo_2


title: Control 2

description: Library name: SAMPLE2

value: Kidney

value: PBS for 6 Days


title: IMR904OHT-siNT1-2

description: Library name: IMR904OHT-siNT1_2_S6

data_processing:
Lowly expressed genes were filtered by excluding those with total log10 counts ≤ 3.5.
Counts were then normalised using the TMM method (edgeR) and transformed to log2CPM using voom (limma), which adjusts for the mean–variance relationship in RNA-seq data.
The final expression matrix is in log2CPM units.
Assembly: hg19
Supplementary files format and content: filtered and normalised expression matrix.
Supplementary files format and content: raw counts obtained directly from VAST-TOOLS;
Supplementary files format and content: alternative splicing inclusion tables obtained directly from VAST-TOOLS;

source_name: Lung

extract_protocol:
RNeasy Kits for RNA Purification (Qiagen)
Library construction was done using the Watchmaker Genomics mRNA Capture kit followed by the Watchmaker Genomics RNA Library Prep Kit according to manufacturers instructions. Libraries were indexed using IDT xGen Unique Dual Index Primers and pooled together for sequencing.

value: Lung

value: Fibroblasts

value: ER:RAS G12V

value: 4OHT siNT1


title: Control 3

description: Library name: SAMPLE3


title: Control 1

description: Library name: SAMPLE1


title: Sample1_MM1S_RNAseq_withoutIL6_24h_rep1

description: Library name: Sample1


title: IMR90_Quiesc_3

value: 0.5percent FBS

value: quiescent


title: IMR904OHT-siNT1-4

description: Library name: IMR904OHT-siNT1_4_S8


title: IMR90_Quiesc_2


title: Reseq-HEK-siDKC1-input-IV-rep2

description: Library name: Library-4

data_processing:
Only R2 reads were used except for the sictrl and siDKC1 samples as described below.
Trim adapter: Adapter sequence of “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” was first trimmed from the 3’ end of poly-A RNA R2
Deduplicate using bbmap clumpify.sh
Trim UMI: Reads R2 from samples generated with superscript III were trimmed 6 nt on the 5’ end and 5 nt on the 3’ end, whereas reads from samples generated with superscript IV was trimmed 7nt on the 5’ end and 5nt on the 3’ end as superscript IV tends to elongate for one more nucleotide.
For the sictrl and siDKC1 IP samples, paired end sequencing were used. Reads R1 and R2 were first merged, then decomplexed based on the internal barcodes. The resulting files are therefore uploaded to GEO as one file for each sample and labeled as "single-end" even though they were merged paired-end reads. The internal barcodes and UMI (8 nt in total on the 5' end and 5 nt in total on the 3' end) need to be trimmed after reads de-duplication. For the sictrl and siDKC1 input samples,single end reads were used. Samples were degerated based on internal barcodes and uploaded to GEO as sinlgle file for each sample. Reads were then removed adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", and then de-duplicated. The internal barcodes and UMI (8 nt in total on the 5' end and 5 nt in total on the 3' end) need to be trimmed after reads de-duplication.
Reads after adapter trimming, deduplication and UMI trimming were mapped to hg38 using hisat2 with options of “--known-splicesite-infile --rna-strandness F --no-softclip”.
Assembly: hg38
Supplementary files format and content: xlsx files containing candidate modification sites or differential modification sites

source_name: HEK 293T

growth_protocol: HEK 293T and HeLa cell lines were grown and maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C with 5% CO2. The day before transfection, 2 × 10⁶ HEK293T cells were seeded onto each 15 cm cell culture plate.

treatment_protocol: For siRNA knockdown experiments, transfection was performed using RNAiMax transfection reagent following manufacturer's instructions. For one 15 cm plate, 20 μL of 20 μM siDKC1 (Qiagen, Hs_DKC1_6 FlexiTube siRNA) or siCtrl (Sigma Aldrich, catalog # sic001) was used. Cells were harvested 72–96 hours post-transfection.

value: HEK 293T

value: cancer cells

value: DKC1 KD


title: IMR90_Doxo_1


title: IMR904OHT-siNT1-1

description: Library name: IMR904OHT-siNT1_1_S5


title: IMR90DMSO-siNT1-3

description: Library name: IMR90DMSO-siNT1_3_S3

value: DMSO siNT1


title: IMR90DMSO-siNT1-4

description: Library name: IMR90DMSO-siNT1_4_S4


title: sample3_tet- WT_1, WT_2, WT_noncoding mRNA_GEX

city: SAINT LOUIS

first: Suin

last: Jo

state: MO

address: 4939 Childrens PI

department: Division of Biology & Biomedical Sciences

institute: Washington University in St. Louis

description:
Library name: tet- WT_1, WT_2, WT_noncoding mRNA_GEX
sample3_GEX

data_processing:
The multiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software ver 9.9.0
Assembly: 10x Genomics reference transcriptome mm10-2020-A (Ensembl 98, GRCm38/mm10).
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Spleen

extract_protocol:
Prior to fluorescence-activated cell sorting (FACS), cells from each individual mouse were stained with hashtag oligonucleotides (HTOs) to enable multiplexing and improve sample throughput. T cells sorted from spleens of non-coding mRNA or OVA mRNA vaccinated mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a GEM-X Single Cell V(D)J Reagent Kit (5' chemistry; 10x Genomics) following the manufacturer’s protocol.
Libraries were quantified using the Qubit dsDNA High Sensitivity (HS) Assay Kit (Invitrogen) and quality-checked using a High Sensitivity DNA chip on a Bioanalyzer 2100 system (Agilent Technologies). The sequencing was carried out on an Illumina NovaSeq 6000 system using an S4 flow cell with paired-end reads (2 × 150 cycles). Raw reads from scRNA-seq libraries were aligned to the mouse reference genome mm10-2020-A using Cell Ranger v9.0.0 (10x Genomics). Filtered feature-barcode matrices, containing only high-confidence cellular barcodes, were used for downstream analysis. Single-cell TCR reads were aligned to the mouse reference genome vdj_GRCm38_alts_ensembl-7.0.0. Only productive TCRα and TCRβ chains were retained for subsequent analyses.

value: Spleen

value: CD8 T cell

value: WT

value: tetramer- sorted


title: sample3_tet- WT_1, WT_2, WT_noncoding mRNA_HTO

description:
Library name: tet- WT_1, WT_2, WT_noncoding mRNA_HTO
sample3_HTO


title: IMR904OHT-siNT1-3

description: Library name: IMR904OHT-siNT1_3_S7


title: sample2_tet+ WT_2, d32_2, d123_2_TCR

description:
Library name: tet+ WT_2, d32_2, d123_2_TCR
sample2_TCR

value: tetramer+ sorted


title: Reseq-HEK-siDKC1-input-IV-rep1

description: Library name: Library-3


title: IMR90_Quiesc_4


title: Reseq-HEK-sictrl-input-IV-rep1

description: Library name: Library-1


title: Reseq-HEK-sictrl-input-IV-rep2

description: Library name: Library-2


title: IMR90_Doxo_3

value: doxorubicin

value: senescent


title: IMR90DMSO-siNT1-2

description: Library name: IMR90DMSO-siNT1_2_S2

value: Lung


title: spikein-NNUNN-click-ctrl-IP-rep2

description: Library name: Library-60

data_processing:
Only R2 reads were used except for the sictrl and siDKC1 samples as described below.
Trim adapter: Adapter sequence of “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” was first trimmed from the 3’ end of poly-A RNA R2
Deduplicate using bbmap clumpify.sh
Trim UMI: Reads R2 from samples generated with superscript III were trimmed 6 nt on the 5’ end and 5 nt on the 3’ end, whereas reads from samples generated with superscript IV was trimmed 7nt on the 5’ end and 5nt on the 3’ end as superscript IV tends to elongate for one more nucleotide.
For the sictrl and siDKC1 samples, paired end sequencing were used. However, reads R1 and R2 were first merged, then decomplexed based on the internal barcodes. The resulting files are therefore uploaded as one file for each sample and labeled as "single-end" even though they were merged paired-end reads. The internal barcodes and UMI (8 nt in total on the 5' end and 5 nt in total on the 3' end) need to be trimmed after reads de-duplication.
Reads after adapter trimming, deduplication and UMI trimming were mapped to hg38 using hisat2 with options of “--known-splicesite-infile --rna-strandness F --no-softclip”.
Assembly: hg38
Supplementary files format and content: The .xlsx files contain information of candidate modification sites identified in different cell lines and under different conditions and the change of enrichment levels under the control and DKC1 knockdown conditions.

extract_protocol:
RNAs were extracted from cells using Trizol reagent and polyA RNA were extracted using Dynabeads® mRNA DIRECT™ Kit for two rounds. Messenger RNAs were extracted with an additional ribosome RNA removal step using the RiboMinus™ Eukaryote Kit v2.
Libraries were constructed using a customized protocol. For the experiments of DKC1 knockdown, internally barcoded RNA adapters, wo that the four input samples (2 sictrl reps and 2 siDKC1 reps) and the four pull-down samples can be pooled together right after the RNA ligation. For IVT RNA, the RNA was mixed with rice mRNA in 1:1 ratio and then proceeded with library construction using ELAP-seq.


title: sample3_tet- WT_1, WT_2, WT_noncoding mRNA_TCR

description:
Library name: tet- WT_1, WT_2, WT_noncoding mRNA_TCR
sample3_TCR


title: IMR90_Quiesc_1


title: spikein-NNUNN-IP-rep2

description: Library name: Library-58


title: IMR90_Control_3

value: DMSO

value: growing


title: sample2_tet+ WT_2, d32_2, d123_2_HTO

description:
Library name: tet+ WT_2, d32_2, d123_2_HTO
sample2_HTO


title: IMR90_Control_1


title: Mutant BACHD sample 2, BACHD;Dlx1-EGFP+ FACsorted Medial Ganglionic Eminence cells (GABAergic) dissociated at E12.5

city: Bronx

first: Aldrin

middle: Enrique

last: Molero

state: US-NY

address: 1410 Pelham Parkway S

department: Neurology

institute: Albert Einstein College of Medicine

description:
Library name: BACHD2
10X Genomics

data_processing:
Raw count matrix preprocessing and ambient RNA correction: Raw gene–cell count matrices generated by the 10x Genomics Cell Ranger pipeline were imported into R (v4.4.3) and processed using Seurat (v5.2.0). Ambient RNA contamination was estimated and removed on a per-sample basis using the SoupX package, yielding corrected count matrices for downstream analysis.
Quality control and doublet removal: Each sample was processed independently for quality control. Cells were retained if they expressed >200 genes and >500 UMIs, and genes detected in fewer than 10 cells were excluded. Cells with >15% mitochondrial transcript content were removed. Heterotypic doublets were identified and excluded using DoubletFinder. High-quality, filtered Seurat objects from all samples were subsequently merged into a single dataset
Normalization, scaling, and batch correction: Merged data were normalized using Seurat’s NormalizeData function, and the top 2,000 variable features were identified. Data were scaled while regressing out technical covariates (nFeature_RNA, mitochondrial and ribosomal transcript percentages) and cell-cycle scores. Cell-cycle scores were regressed out for clustering and integration but retained for downstream cell-cycle–resolved analyses. Batch effects across samples were corrected using Harmony applied to principal component embeddings
Dimensionality reduction, clustering, and cell-type annotation: Principal component analysis (PCA) was performed on the integrated dataset, and the number of components used was selected based on elbow plot inspection. A shared nearest neighbor graph was constructed, and clustering was performed using the Leiden algorithm (resolution = 0.5). Cluster quality and stability were assessed using ROGUE and SCCAF, resulting in 29 transcriptionally distinct clusters. Clusters were visualized using UMAP and annotated by manual curation based on established canonical marker genes. Related clusters were consolidated into 11 major cell-type categories
Differential expression and functional enrichment analyses: Differential gene expression between BACHD and control samples was assessed using pseudobulk aggregation followed by DESeq2, treating pooled samples as biological replicates. MA plots were generated from these analyses. Gene Ontology enrichment for Biological Process and Cellular Component categories was performed using ShinyGO v0.77. Gene expression patterns were visualized using Seurat plotting functions (DimPlot, FeaturePlot, VlnPlot) and heatmaps generated with the pheatmap package
Assembly: refdata-gex-mm10-2020-A (mm10)
Supplementary files format and content: Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v2.1.1

source_name: E12.5 Medial Ganglionic Eminence

extract_protocol:
After dissociation, the sample consisted of two independent pools of cell suspensions per genotype (BACHD and WT). Each pool was fluorescence-activated cell sorted (FACS) using a MoFlo XDP high-speed cell sorter (Beckman Coulter) equipped with a 120-µm nozzle and operated at a sheath pressure of 16.6 PSI, yielding >80% cell viability. Each independent pool of single-cell suspensions (up to 10,000 cells per sample) was then separately processed for scRNA-seq library preparation.
Chromium Next GEM Single Cell 3′ v3.1 kit (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol.  Within the Chromium microfluidic chip, single cells were encapsulated in oil droplets (Gel Beads-in-Emulsion, or GEMs) together with barcoded gel beads and lysis reagents. Upon partitioning, cells were lysed within GEMs and released RNA was immediately hybridized to barcoded oligonucleotides on the gel beads. Reverse transcription (RT) was performed within GEMs to convert captured polyadenylated RNA into barcoded cDNA. Each cDNA molecule contains a unique cell barcode and unique molecular identifier (UMI), enabling identification of the cell of origin and molecule counting after sequencing. After RT, emulsions were broken, and pooled, barcoded cDNA was recovered, amplified by PCR, and used for library preparation according to the 10x Genomics protocol.

value: E12.5 Medial Ganglionic Eminence

value: BACHD;Dlx1-EGFP, C57BL

value: Embryonic Brain

value: BACHD


title: IMR90DMSO-siNT1-1

description: Library name: IMR90DMSO-siNT1_1_S1

value: Fibroblasts

value: ER:RAS G12V


title: IMR90_Control_4

data_processing:
Primary analysis RTA 1.18.64 and Secondary analysis CASAVA- 1.8.4
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to hg19 genome using Tophat 2.0.11
Gene based counting was performed using the Rsubread package.
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.18.1 )
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file include raw counts for each Sample generated by  Rsubread.


title: spikein-NNUNN-click-ctrl-IP-rep1

first: Chuan

last: He

address: 929 E 57th St

institute: University of Chicago

description: Library name: Library-59

value: HEK 293T

value: cancer cells


title: sample2_tet+ WT_2, d32_2, d123_2_GEX

description:
Library name: tet+ WT_2, d32_2, d123_2_GEX
sample2_GEX

value: Spleen

value: CD8 T cell


title: Patient-derived Organoid pid96 replicate1

status: Public on Feb 14 2026

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

institute: Indian Institite of Technology Jammu

description: Library name: CC-CC-96_PDO_R1

data_processing:
Adapter sequences were removed from the FASTQ files using Cutadapt (v5.1). Cleaned and  trimmed paired-end reads were aligned to the human reference genome hg38 release 113 using STAR (v2.6.1a_08-27) aligner to generate BAM files.
The gene-level count matrix was summarized from BAM files using featureCounts (v2.0.2). Gene annotation from Ensembl GRCh38 release 113 was used for quantification.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for individual samples

source_name: Organoid

growth_protocol: Endometrial tissues were minced until tissue was roughly 1mm in diameter and washed twice with PBS. Tissue samples were digested in collagenase IV (Sigma Aldrich, C9407) in the presence of Y-27632 dihydrochloride (Tocris, 1254) for 2-3 hours. Tissues were then incubated in TrypLE Express (Thermo Fisher, 12604) in the presence of Y-27632 dihydrochloride for 10-20 minutes and confirmed microscopically for isolated single-cells. Digestion was stopped with Advanced DMEM F-12 (Gibco, 12634028) and after centrifugation, the specimens were resuspended in 70% Matrigel (Corning, 356234) and 30% corresponding media (PMID:39512886 and 37124727) and plated on pre-warmed plates. Media was refreshed every three days. Organoids were split every 10-20 days depending on the assessment of cell health. Media was removed and Matrigel was removed by Cell Recovery Solution (Corning, 354253) for thirty minutes and then digested with TrypLE supplemented with Y-Factor for 10-20 minutes and confirmed microscopically for single-cells. Single cells were then plated to a density of 5,000 cells/ 10μL.

extract_protocol:
Organoids were collected in Cell Recovery Solution (Corning), and their RNAs were harvested with TRIzol reagent (Thermo Fisher, 15596026). RNA was extracted from organoids using the Zymogen Direct-zol RNA kits (Zymo research, R2062) according to the manufacturer’s instructions.
RNA depletion and library preparation was performed using NEBNextⓇ Ultra II Directional RNA Library Prep Kit for IlluminaⓇ(Illumina, E7765S/L) according to the manufacturer’s protocol. Prepared library was analyzed using the Agilent Bioanalyzer 2100 using high sensitivity DNA chips (Agilent, 5067-4626).  Sequencing was performed using NextSeq500.

value: Organoid

value: Patient-derived Organoid


title: Organoid from matched normal or biopsy pid96 replicate1

description: Library name: CC-CC-96_CTL_R1

value: Organoid from matched normal or biopsy


title: Control sample 2, WT;Dlx1-EGFP+ FACsorted Medial Ganglionic Eminence cells (GABAergic) dissociated at E12.5

description:
Library name: WT2
10X Genomics

value: WT;Dlx1-EGFP, C57BL

value: WT


title: sample1_tet+ WT_1, d32_1, d123_1_TCR

description:
Library name: tet+ WT_1, d32_1, d123_1_TCR
sample1_TCR

value: tetramer+ sorted


title: Organoid from matched normal or biopsy pid95 replicate1

description: Library name: CC-CC-95_CTL_R1


title: Patient-derived Organoid pid93 replicate1

description: Library name: CC-CC-93_PDO_R1


title: Control sample 1, WT;Dlx1-EGFP+ FACsorted Medial Ganglionic Eminence cells (GABAergic) dissociated at E12.5

description:
Library name: WT1
10X Genomics


title: spikein-NNUNN-IP-rep1

city: Chicago

description: Library name: Library-57


title: IMR90_Control_2

value: DMSO

value: growing


title: Patient-derived Organoid pid92 replicate1

description: Library name: CC-CC-92_PDO_R1


title: IgG-Seq Sample IgG39A

description:
Library name: IgG39A
Novogene
IGGSEQ.rds

value: Stool

value: Pre-vitamin D


title: Organoid from matched normal or biopsy pid92 replicate1

description: Library name: CC-CC-92_CTL_R1


title: spikein-NNUNN-input-rep2

description: Library name: Library-56


title: sample1_tet+ WT_1, d32_1, d123_1_HTO

description:
Library name: tet+ WT_1, d32_1, d123_1_HTO
sample1_HTO


title: sample1_tet+ WT_1, d32_1, d123_1_GEX

description:
Library name: tet+ WT_1, d32_1, d123_1_GEX
sample1_GEX


title: Patient-derived Organoid pid90 replicate1

description: Library name: CC-CC-90_PDO_R1


title: spikein-NNUNN-input-rep1

description: Library name: Library-55


title: Mutant BACHD sample 1, BACHD;Dlx1-EGFP+ FACsorted Medial Ganglionic Eminence cells (GABAergic) dissociated at E12.5

description:
Library name: BACHD1
10X Genomics

value: E12.5 Medial Ganglionic Eminence

value: BACHD;Dlx1-EGFP, C57BL

value: Embryonic Brain

value: BACHD


title: Patient-derived Organoid pid95 replicate1

description: Library name: CC-CC-95_PDO_R1


title: Organoid from matched normal or biopsy pid94 replicate1

description: Library name: CC-CC-94_CTL_R1


title: Organoid from matched normal or biopsy pid90 replicate1

description: Library name: CC-CC-90_CTL_R1


title: Organoid from matched normal or biopsy pid89 replicate1

description: Library name: CC-CC-89_CTL_R1


title: Patient-derived Organoid pid89 replicate1

description: Library name: CC-CC-89_PDO_R1


title: Patient-derived Organoid pid94 replicate1

description: Library name: CC-CC-94_PDO_R1


title: Organoid from matched normal or biopsy pid93 replicate1

description: Library name: CC-CC-93_CTL_R1


title: Patient-derived Organoid pid91 replicate1

description: Library name: CC-CC-91_PDO_R1


title: Patient-derived Organoid pid87 replicate1

description: Library name: CC-CC-87_PDO_R1


title: Organoid from matched normal or biopsy pid91 replicate1

description: Library name: CC-CC-91_CTL_R1


title: Organoid from matched normal or biopsy pid84 replicate1

description: Library name: CC-CC-84_CTL_R1


title: Patient-derived Organoid pid83 replicate1

description: Library name: CC-CC-83_PDO_R1


title: Organoid from matched normal or biopsy pid88 replicate1

description: Library name: CC-CC-88_CTL_R1


title: Organoid from matched normal or biopsy pid82 replicate1

description: Library name: CC-CC-82_CTL_R1


title: Organoid from matched normal or biopsy pid87 replicate1

description: Library name: CC-CC-87_CTL_R1


title: Patient-derived Organoid pid88 replicate1

description: Library name: CC-CC-88_PDO_R1


title: Organoid from matched normal or biopsy pid86 replicate1

description: Library name: CC-CC-86_CTL_R1


title: Patient-derived Organoid pid86 replicate1

description: Library name: CC-CC-86_PDO_R1


title: Patient-derived Organoid pid78 replicate1

description: Library name: CC-CC-78_PDO_R1


title: Organoid from matched normal or biopsy pid79 replicate1

description: Library name: CC-CC-79_CTL_R1


title: Organoid from matched normal or biopsy pid85 replicate1

description: Library name: CC-CC-85_CTL_R1


title: Patient-derived Organoid pid85 replicate1

description: Library name: CC-CC-85_PDO_R1


title: Patient-derived Organoid pid84 replicate1

description: Library name: CC-CC-84_PDO_R1


title: Organoid from matched normal or biopsy pid77 replicate1

description: Library name: CC-CC-77_CTL_R1


title: Organoid from matched normal or biopsy pid81 replicate1

description: Library name: CC-CC-81_CTL_R1


title: Patient-derived Organoid pid76 replicate1

description: Library name: CC-CC-76_PDO_R1


title: Organoid from matched normal or biopsy pid78 replicate1

description: Library name: CC-CC-78_CTL_R1


title: Organoid from matched normal or biopsy pid83 replicate1

description: Library name: CC-CC-83_CTL_R1


title: Patient-derived Organoid pid73 replicate1

description: Library name: CC-CC-73_PDO_R1


title: Patient-derived Organoid pid74 replicate1

description: Library name: CC-CC-74_PDO_R1


title: Patient-derived Organoid pid82 replicate1

description: Library name: CC-CC-82_PDO_R1


title: Organoid from matched normal or biopsy pid71 replicate1

description: Library name: CC-CC-71_CTL_R1


title: Patient-derived Organoid pid71 replicate1

description: Library name: CC-CC-71_PDO_R1


title: Organoid from matched normal or biopsy pid80 replicate1

description: Library name: CC-CC-80_CTL_R1


title: Organoid from matched normal or biopsy pid75 replicate1

description: Library name: CC-CC-75_CTL_R1


title: Organoid from matched normal or biopsy pid73 replicate1

description: Library name: CC-CC-73_CTL_R1


title: Patient-derived Organoid pid72 replicate1

description: Library name: CC-CC-72_PDO_R1


title: Organoid from matched normal or biopsy pid66 replicate1

description: Library name: CC-CC-66_CTL_R1


title: Organoid from matched normal or biopsy pid70 replicate1

description: Library name: CC-CC-70_CTL_R1


title: Patient-derived Organoid pid69 replicate1

description: Library name: CC-CC-69_PDO_R1


title: Patient-derived Organoid pid47 replicate2

description: Library name: CC-CC-47_PDO_R2


title: Organoid from matched normal or biopsy pid68 replicate1

description: Library name: CC-CC-68_CTL_R1


title: Patient-derived Organoid pid65 replicate1

description: Library name: CC-CC-65_PDO_R1


title: Organoid from matched normal or biopsy pid44 replicate2

description: Library name: CC-CC-44_CTL_R2


title: Organoid from matched normal or biopsy pid67 replicate1

description: Library name: CC-CC-67_CTL_R1


title: Patient-derived Organoid pid45 replicate2

description: Library name: CC-CC-45_PDO_R2


title: Organoid from matched normal or biopsy pid42 replicate1

description: Library name: CC-CC-42_CTL_R1


title: Organoid from matched normal or biopsy pid47 replicate2

description: Library name: CC-CC-47_CTL_R2


title: Patient-derived Organoid pid43 replicate2

description: Library name: CC-CC-43_PDO_R2


title: Patient-derived Organoid pid37 replicate2

description: Library name: CC-CC-37_PDO_R2


title: Organoid from matched normal or biopsy pid39 replicate1

description: Library name: CC-CC-39_CTL_R1


title: Organoid from matched normal or biopsy pid64 replicate1

description: Library name: CC-CC-64_CTL_R1


title: Organoid from matched normal or biopsy pid46 replicate2

description: Library name: CC-CC-46_CTL_R2


title: Patient-derived Organoid pid35 replicate2

description: Library name: CC-CC-35_PDO_R2


title: Organoid from matched normal or biopsy pid63 replicate1

description: Library name: CC-CC-63_CTL_R1


title: Organoid from matched normal or biopsy pid45 replicate2

description: Library name: CC-CC-45_CTL_R2


title: Patient-derived Organoid pid46 replicate2

description: Library name: CC-CC-46_PDO_R2


title: Patient-derived Organoid pid18 replicate5

description: Library name: CC-CC-18_PDO_R5


title: Patient-derived Organoid pid42 replicate2

description: Library name: CC-CC-42_PDO_R2


title: Patient-derived Organoid pid39 replicate1

description: Library name: CC-CC-39_PDO_R1


title: Patient-derived Organoid pid21 replicate3

description: Library name: CC-CC-21_PDO_R3


title: Organoid from matched normal or biopsy pid59 replicate1

description: Library name: CC-CC-59_CTL_R1


title: Patient-derived Organoid pid59 replicate1

description: Library name: CC-CC-59_PDO_R1


title: Organoid from matched normal or biopsy pid58 replicate1

description: Library name: CC-CC-58_CTL_R1


title: Organoid from matched normal or biopsy pid57 replicate1

description: Library name: CC-CC-57_CTL_R1


title: Organoid from matched normal or biopsy pid62 replicate1

description: Library name: CC-CC-62_CTL_R1


title: Organoid from matched normal or biopsy pid60 replicate2

description: Library name: CC-CC-60_CTL_R2


title: Patient-derived Organoid pid60 replicate1

description: Library name: CC-CC-60_PDO_R1


title: Organoid from matched normal or biopsy pid55 replicate1

description: Library name: CC-CC-55_CTL_R1


title: Patient-derived Organoid pid53 replicate1

description: Library name: CC-CC-53_PDO_R1


title: Organoid from matched normal or biopsy pid54 replicate1

description: Library name: CC-CC-54_CTL_R1


title: Patient-derived Organoid pid47 replicate1

description: Library name: CC-CC-47_PDO_R1


title: Organoid from matched normal or biopsy pid56 replicate1

description: Library name: CC-CC-56_CTL_R1


title: Organoid from matched normal or biopsy pid38 replicate1

description: Library name: CC-CC-38_CTL_R1


title: Patient-derived Organoid pid52 replicate1

description: Library name: CC-CC-52_PDO_R1


title: Organoid from matched normal or biopsy pid47 replicate1

description: Library name: CC-CC-47_CTL_R1


title: Patient-derived Organoid pid51 replicate1

description: Library name: CC-CC-51_PDO_R1


title: Organoid from matched normal or biopsy pid50 replicate1

description: Library name: CC-CC-50_CTL_R1


title: Organoid from matched normal or biopsy pid46 replicate1

description: Library name: CC-CC-46_CTL_R1


title: Patient-derived Organoid pid45 replicate1

description: Library name: CC-CC-45_PDO_R1


title: Patient-derived Organoid pid44 replicate1

description: Library name: CC-CC-44_PDO_R1


title: Organoid from matched normal or biopsy pid44 replicate1

description: Library name: CC-CC-44_CTL_R1


title: Patient-derived Organoid pid43 replicate1

description: Library name: CC-CC-43_PDO_R1


title: Patient-derived Organoid pid49 replicate1

description: Library name: CC-CC-49_PDO_R1


title: Organoid from matched normal or biopsy pid69 replicate1

description: Library name: CC-CC-69_CTL_R1


title: Patient-derived Organoid pid48 replicate1

description: Library name: CC-CC-48_PDO_R1


title: Patient-derived Organoid pid46 replicate1

description: Library name: CC-CC-46_PDO_R1


title: Patient-derived Organoid pid42 replicate1

description: Library name: CC-CC-42_PDO_R1