title: OE33-shAPE1#3-ABS-3

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

description: Library name: OA3-BS3

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality nucleotides using Trimmomatic v0.36. The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome available from Ensembl using STAR v2.5.2b. Unique gene-level read counts were generated using featureCounts from the Subread package v1.5.2. Counts were summarized using the gene_id feature in the annotation file, and only uniquely mapped reads falling within annotated exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: The processed data file, APE1_ABS_36samples_raw_count_matrix.tsv.gz, is a gzip-compressed, tab-delimited gene-level raw-count matrix. Rows represent genes identified by Ensembl gene_id identifiers, columns represent the 36 biological samples, and values are unnormalized integer read counts.

source_name: esophageal adenocarcinoma (EAC)

growth_protocol: FLO1 cells were culture with DMEM and OE33 cells were cultured with  RPMI1640, supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Standard RNA-sequencing (mRNA-Seq) in eukaryotic samples. Polyadenylated mRNA is selectively enriched from total RNA using oligo(dT) magnetic beads. High-temperature thermal treatment in divalent cation buffer fragments the mRNA to ~250–300 bp.

treatment_protocol: The two human EAC cell lines (OE33 and FLO-1) were stably transduced with either a non-targeting control shRNA (shCtrl) or two distinct APE1-targeted shRNAs (shAPE1#1 and shAPE1#3). To model GERD pathophysiology, shCtrl cells and two shAPE1 cells (shAPE1#1 and shAPE1#3) were exposed to an acidic bile salt cocktail (200 µM, pH 4.0) for 20 minutes and allowed to recover in complete medium for 6 h.

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: shAPE1#3 knockdown with ABS exposure


title: OE33-shAPE1#3-ABS-2

status: Public on Aug 06 2026

type: SRA

country: USA

description: Library name: OA3-BS2

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: OE33-shAPE1#3-ABS-1

description: Library name: OA3-BS1


title: OE33-shAPE1#3-3

description: Library name: OA3-3

value: shAPE1#3 knockdown


title: OE33-shAPE1#3-1

description: Library name: OA3-1


title: OE33-shAPE1#3-2

description: Library name: OA3-2


title: OE33-shAPE1#1-ABS-3

description: Library name: OA1-BS3

value: shAPE1#1 knockdown with ABS exposure


title: OE33-shAPE1#1-ABS-2

description: Library name: OA1-BS2


title: OE33-shAPE1#1-2

description: Library name: OA1-2

value: shAPE1#1 knockdown


title: OE33-shAPE1#1-3

description: Library name: OA1-3


title: OE33-shAPE1#1-1

description: Library name: OA1-1


title: OE33-shContorl-ABS-2

description: Library name: OCBS2

value: shControl with ABS exposure


title: OE33-shControl-3

description: Library name: OC3

value: shControl RNA


title: OE33-shControl-2

description: Library name: OC2


title: OE33-shControl-1

description: Library name: OC1


title: FLO1-shAPE1#3-ABS-2

description: Library name: FA3-BS2


title: FLO1-shAPE1#3-ABS-3

description: Library name: FA3-BS3


title: OE33-shContorl-ABS-1

description: Library name: OCBS1


title: GM12878_Express_P3_S2

status: Public on Aug 07 2026

city: New York

first: Viviana

middle: I

last: Risca

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: GM12878_Express_P3_S2

library_source: genomic

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using bwa-mem2, converted to BAM format, and processed with a pairtools-based pipeline to parse contacts, correct orientation, sort, remove duplicates, and generate final high-confidence contact pairs for downstream analysis.
Assembly: hg38
Supplementary files format and content: cool

molecule: genomic DNA

growth_protocol: K562 cells were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10 % fetal bovine serum and 1 % penicillin–streptomycin. hTERT RPE-1 and GM12878 cells were cultured in the media and conditions recommended by ATCC and Coriell Institute for Medical Research, respectively.

extract_protocol:
For Classic CAD-C, crosslinked cells were subjected to RNase treatment and CAD digestion, followed by in situ end repair, biotin fill-in, and proximity ligation; nuclei were then treated with Exonuclease III, crosslinks were reversed by proteinase K digestion, and DNA was purified by phenol–chloroform extraction with ethanol precipitation or by column-based cleanup. For Express CAD-C, DNA extraction followed the Classic CAD-C workflow through CAD digestion, end repair, biotin fill-in, proximity ligation, Exonuclease III treatment, and crosslink reversal, yielding purified CAD-C DNA that was subsequently used directly as input for library preparation. For Direct CAD-C, crosslinked cells were processed by CAD digestion and in situ proximity ligation without end repair or biotin labeling; proximity-ligation concatemer DNA was isolated after crosslink reversal and protein digestion.
Purified DNA was either sonicated and subjected to streptavidin-based enrichment followed by Illumina library preparation, processed directly with the NEBNext UltraExpress FS kit, followed by PCR amplification and sequencing.

value: B lymphoblastoid cell line

tag: genotype

value: WT


title: Lung, MNX CH, female, rep3

city: Kansas City

first: Emily

last: Schueddig

state: KS

address: 2901 Rainbow Boulevard

department: Department of Biostatistics & Data Science

institute: University of Kansas Medical Center

description: Library name: RSB491-06

data_processing:
Read quality was assessed using FastQC (v0.12.1, RRID:SCR_014583). UMI-tools (v1.1.6, RRID:SCR_017048) was used for UMI and read extraction, then cutadapt (v5.0, RRID:SCR_011841) was used to retain reads with a minimum read length of 14 base pairs and maximum of 100 base pairs. BWA (v0.7.18, RRID:SCR_010910) with the aln algorithm was used for mapping with parameters set for no gaps (-o 0) and no mismatches (-n 0). Reads were aligned to the genomic sequence of aminoacetylated, mature mitochondrial mt-TR. Since there are known SNP in the mt-tRNA-Arg sequence for different mouse strains, each sample was mapped to its respective reference sequence. Aligned reads were deduplicated using UMI-tools. The resulting set of aligned reads were then mapped to the full mouse genome with the UCSC mm10 assembly as the reference using the bowtie (v1.3.1, RRID:SCR_005476) aligner. If the sequence mapped to another location, it was marked as a false positive and removed from downstream analysis. The number of reads for each unique sequence was extracted for each sample.
Assembly: NC_005089.1, CM004255.1, CM004184.1
Supplementary files format and content: counts.txt is a matrix of tRFs x samples that contains the extracted counts of sequences to the mt-tRNA-Arg gene

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Tissues were preserved in RNAlater (Invitrogen, AM7024) and frozen prior to RNA extraction. Small RNA was isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, AM1560) according to the manufacturer’s instructions with one exception: rather than being discarded, the corresponding large RNA fractions of small RNA isolations were retained, washed, and eluted to assess RNA integrity by visualization of 28S and 18S rRNA bands following agarose gel electrophoresis. Intact RNA samples were pooled by sodium acetate-propanol precipitation, followed by resuspension in nuclease-free water. RNA concentration was quantified using the Qubit microRNA Assay Kit (ThermoFisher Scientific, Q32881).
RNA isolated from mouse lungs using the mirVana miRNA Isolation Kit was sent to RealSeq (Santa Cruz, CA) for exploratory tRNA fragment sequencing using a single-adapter circularization-based library preparation approach.

value: lung

value: CH

tag: batch


title: VS_Cas9_R2_fraction_1

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

country: Canada

institute: Montreal Heart Institute

description: Library name: VS_sample_7

data_processing:
Using gRNA list, gRNA counts were establsihed from fastq files. The raw counts were normalized without suppervision to remove sequenciing batch effect to create normalized counts.
Assembly: Homo_sapiens.GRCh38.cdna.all
Supplementary files format and content: Unsuppervised normalized count for each gRNA in the given Percoll gradient fraction. Each file contain the data for 1 fraction. First column: gRNA name, second column: normalized count (relative gRNA abundance in the fraction)
Library strategy: CRISPR Screen

growth_protocol: HUDEP-2 were culture in StemSpan medium supplemented with 1 µg/ml doxycycline, 0.4 µg/ml dexamethasone, 0.1 µg/ml Stem Cell Factor, 3 units/ml erythropoietin, 2 mM L-glutamine, 200 IU penicillin, 200 µg/ml streptomycin and incubated at 37°C and 5% CO2.

extract_protocol:
The gDNA was extracted using the Qiagen DNeasy blood and tissue kit. PCR products from gDNA was purified with either the Qiagen QIAquick PCR Purification Kit or SPRISelect reagen. 2 µg of purified PCR product was purified on agarose gel using Qiagen QIAquick gel extraction kit.
The PCR amplification was adding the Illumina TruSeq LT adapator and sample index.

treatment_protocol: gRNA either librairies or single gRNA were transduced in HUDEP-2 cells using lentivirus. The MOI for gRNA librarie was 0.3, while 200 Kcells were infected with 300 µl of viral suspension for single gRNA. Selection with appropriate antibiotic was performed 6 days for Cas9, 5 days for dCas9-KRAB, and 4 days for dCas9-VP64

value: erythropoietic

value: gRNA transduction

value: VS


title: FLO1-shAPE1#3-3

description: Library name: FA3-3


title: FLO1-shAPE1#1-ABS-3

description: Library name: FA1-BS3


title: FLO1-shAPE1#3-2

description: Library name: FA3-2


title: FLO1-shAPE1#3-1

description: Library name: FA3-1


title: FLO1-shAPE1#1-ABS-1

description: Library name: FA1-BS1


title: FLO1-shAPE1#1-ABS-2

description: Library name: FA1-BS2


title: FLO1-shAPE1#1-2

description: Library name: FA1-2


title: FLO1-shAPE1#1-3

description: Library name: FA1-3


title: FLO1-shControl-ABS-3

description: Library name: FCBS3


title: FLO1-shControl-ABS-2

description: Library name: FCBS2


title: FLO1-shAPE1#1-1

description: Library name: FA1-1


title: FLO1-shControl-ABS-1

description: Library name: FCBS1


title: FLO1-shControl-2

description: Library name: FC2


title: FLO1-shControl-3

description: Library name: FC3


title: FLO1-shControl-1

description: Library name: FC1


title: LCL 45 treated with FLS-359 48 hours

city: Durham

first: Ashley

last: Barry

state: NC

address: 213 Research Drive Room 0045 CARL, DUMC box 3054, General Delivery

department: MGM

institute: Duke University

description: Library name: TX_45_48

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, and Cufflink
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
Supplementary files format and content: raw counts with associated gene names are in an excel file
Supplementary files format and content: 24 hour differential expression between SIRT2 modulator treated and DMSO treated LCLs in excel
Supplementary files format and content: 48 hour differential expression between SIRT2 modulator treated and DMSO treated LCLs in excel

source_name: LCL 45

growth_protocol: lymphoplastoid cell lines (LCLs) were grown in RPMI media supplemented with 10% fetal bovine serum (FBS) in humified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the RNeasy MicroKit (Qiagen), ), including on-column DNase digestion.
RNA library preparation and transcriptome sequencing was performed using a Novogene Co. LTD kit (Beijing, China).

treatment_protocol: LCLs (44 and 45) were seeded at 3e5/mL and treated with 10µM FLS-359 or an equivalent concentration of DMSO for 24 and 48 hours and  then pelleted, washed with PBS, and harvested for RNA extraction

value: LCL 45

value: lymphoblastoid cell line

value: 10µM FLS-359 48 hours


title: LCL 45 treated with FLS-359 24 hours

description: Library name: TX_45_24

value: 10µM FLS-359 24 hours


title: LCL 44 treated with FLS-359 24 hours

description: Library name: TX_44_24

source_name: LCL 44

value: LCL 44


title: LCL 45 treated with DMSO 48 hours

description: Library name: DM_45_48

value: DMSO 48 hours


title: LCL 45 treated with DMSO 24 hours

description: Library name: DM_45_24

value: DMSO 24 hours


title: LCL 44 treated with DMSO 48 hours

description: Library name: DM_44_48


title: LCL 44 treated with DMSO 24 hours

description: Library name: DM_44_24


title: OE33-control-2

description: Library name: Ctrl2

data_processing:
Raw paired-end reads were filtered to remove reads containing adapter contamination, reads containing more than 10% undetermined nucleotides, and reads for which more than 50% of bases had quality scores below 5. The resulting clean reads were aligned to the human hg38 reference genome using HISAT2 v2.0.5. Gene-level raw read counts were generated using featureCounts v1.5.0-p3 based on the gene annotation supplied with the hg38 reference.
Assembly: GRCh38
Supplementary files format and content: The processed data file, RNAseq_Novogene_ABS_6samples_count_matrix.tsv.gz, is a gzip-compressed, tab-delimited gene-level raw-count matrix. Rows represent genes identified by gene_id identifiers from the hg38 annotation file, columns represent the 6 biological samples, and values are unnormalized integer raw read counts.

growth_protocol: OE33 cells were cultured RPMI1640 supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Standard RNA-sequencing (mRNA-Seq) in eukaryotic samples:Polyadenylated mRNA is selectively enriched from total RNA using oligo(dT) magnetic beads. High-temperature thermal treatment in divalent cation buffer fragments the mRNA to ~250–300 bp.

treatment_protocol: Cells were exposed to an acidic bile salt (ABS) cocktail (200 µM in pH4.0 unsupplemented medium) for 20 min and allowed to recover in complete medium for 6 h. Untreated cells work as control (Ctrl).

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: untreated


title: OE33-ABS-1

description: Library name: ABS1

value: ABS exposure


title: OE33-ABS-2

description: Library name: ABS2


title: OE33-control-1

description: Library name: Ctrl1


title: SK-MEL-28, 2 uM ASO550 (dIRE), biol rep 2

city: Seattle

first: Benjamin

last: Logsdon

state: WA

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

description:
Library name: AN98-ASO550-RNA-14
column AN98-ASO550-RNA-14 in AN98_deseq2_tmm_norm_counts.tsv

data_processing:
Bcl -> FASTQ demultiplexing performed by Azenta (bcl2fastq).
Transcript-level quantification with Salmon v1.10.0 against the GENCODE human transcriptome (confirm release).
Transcript counts aggregated to gene level with tximport; gene-level counts normalized in DESeq2 v1.38.3 using TMM.
Differential expression testing with DESeq2 (Wald test).
Assembly: GRCh38 (GENCODE release to be confirmed)
Supplementary files format and content: AN98_deseq2_tmm_norm_counts.tsv: tab-delimited gene x sample matrix of DESeq2 TMM-normalized counts. 14,473 Ensembl gene IDs x 12 samples with headers matching *library name values.

growth_protocol: SK-MEL-28 cells (ATCC HTB-72) cultured in EMEM (ATCC 30-2003) + 10% FBS + 1% Penicillin/Streptomycin. Cells were thawed at passage 9, expanded to passage 10, and plated on 2026-02-09 into 24-well plates at 100,000 cells/well (viability 96%) in 1 mL medium and grown ~24 h before transfection.

extract_protocol:
Cell pellets lysed in 250 uL cold Trizol on ice, vortexed 2 x 30 s, incubated 5 min at RT; 50 uL chloroform added, shaken 15 s, incubated 3 min at RT, centrifuged 15 min at 12,000 x g / 4 C. Aqueous phase mixed 1:1 with 250 uL of 70% ethanol and purified on Qiagen RNeasy MinElute Micro columns (UPenn hybrid protocol; RW1 wash, two RPE washes, 80% EtOH wash, 3 min dry spin, elution in 15 uL water). RNA quantified by NanoDrop (A260/A280 1.97-2.04, A260/A230 1.78-2.28, concentrations 205-366 ng/uL). Twelve of 16 samples passed QC and were normalized to 40 ng/uL in 30 uL (1.2 ug total) for shipping to Azenta.
RNA (1,200 ng in 30 uL at 40 ng/uL) submitted to Azenta Life Sciences (project 30-1296162709) for Standard RNA-Seq with polyA selection (rRNA removal = PolyA selection for mRNA species, eukaryotic; 30 M reads/sample; Illumina 2x150 bp paired-end). (Exact library-prep kit chemistry to be confirmed with Azenta; likely NEBNext Ultra II Directional RNA Library Prep Kit.)

treatment_protocol: On 2026-02-10, cells were transfected with one of four ASOs (ASO2 non-targeting control, ASO3 pan-SNCA, ASO43 dIRE-selective from IDT; ASO550 dIRE-selective from Biospring) at 2 uM final in-well concentration; n=4 biological replicates prepared per ASO. ASO stocks were diluted to 200 uM in water; 7.7 uL of 200 uM ASO + 27.3 uL Opti-MEM were combined with 2.1 uL Lipofectamine RNAiMAX + 32.9 uL Opti-MEM (pre-mixed dilute-lipo master mix); after 5 min at RT, 60 uL of the ASO/lipid complex added to 600 uL medium per well (final [ASO] = 2 uM). Cell pellets were collected 3 days post-transfection (2026-02-13) by PBS wash x 2, Trypsin/Accutase (5 min), quench with FBS-containing medium, centrifugation at 350-400 x g / 5 min / 4 C, PBS wash, second spin, and -80 C storage.

value: melanoma (metastatic melanoma-derived)

value: wild type

value: SNCA-dIRE-selective ASO (ASO0550, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

tag: dose

value: 2 uM

tag: replicate


title: SK-MEL-28, 2 uM ASO550 (dIRE), biol rep 1

description:
Library name: AN98-ASO550-RNA-13
column AN98-ASO550-RNA-13 in AN98_deseq2_tmm_norm_counts.tsv


title: Telencephalon_DMSOforRU486_WT_rep2

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: Telencephalon_DMSOforRU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: Telencephalon

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Telencephalon

value: WT

tag: strain

tag: Sex

value: Male

tag: age

value: 3 months

tag: mouse id


title: SK-MEL-28, 2 uM ASO43 (dIRE), biol rep 2

description:
Library name: AN98-ASO43-RNA-11
column AN98-ASO43-RNA-11 in AN98_deseq2_tmm_norm_counts.tsv

value: SNCA-dIRE-selective ASO (ASO0043, IDT; 2'-O-methoxyethyl/DNA gapmer targeting the dIRE splice junction); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 2 uM ASO3 (pan-SNCA), biol rep 3

description:
Library name: AN98-ASO3-RNA-7
column AN98-ASO3-RNA-7 in AN98_deseq2_tmm_norm_counts.tsv

value: Pan-SNCA ASO (ASO0003, IDT; 2'-O-methoxyethyl/DNA gapmer targeting SNCA intron 4); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 2 uM ASO3 (pan-SNCA), biol rep 1

description:
Library name: AN98-ASO3-RNA-5
column AN98-ASO3-RNA-5 in AN98_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO2 (NTC), biol rep 2

description:
Library name: AN98-ASO2-RNA-3
column AN98-ASO2-RNA-3 in AN98_deseq2_tmm_norm_counts.tsv

value: Non-targeting control ASO (ASO0002, IDT); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 10 uM ASO387 (IRE), biol rep 3

description:
Library name: MB107-10uM-ASO387-rep3-36
column MB107-10uM-ASO387-rep3-36 in MB107_deseq2_tmm_norm_counts.tsv

data_processing:
Bcl -> FASTQ demultiplexing performed by Azenta (bcl2fastq).
Transcript-level quantification with Salmon v1.10.0 against the GENCODE human transcriptome (confirm release).
Transcript counts aggregated to gene level with tximport.
Gene-level counts normalized in DESeq2 v1.38.3 (TMM); differential expression testing by DESeq2 Wald test.
Assembly: GRCh38 (GENCODE release to be confirmed)
Supplementary files format and content: MB107_deseq2_tmm_norm_counts.tsv: tab-delimited gene x sample matrix of DESeq2 TMM-normalized counts. 14,892 Ensembl gene IDs x 36 samples; column names match *library name values (with ASO2-REP2-29 and ASO2-REP2-30 corresponding to library indices 29 and 30 -- see naming note in accompanying documentation).

growth_protocol: SK-MEL-28 cells (ATCC HTB-72; working stock SKMEL28_P4) cultured in EMEM (ATCC 30-2003) + 10% FBS (Atlas Biologicals F-0500-A) + 1% Penicillin/Streptomycin (Thermo Scientific 15140122). Cells were thawed at passage 4 in a 10 cm plate at 1.478e6 cells (~2.6e4 cells/cm^2), grown 3 days, then plated on 2025-09-29 into 24-well plates at 80,000 cells/well in 550 uL medium and grown ~24 h before transfection.

extract_protocol:
Cell pellets were lysed in 1 mL cold Trizol (Invitrogen 15596026) on ice, vortexed 2 x 30 s, incubated 5 min at RT; 200 uL chloroform added, shaken 15 s, incubated 3 min at RT, centrifuged 15 min at 12,000 x g / 4 C. The aqueous phase was mixed 1:1 with 70% ethanol and purified on Qiagen RNeasy MinElute Micro columns per the UPenn Trizol/Qiagen hybrid protocol (Buffer RW1 wash, two RPE washes, 80% EtOH wash, 5 min dry spin, elution in 15 uL nuclease-free water). RNA was quantified by NanoDrop (A260/A280 1.98-2.05, A260/A230 1.83-2.22 across 36 samples).
Total RNA (12 uL per sample, 160-427 ng/uL) was submitted to Azenta Life Sciences (project 30-1251841615) for standard bulk poly(A) RNA-Seq library preparation. Illumina 2x150 bp paired-end, ~25-35 M reads/sample. (Exact kit and stranded chemistry to be confirmed with Azenta; likely NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.)

treatment_protocol: On 2025-09-30, cells were transfected with one of four ASOs (ASO2 non-targeting control, ASO43 SNCA-dIRE-selective, ASO550 SNCA-dIRE-selective from Biospring; ASO387 SNCA-IRE-selective from IDT) at 0.2 uM, 2 uM, or 10 uM final concentration in the well. ASO stocks were pre-diluted to 2 mM in PBS, then serially diluted in water. For each transfection, 5.5 uL of 100x ASO in Opti-MEM (Gibco 31985062) and 1.5 uL Lipofectamine RNAiMAX (Thermo Fisher 13778150) in Opti-MEM were mixed 1:1, incubated 5 min at RT, and 50 uL of the ASO/lipid complex added dropwise to 500 uL of medium per well. n=3 biological replicates per (ASO x dose) condition. Cell pellets were collected 3 days post-transfection (2025-10-03) using Accutase, centrifuged at 500 x g / 5 min / 4 C, and stored at -80 C.

value: SNCA-IRE-selective ASO (ASO0387, IDT; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

value: 10 uM


title: SK-MEL-28, 10 uM ASO550 (dIRE), biol rep 3

description:
Library name: MB107-10uM-ASO550-rep3-35
column MB107-10uM-ASO550-rep3-35 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 10 uM ASO43 (dIRE), biol rep 3

description:
Library name: MB107-10uM-ASO43-rep3-34
column MB107-10uM-ASO43-rep3-34 in MB107_deseq2_tmm_norm_counts.tsv

value: SNCA-dIRE-selective ASO (ASO0043, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 10 uM ASO387 (IRE), biol rep 2

description:
Library name: MB107-10uM-ASO387-rep2-32
column MB107-10uM-ASO387-rep2-32 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 10 uM ASO2 (NTC), biol rep 2

description:
Library name: ASO2-REP2-29
column ASO2-REP2-29 in MB107_deseq2_tmm_norm_counts.tsv

value: Non-targeting control ASO (ASO0002, Biospring); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 10 uM ASO43 (dIRE), biol rep 2

description:
Library name: ASO2-REP2-30
column ASO2-REP2-30 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 10 uM ASO550 (dIRE), biol rep 1

description:
Library name: MB107-10uM-ASO550-rep1-27
column MB107-10uM-ASO550-rep1-27 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 10 uM ASO43 (dIRE), biol rep 1

description:
Library name: MB107-10uM-ASO43-rep1-26
column MB107-10uM-ASO43-rep1-26 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 10 uM ASO387 (IRE), biol rep 1

description:
Library name: MB107-10uM-ASO387-rep1-28
column MB107-10uM-ASO387-rep1-28 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO387 (IRE), biol rep 3

description:
Library name: MB107-2uM-ASO387-rep3-24
column MB107-2uM-ASO387-rep3-24 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO43 (dIRE), biol rep 3

description:
Library name: MB107-2uM-ASO43-rep3-22
column MB107-2uM-ASO43-rep3-22 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO2 (NTC), biol rep 3

description:
Library name: MB107-2uM-ASO2-rep3-21
column MB107-2uM-ASO2-rep3-21 in MB107_deseq2_tmm_norm_counts.tsv


description:
Library name: MB107-2uM-ASO550-rep2-19
column MB107-2uM-ASO550-rep2-19 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO550 (dIRE), biol rep 3

description:
Library name: MB107-2uM-ASO550-rep3-23
column MB107-2uM-ASO550-rep3-23 in MB107_deseq2_tmm_norm_counts.tsv


description:
Library name: MB107-2uM-ASO43-rep2-18
column MB107-2uM-ASO43-rep2-18 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO2 (NTC), biol rep 2

description:
Library name: MB107-2uM-ASO2-rep2-17
column MB107-2uM-ASO2-rep2-17 in MB107_deseq2_tmm_norm_counts.tsv


title: RPE1_Classic_P2_TR3

description: Library name: RPE1_Classic_P2_TR3

value: Retinal Pigment Epithelial cell


title: SK-MEL-28, 2 uM ASO387 (IRE), biol rep 1

description:
Library name: MB107-2uM-ASO387-rep1-16
column MB107-2uM-ASO387-rep1-16 in MB107_deseq2_tmm_norm_counts.tsv


description:
Library name: MB107-2uM-ASO550-rep1-15
column MB107-2uM-ASO550-rep1-15 in MB107_deseq2_tmm_norm_counts.tsv


title: DSA+CAMR, glomerulus, ROI003

city: Goyang-si

first: Sung-Eun

last: Choi

state: --- Select One ---

address: 100 Ilsan-ro, Ilsan-donggu

country: South Korea

institute: NHIS Ilsan hospital

description:
Library name: ROI003
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D04; AOI surface area 21766.5 um2; nuclei count 136; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI003

data_processing:
GeoMx NGS Pipeline v3.1.1.6
Paired-end FASTQ reads were quality-trimmed, adapter-trimmed, and stitched, then aligned to Readout Tag Sequence (RTS) barcodes; PCR duplicates were removed using unique molecular identifiers (UMIs), yielding deduplicated probe counts in DCC files (one per ROI).
DCC files were uploaded to the GeoMx DSP Data Analysis Suite and interpreted using the Hs_R_NGS_WTA_v1.0.pkc probe configuration file to collapse probe-level counts to gene-level (target-level) counts for 18,677 WTA targets.
Gene-level counts were normalized using the third-quartile (Q3) method across the 48 ROIs.
Assembly: GRCh38.p13
Supplementary files format and content: GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: tab-delimited text file. Rows are the 18,677 WTA gene targets; columns are the 48 ROIs (ROI001-ROI048); values are Q3-normalized counts. Column names correspond to the 'library name' field of each sample.
Supplementary files format and content: DCC files (one per ROI): raw deduplicated read counts per RTS_ID (probe barcode). RTS_IDs are interpreted using Hs_R_NGS_WTA_v1.0.pkc, provided as a study-level supplementary file.
Library strategy: Spatial Transcriptomics

source_name: kidney allograft biopsy

extract_protocol:
Formalin-fixed paraffin-embedded kidney biopsy sections (5 um) were mounted on slides, deparaffinized, subjected to target retrieval and proteinase K digestion, and hybridized overnight with the GeoMx Human NGS Whole Transcriptome Atlas RNA probe set (v1.0), in which each target-specific probe carries a UV-photocleavable oligonucleotide barcode. Slides were stained with morphology markers and imaged on the GeoMx DSP. Regions of interest corresponding to glomeruli, peritubular capillaries, and vessels were selected, and barcodes were released by UV illumination and collected into a microplate.
Collected oligonucleotide barcodes were uniquely indexed by PCR using GeoMx Seq Code primers, pooled, and purified with AMPure XP beads. Libraries were sequenced paired-end on an Illumina NovaSeq 6000.

value: kidney allograft biopsy

tag: patient id

value: patient 1

tag: diagnosis

value: chronic antibody-mediated rejection

tag: dsa status

value: positive

tag: anatomical compartment

value: glomerulus

tag: roi id


title: SK-MEL-28, 2 uM ASO387 (IRE), biol rep 2

description:
Library name: MB107-2uM-ASO387-rep2-20
column MB107-2uM-ASO387-rep2-20 in MB107_deseq2_tmm_norm_counts.tsv

value: melanoma (metastatic melanoma-derived)

value: wild type

value: 2 uM


title: iHPC_CNS_LPS_rep1

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: human_ec11brainMGLPS1

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Batch correction was performed using CombatSeq and the sva package (v3.52.0)
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: iPSC-derived cells

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

tag: tissue

value: iPSC-derived cells

value: iHPC

value: LPS


title: CD34_CNS_LPS_rep2

description: Library name: human_CD34brainMGLPS2

source_name: umbilical cord blood

value: umbilical cord blood

tag: cell line


title: SK-MEL-28, 0.2 uM ASO550 (dIRE), biol rep 3

description:
Library name: MB107-0x2uM-ASO550-rep3-11
column MB107-0x2uM-ASO550-rep3-11 in MB107_deseq2_tmm_norm_counts.tsv

tag: cell type

value: SNCA-dIRE-selective ASO (ASO0550, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 0.2 uM ASO43 (dIRE), biol rep 3

description:
Library name: MB107-0x2uM-ASO43-rep3-10
column MB107-0x2uM-ASO43-rep3-10 in MB107_deseq2_tmm_norm_counts.tsv

tag: treatment


title: OE33-shContorl-ABS-3

description: Library name: OCBS3

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: shControl with ABS exposure


title: SK-MEL-28, 0.2 uM ASO2 (NTC), biol rep 3

description:
Library name: MB107-0x2uM-ASO2-rep3-9
column MB107-0x2uM-ASO2-rep3-9 in MB107_deseq2_tmm_norm_counts.tsv

tag: genotype

value: Non-targeting control ASO (ASO0002, Biospring); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: OE33-shAPE1#1-ABS-1

description: Library name: OA1-BS1

value: shAPE1#1 knockdown with ABS exposure


title: SK-MEL-28, 0.2 uM ASO387 (IRE), biol rep 2

description:
Library name: MB107-0x2uM-ASO387-rep2-8
column MB107-0x2uM-ASO387-rep2-8 in MB107_deseq2_tmm_norm_counts.tsv

value: SNCA-IRE-selective ASO (ASO0387, IDT; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: FLO1-shAPE1#3-ABS-1

description: Library name: FA3-BS1

value: shAPE1#3 knockdown with ABS exposure


title: SK-MEL-28, 0.2 uM ASO550 (dIRE), biol rep 2

description:
Library name: MB107-0x2uM-ASO550-rep2-7
column MB107-0x2uM-ASO550-rep2-7 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 0.2 uM ASO43 (dIRE), biol rep 2

description:
Library name: MB107-0x2uM-ASO43-rep2-6
column MB107-0x2uM-ASO43-rep2-6 in MB107_deseq2_tmm_norm_counts.tsv

value: SNCA-dIRE-selective ASO (ASO0043, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SK-MEL-28, 0.2 uM ASO387 (IRE), biol rep 1

description:
Library name: MB107-0x2uM-ASO387-rep1-4
column MB107-0x2uM-ASO387-rep1-4 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 0.2 uM ASO2 (NTC), biol rep 2

description:
Library name: MB107-0x2uM-ASO2-rep2-5
column MB107-0x2uM-ASO2-rep2-5 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 0.2 uM ASO550 (dIRE), biol rep 1

description:
Library name: MB107-0x2uM-ASO550-rep1-3
column MB107-0x2uM-ASO550-rep1-3 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 0.2 uM ASO43 (dIRE), biol rep 1

description:
Library name: MB107-0x2uM-ASO43-rep1-2
column MB107-0x2uM-ASO43-rep1-2 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 2 uM ASO43 (dIRE), biol rep 1

description:
Library name: MB107-2uM-ASO43-rep1-14
column MB107-2uM-ASO43-rep1-14 in MB107_deseq2_tmm_norm_counts.tsv


title: SK-MEL-28, 0.2 uM ASO2 (NTC), biol rep 1

description:
Library name: MB107-0x2uM-ASO2-rep1-1
column MB107-0x2uM-ASO2-rep1-1 in MB107_deseq2_tmm_norm_counts.tsv


title: Pro.347.Nutlin, rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Library name: Pro.347.Nutlin

library_source: other

data_processing:
Base calls were demultiplexed to FASTQ files using bcl2fastq v2.20.0.422. Adapter-trimmed small RNA-seq reads were aligned to a custom human small RNA reference using Bowtie v1.3.1. Multi-mapping reads were retained and fractionally assigned.
Assembly: GRCh38
Supplementary files format and content: Combined raw and normalized counts in two separate csv file.

molecule: other

growth_protocol: SJSA-1 cells (ATCC, Cat# CRL-2098; RRID: CVCL_1697) were maintained in DMSO supplemented with 10 % FCS, 2mM Glutamine and 50 U/mL Penicillin, 50 μg/mL Streptomycin.

extract_protocol:
Approximately 0.5 million cells per sample were lysed in 1 ml TRIzol. Small RNA-enriched RNA fractions (<200 nt) were isolated, spike-ins were added, and RNA was treated with RppH to enable 5′ adapter ligation. RNA was purified and quality-checked using LabChip, TapeStation, or equivalent.
RppH-treated small RNA was used for adapter ligation, reverse transcription, and 21-cycle PCR amplification with NEXTFLEX primers. Adapter dimers were depleted, libraries were QC-checked, and sequencing was performed as 2 × 50 bp paired-end reads on a NovaSeq 6000 S1 flow cell at the NGS-Integrative Genomics Core Unit, UMG.

treatment_protocol: SJSA-1 cells were seeded. Next day, DMSO, MI-1061 (1µM), MD-224 (1µM) and Nutlin-3a (20 µM) were applied for 12h.

value: osteosarcoma cells

tag: time


title: Pro..346.Nutlin, rep1

description: Library name: Pro..346.Nutlin


title: Pro.348.MI, rep3

description: Library name: Pro.348.MI


title: Pro.348.MD, rep3

description: Library name: Pro.348.MD


title: Pro..346.MD, rep1

description: Library name: Pro..346.MD


title: LCL 44 treated with FLS-359 48 hours

description: Library name: TX_44_48

value: LCL 44

value: lymphoblastoid cell line

value: 10µM FLS-359 48 hours


title: SK-MEL-28, 0.2 uM ASO387 (IRE), biol rep 3

description:
Library name: MB107-0x2uM-ASO387-rep3-12
column MB107-0x2uM-ASO387-rep3-12 in MB107_deseq2_tmm_norm_counts.tsv

value: melanoma (metastatic melanoma-derived)

value: wild type

tag: dose


title: SK-MEL-28, 2 uM ASO2 (NTC), biol rep 1

description:
Library name: MB107-2uM-ASO2-rep1-13
column MB107-2uM-ASO2-rep1-13 in MB107_deseq2_tmm_norm_counts.tsv

value: 2 uM

tag: replicate


title: Pro..346.MI, rep1

description: Library name: Pro..346.MI


title: Pro.348.DMSO, rep3

description: Library name: Pro.348.DMSO

value: DMSO


title: OE33-ABS-3

description: Library name: ABS3

value: ABS exposure


title: Pro.347.DMSO, rep2

description: Library name: Pro.347.DMSO


title: Pro.346.DMSO, rep1

description: Library name: Pro.346.DMSO


title: OE33-control-3

description: Library name: Ctrl3

value: esophageal adenocarcinoma (EAC)

value: untreated


title: SJSA-1 cells, NCS 72h, MI-1061 24h, rep3

city: Göttingen

first: Sabrina

last: Weber

state: Lower Saxony

address: Justus-von-Liebig Weg 11

department: Molecular Oncology

institute: University Medical Center

description: Library name: SW_3_N_Mi

data_processing:
Galaxy environment provided by the GWDG (Gesellschaft für wissenschafltiche Datenverarbeitung mbH Göttingen, https://galaxy.gwdg.de/)
Sequences were trimmed for 11 nucleotides (Trim, version 0.0.2).
Alignment was performed on GRCh38 using HISAT2 (version 2.0.5.2).
Read counts were acquired via featureCounts (version 1.6.3+galaxy2).
DeSeq2 (version 2.11.40.6+galaxy1) was used to perform differential gene expression analysis and to obtain normalized counts.
Assembly: CRCh38
Supplementary files format and content: tab-delimited file contains normalized count data

extract_protocol:
Total RNA was extracted from cells using TRIzol®. 200 µL Chloroform was added per 500 µL TRIzol. For phase separation, samples were centrifuged, and the aqueous phase was used to precipitate the RNA with 250 µL isopropanol. Two washing steps with 80 % ethanol were performed before the RNA was resuspended in nuclease-free water. 400 ng RNA was used for sequencing.
mRNA library preparation (poly A enrichment) and reverse transcription into cDNA followed by QC at Novogene

treatment_protocol: SJSA-1 cells were seeded. Next day, Neocarzinostatin (1 µg/mL) or DMSO was applied to the cells for the following 48h. After the  48h the treatment was refreshed and DMSO, MI-1016 or MD-224 (1µM) treatment was applied for further 24h.

value: cell line

value: Neocarzinostatin, MI-1061


title: SJSA-1 cells, NCS 72h, DMSO 24h, rep3

description: Library name: SW_3_N_D

value: Neocarzinostatin, DMSO


title: SJSA-1 cells, NCS 72h, MD-224 24h, rep3

description: Library name: SW_3_N_Md

value: Neocarzinostatin, MD-224


title: SK-MEL-28, 2 uM ASO550 (dIRE), biol rep 3

description:
Library name: AN98-ASO550-RNA-16
column AN98-ASO550-RNA-16 in AN98_deseq2_tmm_norm_counts.tsv

value: SNCA-dIRE-selective ASO (ASO0550, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: SJSA-1 cells, DMSO 72h, MD-224 24h, rep3

description: Library name: SW_3_D_Md

value: DMSO, MD-224


title: SJSA-1 cells, DMSO 72h, MI-1061 24h, rep3

description: Library name: SW_3_D_Mi

value: osteosarcoma cells

value: DMSO, MI-1061


title: SJSA-1 cells, DMSO 72h, DMSO 24h, rep3

description: Library name: SW_3_D_D

value: DMSO, DMSO


title: SK-MEL-28, 2 uM ASO43 (dIRE), biol rep 3

description:
Library name: AN98-ASO43-RNA-12
column AN98-ASO43-RNA-12 in AN98_deseq2_tmm_norm_counts.tsv

value: SNCA-dIRE-selective ASO (ASO0043, IDT; 2'-O-methoxyethyl/DNA gapmer targeting the dIRE splice junction); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: VU591- 203440060073_R01C01

type: genomic

city: Amsterdam

first: Bart A.

last: Westerman

address: van der Boechorststraat 6b

department: Human Genetics

country: Netherlands

institute: Amsterdam UMC

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

hyb_protocol: According to Infinium Methylation HD EPIC manufacturers protocol

data_processing:
CNV analysis and graphing was done using the Bioconductor minfi and conumee R packages 28 or by using Python pylluminator==2.2. Gene locations for annotation were derived with the UCSC genome browser database, using the Table browser tool 29. Assembly hg19 was used as reference genome.
Processed values consist of NOOB background-corrected and nonlinear dye-bias-corrected DNA-methylation beta values for Infinium MethylationEPIC CpG probes, together with corresponding pOOBAH detection P values. Beta values range from 0 to 1 and represent the proportion of methylated signal at each CpG site. Detection P values indicate whether the measured probe signal is distinguishable from background.

label: Cy3, Cy5

source_name: Human GBM brain tumor

growth_protocol: According to Krishna P L Bhat. Mesenchymal differentiation mediated by NF-κB promotes radiation resistance in glioblastoma. Cancer Cell 2013 Sep 9;24(3):331-46.

extract_protocol: Genomic DNA was isolated from untreated cell pellets using the DNeasy Blood & Tissue Kit (Qiagen, 69504), according to manufacturer’s protocol. Additionally, samples were treated with RNase A (DNase and protease-free, 10 mg/mL, Thermo Scientific™, EN0531) to remove RNA from samples.

treatment_protocol: Cells were grown in steady state

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.43 to 1.1EGFR min to max

value: None (steady state culture)


title: SJSA-1 cells, NCS 72h, MD-224 24h, rep2

description: Library name: SW_2_N_Md


title: SJSA-1 cells, NCS 72h, MI-1061 24h, rep2

description: Library name: SW_2_N_Mi


description:
Library name: AN98-ASO43-RNA-10
column AN98-ASO43-RNA-10 in AN98_deseq2_tmm_norm_counts.tsv

value: melanoma (metastatic melanoma-derived)

value: wild type

value: 2 uM


title: SJSA-1 cells, NCS 72h, DMSO 24h, rep2

description: Library name: SW_2_N_D

value: cell line


title: SJSA-1 cells, DMSO 72h, MI-1061 24h, rep2

description: Library name: SW_2_D_Mi


title: SJSA-1 cells, DMSO 72h, MD-224 24h, rep2

description: Library name: SW_2_D_Md


title: SJSA-1 cells, NCS 72h, MI-1061 24h, rep1

description: Library name: SW_1_N_Mi

value: Neocarzinostatin, MI-1061


title: SJSA-1 cells, NCS 72h, MD-224 24h, rep1

description: Library name: SW_1_N_Md


title: SJSA-1 cells, NCS 72h, DMSO 24h, rep1

description: Library name: SW_1_N_D

value: Neocarzinostatin, DMSO


title: SJSA-1 cells, DMSO 72h, MI-1061 24h, rep1

description: Library name: SW_1_D_Mi


title: SJSA-1 cells, DMSO 72h, MD-224 24h, rep1

description: Library name: SW_1_D_Md


title: SET7-deficient THP-1 cells, infection with VSV for 8 h, 2

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: KO-VSV2

data_processing:
Fastp version 0.23.2 was used to perform basic statistics on the quality of the raw reads.
The clean reads were mapped to the human reference genome (hg38) using HISAT2 version 2.2.1.
FeatureCounts version 2.0.1 was used to calculate gene and transcript expression levels expressed as fragments per kilobase of transcript per million fragments mapped (FPKM).
Assembly: Hg38
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: THP-1 cells

growth_protocol: THP-1 cells (originally obtained from ATCC) were cultured in RPMI 1640 medium (VivaCell) supplemented with 10% FBS. All cells were grown at 37 °C in a humidified atmosphere incubator containing 5% CO2.

extract_protocol:
Total RNAs were extracted using RNAiso Plus (TaKaRa Bio),and then purified using the RNeasy Mini Kit (QIAGEN, 74104).
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) according to the manufacturer’s protocol. Qualified libraries were pooled and sequenced on Illumina NovaSeq platforms using PE150 strategy.

treatment_protocol: SET7-deficient or wild-type THP-1 cells infected without or with VSV or HSV-1 for 8 hours.

value: THP-1 cells

value: monocytes

value: Wild-type

value: infection with VSV for 8 h


title: SET7-deficient THP-1 cells, infection with VSV for 8 h, 1

description: Library name: KO-VSV1


title: SET7-deficient THP-1 cells, infection with HSV-1 for 8 h, 3

description: Library name: KO-HSV3

value: infection with HSV-1 for 8 h


title: SET7-deficient THP-1 cells, infection with HSV-1 for 8 h, 1

description: Library name: KO-HSV1


title: SET7-deficient THP-1 cells, 2

description: Library name: KO-con2

value: control


title: SET7-deficient THP-1 cells, 3

description: Library name: KO-con3


title: SET7-deficient THP-1 cells, infection with HSV-1 for 8 h, 2

description: Library name: KO-HSV2


title: SET7-deficient THP-1 cells, 1

description: Library name: KO-con1


title: A549 hnRNPM knockdown, untreated, replicate 3

city: Shenyang

first: Xu

last: Yang

state: Liaoning Province

address: No. 77, Puhe Road, Shenbei New District

institute: China Medical University

description:
Library name: hnRNPM_KD_untreated_rep3
hnRNPM_KD3

data_processing:
Raw reads quality control: FastQC v0.11.9 was used to assess raw read quality.
UID deduplication: Unique molecular identifiers (UMIs/UIDs) were used to remove PCR duplicates using fgbio v2.0.2, generating deduplicated clean reads (stored in "UID" folder).
Genome alignment: Clean reads were aligned to human reference genome GRCh38 (hg38) using HISAT2 v2.2.1. Aligned reads were sorted and indexed using SAMtools v1.15.1, generating sorted BAM files (stored in "mapping" folder).
Gene expression quantification: StringTie v2.1.4 was used to calculate gene-level read counts and FPKM values.
Differential expression analysis: DESeq2 v1.32.0 was used to identify differentially expressed genes (adjusted P-value < 0.05,log2FC> 1).
Alternative splicing analysis: rMATS v4.1.2 was used to detect differential alternative splicing events ΔPSI> 10%, P-value < 0.05).
Assembly: GRCh38 (hg38)
Supplementary files format and content: counts and rpkm

extract_protocol:
Total RNA was extracted from A549 cells using TRIzol reagent (Invitrogen, Cat# 15596026) according to the manufacturer's instructions. RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies), and only samples with RIN ≥ 8.0 were used for library construction. RNA concentration was quantified by Qubit 3.0 Fluorometer (Thermo Fisher Scientific).
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads (NEB, Cat# E7490L). The enriched mRNA was fragmented into ~200bp fragments using divalent cations at 94℃ for 5min. First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (NEB, Cat# M0253L). Second-strand cDNA was synthesized using DNA Polymerase I and RNase H. After end repair, dA-tailing and adapter ligation, the cDNA fragments were amplified by PCR for 12-15 cycles. Libraries were purified using AMPure XP beads (Beckman Coulter, Cat# A63881) and quantified by Qubit 3.0. Library insert size was verified by Agilent 2100 Bioanalyzer.

value: hnRNPM stable knockdown

value: Untreated


title: A549 hnRNPM knockdown, untreated, replicate 1

description:
Library name: hnRNPM_KD_untreated_rep1
hnRNPM_KD1


title: SJSA-1 cells, DMSO 72h, DMSO 24h, rep1

description: Library name: SW_1_D_D

value: osteosarcoma cells

value: DMSO, DMSO


title: A549 hnRNPM knockdown, untreated, replicate 2

description:
Library name: hnRNPM_KD_untreated_rep2
hnRNPM_KD2


title: A549 MagoHB knockdown, untreated, replicate 1

description:
Library name: MagoHB_KD_untreated_rep1
MagoHB_KD1

value: MagoHB stable knockdown


title: A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 1

description:
Library name: S100A16_KD_H2O2_rep1
S100A16KDH1

value: S100A16 stable knockdown

value: 100μM H₂O₂, 2h


title: A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 2

description:
Library name: S100A16_KD_H2O2_rep2
S100A16KDH2


title: A549 S100A16 knockdown, untreated, replicate 3

description:
Library name: S100A16_KD_untreated_rep3
S100A16_KD3


title: A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 3

description:
Library name: S100A16_KD_H2O2_rep3
S100A16KDH3


title: A549 S100A16 knockdown, untreated, replicate 1

description:
Library name: S100A16_KD_untreated_rep1
S100A16_KD1


title: A549 wild type, 100μM H₂O₂ 2h, replicate 2

description:
Library name: Ctrl_H2O2_rep2
Ctrl_H2

value: Wild type


title: A549 MagoHB knockdown, untreated, replicate 3

description:
Library name: MagoHB_KD_untreated_rep3
MagoHB_KD3


title: A549 wild type, untreated, replicate 2

description:
Library name: Ctrl_untreated_rep2
Ctrl2


title: A549 wild type, untreated, replicate 1

description:
Library name: Ctrl_untreated_rep1
Ctrl1


title: ccRCC tumor-infiltrating lymphocytes, Patient 2 (pT2b)

city: Suwon

first: WonJoon

last: Oh

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do

institute: Sunkyunkwan university

description:
Library name: ccRCC_Patient2_Tumor
10x Genomics 5' scRNA-seq; pT2b; 10.3x7.3 cm; clear cell RCC grade III/IV

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics). scRNA-seq data were analyzed using Seurat v5.3.1 with Harmony v1.2.4 batch correction.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: RDS object: integrated Seurat object with normalized gene expression, UMAP, and cluster annotations for all three patients.

source_name: Kidney tumor

extract_protocol:
Tumor tissues were mechanically dissociated into single-cell suspensions. Lymphocytes were isolated by Ficoll-Paque PLUS density gradient centrifugation. gdT cells and B cells were sorted using BD FACSAria III cell sorter.
5' gene expression libraries were prepared using the 10x Genomics Chromium Controller. Libraries were quantified by qPCR (KAPA) and quality-assessed using Agilent 4200 TapeStation.

value: Kidney tumor

value: gdT cells and B cells


title: HUVEC-OSVEC1

city: Guangzhou

first: Jinming

last: Di

address: No. 600, Zhongshan Avenue, Tianhe District

department: Urology

institute: The Third Affiliated Hospital, Sun Yat-sen University

description:
Library name: Sample 10
HUVEC cells, treated with conditioned medium from vector-control OS-RC-2 cells_1

data_processing:
Raw sequencing reads generated by Illumina NovaSeq 6000 were quality-controlled using FastQC v0.11.9; low-quality reads (Q<20), adapter sequences, and poly-N stretches were trimmed using Trimmomatic v0.39 with parameters: LEADING:20, TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:50.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 v2.2.1 with default parameters; aligned reads were sorted and indexed using SAMtools v1.15.1.
Gene expression levels (raw read counts) were quantified from aligned reads using featureCounts v2.0.3, with annotation files from Ensembl (GRCh38.109).
Differentially expressed genes (DEGs) were identified using DESeq2 v1.38.3 in R (v4.3.1) with the threshold of log2FC > 1 and adjusted P < 0.05; raw read counts were normalized by DESeq2's regularized log transformation.
Functional enrichment analysis (GO/KEGG) was performed on differentially expressed genes using clusterProfiler v4.6.2 in R (v4.3.1).
Assembly: GRCh38/hg38 (human reference genome, Ensembl release 109)
Supplementary files format and content: raw_counts_All_Samples.txt: Tab-delimited text file containing raw read counts for all 12 samples (OS-RC-2 and HUVEC, 3 biological replicates each for SBSN overexpression and vector control); each row represents a gene (Ensembl ID + gene symbol), each column represents a sample (matching library name in SAMPLES section).

source_name: HUVEC

growth_protocol: OS-RC-2 renal carcinoma cells and HUVECs were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 100 U/mL penicillin-streptomycin (Solarbio). Cultures were maintained in a humidified incubator at 37 °C with 5% CO₂. OS-RC-2 cells were stably transfected with SBSN overexpression lentiviral vector or empty vector (vecControl).

extract_protocol:
Total RNA was extracted from OS-RC-2 cells and CM-treated HUVECs using TRIzol reagent (Invitrogen) following the manufacturer's standard protocol. RNA purity and concentration were verified by Nanodrop spectrophotometry and agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer's instructions. Briefly, poly(A)+ mRNA was enriched from total RNA, fragmented, reverse-transcribed into cDNA, end-repaired, adenylated, and ligated with index adapters. The ligated products were PCR-amplified and size-selected to generate final cDNA libraries (200-300 bp).

treatment_protocol: HUVECs were treated with conditioned medium (CM) collected from SBSN-overexpressing OS-RC-2 cells or vector control OS-RC-2 cells for 48 h; no additional treatment was applied to OS-RC-2 cells.

value: HUVEC

value: human umbilical vein endothelial cell

tag: genetic modification

value: conditioned medium from OS-RC-2 vector control

tag: batch


title: HUVEC-OSVEC2

description:
Library name: Sample 11
HUVEC cells, treated with conditioned medium from vector-control OS-RC-2 cells_2


title: ccRCC tumor-infiltrating lymphocytes, Patient 1 (pT3a)

description:
Library name: ccRCC_Patient1_Tumor
10x Genomics 5' scRNA-seq; pT3a Nx; 11x7 cm; clear cell RCC grade III/IV


title: HUVEC-OSOESBSN1

description:
Library name: Sample 7
HUVEC cells, treated with conditioned medium from SBSN overexpression OS-RC-2 cells_1

value: conditioned medium from OS-RC-2 SBSN overexpression


title: OSRC2-VEC2

description:
Library name: Sample 5
OS-RC-2 cells, empty vector control_2

value: renal carcinoma epithelial cell

value: vector control


title: A549 S100A16 knockdown, untreated, replicate 2

description:
Library name: S100A16_KD_untreated_rep2
S100A16_KD2


title: OSRC2-OESBSN2

description:
Library name: Sample 2
OS-RC-2 cells, SBSN overexpression_2

value: SBSN overexpression


title: AC63_T4

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

description:
Library name: Sample 83
Column name in raw counts file: AC63_T4

data_processing:
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9). Raw reads were quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were mapped to the human Grch38 reference genome using a splice aware aligner HiSat2 (v2.2.1), resulting BAM files were processed using samtools (v.1.3), and gene expression was quantified with featureCounts (subread v2.0.1, featureCounts v1.5.0-p3) as raw counts
Assembly: Grch38 reference genome
Supplementary files format and content: The excel file named "MONOCYTE RNA SEQ healthy.xlsx" includes counts for each sample

source_name: Blood (monocytes)

extract_protocol:
Total RNA for transcriptome analysis was extracted from isolated monocytes using TRIzol® (Gibco BRL Life Technologies, Rockville, MD). RNA was purified using Qiagen-RNeasy Mini Kit. RNA pellets were resuspended in diethyl pyrocarbonate-treated water. RNA integrity was assessed (prior to beginning target processing) using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). We analyzed samples with RNA Integrity Number (RIN) between 6.7 and 10 (average 9.59).
The libraries were constructed using the Illumina stranded mRNA sample preparation kit. The construction begins mRNA enrichment using oligodT beads and fragmentation of the RNA. First strand synthesis uses random primers and reverse transcriptase. Second strand synthesis is completed with a marking mix that allows retention of the strandedness. The cDNA end repaired and adenylated before ligation of the Illumina barcoded adapters. Adapter ligated libraries are PCR amplified and then quantified by Kapa qPCR and multiplexed.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-treated blood using OptiPrep® Density Gradient Medium (SIGMA). Monocytes were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Monocyte Isolation Kit II Human and the autoMACS® Pro Separator). The Monocyte Isolation Kit was developed to isolate monocytes from human PBMCs with minimum perturbation. Non-monocytes, i.e., T cells, NK cells, B cells, dendritic cells and basophils, are indirectly magnetically labeled using a cocktail of biotin-conjugated antibodies against CD3, CD7, CD16, CD19, CD56, CD123 and Glycophorin A, and Anti-Biotin MicroBeads. Our monocyte isolation procedure consistently yielded high-purity monocytes, with an average purity of 90.8% (ranging from 79% to 97%), as shown by flow cytometry (stained with CD14-FITC).

value: Blood (monocytes)

tag: age

tag: Sex

value: male


title: HUVEC-OSVEC3

description:
Library name: Sample 12
HUVEC cells, treated with conditioned medium from vector-control OS-RC-2 cells_3


title: OSRC2-OESBSN1

description:
Library name: Sample 1
OS-RC-2 cells, SBSN overexpression_1


title: AC63_T3

description:
Library name: Sample 82
Column name in raw counts file: AC63_T3


title: AC63_T2

description:
Library name: Sample 81
Column name in raw counts file: AC63_T2


title: AC63_T1

description:
Library name: Sample 80
Column name in raw counts file: AC63_T1


title: OSRC2-VEC3

description:
Library name: Sample 6
OS-RC-2 cells, empty vector control_3


title: AC62_T4

description:
Library name: Sample 79
Column name in raw counts file: AC62_T4


title: AC62_T2

description:
Library name: Sample 77
Column name in raw counts file: AC62_T2


title: AC62_T3

description:
Library name: Sample 78
Column name in raw counts file: AC62_T3


title: AC62_T1

description:
Library name: Sample 76
Column name in raw counts file: AC62_T1


title: AC61_T3

description:
Library name: Sample 74
Column name in raw counts file: AC61_T3


title: AC61_T1

description:
Library name: Sample 72
Column name in raw counts file: AC61_T1


title: AC60_T4

description:
Library name: Sample 71
Column name in raw counts file: AC60_T4


title: AC60_T2

description:
Library name: Sample 69
Column name in raw counts file: AC60_T2


title: AC60_T1

description:
Library name: Sample 68
Column name in raw counts file: AC60_T1


title: AC59_T3

description:
Library name: Sample 66
Column name in raw counts file: AC59_T3


title: AC59_T4

description:
Library name: Sample 67
Column name in raw counts file: AC59_T4


title: AC59_T2

description:
Library name: Sample 65
Column name in raw counts file: AC59_T2


title: AC58_T4

description:
Library name: Sample 63
Column name in raw counts file: AC58_T4


title: AC58_T3

description:
Library name: Sample 62
Column name in raw counts file: AC58_T3


title: AC58_T2

description:
Library name: Sample 61
Column name in raw counts file: AC58_T2


title: AC58_T1

description:
Library name: Sample 60
Column name in raw counts file: AC58_T1


title: AC57_T4

description:
Library name: Sample 59
Column name in raw counts file: AC57_T4


title: AC60_T3

description:
Library name: Sample 70
Column name in raw counts file: AC60_T3


title: AC57_T3

description:
Library name: Sample 58
Column name in raw counts file: AC57_T3


title: AC57_T2

description:
Library name: Sample 57
Column name in raw counts file: AC57_T2


title: AC57_T1

description:
Library name: Sample 56
Column name in raw counts file: AC57_T1


title: AC56_T4

description:
Library name: Sample 55
Column name in raw counts file: AC56_T4


title: AC56_T3

description:
Library name: Sample 54
Column name in raw counts file: AC56_T3


title: AC56_T2

description:
Library name: Sample 53
Column name in raw counts file: AC56_T2


title: AC59_T1

description:
Library name: Sample 64
Column name in raw counts file: AC59_T1


title: AC56_T1

description:
Library name: Sample 52
Column name in raw counts file: AC56_T1


title: SJSA-1 cells, DMSO 72h, DMSO 24h, rep2

description: Library name: SW_2_D_D

value: osteosarcoma cells

value: cell line


title: SET7-deficient THP-1 cells, infection with VSV for 8 h, 3

description: Library name: KO-VSV3

value: THP-1 cells

value: monocytes

value: Wild-type

value: infection with VSV for 8 h


title: AC54_T4

description:
Library name: Sample 51
Column name in raw counts file: AC54_T4


title: AC54_T3

description:
Library name: Sample 50
Column name in raw counts file: AC54_T3


title: AC54_T1

description:
Library name: Sample 48
Column name in raw counts file: AC54_T1


title: A549 MagoHB knockdown, untreated, replicate 2

description:
Library name: MagoHB_KD_untreated_rep2
MagoHB_KD2

value: MagoHB stable knockdown

value: Untreated


title: AC54_T2

description:
Library name: Sample 49
Column name in raw counts file: AC54_T2


title: AC53_T4

description:
Library name: Sample 47
Column name in raw counts file: AC53_T4


title: AC53_T3

description:
Library name: Sample 46
Column name in raw counts file: AC53_T3


title: AC53_T2

description:
Library name: Sample 45
Column name in raw counts file: AC53_T2


title: AC53_T1

description:
Library name: Sample 44
Column name in raw counts file: AC53_T1


title: AC52_T4

description:
Library name: Sample 43
Column name in raw counts file: AC52_T4


title: A549 wild type, 100μM H₂O₂ 2h, replicate 3

description:
Library name: Ctrl_H2O2_rep3
Ctrl_H3

value: Wild type

value: 100μM H₂O₂, 2h


title: AC52_T2

description:
Library name: Sample 41
Column name in raw counts file: AC52_T2


title: AC52_T3

description:
Library name: Sample 42
Column name in raw counts file: AC52_T3


title: AC52_T1

description:
Library name: Sample 40
Column name in raw counts file: AC52_T1


title: AC51_T4

description:
Library name: Sample 39
Column name in raw counts file: AC51_T4


title: ccRCC tumor-infiltrating lymphocytes, Patient 3 (pT1a)

description:
Library name: ccRCC_Patient3_Tumor
10x Genomics 5' scRNA-seq; pT1a; 3.5x2.7 cm; clear cell RCC grade III/IV

value: Kidney tumor

value: gdT cells and B cells


title: A549 wild type, untreated, replicate 3

description:
Library name: Ctrl_untreated_rep3
Ctrl3


title: A549 wild type, 100μM H₂O₂ 2h, replicate 1

description:
Library name: Ctrl_H2O2_rep1
Ctrl_H1


title: AC51_T3

description:
Library name: Sample 38
Column name in raw counts file: AC51_T3


title: AC51_T2

description:
Library name: Sample 37
Column name in raw counts file: AC51_T2


title: AC51_T1

description:
Library name: Sample 36
Column name in raw counts file: AC51_T1


title: AC16_T4

description:
Library name: Sample 35
Column name in raw counts file: AC16_T4

value: female


title: AC16_T3

description:
Library name: Sample 34
Column name in raw counts file: AC16_T3


title: AC16_T2

description:
Library name: Sample 33
Column name in raw counts file: AC16_T2


title: HUVEC-OSOESBSN3

description:
Library name: Sample 9
HUVEC cells, treated with conditioned medium from SBSN overexpression OS-RC-2 cells_3

value: HUVEC

value: human umbilical vein endothelial cell

value: conditioned medium from OS-RC-2 SBSN overexpression


title: AC16_T1

description:
Library name: Sample 32
Column name in raw counts file: AC16_T1

value: Blood (monocytes)


title: AC15_T4

description:
Library name: Sample 31
Column name in raw counts file: AC15_T4


title: AC15_T3

description:
Library name: Sample 30
Column name in raw counts file: AC15_T3


title: AC15_T2

description:
Library name: Sample 29
Column name in raw counts file: AC15_T2


title: AC15_T1

description:
Library name: Sample 28
Column name in raw counts file: AC15_T1


title: HUVEC-OSOESBSN2

description:
Library name: Sample 8
HUVEC cells, treated with conditioned medium from SBSN overexpression OS-RC-2 cells_2


title: AC13_T4

description:
Library name: Sample 27
Column name in raw counts file: AC13_T4


title: OSRC2-OESBSN3

description:
Library name: Sample 3
OS-RC-2 cells, SBSN overexpression_3

value: renal carcinoma epithelial cell

value: SBSN overexpression


title: OSRC2-VEC1

description:
Library name: Sample 4
OS-RC-2 cells, empty vector control_1

value: vector control


title: AC13_T3

description:
Library name: Sample 26
Column name in raw counts file: AC13_T3


title: AC13_T2

description:
Library name: Sample 25
Column name in raw counts file: AC13_T2


title: AC11_T3

description:
Library name: Sample 22
Column name in raw counts file: AC11_T3


title: AC11_T4

description:
Library name: Sample 23
Column name in raw counts file: AC11_T4


title: AC13_T1

description:
Library name: Sample 24
Column name in raw counts file: AC13_T1


title: AC11_T2

description:
Library name: Sample 21
Column name in raw counts file: AC11_T2


title: AC11_T1

description:
Library name: Sample 20
Column name in raw counts file: AC11_T1


title: AC09_T3

description:
Library name: Sample 18
Column name in raw counts file: AC09_T3


title: AC09_T4

description:
Library name: Sample 19
Column name in raw counts file: AC09_T4


title: AC09_T2

description:
Library name: Sample 17
Column name in raw counts file: AC09_T2


title: AC09_T1

description:
Library name: Sample 16
Column name in raw counts file: AC09_T1


title: AC08_T4

description:
Library name: Sample 15
Column name in raw counts file: AC08_T4


title: SK-MEL-28, 2 uM ASO3 (pan-SNCA), biol rep 2

description:
Library name: AN98-ASO3-RNA-6
column AN98-ASO3-RNA-6 in AN98_deseq2_tmm_norm_counts.tsv

value: melanoma (metastatic melanoma-derived)

value: wild type

value: Pan-SNCA ASO (ASO0003, IDT; 2'-O-methoxyethyl/DNA gapmer targeting SNCA intron 4); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

value: 2 uM


title: AC08_T3

description:
Library name: Sample 14
Column name in raw counts file: AC08_T3


title: AC08_T1

description:
Library name: Sample 12
Column name in raw counts file: AC08_T1


title: AC08_T2

description:
Library name: Sample 13
Column name in raw counts file: AC08_T2


title: AC07_T4

description:
Library name: Sample 11
Column name in raw counts file: AC07_T4


title: AC07_T3

description:
Library name: Sample 10
Column name in raw counts file: AC07_T3


title: AC06_T3

description:
Library name: Sample 7
Column name in raw counts file: AC06_T3


title: AC07_T1

description:
Library name: Sample 8
Column name in raw counts file: AC07_T1


title: AC07_T2

description:
Library name: Sample 9
Column name in raw counts file: AC07_T2


title: SK-MEL-28, 2 uM ASO2 (NTC), biol rep 1

description:
Library name: AN98-ASO2-RNA-1
column AN98-ASO2-RNA-1 in AN98_deseq2_tmm_norm_counts.tsv

value: Non-targeting control ASO (ASO0002, IDT); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation


title: AC06_T2

description:
Library name: Sample 6
Column name in raw counts file: AC06_T2


title: AC06_T1

description:
Library name: Sample 5
Column name in raw counts file: AC06_T1


title: AC03_T4

description:
Library name: Sample 4
Column name in raw counts file: AC03_T4


title: AC03_T3

description:
Library name: Sample 3
Column name in raw counts file: AC03_T3


title: AC03_T2

description:
Library name: Sample 2
Column name in raw counts file: AC03_T2


title: SJOS030605_D1_DYE7028

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description: Library name: SJOS030605_D1

data_processing:
Single-cell (scRNA-seq) and single-nucleus (snRNA-seq) RNA sequencing data were generated from patient tumors, patient-derived xenografts (PDXs), and in vitro culture models (2D, 3D, and Cancer Cell Line Factory [CCLF]) representing multiple pediatric solid tumor types. Analyses were conducted using consistent methodological principles within an evolving computational framework. Although individual datasets were processed with slightly different versions of analytical tools, all followed a unified workflow for alignment, quality control, normalization, integration, and downstream analysis as described below.
Raw sequencing reads in FASTQ format were first assessed for quality using FASTQC (v0.11.5). Alignment and gene quantification were performed using Cell Ranger (v7.0.0 or v8.0.1, 10x Genomics) against the appropriate genome references. Patient samples were aligned to the human GRCh38 reference genome, whereas xenograft and mixed-origin datasets (PDX, 3D) were aligned to a dual human–mouse reference (GRCh38 + mm10 or GRCh38 + GRCm39). In all cases, intronic reads were included during counting to enhance transcript detection sensitivity. For rhabdomyosarcoma samples, the cell count parameter in Cell Ranger was fixed at 10,000 to mitigate barcode overestimation.
Comprehensive quality control (QC) filtering was applied to remove debris, damaged cells, multiplets, and nonhuman contaminants. Cells were excluded based on a combination of criteria, including the number of detected genes, total UMI counts, and the proportion of mitochondrial reads. Typical thresholds included the retention of cells with at least 100–1,000 detected genes and ≥500 UMIs, and exclusion of cells with >5–25% mitochondrial transcripts, depending on dataset type (≤10% for most scRNA-seq, ≤1% for snRNA-seq). For select samples, Outlier cells exceeding three median absolute deviations (MADs) from the median number of detected genes or UMIs were also removed.For select samples, doublets were detected and filtered using demuxafy (PMID 38622708) and Seurat-based outlier identification. In xenograft and culture samples, potential mouse contamination was addressed by removing barcodes showing predominant alignment to the mouse genome. For select tumor datasets, background ambient RNA contamination was further reduced using CellBender (v0.2.0) (PMID 37550580).
Quality-controlled gene expression matrices were processed using Seurat (v4.4.0 or v5.0; Hao et al., 2021). Data were normalized using the NormalizeData() function (log-normalization with a scale factor of 10,000) and scaled via linear regression to account for differences in sequencing depth and mitochondrial content. Highly variable genes (typically 2,000–3,000 per dataset) were identified for downstream analysis. Dimensionality reduction was performed using principal component analysis (PCA), with the top 30 principal components retained for nonlinear projection via Uniform Manifold Approximation and Projection (UMAP). Graph-based clustering was implemented using the Leiden algorithm (Traag et al., 2019) through Seurat’s FindClusters() function at resolutions between 0.1 and 0.4.
To integrate datasets across experimental models, replicates, and biological conditions, multiple batch-correction frameworks were employed, including Harmony (Korsunsky et al., 2019), Reciprocal PCA (RPCA) (Stuart et al., 2019), fastMNN (Haghverdi et al., 2018), and scVI (Lopez et al., 2018). The choice of integration method was dataset-dependent and guided by visual inspection of inter-sample mixing and Local Inverse Simpson’s Index (LISI) metrics (Korsunsky et al., 2019). All integrated datasets were subsequently clustered and analyzed uniformly.
Automated annotation was performed using SingleR (Aran et al., 2019) by comparison with the Human Cell Atlas and the Database of Immune Cell Expression (DICE). Clusters identified as immune populations or doublets were excluded prior to reintegration. For select datasets, copy-number variation (CNV) inference was carried out using inferCNV (https://github.com/broadinstitute/inferCNV/wiki), supplemented by Numbat for single-nucleus variant calling (PMID 36163550). In some analyses, cell cycle scores were computed using Seurat’s CellCycleScoring() function to quantify the proportion of S- and G2/M-phase genes. Differential gene expression analysis was performed using Seurat’s FindMarkers() function (Wilcoxon rank-sum test) with thresholds of log₂ fold change ≥ 0.25, a minimum expression frequency of 0.1, and adjusted p < 0.01.Additionally, cells were annotated using known gene expression profiles from a reference dataset (Patel et al., 2022) using scRNA-seq reference label transfer method, FindTransferAnchors(), from Seurat, enabling the classification of cells in query datasets at specified clustering resolution.
For multi-tumor cohorts (Ewing sarcoma, neuroblastoma, osteosarcoma, and rhabdomyosarcoma), analyses were executed using the Snap workflow (https://github.com/stjude-dnb-binfcore/sc-rna-seq-snap), a containerized and reproducible pipeline maintained by the St. Jude Bioinformatics Core. All dependencies were configured for R v4.4.0 and Seurat v4.4.0, ensuring full computational reproducibility (see GitHub repository for versioning reports). Each cohort was subdivided into three analytical groups: 1. Dual-genome cohort (PDX and 3D samples): aligned to GRCh38 + GRCm39 and filtered for low-quality and mouse-derived cells. 2. Human-genome cohort (patient, 2D, CCLF samples): aligned to GRCh38 and processed using identical QC parameters. 3. Integrated cohort: merged from the two above and analyzed jointly after Harmony-based integration. Cells with fewer than 500 UMIs, fewer than 300–1,000 genes (depending on tumor type), or >10% mitochondrial reads were removed prior to normalization and scaling. Highly variable features (n = 3,000) were used for PCA, followed by clustering with Leiden at resolution 0.1. Marker genes were identified per cluster, and top-ranked genes were examined for biological interpretability.
Interactive visualization and exploratory analysis were facilitated using ShinyCell (v2.1.0) (Ouyang et al., 2021). Processed datasets and interactive R Shiny applications are available through institutional repositories and project-specific GitHub resources (URLs to be provided upon publication).
Assembly: hg38
Supplementary files format and content: barcodes, matrix, features

source_name: tumor

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

extract_protocol:
Extract protocol: To dissociate organoids into single-cell suspension 40U papain was added to 400uL of papain buffer(1mM L-cystein, 0.5mM EDTA in PBS -/-) and incubated at 37°C for ~5 min. The organoids were added and incubating at 37°C for ~5 min with occasional flicking until the organoid dissociated to the point of floating. 40uL of DNase was added and the dissociated cells were incubated at 37 °C for an additional 5 min. The cell suspension was filtered with a 40-μm mesh cell strainer and washed with 2mL PBS−/−. The filtered cells were slowly added to a 5 ml BSA cushion medium (4% BSA in Retinal Explant media) and spun at 500g for 10 min at 4 °C to separate the cells from the debris. The supernatant was removed and resuspend the cell pellet in 400 μl of explant culture medium. To generate single-nucleus suspensions from flash-frozen tissue frozen fragments were manually dissociated using Noyes spring scissors in 1 mL TST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride, 0.01% bovine serum albumin, 0.03% Tween-20). Nuclear suspensions were filtered through a 40 μm strainer and diluted with an additional 1 mL TST buffer and 3 mL ST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride) and centrifuged at 500xg at 4°C for 5 min. The nuclear pellet was resuspended in ST buffer and filtered through a 40 μm strainer to generate single-nuclear suspensions for snRNA-seq. To generate single-cell suspensions from fresh tissue, samples were rinsed with PBS -/-, minced with a scalpel, and processed using the Papain Dissociation System (Worthington). The tumors were incubated in 5 mL papain-DNase I solution at 37°C for 15-30 min, filtered through a 40 μm strainer, and centrifuged at 500 x g for 5 min. The cell pellets were then resuspended in 3.1 mL resuspension buffer (2.7 mL Earle’s buffered saline solution, 300 μL albumin-ovomucoid inhibitor, 150 μL DNase I) and layered over 5 mL albumin-ovomucoid inhibitor cushion and centrifuged at 100xg for 6 min. The pellet was resuspended in PBS and filtered through a 40 μm strainer.
Single cell RNA sequencing and library preparation was preformed using the 10X genomics 3’ gene expression kits.

value: tumor

tag: disease

value: OST

value: Patient


title: AC03_T1

description:
Library name: Sample 1
Column name in raw counts file: AC03_T1


title: SJNBL030513_X1_DYE4558

description: Library name: SJNBL030513_X1

value: NBL

value: PDX


title: SJNBL015724_D1_DYE4557

description: Library name: SJNBL015724_D1


title: SJNBL012407_X1_DYE4556

description: Library name: SJNBL012407_X1


title: SJNBL063821_X1_DYE4555

description: Library name: SJNBL063821_X1


title: SJNBL030721_D5_DYE3129

description: Library name: SJNBL030721_D5


title: SJNBL012407_D1_DYE3066

description: Library name: SJNBL012407_D1


title: SJEWS063826_D1_DYE3065

description: Library name: SJEWS063826_D1

value: EWS


title: SJNBL030721_D1_DYE3128

description: Library name: SJNBL030721_D1


title: SJRHB000026_R2_DYE2840

description: Library name: SJRHB000026_R2

value: RMS


title: SJRHB013758_D1_DYE2839

description: Library name: SJRHB013758_D1


title: SJRHB013759_A1_DYE2835

description: Library name: SJRHB013759_A1


title: SJRHB010928_R1_DYE2661

description: Library name: SJRHB010928_R1


title: SJRHB013758_D2_DYE2837

description: Library name: SJRHB013758_D2


title: SJRHB013758_X2_DYE2618

description: Library name: SJRHB013758_X2


title: SJRHB010927_X1_DYE2580

description: Library name: SJRHB010927_X1


title: SJNBL031239_X1_DYE2577

description: Library name: SJNBL031239_X1


title: SJNBL031239_D1_DYE2515

description: Library name: SJNBL031239_D1


title: SJRHB000026_X1_DYE2379

description: Library name: SJRHB000026_X1


title: SJNBL046_X_DYE2340

description: Library name: SJNBL046_X


title: SJOS030605_X2_DYE1707

description: Library name: SJOS030605_X2


title: SJEWS063826_X1_DYE1472

description: Library name: SJEWS063826_X1


title: snRNA (10x-Flex), tumor 24, kidney

city: Boston

first: Prathyusha

last: Konda

state: Massachusetts

address: 450 BROOKLINE AVENUE

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: Tumor 24

data_processing:
Sequencing data were demultiplexed, aligned, and quantified using the 10x Genomics Cell Ranger pipeline (v3.1.0). Reads were aligned to the GRCh38 reference genome (Gencode annotation), and gene-by-cell UMI count matrices were generated.
Assembly: GRCh38
Supplementary files format and content: Count matrices

source_name: Kidney

extract_protocol:
FFPE tissue processing and RNA isolation were performed using the RNeasy FFPE Kit (Qiagen) on two 10-μm scrolls per sample, following the manufacturer’s protocol. RNA quality was assessed via DV200 analysis using the Agilent 2100 Bioanalyzer. For nuclei isolation, three 30-μm scrolls per sample were deparaffinized in xylene, rehydrated through graded ethanol washes, and incubated in Milli-Q water followed by cold PBS. Tissue dissociation was performed using enzymes from the Miltenyi FFPE Tissue Dissociation Kit and Liberase™ TM, followed by mechanical dissociation with the gentleMACS Octo Dissociator. Nuclei were filtered, centrifuged, and resuspended in 10x Genomics quenching buffer, and counted using AO staining with a Cellometer-K2 Fluorescent Cell Counter. All steps were performed independently for each sample.
Approximately one million nuclei per sample were hybridized with Human WTA Probes (10x Genomics) for 23 hours at 42°C, washed three times per the manufacturer’s protocol (CG000527-Rev E), and counted. Around 50,000 nuclei per sample were pooled, filtered, and assessed for quality. A total of ∼144,000 pooled nuclei were processed using the Chromium Next GEM Single Cell Fixed RNA for Multiplexed Samples workflow. GEM formation, reverse transcription, cleanup, and pre-amplification were performed according to the user guide, followed by FLEX-GEX library construction. Final libraries were quantified on the Agilent Bioanalyzer 2100.

value: Kidney


title: snRNA (10x-Flex), tumor 23, kidney

description: Library name: Tumor 23


title: snRNA (10x-Flex), tumor 22, kidney

description: Library name: Tumor 22


title: snRNA (10x-Flex), tumor 21, kidney

description: Library name: Tumor 21


title: snRNA (10x-Flex), tumor 14, kidney

description: Library name: Tumor 14


title: snRNA (10x-Flex), tumor 13, kidney

description: Library name: Tumor 13


title: Multiome ATAC, normal 19

description: Library name: Normal 19, ATAC

library_source: genomic single cell

data_processing:
Sequencing data were demultiplexed, aligned, and quantified using the 10x Genomics Cell Ranger pipeline (v3.1.0). Reads were aligned to the GRCh38 reference genome (Gencode annotation), and gene-by-cell UMI count matrices were generated.
Assembly: GRCh38
Supplementary files format and content: fragments and Count matrices

extract_protocol:
From fresh frozen tissues, nuclei isolation was performed using low-retention microcentrifuge tubes throughout the procedure to minimize nuclei loss. Briefly, OCT-embedded tissue fragments were rapidly thawed on wet ice to remove excess OCT, mechanically dissociated by pipetting, and homogenized in TST solution. The homogenate was filtered through a 30 µm MACS SmartStrainer and pelleted by centrifugation for 4 minutes at 500 × g at 4°C. The resulting nuclei pellet was resuspended in 150 µL of 10x Genomics Diluted Nuclei Buffer. Trypan blue-stained nuclei were counted manually using INCYTO C-Chip Neubauer Improved Disposable Hemacytometers.
Library construction according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide, Rev D or Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, Rev F). Libraries were normalized and pooled for sequencing on a NovaSeq SP-100 flow cell (Illumina, Inc., San Diego, CA, USA).

tag: disease state

value: translocation renal cell carcinoma


title: Multiome ATAC, tumor 19

description: Library name: Tumor 19, ATAC


title: NC-1

type: RNA

city: Beijing

first: Shunchang

last: Ma

address: No. 119, South Fourth Ring West Road, Fengtai District

department: Beijing Tiantan Hospital

institute: Capital Medical University

description:
Gene expression data from NC-1
NC-1_(HTA-2_0).sst-rma-gene-full-Signal

hyb_protocol: The labeled cDNA was fragmented and then hybridized to the GPL17586 for 16 hours at 45°C in a Hybridization Oven 640 (Thermo Fisher Scientific, USA). Following hybridization, the arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G (Thermo Fisher Scientific, USA). The Affymetrix GeneChip Command Console (AGCC) software was used to control the scanner and generate .CEL files from the scanned images.

data_processing:
The .CEL files were normalized using the Signal Space Transformation-Robust Multichip Analysis (SST-RMA) algorithm with default settings in the Affymetrix Expression Console software (Thermo Fisher Scientific, Pittsburgh, PA, USA) .
The final output is the log2-transformed signal intensity value for each probe set (transcript cluster), representing the relative abundance of the corresponding transcript.

label: biotin

source_name: transfected with a CLDN5-specific siRNA

label_protocol: Biotinylated cDNA was synthesized from 100 ng of total RNA using the Affymetrix GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific, Pittsburgh, PA, USA) according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA quality and concentration were assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: hCMEC/D3 cells were transfected with either a CLDN5-overexpressing plasmid or CLDN5-specific siRNA to establish overexpression and knockdown models, respectively. After 48 hours of transfection, total RNA was extracted and subjected to Affymetrix HTA 2.0 microarray analysis, with qRT-PCR performed for validation of the differentially expressed genes.

value: human brain vascular endothelial (hCMEC/D3) cells

value: transfected with a CLDN5-specific siRNA


title: Multiome ATAC, tumor 18, liver 2

description: Library name: Tumor 18 Liver 2, ATAC

source_name: Liver

value: Liver


title: Multiome RNA, normal 19

description: Library name: Normal 19

molecule: nuclear RNA


title: E-2

description:
Gene expression data from E-2
E-2_(HTA-2_0).sst-rma-gene-full-Signal

source_name: transfected with a CLDN5-overexpressing plasmid


title: Experiment 1_LV_T_7

city: Leiden

first: Sen

last: Zhang

address: Albinusdreef 2, Einthoven Laboratory, D4-29

institute: Leiden Univesity Medical Center

description:
Library name: LV_T_7
column X

data_processing:
The raw data end reads were trimmed and quality controlled by FASTQ with default parameters (https://github.com/OpenGene/fastp), and the clean reads were separately aligned to the reference genome (GRCm38) with orientation mode (5′ to 3′ orientation) using the HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). The overall consistency of Q20% and GC% across all samples indicates a stable, consistent sequencing run. Q20 values ranged from 96.21–98.40% and GC content ranged from 46.18–48.39% across all samples, indicating consistent sequencing quality. The mapped reads of each sample were assembled by StringTie in a reference-based approach (https://ccb.jhu.edu/software/stringtie/). To identify differentially expressed genes (DEGs) between the vehicle and SXB groups, the expression levels of each gene were calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundance. Analysis of DEGs was performed using DESeq2, and the resulting P-values were adjusted for multiple comparisons using the Benjamini–Hochberg FDR method. DEGs are defined as fold changes > 2 and adjusted P-values (padj) P < 0.05. Volcano plots were generated using the EnhancedVolcano feature (https://github.com/kevinblighe/EnhancedVolcano). KEGG pathway enrichment analysis was carried out by KOBAS (http://kobas.cbi.pku.edu.cn/home.do). GSEA was conducted to identify gene sets that share common biological function and significantly enriched gene sets were annotated based on the Molecular Signatures Database.
Assembly: clean reads were separately aligned to the reference genome (GRCm38) with orientation mode (5′ to 3′ orientation) using the HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml)
Supplementary files format and content: Liver RNA-seq_processed data_P.xlsx
Supplementary files format and content: Liver RNA-seq_processed data_T.xlsx

extract_protocol:
TRIzol RNA isolation reagent
The Illumina HiSeq 2500 platform was used to construct RNA libraries and generate reads of 2 × 150 bp long paired ends (Illumina, San Diego, CA, USA).


title: Multiome RNA, tumor 19

description: Library name: Tumor 19


title: E-1

description:
Gene expression data from E-1
E-1_(HTA-2_0).sst-rma-gene-full-Signal

value: transfected with a CLDN5-overexpressing plasmid


title: Experiment 1_LV_T_3

description:
Library name: LV_T_3
column W


title: NC-2

description:
Gene expression data from NC-2
NC-2_(HTA-2_0).sst-rma-gene-full-Signal


title: Experiment 1_LV_T_2

description:
Library name: LV_T_2
column V


title: Multiome RNA, tumor 18, RPLN

description: Library name: Tumor 18 RPLN

source_name: RPLN

value: RPLN


title: Multiome RNA, tumor 18, liver 4

description: Library name: Tumor 18 Liver 4


title: Experiment 1_LV_T_9

description:
Library name: LV_T_9
column Y


title: Experiment 1_LV_T_13

description:
Library name: LV_T_13
column T


title: snRNA, tumor 14, kidney

description: Library name: Tumor 14


title: Experiment 1_LV_T_12

description:
Library name: LV_T_12
column S


title: Experiment 1_LV_T_1

description:
Library name: LV_T_1
column R


title: snRNA, tumor 10, kidney

description: Library name: Tumor 10


title: Experiment 1_LV_T_6

description:
Library name: LV_T_6
column P


title: Experiment 1_LV_T_4

description:
Library name: LV_T_4
column O


title: snRNA, tumor 6, kidney

description: Library name: Tumor 6


title: Experiment 1_LV_T_18

description:
Library name: LV_T_18
column N


title: RNA-seq CNOT11-KD replicate 1

city: Onna

first: Saori

last: Nishijima

state: Okinawa

address: 1919-1 Tahncha

department: cell signal unit

country: Japan

institute: OIST

description:
Library name: index3
HeLa cells transfected with siRNA targeting CNOT11 (rep 1)

data_processing:
Adapter sequences were removed using Cutadapt.
Reads were aligned to the human reference genome (GRCh38) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: txt file, raw counts

source_name: HeLa

growth_protocol: DMEM high glucose with 10% FBS, streptomycin, and penicillin

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with polyA selection.

treatment_protocol: Cells were transfected with either scramble siRNA or siRNA targeting CNOT11 using standard transfection reagents.

value: HeLa

value: tumor cell


title: Experiment 1_LV_T_15

description:
Library name: LV_T_15
column M


title: RNA-seq Scramble replicate 2

description:
Library name: index2
HeLa cells transfected with scramble siRNA (rep 2)

value: scramble


title: Experiment 1_LV_T_11

description:
Library name: LV_T_11
column K


title: RNA-seq Scramble replicate 1

description:
Library name: index1
HeLa cells transfected with scramble siRNA (rep 1)


title: SW1463, 50nM Soto, 10 Days_3

first: Jonas

last: Buchloh

address: Robert-Koch-Straße 40

institute: University Medicine Göttingen

description: Library name: Soto_10d_3

data_processing:
Reads were aligned with the STAR aligner (version v2.7.11) based on the GRCh38 genome
Counts were quantified using Salmon (version v1.10.0)
Assembly: GRCh38
Supplementary files format and content: FASTQ format

source_name: Cell line

extract_protocol:
RNA isolation was conducted with Rneasy Mini Kit (Qiagen, #74106).
RNA sequencing library was prepared with PE150.

value: Sotorasib


title: Experiment 2_LV_P_30

description:
Library name: LV_P_30
column Y


title: SW1463, 50nM Soto, 10 Days_1

description: Library name: Soto_10d_1