title: SUB10, B cells, A/H3N2, Day2

description:
Library name: SUB10_D2_BCR
SUB10_D2_BCR


title: SUB10, T cells, A/H3N2, Day1

status: Public on Jul 29 2026

type: SRA

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

country: USA

institute: The Emmes Company

description:
Library name: SUB10_D1_TCR
SUB10_D1_TCR

library_source: transcriptomic

data_processing:
Human reference genome assembly (GRCh38), gene models, and associated gene annotation information were obtained from the ENSEMBL database (Version 99). The genomic reference was built by merging all human chromosomes except for X and Y chromosomes (to avoid gender-specific effects). Adapter sequences and low-quality 5′ ending sequences were removed from raw sequencing reads using the Trimmomatic software (Version 0.39). Following adapter removal, sequence reads were aligned to the reference transcriptome/genome using HISAT2 splice-aware sequence aligner (Version 2.2.0).  For each sample, the quality of reference alignments was evaluated using the RSeQC software (Version 3.0.1). Gene expression quantification was conducted on the gene level using Subread v2.0.0 counting mapped paired-reads to obtain fragment counts per gene.
Assembly: GRCh38 ENSEMBL database (Version 99)
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: T cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were recovered from phlebotomy samples and processed immediately. Magnetic sorting (AutoMACS Pro) was used to isolate individual immune cells using microbeads coated with CD15 (PMN), CD19 (B-cells), CD3 (T-cells), CD56 (NK cells), CD11c (dendritic cells), and CD14 (monocytes). During optimization, flow cytometric analysis confirmed >99% purity of each immune cell compartment. RNA was extracted from PBMC using the Promega simplyRNA Cell Kit according to the manufacturer’s protocol.
Polyadenylated RNAs were captured using NEBNext Magnetic Oligo d(T)25 Beads, and the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was used to prepare individually bar-coded libraries as per manufacturer’s recommended protocol. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).
Paired-end sequencing (25 million, 75-bp, paired-end reads) was performed on an Illumina Novaseq 6000 sequencers (Illumina, Inc., San Diego, CA, USA) as per manufacturer’s recommended protocol.

tag: tissue

value: T cells

tag: treatment

tag: day


title: SUB10, Neutrophils, A/H3N2, Day1

description:
Library name: SUB10_D1_NER
SUB10_D1_NER

source_name: Neutrophils

value: Neutrophils


title: SUB10, NK cells, A/H3N2, Day1

description:
Library name: SUB10_D1_NKR
SUB10_D1_NKR

source_name: NK cells

value: NK cells


title: SUB10, Dendritic cells, A/H3N2, Day1

description:
Library name: SUB10_D1_DNR
SUB10_D1_DNR

source_name: Dendritic cells

value: Dendritic cells


title: SUB10, Monocytes, A/H3N2, Day1

description:
Library name: SUB10_D1_MNR
SUB10_D1_MNR

source_name: Monocytes

value: Monocytes


title: SUB10, B cells, A/H3N2, Day-7

description:
Library name: SUB10_D.7_BCR
SUB10_D.7_BCR

source_name: B cells

value: B cells


title: SUB10, NK cells, A/H3N2, Day-7

description:
Library name: SUB10_D.7_NKR
SUB10_D.7_NKR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_TCR
SUB09_D4_TCR

value: A/H7N9 vaccine with AS03 adjuvant


title: SUB10, Neutrophils, A/H3N2, Day-7

description:
Library name: SUB10_D.7_NER
SUB10_D.7_NER


title: SUB10, B cells, A/H3N2, Day1

description:
Library name: SUB10_D1_BCR
SUB10_D1_BCR


title: SUB10, Monocytes, A/H3N2, Day-7

description:
Library name: SUB10_D.7_MNR
SUB10_D.7_MNR


title: SUB10, Dendritic cells, A/H3N2, Day-7

description:
Library name: SUB10_D.7_DNR
SUB10_D.7_DNR


title: SUB10, T cells, A/H3N2, Day-7

description:
Library name: SUB10_D.7_TCR
SUB10_D.7_TCR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_NER
SUB09_D4_NER


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_NKR
SUB09_D4_NKR


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_MNR
SUB09_D4_MNR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_DNR
SUB09_D4_DNR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day4

description:
Library name: SUB09_D4_BCR
SUB09_D4_BCR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day36

description:
Library name: SUB09_D36_NKR
SUB09_D36_NKR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day36

description:
Library name: SUB09_D36_NER
SUB09_D36_NER


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day36

description:
Library name: SUB09_D36_MNR
SUB09_D36_MNR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day36

description:
Library name: SUB09_D36_DNR
SUB09_D36_DNR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_TCR
SUB09_D32_TCR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_NKR
SUB09_D32_NKR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_NER
SUB09_D32_NER


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_MNR
SUB09_D32_MNR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_DNR
SUB09_D32_DNR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_NKR
SUB09_D30_NKR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_DNR
SUB09_D30_DNR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_NER
SUB09_D30_NER


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_MNR
SUB09_D30_MNR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_BCR
SUB09_D30_BCR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_NER
SUB09_D2_NER


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_NKR
SUB09_D2_NKR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_TCR
SUB09_D2_TCR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_DNR
SUB09_D2_DNR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_TCR
SUB09_D29_TCR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_NKR
SUB09_D29_NKR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_NER
SUB09_D29_NER


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_MNR
SUB09_D29_MNR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_BCR
SUB09_D29_BCR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_BCR
SUB09_D1_BCR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_NER
SUB09_D1_NER


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_DNR
SUB09_D1_DNR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_NKR
SUB09_D.7_NKR


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_MNR
SUB09_D.7_MNR


title: SUB09, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_NER
SUB09_D.7_NER


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_TCR
SUB09_D.7_TCR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_DNR
SUB09_D.7_DNR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day-7

description:
Library name: SUB09_D.7_BCR
SUB09_D.7_BCR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_NKR
SUB08_D4_NKR

value: A/H7N9 vaccine unadjuvanted


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_TCR
SUB08_D4_TCR


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_MNR
SUB08_D4_MNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_BCR
SUB08_D4_BCR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_NKR
SUB08_D36_NKR


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_MNR
SUB08_D36_MNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_BCR
SUB08_D36_BCR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_NER
SUB08_D32_NER


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_MNR
SUB08_D32_MNR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_DNR
SUB08_D32_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_BCR
SUB08_D32_BCR


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_TCR
SUB08_D30_TCR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_NKR
SUB08_D30_NKR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_DNR
SUB08_D30_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_BCR
SUB08_D30_BCR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_NKR
SUB08_D2_NKR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_NER
SUB08_D2_NER


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_MNR
SUB08_D2_MNR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_DNR
SUB08_D2_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_BCR
SUB08_D2_BCR


title: SUB09, NK cells, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_NKR
SUB09_D1_NKR


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_MNR
SUB09_D1_MNR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day1

description:
Library name: SUB09_D1_TCR
SUB09_D1_TCR


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_TCR
SUB08_D29_TCR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_NER
SUB08_D29_NER


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_DNR
SUB08_D4_DNR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_DNR
SUB08_D29_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_BCR
SUB08_D29_BCR


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_TCR
SUB08_D1_TCR


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_MNR
SUB08_D29_MNR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_NER
SUB08_D36_NER


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_NKR
SUB08_D32_NKR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_NKR
SUB08_D1_NKR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_NER
SUB08_D1_NER


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_MNR
SUB08_D1_MNR


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_NKR
SUB08_D.7_NKR


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_NER
SUB08_D.7_NER


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_MNR
SUB08_D.7_MNR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_DNR
SUB08_D.7_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_BCR
SUB08_D.7_BCR


title: SUB07, T cells, A/H3N2, Day8

description:
Library name: SUB07_D8_TCR
SUB07_D8_TCR


title: SUB07, NK cells, A/H3N2, Day8

description:
Library name: SUB07_D8_NKR
SUB07_D8_NKR


title: SUB07, Neutrophils, A/H3N2, Day8

description:
Library name: SUB07_D8_NER
SUB07_D8_NER


title: SUB07, Dendritic cells, A/H3N2, Day8

description:
Library name: SUB07_D8_DNR
SUB07_D8_DNR


title: SUB07, B cells, A/H3N2, Day8

description:
Library name: SUB07_D8_BCR
SUB07_D8_BCR


title: SUB07, T cells, A/H3N2, Day4

description:
Library name: SUB07_D4_TCR
SUB07_D4_TCR


title: SUB07, Neutrophils, A/H3N2, Day4

description:
Library name: SUB07_D4_NER
SUB07_D4_NER


title: SUB07, NK cells, A/H3N2, Day4

description:
Library name: SUB07_D4_NKR
SUB07_D4_NKR


title: SUB07, Dendritic cells, A/H3N2, Day4

description:
Library name: SUB07_D4_DNR
SUB07_D4_DNR


title: SUB07, T cells, A/H3N2, Day2

description:
Library name: SUB07_D2_TCR
SUB07_D2_TCR


title: SUB07, B cells, A/H3N2, Day4

description:
Library name: SUB07_D4_BCR
SUB07_D4_BCR


title: SUB07, NK cells, A/H3N2, Day2

description:
Library name: SUB07_D2_NKR
SUB07_D2_NKR


title: SUB07, Neutrophils, A/H3N2, Day2

description:
Library name: SUB07_D2_NER
SUB07_D2_NER


title: SUB07, Monocytes, A/H3N2, Day2

description:
Library name: SUB07_D2_MNR
SUB07_D2_MNR


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB08_D.7_TCR
SUB08_D.7_TCR


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_DNR
SUB08_D1_DNR


title: SUB08, B cells, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB08_D1_BCR
SUB08_D1_BCR


title: SUB07, Dendritic cells, A/H3N2, Day2

description:
Library name: SUB07_D2_DNR
SUB07_D2_DNR


title: SUB07, B cells, A/H3N2, Day2

description:
Library name: SUB07_D2_BCR
SUB07_D2_BCR


title: SUB07, T cells, A/H3N2, Day1

description:
Library name: SUB07_D1_TCR
SUB07_D1_TCR


title: SUB07, NK cells, A/H3N2, Day1

description:
Library name: SUB07_D1_NKR
SUB07_D1_NKR


title: SUB07, Neutrophils, A/H3N2, Day1

description:
Library name: SUB07_D1_NER
SUB07_D1_NER


title: SUB07, Monocytes, A/H3N2, Day1

description:
Library name: SUB07_D1_MNR
SUB07_D1_MNR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day36

description:
Library name: SUB09_D36_TCR
SUB09_D36_TCR


title: SUB07, Dendritic cells, A/H3N2, Day1

description:
Library name: SUB07_D1_DNR
SUB07_D1_DNR


title: SUB07, Monocytes, A/H3N2, Day8

description:
Library name: SUB07_D8_MNR
SUB07_D8_MNR


title: SUB07, B cells, A/H3N2, Day1

description:
Library name: SUB07_D1_BCR
SUB07_D1_BCR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day32

description:
Library name: SUB09_D32_BCR
SUB09_D32_BCR


title: SUB07, T cells, A/H3N2, Day-7

description:
Library name: SUB07_D.7_TCR
SUB07_D.7_TCR


title: SUB09, T cells, A/H7N9 vaccine with AS03 adjuvant, Day30

description:
Library name: SUB09_D30_TCR
SUB09_D30_TCR


title: SUB07, NK cells, A/H3N2, Day-7

description:
Library name: SUB07_D.7_NKR
SUB07_D.7_NKR


title: SUB07, Neutrophils, A/H3N2, Day-7

description:
Library name: SUB07_D.7_NER
SUB07_D.7_NER


title: SUB07, Monocytes, A/H3N2, Day-7

description:
Library name: SUB07_D.7_MNR
SUB07_D.7_MNR


title: WT_Rrp5_H375A_noDMS_2

status: Public on Jul 30 2026

city: Nashville

first: zahrat el oula

last: hassoun

state: TN

address: 200 Robinson research

department: Biochemistry

institute: Vanderbilt University

description: Library name: WT_H375A_noDMS_rep2

data_processing:
Adapter trimming and quality filtering were performed using Skewer. PCR duplicates were removed using SeqKit, and reads were trimmed at both ends. Processed reads were aligned to the Saccharomyces cerevisiae RDN37 pre_rRNA reference sequence using ShapeMapper v2.3.0 with Bowtie2 in DMS mode. Mutation frequencies were calculated using ShapeMapper after quality filtering. DMS_induced mutation frequencies were obtained by subtracting untreated from DMS_treated samples, and statistical analyses were performed using three biological replicates per condition.
Assembly: Saccharomyces cerevisiae RDN37 pre_rRNA reference sequence.
Supplementary files format and content: Tab_delimited text files containing per_nucleotide mutation frequencies and sequencing coverage.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cell

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium to mid_log phase before harvesting.

extract_protocol:
RNA was purified by phenol_chloroform extraction followed by ethanol precipitation.
RNA was fragmented, size_selected by denaturing polyacrylamide gel electrophoresis, dephosphorylated with T4 polynucleotide kinase, ligated to a pre_adenylated 3′ DNA adapter using truncated T4 RNA ligase 2 (K227Q), reverse transcribed using TGIRT_III reverse transcriptase, circularized with CircLigase II, amplified by indexed PCR, size_selected by native polyacrylamide gel electrophoresis, and quantified prior to sequencing. Libraries were sequenced on an Illumina NovaSeq X platform using single_end 100_bp reads.

treatment_protocol: Purified pre_40S ribosomes or mature 40S ribosomes were treated with 1% dimethyl sulfate (DMS) at 30°C for 5 min in the presence of 800 mM HEPES (pH 7.4), 500 mM NaCl, 50 mM Mg(OAc)2, and 0.2 μM Bacillus subtilis RNase P RNA. Untreated control samples were processed in parallel without DMS. Reactions were quenched with β_mercaptoethanol/NaOAc and RNA was purified by phenol_chloroform extraction.

tag: cell line

value: Saccharomyces cerevisiae cell


title: MSKCC-EF1-sgSCR-1

city: Durham

first: Jung Wook

last: Park

state: NC

address: 905 South Lasalle St.

department: Pathology

institute: Duke University

description: Library name: UUID_1

data_processing:
The sequencing libraries were multiplexed and clustered onto 3 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. The HiSeq Control Software (HCS) conducted image analysis and base calling. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software.
we used a pipeline developed at UCSC (UCSC Toil RNA-seq Recompute, https://xenabrowser.net/datapages/?hub=https://toil.xenahubs.net:443). CutAdapt was employed for adapter trimming, STAR for alignment, and RSEM and Kallisto served as quantifiers.
Assembly: hg18
Supplementary files format and content: normalized read counts

source_name: Prostate

growth_protocol: Growing in suspension (T75 flask) in B27-supplemented advanced DMEM/F12K media

extract_protocol:
RNeasy Mini Kit (Qiagen, Cat. #74104)
NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: NCI-H660 or MSKCC-EF1 cells were treated by sgDNMT3B or sgScrambe expressing lentiviruses

value: Prostate

tag: cell type

value: Neuroendocrine prostate cancer cell line

tag: genotype

value: sgSCR


title: SUB09, Monocytes, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_MNR
SUB09_D2_MNR


title: SUB07, Dendritic cells, A/H3N2, Day-7

description:
Library name: SUB07_D.7_DNR
SUB07_D.7_DNR


title: SUB07, B cells, A/H3N2, Day-7

description:
Library name: SUB07_D.7_BCR
SUB07_D.7_BCR


title: SUB09, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day29

description:
Library name: SUB09_D29_DNR
SUB09_D29_DNR


title: SUB09, B cells, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB09_D2_BCR
SUB09_D2_BCR


title: SUB06, T cells, A/H3N2, Day8

description:
Library name: SUB06_D8_TCR
SUB06_D8_TCR


title: NDM_3h_rep1

type: RNA

city: Numazu

first: Takefumi

last: Onodera

address: 18-24 Miyamoto

department: Numazu

country: Japan

institute: Institute of microbial chemistry

description: Gene expression in PANC-1 cells after NDM treatment 3h

hyb_protocol: For each array, 1.65 µg of Cy3-labeled cRNA was fragmented according to the manufacturer’s one-color gene expression protocol and combined with Agilent gene expression hybridization buffer. The hybridization mixture was loaded onto the Agilent Whole Human Genome 4×44K v2 microarray slide and hybridized at 65°C for 17 h with rotating Agilent hybridization oven. After hybridization, slides were washed according to the manufacturer’s recommended one-color gene expression wash procedure and then dried prior to scanning.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10 %).

data_processing:
Feature Extraction output files were generated using Feature Extraction Software 9.5.3.1 (Agilent) with protocol GE1-v5_95 and grid 014850_D_20070820. Data were imported into GeneSpring GX, thresholded to 1.0, log2-transformed (log base 2), normalized across arrays by 75th percentile shift, and baseline-transformed to the median of all samples. Processed expression matrices were exported from GeneSpring GX.
DEG list generated in GeneSpring GX after re-normalization within the subset of samples used for this comparison.

source_name: Nutrient-deprived medium, 3h, replicate 1

label_protocol: Total RNA (200 ng per sample) was labeled using the Agilent Low Input Quick Amp Labeling Kit, One-Color (manufacturer’s protocol). Briefly, double-stranded cDNA was synthesized from total RNA using an oligo(dT)-T7 primer. Cy3-labeled cRNA was then generated by in vitro transcription with T7 RNA polymerase. Approximately 10 µg of cRNA was obtained per sample. Labeled cRNA was purified according to the kit protocol and quantified prior to hybridization.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The gene expression profile under nutrient deprivation consisted of PANC-1 samples exposed to nutrient-deprived medium (NDM) for 0, 3, 6, 12, 24, and 48 h.

tag: condition

value: NDM treatment 3h


title: SUB06, NK cells, A/H3N2, Day8

description:
Library name: SUB06_D8_NKR
SUB06_D8_NKR


title: SUB06, Neutrophils, A/H3N2, Day8

description:
Library name: SUB06_D8_NER
SUB06_D8_NER


title: SUB06, Dendritic cells, A/H3N2, Day8

description:
Library name: SUB06_D8_DNR
SUB06_D8_DNR


title: SUB06, Monocytes, A/H3N2, Day8

description:
Library name: SUB06_D8_MNR
SUB06_D8_MNR


title: SUB06, B cells, A/H3N2, Day8

description:
Library name: SUB06_D8_BCR
SUB06_D8_BCR


title: SUB06, T cells, A/H3N2, Day4

description:
Library name: SUB06_D4_TCR
SUB06_D4_TCR


title: SUB07, Monocytes, A/H3N2, Day4

description:
Library name: SUB07_D4_MNR
SUB07_D4_MNR


title: SUB06, NK cells, A/H3N2, Day4

description:
Library name: SUB06_D4_NKR
SUB06_D4_NKR


title: siNC_2

city: Xi'an

first: Renji

last: Wei

address: Changle West Road, Xincheng District

country: China

institute: Fourth Military Medical University

description:
Library name: siNC_2
siNC, control

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: cell culture

value: siNC, control


title: siNC_1

description:
Library name: siNC_1
siNC, control


title: siANKRD52_2

description:
Library name: siANKRD52_2
siANKRD52, treatment

value: siANKRD52, treatment


title: siANKRD52_1

description:
Library name: siANKRD52_1
siANKRD52, treatment


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB08_D4_NER
SUB08_D4_NER


title: shANKRD52

description:
Library name: shANKRD52
shANKRD52, treatment

value: shANKRD52, treatment


title: shNC

description:
Library name: shNC
shNC, control

value: shNC, control


title: GES-1, IGF2BP1 overexpression, rep3

city: Beijing

first: Jing

last: Ning

state: Not required for this country

address: 49 North Garden Rd.,Haidian District，

institute: Peking University Third Hospital

description: Library name: GES-1 IGF2BP1-3

data_processing:
After the library is qualified, the different libraries are pooling according totheeffective concentration and the target amount of data off the machine, then beingsequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairingisgenerated. The basic principle of sequencing is to synthesize and sequence at the sametime (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNApolymeraseand splice primers were added to the sequenced flowcell and amplified. Whenthesequence cluster extends the complementary chain, each dNTP labeledbyfluorescence can release the corresponding fluorescence. The sequencer captures thefluorescence signal and converts the optical signal into the sequencing peakbycomputer software, so as to obtain the sequence information of the fragment tobetested
Assembly: GRCh38.p13
Supplementary files format and content: Exp_G_RSEM_TPM_20210310.txt include TPM values for GES-1 control cells and GES-1 with H. pylori infection
Supplementary files format and content: gene_fpkm.txt include FPKM values for GES-1 PCDH control cells and GES-1 with IGF2BP1 overexpression samples.

source_name: IGF2BP1-overexpressing GES-1 gastric epithelial cells

growth_protocol: GES-1 cells were cultured in standard gastric epithelial cell culture conditions and treated as described in the manuscript.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNANano 6000Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. In order to select cDNA fragments of preferentially 370~420 bpinlength, the library fragments were purified with AMPure XP system(BeckmanCoulter, Beverly, USA). Then PCR amplification, the PCR product was purifiedbyAMPure XP beads, and the library was finally obtained. Afterthe construction of the library, the library was initially quantified by Qubit2.0Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detectedbyAgilent 2100 bioanalyzer.

value: stomach

value: gastric epithelial cells

value: IGF2BP1 overexpressed


title: GES-1, IGF2BP1 overexpression, rep2

description: Library name: GES-1 IGF2BP1-2


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_TCR
SUB08_D36_TCR

value: T cells


title: GES-1, pCDH vector control, rep3

description: Library name: GES-1 PCDH-3

source_name: empty pCDH vector control GES-1

value: empty pCDH vector control


title: GES-1, pCDH vector control, rep2

description: Library name: GES-1 PCDH-2


title: GES-1, H.pylori infected 6 hours, rep3

description: Library name: GES-1 HP6h-3

source_name: H. pylori 26695 infected, MOI=100:1,infection duration: 6 hours

value: WT

value: H. pylori-infected


title: GES-1, H.pylori infected 6 hours, rep1

description: Library name: GES-1 HP6h-1


title: GES-1, H.pylori infected 6 hours, rep2

description: Library name: GES-1 HP6h-2


title: GES-1, negative control, rep1

description: Library name: GES-1 NC1

source_name: uninfected GES-1 control


title: 24h Glass (3)

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Library name: S24

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (hg38, v44) and read counts obtained for each gene
Assembly: hg38, v44
Supplementary files format and content: A matrix is generated as a plain text file (*.csv) with the Program featureCounts, in which each column is a sample, each row is a gene (Entrez_ID), and each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: bone marrow

growth_protocol: DMEM with fetal bovine serum, 37ºC on different culture surfaces

extract_protocol:
RNA was isolated using the RNAqueous-Micro Kit (AM1931, Thermo Fisher) following the manufacturer’s instructions.
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (mRNAseq)

value: bone marrow

value: mesenchymal stem cell


title: 24h PVDF (non poled) (3)

description: Library name: S23


title: 24h PVDF (+) (3)

description: Library name: S21


title: 4 days Glass (3)

description: Library name: S20


title: 4 days PVDF (-) (3)

description: Library name: S18


title: 4 days PVDF (+) (3)

description: Library name: S17


title: 24h Glass (2)

description: Library name: S16


title: 24h PVDF (non poled) (2)

description: Library name: S15


title: SUB23, Neutrophils, A/H7N9 vaccine with AS03 adjuvant, Day2

description:
Library name: SUB23_D2_NER
SUB23_D2_NER

value: Neutrophils

value: A/H7N9 vaccine with AS03 adjuvant


title: 24h PVDF (+) (2)

description: Library name: S13


title: 24h PVDF (-) (2)

description: Library name: S14


title: 4 days PVDF (non poled) (2)

description: Library name: S11


title: 4 days PVDF (+) (2)

description: Library name: S09


title: 4 days PVDF (-) (2)

description: Library name: S10


title: 4 days PVDF (-)

description: Library name: S06


title: 4 days PVDF (+)

description: Library name: S05


title: 24h PVDF (non poled)

description: Library name: S03


title: 24h Glass

description: Library name: S04


title: 24h PVDF (-)

description: Library name: S02


title: 24h PVDF (+)

description: Library name: S01


title: luad1

city: shanghai

first: Jian

last: Li

address: huaihai road

institute: shanghai chest hospital

description:
Library name: sample1
one sample from non small cell lung cancer

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed and converted into FASTQ format using the mkfastq pipeline in the Cell Ranger software suite (10x Genomics). The resulting FASTQ files were then processed using the Cell Ranger count pipeline, which performed read alignment, barcode processing, and Unique Molecular Identifier (UMI) counting. This pipeline generated the raw and filtered gene-barcode expression matrices utilized for downstream bioinformatic analyses.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: tumor

extract_protocol:
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller to generate Gel Bead-in-Emulsions (GEMs). Within each individual GEM, single cells were lysed, and the released intracellular polyadenylated mRNA transcripts were captured by the barcoded oligonucleotides present on the 10x Gel Beads. Reverse transcription was subsequently performed within the intact GEMs to synthesize single-cell barcoded full-length cDNA.
Following reverse transcription, the emulsion was disrupted, and the uniquely barcoded cDNA was pooled and amplified via polymerase chain reaction (PCR). The amplified cDNA was purified using SPRIselect beads. The purified cDNA then underwent enzymatic fragmentation, end repair, and A-tailing. Finally, sequencing adapters and sample-specific indices were incorporated via PCR to construct the final single-cell RNA-seq libraries, adhering strictly to the manufacturer's protocol for the 10x Genomics Chromium Single Cell 3' Reagent Kits.

value: tumor

value: lung cancer cell


title: HCT116 cells, SETD8 overexpression replicate 3

city: Wuhan

first: Nie

last: Haihang

address: donghu road 169

institute: Zhongnan Hospital of Wuhan University

description: Library name: Sample6

data_processing:
Raw sequencing reads (FASTQ format) were first quality-controlled by removing adaptor sequences, reads containing N, and low-quality reads.
Clean reads were then aligned to the human reference genome (GRCh38/hg38) using HISAT2/STAR.
Gene-level read counts were obtained using featureCounts (or HTSeq), which summarizes the number of reads uniquely mapped to the exonic regions of each gene according to the annotation (GTF file).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colorectal cancer

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s instructions. RNA integrity was assessed with Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using poly(A) selection and the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Cells were transduced with lentiviral Vector or SETD8 overexpression plasmids, and stable clones were selected using puromycin.

value: Colorectal cancer

value: Colon adenocarcinoma cells

value: SETD8 overexpression


title: HCT116 cells, SETD8 overexpression replicate 1

description: Library name: Sample4


title: HCT116 cells,Vector replicate 3

description: Library name: Sample3

value: Vector


title: HCT116 cells,Vector replicate 2

description: Library name: Sample2


title: ES2 cells siUAP1-3

city: Hong Kong

first: Michelle

middle: KY

last: Siu

address: Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: O&G

country: Hong Kong

institute: University of Hong Kong

description: Library name: ES2U12_13_3

data_processing:
Differentially expressed genes (DEGs) between groups (n = 3) were identified using the DESeq2 method, with multiple testing correction performed using the Benjamini–Hochberg (BH) procedure
Genes were defined as differentially expressed if they showed a log2 fold change greater than 0.5 and an adjusted p-value below 0.05. KEGG pathway enrichment analysis was then conducted based on these DEGs
Assembly: GRCh38.p12
Supplementary files format and content: tab delimited text file contains FPKM list with the annotation of each gene
Supplementary files format and content: tab delimited text file contains readcount list with the annotation of each gene

molecule: polyA RNA

source_name: ovarian

growth_protocol: ES2 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin. Cells were incubated at 37°C in a humidified incubatorwith 5% CO₂

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA kit (Macherery-Nagel) according to the manufacturer’s instructions
Library preparation and next-generation RNA-Seq were performed by Novogene. RNA libraries were generated using poly(A) enrichment (or rRNA depletion) followed by cDNA synthesis. Sequencing was carried out on an Illumina NovaSeq 6000 platform

treatment_protocol: ES2 cells were transfected with UAP1 siRNAs (s13338 and s13337, Thermo Fisher Scientific) or a control siRNA (4390846, Thermo Fisher Scientific) using Lipid siLentfect reagent (Bio-Rad) following the manufacturer’s protocol. Six hours after transfection, the transfection medium was replaced with complete medium. Total RNA was isolated from the transfected cells 48 hours post-transfection

value: ovarian

value: high-grade serous carcinoma

value: UAP1 knockdown


title: ES2 cells siUAP1-2

description: Library name: ES2U12_31_2


title: ES2 cells control siRNA-3

description: Library name: ES2C12_13_3


title: ES2 cells siUAP1-1

description: Library name: ES2U4_1_1


title: ES2 cells control siRNA-1

description: Library name: ES2C4_1_1


title: CST-CREB, NGP, CREB (ChIP)

city: Washington

first: Yang

last: Yu

state: DC

address: 111 Michigan Ave NW

institute: Children's national hospital

description: Library name: CST-CREB, ChIP

library_source: genomic

data_processing:
CREB ChIP-seq data from three biological replicates were aligned to the human hg38 genome using Bowtie2, and peaks were called with MACS2 (q < 0.05) using matched input controls.
Gene transcription start sites (TSSs) were annotated based on UCSC refGene annotations hg38, and genes were considered CREB-associated if at least one CREB ChIP-seq peak overlapped a ±50 kb window surrounding the TSS.
Assembly: hg38
Supplementary files format and content: narrowPeak, tsv

molecule: genomic DNA

source_name: NGP

growth_protocol: NGP cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ChIP assays were performed by using a chromatin immunoprecipitation (ChIP) kit (Active Motif).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit . 4 ng of DNA was used as starting material for input and ip samples. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: When cell confluency was 80 to 90%, NGP cells were harvested for ChIP assay.

value: NGP

value: human neuroblastoma


title: PKDL 4

city: Kolkata

first: Mitali

last: Chatterjee

state: West Bengal

address: 244B, AJC Bose Road

department: Pharmacology

country: India

institute: Institute of Post Graduate Medical Education & Research, Kolkata

description: Library name: P709

data_processing:
Illumina Novaseq 6000 platform was used for basecalling to generate paired-end reads of 100 bases
Sequenced reads were trimmed for adaptor sequences using CutAdapt, quality trimmed at the 5' and 3′ ends, then mapped to the human genome (hg19/GRCh37) using STAR v2.7.11b
The mapped reads were filtered based on mapping quality using samtools view with parameter -q 10
Raw read counts of genes were generated using HTSeq-count v2.1.2 with parameters -s reverse --nonunique all
Differential expression analysis was carried out using Deseq2
Assembly: hg19/GrCh37
Supplementary files format and content: Tab-delimited text files include raw read counts for all known genes for each sample.

source_name: Dermal biopsy from patient with PKDL

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit following the manufacturer’s instructions. Briefly, tissues were snap-frozen in liquid nitrogen, crushed using a mortar and pestle, and transferred to microcentrifuge tubes containing 1 ml TRIzol reagent. Phase separation was performed using chloroform, and the aqueous phase was collected for further processing. Ethanol was added to facilitate RNA binding, and the sample was applied to an RNeasy Mini spin column, allowing total RNA to bind to the membrane. On-column DNase treatment was performed to remove genomic DNA, followed by washing steps to eliminate contaminants. Finally, high-quality RNA was eluted in 30 µl of nuclease-free water. RNA quality was assessed using the Agilent RNA ScreenTape on the Agilent 2200 TapeStation system, and quantification was performed using a NanoDrop spectrophotometer and Qubit fluorometer (Thermo Scientific).
RNA-seq libraries were prepared from 100 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions (KR1351-v2.17). Ribosomal RNA was depleted by hybridization with complementary DNA oligonucleotides followed by RNase H and DNase treatment. The rRNA-depleted RNA was then fragmented using heat and magnesium, and first-strand cDNA synthesis was performed using random priming, followed by second-strand synthesis with A-tailing to generate double-stranded cDNA incorporating dUTP in the second strand. Adapter ligation with 3′ dTMP overhangs was carried out, followed by limited-cycle high-fidelity PCR amplification to produce strand-specific libraries. Library quality was evaluated using High Sensitivity D1000 ScreenTape on the Agilent 2200 TapeStation system, and final library quantification was performed using Real-Time PCR (QuantStudio 7 Flex). Paired-end sequencing (2 × 100 bp or 2 × 150 bp, depending on insert size) was performed on the Illumina NovaSeq 6000 platform.

value: Lesional biopsy from patient with PKDL

tag: age of_onset


title: PKDL 2

description: Library name: P641


title: Healthy control 3

description: Library name: H44

source_name: Healthy control normal skin from lab volunteer


title: PKDL 1

description: Library name: P634


title: Healthy control 2

description: Library name: H42a

value: Healthy control normal skin from lab volunteer


title: MCF7 cells,VI-10H,rep2

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

description: Library name: Sample 8

data_processing:
For RNAseq, raw fastq reads underwent alignment to the mouse genome (hg38) utilizing HISAT2 version 2.1.0. The raw read counts were normalized to Reads per Million (RPM) per sample. To quantify read counts within specific genomic regions, featurecounts was employed, and these counts were subsequently utilized by DESeq2 (version 1.32.0) for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
For RNAseq, poly(A)-containing mRNA was selectively enriched from 1 μg of total RNA utilizing VAHTS mRNA capture beads (Vazyme, N401-02).
To generate fragments of 200-500 nucleotides in length, the enriched mRNA was fragmented through treatment with 2× ProtoScript II buffer (NEB, M0368). Following fragmentation, the first- and second-strand cDNA were generated, and adaptor ligation was carried out, followed by 12-15 cycles of PCR amplification.

value: human breast cancer

value: WT


title: MCF7 cells,VI-10J,rep3

description: Library name: Sample 6


title: MCF7 cells,VI-10J,rep1

description: Library name: Sample 4


title: MCF7 cells,DMSO,rep3

description: Library name: Sample 3

value: DMSO


title: MCF7 cells,DMSO,rep2

description: Library name: Sample 2


title: MCF7 cells,DMSO,rep1

description: Library name: Sample 1


title: Patient 8_2

city: Lexington

first: Robert

middle: N

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

institute: University of Kentucky

description:
Library name: Sample 17
S17

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogenes methods
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: xls files include RPKM and total counts for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from livers using the Qiagen Rneasy Mini kit. Novogene isolated mRNA from the total RNA provided by the investigators using poly-T oligo-attached magnetic beads.
mRNA libraries were constructed by Novogene using random hexamers and dUTP. The library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, following Novogenes methods.

value: Liver

value: Tumor


title: Patient 8_1

description:
Library name: Sample 16
S16

value: Adjacent


title: Patient 7_2

description:
Library name: Sample 15
S15


title: Patient 7_1

description:
Library name: Sample 14
S14


title: Patient 6_3

description:
Library name: Sample 13
S13


title: Patient 5_2

description:
Library name: Sample 10
S10


title: Patient 4_2

description:
Library name: Sample 8
S8


title: Patient 3_2

description:
Library name: Sample 6
S6


title: SUB21, NK cells, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB21_D36_NKR
SUB21_D36_NKR

source_name: NK cells

value: NK cells

value: A/H7N9 vaccine unadjuvanted


title: SUB22, B cells, A/H3N2, Day-7

description:
Library name: SUB22_D.7_BCR
SUB22_D.7_BCR

source_name: B cells

value: B cells


title: Patient 3_1

description:
Library name: Sample 5
S5


title: Patient 2_2

description:
Library name: Sample 4
S4


title: Patient 2_1

description:
Library name: Sample 3
S3


title: Patient 1_2

description:
Library name: Sample 2
S2


title: Patient 1_1

description:
Library name: Sample 1
S1


title: WM266_EPACi-3_24h

city: Madison

first: Sireesh Kumar

last: Teertam

state: WI

address: 1111 Highland Ave

department: Dermatology

institute: UW-Madison

description: Library name: Sample-72

data_processing:
Rosalind cloud based RNA seq analysis platform
Assembly: Reads were mapped to GRCh38
Supplementary files format and content: XL format

growth_protocol: Patient matched primary and LN-Met melanoma cells were cultured in Tumor specific media composed of MCDB media, Lebovitz's L-15, Sodium Bicabonate, 2% heat inactivated FBS.

extract_protocol:
RNA was extracted using Qiagen RNA isolation kit.
RNA libraries were prepared by UW gene expression center RNA seq library preparation services.

treatment_protocol: Cells were treated with 2.5 μM of ESI-09 (EPACi) for 6, 12, & 24h.

value: Lymph node Met

tag: time


title: WM266_EPACi-2_24h

description: Library name: Sample-71


title: WM266_EPACi-1_24h

description: Library name: Sample-70


title: WM266_DMSO-3_24h

description: Library name: Sample-69


title: WM266_DMSO-2_24h

description: Library name: Sample-68


title: WM266_DMSO-1_24h

description: Library name: Sample-67


title: WM266_EPACi-2_12h

description: Library name: Sample-65


title: Patient 6_1

description:
Library name: Sample 11
S11


title: WM266_EPACi-1_12h

description: Library name: Sample-64


title: WM266_DMSO-2_12h

description: Library name: Sample-62


title: WM266_DMSO-1_12h

description: Library name: Sample-61


title: WM266_EPACi-3_6h

description: Library name: Sample-60


title: SUB21, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day1

description:
Library name: SUB21_D1_DNR
SUB21_D1_DNR

source_name: Dendritic cells

value: Dendritic cells


title: SUB21, B cells, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB21_D29_BCR
SUB21_D29_BCR


title: WM266_EPACi-2_6h

description: Library name: Sample-59


title: WM266_DMSO-3_6h

description: Library name: Sample-57


title: WM266_EPACi-1_6h

description: Library name: Sample-58


title: WM266_DMSO-2_6h

description: Library name: Sample-56


title: WM266_DMSO-1_6h

description: Library name: Sample-55


title: WM165_EPACi-3_24h

description: Library name: Sample-54


title: WM165_EPACi-1_24h

description: Library name: Sample-52


title: GES-1, negative control, rep2

description: Library name: GES-1 NC2

value: stomach

value: gastric epithelial cells


title: GES-1, pCDH vector control, rep1

description: Library name: GES-1 PCDH-1

value: empty pCDH vector control


title: WM165_EPACi-2_24h

description: Library name: Sample-53


title: WM165_DMSO-2_24h

description: Library name: Sample-50


title: WM165_DMSO-3_24h

description: Library name: Sample-51


title: 4 days PVDF (non poled) (3)

description: Library name: S19

value: bone marrow

value: mesenchymal stem cell


title: 24h PVDF (-) (3)

description: Library name: S22


title: WM165_DMSO-1_24h

description: Library name: Sample-49


title: 4 days Glass (2)

description: Library name: S12


title: WM165_EPACi-3_12h

description: Library name: Sample-48


title: WM165_EPACi-2_12h

description: Library name: Sample-47


title: WM165_EPACi-1_12h

description: Library name: Sample-46


title: WM165_DMSO-3_12h

description: Library name: Sample-45


title: WM165_DMSO-1_12h

description: Library name: Sample-43


title: WM165_DMSO-2_12h

description: Library name: Sample-44


title: 4 days PVDF (non poled)

description: Library name: S07


title: 4 days Glass

description: Library name: S08


title: WM165_EPACi-3_6h

description: Library name: Sample-42


title: WM266_EPACi-3_12h

description: Library name: Sample-66


title: WM165_EPACi-2_6h

description: Library name: Sample-41


title: HCT116 cells, SETD8 overexpression replicate 2

description: Library name: Sample5

value: Colorectal cancer

value: Colon adenocarcinoma cells

value: SETD8 overexpression


title: WM165_EPACi-1_6h

description: Library name: Sample-40


title: HCT116 cells,Vector replicate 1

description: Library name: Sample1

value: WT

value: Vector


title: WM165_DMSO-3_6h

description: Library name: Sample-39

value: DMSO


title: WM165_DMSO-1_6h

description: Library name: Sample-37


title: WM239_EPACi-2_24h

description: Library name: Sample-35


title: WM266_DMSO-3_12h

description: Library name: Sample-63


title: WM165_DMSO-2_6h

description: Library name: Sample-38


title: WM239_EPACi-3_24h

description: Library name: Sample-36


title: WM239_EPACi-1_24h

description: Library name: Sample-34


title: WM239_EPACi-3_12h

description: Library name: Sample-30


title: WM239_DMSO-3_24h

description: Library name: Sample-33


title: WM239_DMSO-1_24h

description: Library name: Sample-31


title: WM239_DMSO-2_24h

description: Library name: Sample-32


title: WM239_EPACi-2_12h

description: Library name: Sample-29


title: WM239_EPACi-1_12h

description: Library name: Sample-28


title: WM239_DMSO-3_12h

description: Library name: Sample-27


title: WM239_DMSO-1_12h

description: Library name: Sample-25


title: WM239_DMSO-2_12h

description: Library name: Sample-26


title: WM239_EPACi-1_6h

description: Library name: Sample-22


title: WM239_DMSO-1_6h

description: Library name: Sample-19


title: WM239_DMSO-2_6h

description: Library name: Sample-20


title: WM239_DMSO-3_6h

description: Library name: Sample-21


title: WM115_EPACi-3_24h

description: Library name: Sample-18

value: Primary melanoma


title: WM115_EPACi-1_24h

description: Library name: Sample-16


title: WM115_DMSO-3_24h

description: Library name: Sample-15


title: WM115_DMSO-2_24h

description: Library name: Sample-14


title: WM115_DMSO-1_24h

description: Library name: Sample-13


title: WM115_EPACi-2_12h

description: Library name: Sample-11


title: WM115_DMSO-3_12h

description: Library name: Sample-9


title: WM115_EPACi-1_12h

description: Library name: Sample-10


title: WM115_DMSO-1_12h

description: Library name: Sample-7


title: WM115_DMSO-2_12h

description: Library name: Sample-8


title: WM115_EPACi-3_6h

description: Library name: Sample-6


title: WM115_EPACi-2_6h

description: Library name: Sample-5


title: WM115_EPACi-1_6h

description: Library name: Sample-4


title: WM115_DMSO-2_6h

description: Library name: Sample-2


title: WM115_DMSO-3_6h

description: Library name: Sample-3


title: WM115_DMSO-1_6h

description: Library name: Sample-1


title: HFF/3_MP 0.2mM

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Library name: H3_M3

data_processing:
Low-quality reads and adapter sequences were trimmed with Trimmomatic  (v0.39), employing the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Alignment and quantification was done using STAR  (v2.7.11b)
Assembly: hg38
Supplementary files format and content: raw read count per gene in tab delimited file

source_name: skin

growth_protocol: Cells were cultured under standard conditions at 37°C and 5% CO2 in appropriate complete growth medium as specified for each cell type and expanded to comparable confluence prior to treatment.

extract_protocol:
Total RNA was isolated using silica membrane spin columns (RNeasy Mini Kit, Qiagen, Hilden, Germany) with on-column DNase digestion according to the manufacturer’s instructions. RNA quantity and purity were assessed spectrophotometrically, and RNA integrity was verified prior to library preparation.
mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. Libraries were indexed, PCR-amplified, purified, and quality-controlled prior to sequencing.

treatment_protocol: Cells were exposed to clinically derived postoperative pancreatic effluents (AES1448, GR1479), monopalmitin (0.2 mM), or medium control for transcriptomic analysis. Treatments were applied for 24, 48, or 72 hours, with three biological replicates per condition and time point. After exposure, cells were washed with PBS and harvested for RNA extraction.

value: skin

value: HFF

value: fibroblast

value: wild type

value: MP


title: HFF/3_AES1448 1:50

description: Library name: H3_A3


title: HFF/3_Ko

description: Library name: H3_K3

value: ctl


title: HFF/3_GR1479 1:50

description: Library name: H3_G3


title: HFF/2_AES1448 1:50

description: Library name: H2_A2


title: HFF/2_Ko

description: Library name: H2_K2


title: HFF/2_GR1479 1:50

description: Library name: H2_G2


title: HFF/2_MP 0.2mM

description: Library name: H2_M2


title: HFF_MP 0.2mM

description: Library name: H1_M1


title: HFF_AES1448 1:50

description: Library name: H1_A1


title: HFF_Ko

description: Library name: H1_K1


title: Pat.6.3/Perit._MP 0.2mM

description: Library name: P6_M3

source_name: peritoneum

value: peritoneum

value: primary cells

value: peritoneum mesothelial cells


title: HFF_GR1479 1:50

description: Library name: H1_G1


title: Pat.6.3/Perit._AES1448 1:50

description: Library name: P6_A3


title: Pat.6.3/Perit._Ko

description: Library name: P6_K3


title: Pat.6.2/Perit._MP 0.2mM

description: Library name: P6_M2


title: Pat.6.2/Perit._AES1448 1:50

description: Library name: P6_A2


title: Pat.6.2/Perit._GR1479 1:50

description: Library name: P6_G2


title: Pat.6.2/Perit._Ko

description: Library name: P6_K2


title: Pat.6/Perit._MP 0.2mM

description: Library name: P6_M1


title: Pat.6/Perit._AES1448 1:50

description: Library name: P6_A1


title: Pat.6/Perit._Ko

description: Library name: P6_K1


title: Pat.5.3/Perit._AES1448 1:50

description: Library name: P5_A3


title: Pat.5.3/Perit._GR1479 1:50

description: Library name: P5_G3


title: Pat.5.2/Perit._MP 0.2mM

description: Library name: P5_M2


title: Pat.5.2/Perit._AES1448 1:50

description: Library name: P5_A2


title: Pat.5.2/Perit._Ko

description: Library name: P5_K2


title: Pat.5.2/Perit._GR1479 1:50

description: Library name: P5_G2


title: Pat.5/Perit._AES1448 1:50

description: Library name: P5_A1


title: Pat.5/Perit._GR1479 1:50

description: Library name: P5_G1


title: Pat.4.3/Perit._AES1448 1:50

description: Library name: P4_A3


title: Pat.4.3/Perit._GR1479 1:50

description: Library name: P4_G3


title: Pat.4.3/Perit._Ko

description: Library name: P4_K3


title: Pat.4.2/Perit._MP 0.2mM

description: Library name: P4_M2


title: Pat.4.2/Perit._AES1448 1:50

description: Library name: P4_A2


title: Pat.4.2/Perit._GR1479 1:50

description: Library name: P4_G2


title: Pat.4.2/Perit._Ko

description: Library name: P4_K2


title: Pat.4/Perit._MP 0.2mM

description: Library name: P4_M1


title: Pat.4/Perit._AES 1:50

description: Library name: P4_A1


title: Pat.4/Perit._GR1479 1:50

description: Library name: P4_G1


title: Pat.4/Perit._Ko

description: Library name: P4_K1


title: Pat.3.3/Perit._GR1479 1:50

description: Library name: P3_G3


title: Pat.3.3/Perit._Ko

description: Library name: P3_K3


title: Pat.3.2/Perit._AES1448 1:50

description: Library name: P3_A2


title: Pat.3.3/Perit._AES1448 1:50

description: Library name: P3_A3


title: Pat.3.2/Perit._GR1479 1:50

description: Library name: P3_G2


title: Pat.3.2/Perit._Ko

description: Library name: P3_K2


title: Pat.3.2/Perit._MP 0,2mM

description: Library name: P3_M2


title: Pat.3/Perit._MP 0,2mM

description: Library name: P3_M1


title: Pat.5/Perit._Ko

description: Library name: P5_K1


title: Pat.4.3/Perit._MP 0.2mM

description: Library name: P4_M3


title: Pat.3/Perit._GR1479 1:50

description: Library name: P3_G1


title: Pat.3/Perit._Ko

description: Library name: P3_K1


title: Pat.1.3/Perit._AES1448 1:50

description: Library name: P1_A3


title: Pat.1.3/Perit._MP 0,2mM

description: Library name: P1_M3


title: Pat.1.3/Perit._GR1479 1:50

description: Library name: P1_G3


title: Pat.1.3/Perit._Ko

description: Library name: P1_K3


title: Pat.1.2/Perit._MP 0,2mM

description: Library name: P1_M2


title: Pat.1.2/Perit._AES1448 1:50

description: Library name: P1_A2


title: Pat.1.2/Perit._GR1479 1:50

description: Library name: P1_G2


title: Pat.3.3/Perit._MP 0,2mM

description: Library name: P3_M3


title: Pat.1.2/Perit._Ko

description: Library name: P1_K2


title: Pat.1/Perit._MP 0,2mM

description: Library name: P1_M1


title: Pat.1/Perit._AES1448 1:50

description: Library name: P1_A1


title: Pat.1/Perit._GR1479 1:50

description: Library name: P1_G1


title: Lung fibroblast, Sh-ZNF469, Rep 3

city: Bangkok

first: Thammachanok

last: Boonto

address: 254 Phaya Thai Rd, Khwaeng Wang Mai, Pathum Wan

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

description: Library name: Sample6

data_processing:
High-quality clean sequencing reads were obtained following stringent filtering of raw reads to remove adaptor sequences and low-quality reads. Filtered reads were aligned to the reference genome using HISAT2, and transcript assembly was performed with StringTie. Differential pathway activity between experimental groups was subsequently interrogated using Gene Set Enrichment Analysis (GSEA) software developed by the Broad Institute, and Over-Representation Analysis (ORA), enabling systematic identification of significantly enriched gene sets and biological pathways.
Assembly: Homo_sapiens.GRCh38_release95.genome.fa.
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

growth_protocol: Human lung fibroblasts IMR-90 (CCL-186™) will be purchased from American Type Culture Collection (Rockville, MD, USA) and will be maintained in Eagle's Minimum Essential Medium (EMEM), supplemented with 10% FBS, 1% anti-anti, GlutaMAX™ (Gibco, USA), and Primocin® (InvivoGen, USA) at 37 °C in 5% CO2. Stable ZNF469 knockdown cells (Sh-ZNF469) were generated using a doxycycline-inducible Tet-pLKO-puro lentiviral vecto. Transduced cells were selected and maintained in culture medium containing puromycin (0.5 µg/mL; Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol:
RNA extraction was performed with GenUP Total RNA Kit (Biotechrabbit, Berlin, Germany), following the manufacturer's protocol.
Total RNA was extracted from ZNF469-knockdown with or without doxycyclince (DOX) induction and then to Beijing Biomarker Technologies Co., Ltd. (Beijing, China) for transcriptomic sequencing. RNA quality and integrity were evaluated according to the BMKGENE standard workflow using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Sequncing libraries were constructed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) and then, sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads (Illumina, San Diego, CA, USA).

treatment_protocol: Sh-ZNF469 expression was induced by doxycycline (DOX; Sigma-Aldrich) treatment at 2 µg/mL to achiceve transient ZNF469 kncokdown.

value: Fibroblast


title: Pat.1/Perit._Ko

description: Library name: P1_K1


title: Lung fibroblast, Sh-ZNF469, Rep 2

description: Library name: Sample5


title: Lung fibroblast, Sh-ZNF469, Rep 1

description: Library name: Sample4


title: Lung fibroblast, Control, Rep 3

description: Library name: Sample3

value: Wild-type


title: Lung fibroblast, Control, Rep 2

description: Library name: Sample2


title: Lung fibroblast, Control, Rep 1

description: Library name: Sample1


title: NGS_rRNA_depleted_U2OS_Rep3

city: Guangzhou

first: Yulong

last: Song

address: No.1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description:
Library name: Sample 14
Stranded rRNA-depleted RNA-seq

data_processing:
CLC Genomics Workbench v 11.0.1
The RNA-seq raw data was initially processed by Cutadapt (version v4.0; -q 30,30 --trim-n --length-tag 'length=' -m 36 -e 0.1), including removing the adapter sequences from the 3' end of reads and trimming the bases with quality scores lower than 30 from both 5’ and 3’ ends
Subsequently, the clean reads were aligned to the human reference genome (hg19) using STAR (version v2.7.10b) with the default parameters. And the corresponding Gencode v19 annotation files were obtained from UCSC table browser
Then, a custom perl script was used to calculate the editing level of each site, which is the percentage of reads with G bases in all reads
Only sites with a minimum coverage depth of 30 were retained for further analysis, and the cutoff of base quality is ≥ 30
Assembly: hg19
Supplementary files format and content: tab-delimited text file with the A-to-I RNA editing level

growth_protocol: HEK293T and U2OS cells were cultured in DMEM, supplemented with 10% fetal bovine serum and 100 U/ml penicillin G and 100 μg/ml streptomycin at 37°C under 5% CO2.

extract_protocol:
Total RNAs were then extracted using the FastPure® Cell/Tissue Total RNA Isolation Kit V2 (Vazyme Biotech Co., Ltd., RC112-01).
For the polyA-based mRNA enrichment, mRNAs were captured using VAHTS mRNA Capture Beads (Vazyme Biotech Co., Ltd., N401). For the rRNA-depleted method, ribosomal-depleted RNA was purified with Ribo-off rRNA Depletion kit (Vazyme Biotech Co., Ltd., N406). Then, the RNA-seq libraries were constructed with VAHTS Universal V8 RNA-Seq Library Prep Kit (Vazyme Biotech Co., Ltd., NRM605).

treatment_protocol: Without any treatment

value: Human osteosarcoma cell line derived from a bone tumour of a 15-year-old girl in 1964


title: NGS_rRNA_depleted_U2OS_Rep2

description:
Library name: Sample 13
Stranded rRNA-depleted RNA-seq


title: NGS_rRNA_depleted_U2OS_Rep1

description:
Library name: Sample 12
Stranded rRNA-depleted RNA-seq


title: NGS_polyA_U2OS_Rep3

description:
Library name: Sample 11
Stranded polyA-selected RNA-seq


title: WM239_EPACi-3_6h

description: Library name: Sample-24

value: Lymph node Met


title: Pat.3/Perit._AES1448 1:50

description: Library name: P3_A1


title: NGS_polyA_U2OS_Rep2

description:
Library name: Sample 10
Stranded polyA-selected RNA-seq

value: WT


title: NGS_polyA_U2OS_Rep1

description:
Library name: Sample 9
Stranded polyA-selected RNA-seq


title: NGS_rRNA_depleted_HEK293T_Rep3

description:
Library name: Sample 6
Stranded rRNA-depleted RNA-seq

value: Epithelial-like cell of Kidney


title: WM115_EPACi-2_24h

description: Library name: Sample-17


title: NGS_rRNA_depleted_HEK293T_Rep2

description:
Library name: Sample 5
Stranded rRNA-depleted RNA-seq


title: NGS_rRNA_depleted_HEK293T_Rep1

description:
Library name: Sample 4
Stranded rRNA-depleted RNA-seq


title: WM115_EPACi-3_12h

description: Library name: Sample-12


title: WM239_EPACi-2_6h

description: Library name: Sample-23


title: NGS_polyA_HEK293T_Rep3

description:
Library name: Sample 3
Stranded polyA-selected RNA-seq


title: NGS_polyA_HEK293T_Rep1

description:
Library name: Sample 1
Stranded polyA-selected RNA-seq


title: NGS_polyA_HEK293T_Rep2

description:
Library name: Sample 2
Stranded polyA-selected RNA-seq


title: Tonsil organoid, Day 21, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), B cell receptor (BCR) library

city: Irvine

first: Timothy

last: Yates

state: CA

address: 501 Aldrich Hall

institute: UC Irvine

description:
Library name: D21_BCR_lib_nonB_GFPplus_B
d21_gfp-pos-b_vdjB_filtered_contig_annotations.csv
d21_gfp-pos-b_vdjB_filtered_contig.fasta

data_processing:
Gene expression and feature barcode libraries were aligned and quantified using Cell Ranger multi (v8.0.1) against GRCh38 with EBV and GFP sequences included.
HTO feature barcode counts were normalized and used for sample demultiplexing with Seurat HTODemux.
BCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
TCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: gex_fb_barcodes.tsv.gz, gex_fb_features.tsv.gz, gex_fb_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: vdjB_filtered_contig_annotations.csv, vdjB_filtered_contig.fasta
Supplementary files format and content: Cellranger output files: vdjT_filtered_contig_annotations.csv, vdjT_filtered_contig.fasta
Library strategy: BCR-Seq

source_name: tonsil

growth_protocol: Human tonsil, spleen, and PBMC-derived organoids were generated from cryopreserved cells and cultured in RPMI-based media supplemented with BAFF.

extract_protocol:
Single-cell suspensions were prepared from ex vivo tissues and organoids by mechanical dissociation, filtering, and density gradient centrifugation.
Single-cell 5′ gene expression, feature barcode (HTO/CITE-seq), and V(D)J libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 5′ v2 platform.

treatment_protocol: Organoids were infected with GFP-expressing EBV (AKATA strain) at MOI 0.0005 and cultured up to 21 days with periodic media replacement.

value: tonsil

tag: sample group

tag: library type

value: BCR


title: Tonsil organoid, Day 21, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), T cell receptor (TCR) library

description:
Library name: D21_TCR_lib_nonB_GFPplusB
d21_gfp-pos-b_vdjT_filtered_contig_annotations.csv
d21_gfp-pos-b_vdjT_filtered_contig.fasta

data_processing:
Gene expression and feature barcode libraries were aligned and quantified using Cell Ranger multi (v8.0.1) against GRCh38 with EBV and GFP sequences included.
HTO feature barcode counts were normalized and used for sample demultiplexing with Seurat HTODemux.
BCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
TCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: gex_fb_barcodes.tsv.gz, gex_fb_features.tsv.gz, gex_fb_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: vdjB_filtered_contig_annotations.csv, vdjB_filtered_contig.fasta
Supplementary files format and content: Cellranger output files: vdjT_filtered_contig_annotations.csv, vdjT_filtered_contig.fasta
Library strategy: TCR-Seq

value: TCR


title: Tonsil organoid, Day 21, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), Gene Expression library

description:
Library name: D21_GEX_lib_nonB_GFPplus_B
d21_gfp-pos-b_gex_barcodes.tsv.gz
d21_gfp-pos-b_gex_features.tsv.gz
d21_gfp-pos-b_gex_matrix.mtx.gz

data_processing:
Gene expression and feature barcode libraries were aligned and quantified using Cell Ranger multi (v8.0.1) against GRCh38 with EBV and GFP sequences included.
HTO feature barcode counts were normalized and used for sample demultiplexing with Seurat HTODemux.
BCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
TCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: gex_fb_barcodes.tsv.gz, gex_fb_features.tsv.gz, gex_fb_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: vdjB_filtered_contig_annotations.csv, vdjB_filtered_contig.fasta
Supplementary files format and content: Cellranger output files: vdjT_filtered_contig_annotations.csv, vdjT_filtered_contig.fasta

value: mRNA


title: Tonsil organoid, Day 21, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), Feature Barcode library

description:
Library name: D21_FB_lib_nonB_GFPplus_B
d21_gfp-pos-b_gex_barcodes.tsv.gz
d21_gfp-pos-b_gex_features.tsv.gz
d21_gfp-pos-b_gex_matrix.mtx.gz

data_processing:
Gene expression and feature barcode libraries were aligned and quantified using Cell Ranger multi (v8.0.1) against GRCh38 with EBV and GFP sequences included.
HTO feature barcode counts were normalized and used for sample demultiplexing with Seurat HTODemux.
BCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
TCR V(D)J sequences were processed using cellranger multi with refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: gex_fb_barcodes.tsv.gz, gex_fb_features.tsv.gz, gex_fb_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: vdjB_filtered_contig_annotations.csv, vdjB_filtered_contig.fasta
Supplementary files format and content: Cellranger output files: vdjT_filtered_contig_annotations.csv, vdjT_filtered_contig.fasta
Library strategy: CITE-seq

value: ADT/HTO


title: Tonsil organoid, Day 21, uninfected B cells and GFP− B cells(EBV cultures), B cell receptor (BCR) library

description:
Library name: D21_BCR_lib_GFPminus_B
d21-gfp-neg-b_vdjB_filtered_contig_annotations.csv
d21-gfp-neg-b_vdjB_filtered_contig.fasta


title: Tonsil organoid, Day 21, uninfected B cells and GFP− B cells(EBV cultures), Feature Barcode library

description:
Library name: D21_FB_lib_GFPminus_B
d21-gfp-neg-b_gex_barcodes.tsv.gz
d21-gfp-neg-b_gex_features.tsv.gz
d21-gfp-neg-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 21, uninfected B cells and GFP− B cells(EBV cultures), Gene Expression library

description:
Library name: D21_GEX_lib_GFPminus_B
d21-gfp-neg-b_gex_barcodes.tsv.gz
d21-gfp-neg-b_gex_features.tsv.gz
d21-gfp-neg-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 14, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), T cell receptor (TCR) library

description:
Library name: D14_TCR_lib_nonB_GFPplusB
d14_gfp-pos-b_vdjT_filtered_contig_annotations.csv
d14_gfp-pos-b_vdjT_filtered_contig.fasta


title: Tonsil organoid, Day 14, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), B cell receptor (BCR) library

description:
Library name: D14_BCR_lib_nonB_GFPplus_B
d14_gfp-pos-b_vdjB_filtered_contig_annotations.csv
d14_gfp-pos-b_vdjB_filtered_contig.fasta


title: Tonsil organoid, Day 14, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), Gene Expression library

description:
Library name: D14_GEX_lib_nonB_GFPplus_B
d14_gfp-pos-b_gex_barcodes.tsv.gz
d14_gfp-pos-b_gex_features.tsv.gz
d14_gfp-pos-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 14, uninfected nonB cells and nonB/GFP+ B cells(EBV cultures), Feature Barcode library

description:
Library name: D14_FB_lib_nonB_GFPplus_B
d14_gfp-pos-b_gex_barcodes.tsv.gz
d14_gfp-pos-b_gex_features.tsv.gz
d14_gfp-pos-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 14, uninfected B cells and GFP− B cells(EBV cultures), B cell receptor (BCR) library

description:
Library name: D14_BCR_lib_GFPminus_B
d14-gfp-neg-b_vdjB_filtered_contig_annotations.csv
d14-gfp-neg-b_vdjB_filtered_contig.fasta


title: Tonsil organoid, Day 14, uninfected B cells and GFP− B cells(EBV cultures), Gene Expression library

description:
Library name: D14_GEX_lib_GFPminus_B
d14-gfp-neg-b_gex_barcodes.tsv.gz
d14-gfp-neg-b_gex_features.tsv.gz
d14-gfp-neg-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 7 uninfected/infected, T cell receptor (TCR) library

description:
Library name: D7_TCR_lib
d7_vdjT_filtered_contig_annotations.csv
d7_vdjT_filtered_contig.fasta


title: Tonsil organoid, Day 14, uninfected B cells and GFP− B cells(EBV cultures), Feature Barcode library

description:
Library name: D14_FB_lib_GFPminus_B
d14-gfp-neg-b_gex_barcodes.tsv.gz
d14-gfp-neg-b_gex_features.tsv.gz
d14-gfp-neg-b_gex_matrix.mtx.gz


title: Tonsil organoid, Day 7 uninfected/infected, B cell receptor (BCR) library

description:
Library name: D7_BCR_lib
d7_vdjB_filtered_contig_annotations.csv
d7_vdjB_filtered_contig.fasta


title: Tonsil organoid, Day 7 uninfected/infected, Gene Expression library

description:
Library name: D7_GEX_lib
d7_gex_barcodes.tsv.gz
d7_gex_features.tsv.gz
d7_gex_matrix.mtx.gz


title: Tonsil organoid, Day 7 uninfected/infected, Feature Barcode library

description:
Library name: D7_FB_lib
d7_gex_barcodes.tsv.gz
d7_gex_features.tsv.gz
d7_gex_matrix.mtx.gz


title: Tonsil organoid, Day 4 uninfected/infected, T cell receptor (TCR) library

description:
Library name: D4_TCR_lib
d4_vdjT_filtered_contig_annotations.csv
d4_vdjT_filtered_contig.fasta


title: Tonsil organoid, Day 4 uninfected/infected, B cell receptor (BCR) library

description:
Library name: D4_BCR_lib
d4_vdjB_filtered_contig_annotations.csv
d4_vdjB_filtered_contig.fasta


title: Tonsil organoid, Day 4 uninfected/infected, Gene Expression library

description:
Library name: D4_GEX_lib
d4_gex_barcodes.tsv.gz
d4_gex_features.tsv.gz
d4_gex_matrix.mtx.gz


title: Pat.6.3/Perit._GR1479 1:50

description: Library name: P6_G3

value: wild type


title: Tonsil organoid, Day 4 uninfected/infected, Feature Barcode library

description:
Library name: D4_FB_lib
d4_gex_barcodes.tsv.gz
d4_gex_features.tsv.gz
d4_gex_matrix.mtx.gz


title: Ex vivo tonsil, Day 0 unstim, T cell receptor (TCR) library

description:
Library name: D0_TCR_lib
d0_vdjT_filtered_contig_annotations.csv
d0_vdjT_filtered_contig.fasta

value: Ex vivo tonsil, Day 0 unstim


title: Ex vivo tonsil, Day 0 unstim, B cell receptor (BCR) library

description:
Library name: D0_BCR_lib
d0_vdjB_filtered_contig_annotations.csv
d0_vdjB_filtered_contig.fasta


title: Ex vivo tonsil, Day 0 unstim, Feature Barcode library

description:
Library name: D0_FB_lib
d0_gex_barcodes.tsv.gz
d0_gex_features.tsv.gz
d0_gex_matrix.mtx.gz


title: Ex vivo tonsil, Day 0 unstim, Gene Expression library

description:
Library name: D0_GEX_lib
d0_gex_barcodes.tsv.gz
d0_gex_features.tsv.gz
d0_gex_matrix.mtx.gz


title: Pat.5.3/Perit._MP 0.2mM

description: Library name: P5_M3

value: MP


title: Pat.6/Perit._GR1479 1:50

description: Library name: P6_G1

value: peritoneum


title: PANC1 PDAC cells treated for 12 hours with 3.3 mM Indisulam, replicate 3

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

description:
Library name: PANC1_IND3
Column name in raw_counts.txt IND_3

data_processing:
Raw pairend-ends reads fastq files were preprocessed with fastp v0.23.2 to remove lower quality bases and adapters.
Trimmed reads were mapped to hg38 using STAR v2.7.9a.
Statistics on strandness reads, genebody coverage, reads distribuition and insert size estimation were performed using RSeQC v.4.0.0 and picard CollectRnaSeqMetrics v.2.26.10.
The uniquely mapped reads from biological replicates were kept and counted with featureCounts v.2.0.3.
Differential gene expression on read counts matrix were performed using DESeq2 v.1.30.0
Alternative splicing analysis on bam files was performed using ASpli v .2.2.0 and CASTDb human database ver3.0.
Assembly: hg38 Gencode
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Pancreas; Duct

growth_protocol: PANC1 cells were cultured in RPMI 1640 medium (Euroclone). Media was supplemented with 10% fetal bovine serum (FBS; Gibco), non-essential amino acids (Thermo Fischer), penicillin and  streptomycin and gentamicin (Thermo Fischer). Cells were grown in a 37°C humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated and DNase digested using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared with Universal Plus mRNA-Seq with NuQuant (Tecan) following manufacturer's instructions and sequenced using a 150 bp paired-end format on an Illumina NovaSeq 6000.

treatment_protocol: Cells were treated for 6 hours with 3.3 nM Pladienolide B (Santa Cruz; sc-391691), for 8 hours with 500 nM Thailastatin A (MedChemExpress; HY-129589) or for 12 hours with 3.3 mM Indisulam (MedChemExpress; HY-13650)

value: Pancreas; Duct

value: human pancreatic ductal adenocarcinoma (PDAC)


title: PANC1 PDAC cells treated for 12 hours with 3.3 mM Indisulam, replicate 1

description:
Library name: PANC1_IND1
Column name in raw_counts.txt IND_1


title: PANC1 PDAC cells treated for 12 hours with 3.3 mM Indisulam, replicate 2

description:
Library name: PANC1_IND2
Column name in raw_counts.txt IND_2


title: PANC1 PDAC cells treated for 8 hours with 500 nM Thailastatin A, replicate 3

description:
Library name: PANC1_ThA3
Column name in raw_counts.txt ThA_3


title: PANC1 PDAC cells treated for 8 hours with 500 nM Thailastatin A, replicate 2

description:
Library name: PANC1_ThA2
Column name in raw_counts.txt ThA_2


title: PANC1 PDAC cells treated for 8 hours with 500 nM Thailastatin A, replicate 1

description:
Library name: PANC1_ThA1
Column name in raw_counts.txt ThA_1


title: Pat.5.3/Perit._Ko

description: Library name: P5_K3

value: primary cells

value: peritoneum mesothelial cells

value: ctl


title: ES2 cells control siRNA-2

description: Library name: ES2C12_31_2

value: ovarian

value: high-grade serous carcinoma


title: PANC1 PDAC cells treated for 6 hours with 3.3 nM Pladienolide B, replicate 3

description:
Library name: PANC1_PdB3
Column name in raw_counts.txt PdB_3

value: 6 hours with 3.3 nM Pladienolide B, replicate 1


title: PANC1 PDAC cells treated for 6 hours with 3.3 nM Pladienolide B, replicate 2

description:
Library name: PANC1_PdB2
Column name in raw_counts.txt PdB_2


title: PANC1 PDAC cells treated with DMSO, replicate 3

description:
Library name: PANC1_DMSO3
Column name in raw_counts.txt DMSO_3

value: DMSO, replicate 3


title: PANC1 PDAC cells treated for 6 hours with 3.3 nM Pladienolide B, replicate 1

description:
Library name: PANC1_PdB1
Column name in raw_counts.txt PdB_1


title: PANC1 PDAC cells treated with DMSO, replicate 1

description:
Library name: PANC1_DMSO1
Column name in raw_counts.txt DMSO_1

value: DMSO, replicate 1


title: Pat.5/Perit._MP 0.2mM

description: Library name: P5_M1


title: PANC1 PDAC cells treated with DMSO, replicate 2

description:
Library name: PANC1_DMSO2
Column name in raw_counts.txt DMSO_2

value: DMSO, replicate 2


title: RNA-seq_HepG2-NTCP-sg9-1

first: Kailong

institute: Peking University

description: Library name: HepG2-NTCP-sg9-1

data_processing:
Sequencing reads were first processed using cutadapt (vX.X) with the following parameters: adapter trimming with explicit Illumina adapter sequences provided for both forward (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and reverse (-A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT) reads, removal of reads containing more than 8 ambiguous bases (--max-n 8), minimum read length filter of 15 bp (--minimum-length 15), and paired-end consistency filtering (--pair-filter=any). Cleaned paired reads were written to output files with 50 parallel threads enabled. Subsequently, adapter-removed reads were subjected to an additional round of quality filtering using Trimmomatic (v0.39) in paired-end mode with the following settings: average read quality threshold of 20 (AVGQUAL:20), sliding window trimming with a window size of 4 and minimum average quality of 15 (SLIDINGWINDOW:4:15), and minimum read length requirement of 15 bp (MINLEN:15). This two-step filtering strategy ensured stringent removal of adapter contamination, low-quality bases, and excessively short or low-confidence reads prior to downstream analyses.
Processed reads were then aligned to human genome assembly hg19 using hisat2  in local alignment mode with default parameters.
Alignment files were processed using samtools (v1.15.1) for sorting and indexing.
The bigWig files were generated using deepTools bamCoverage (v3.5.1) with the following arguments: bin size of 1 bp.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were harvested and total RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
For RNA-seq analysis using the Illumina NovaSeq platform, 500 ng–1 μg of total RNA was processed for library construction

value: Hepatocellular carcinoma derived cell line engineered to express NTCP


title: RNA-seq_HepG2-NTCP-sg9-2

description: Library name: HepG2-NTCP-sg9-2


title: RNA-seq_HepG2-NTCP-sg1-1

description: Library name: HepG2-NTCP-sg1-1


title: RNA-seq_HepG2-NTCP-sg1-2

description: Library name: HepG2-NTCP-sg1-2


title: RNA-seq_HepG2-NTCP-sgNT-1

description: Library name: HepG2-NTCP-sgNT-1

value: sgNT


title: RNA-seq_HepG2-NTCP-sgNT-2

description: Library name: HepG2-NTCP-sgNT-2


title: RNA-seq_sgHBG1_2-1

description: Library name: sgHBG1_2-1

extract_protocol:
Cells were fiex with 1% formaldehyde for 10min\ at RT with shaking.After quenching and cell lysis chromatin was sonicated.
For RNA-seq analysis using the Illumina NovaSeq platform, 500 ng–1 μg of total RNA was processed for library construction

value: Human epithelial-like cell from the kidney


title: RNA-seq_Control-2

description: Library name: Control-2

value: Control


title: RNA-seq_Control-1

description: Library name: Control-1


title: hASCs, si-HDAC4, Osteogenic indution for 7 day

first: liyuan

last: yu

address: 639 Zhizaoju Road, Huangpu District, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: sample 2

data_processing:
Raw reads were processed with fastp (v0.20.0) to obtain clean reads (Q20/Q30/GC metrics calculated). Clean reads were aligned to a reference genome (downloaded from public databases) using BWA (v0.7.12) with MAPQ ≥13 filtering.
Peak calling was performed with MACS2 (v2.1.0) under parameters: q 0.05, f AUTO, call-summits, nomodel, shift 100, extsize 200, keep-dup all.
bigWig files were generated using the genomicRanges R package. Score represents the normalizeccoverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated usingMAcS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: OriCell adult adipose-derived mesenchymal stem cells (HUXMD-01003)

growth_protocol: The hASCs  are cultured in complete medium.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.
Libraries were purified with AMPure beads, quality-checked on an Agilent Bioanalyzer 2100, and sequenced by Novogene (Beijing) on an Illumina platform (TruSeq PE Cluster Kit), generating 150 bp raw reads.

treatment_protocol: The medium was replaced with OriCell™ human adipose-derived mesenchymal stem cell osteogenic differentiation medium (Cyagen, China).

value: HDAC4 Knockdown

value: si-HDAC4, Osteogenic indution for 7 day


title: hASCs, si-NC, Osteogenic indution for 7 day

description: Library name: sample 1

source_name: OriCell adult adipose-derived mesenchymal stem cells (HUXMD-01001)

value: control

value: si-NC, Osteogenic indution for 7 day


title: CAR_19_NOGITRL_1

city: Ribeirão Preto

first: Matheus

middle: Henrique

last: dos Santos

state: SP

address: R. Ten. Catão Roxo, 2501

department: Oncology

country: Brazil

institute: University of Sao Paulo

description:
Library name: LCS10338_CAR_19_NOGITRL_1_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_19_NOGITRL_1

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Assembly: Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Supplementary files format and content: xlsm file include FPKM value for each sample

growth_protocol: CAR-NK cells were cultivated in X-VIVO suplemented with 10% fetal bovine serum and 200U of IL-2/mL. NALM-6 cells were cultivated in RPMI 10% fetal bovine sereum. The cell were co-cultured in X-VIVO 10% FBS.

extract_protocol:
RNA was extracted using RNAeasy mini kit (QIAGEN)
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip

treatment_protocol: After co-culture, CAR-labelled NK cells were separeted from target cells using magnetic columns.

value: Lymphocyte

value: Lentivirally transduced

value: no-treatment


title: CAR_19_NOGITRL_2

description:
Library name: LCS10338_CAR_19_NOGITRL_2_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_19_NOGITRL_2


title: MCF7 cells,VI-10H,rep1

description: Library name: Sample 7

value: human breast cancer

value: WT


title: CAR_19_GITRL_2

description:
Library name: LCS10338_CAR_19_GITRL_2_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_19_GITRL_2


title: CAR_19_GITRL_1

description:
Library name: LCS10338_CAR_19_GITRL_1_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_19_GITRL_1


title: TCR-seq, P35, after RTX treatment

city: Nagoya City

first: Yu

last: Watanabe

state: Aichi Pref

address: 65, Tsurumai Town, Showa Ward

department: Molecular Oncology

institute: Nagoya University

description: Library name: P35_Post_TCR

data_processing:
Droplet-based sequencing data were aligned and quantified using Cell Ranger 8.0.0(10x Genomics).
Assembly: Homo Sapiens, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
Frozen PBMC samples were thawed rapidly in trypsin-stopping solution (D-MEM Low Glucose, 10% FBS, and 1% penicillin/streptomycin) at 37°C, centrifuged at 400g for 10 minutes at 4°C and the supernatant was discarded. To release cell aggregation, 25 μL of DNase Booster Buffer and 10 μL of DNase I stock solution (#79254, QIAGEN) were added to the pellet and incubated at room temperature for 15 minutes. The samples were washed with trypsin-stopping solution and diluted with PBS. To isolate CD3+ T cells, PBMCs collected at both pre and post were stained and sorted at 4°C using pooled monoclonal antibodies and sorted using FACSAria Fusion flow cytometer (BD Biosciences).
Single-cell 5’ and TCR libraries were prepared following the protocol provided by the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index).

value: PBMC

value: CD3+ T-cells

value: after RTX treatment


title: scRNA-seq, P35, after RTX treatment

description: Library name: P35_Post_GEX

data_processing:
Droplet-based sequencing data were aligned and quantified using Cell Ranger 8.0.0(10x Genomics).
Assembly: Homo Sapiens, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files


title: TCR-seq, P35, before RTX treatment

description: Library name: P35_Pre_TCR

value: before RTX treatment


title: scRNA-seq, P35, before RTX treatment

description: Library name: P35_Pre_GEX


title: TCR-seq, P29, after RTX treatment

description: Library name: P29_Post_TCR


title: scRNA-seq, P29, after RTX treatment

description: Library name: P29_Post_GEX


title: TCR-seq, P29, before RTX treatment

description: Library name: P29_Pre_TCR


title: scRNA-seq, P18, after RTX treatment

description: Library name: P18_Post_GEX


title: scRNA-seq, P18, before RTX treatment

description: Library name: P18_Pre_GEX


title: TCR-seq, P15, before RTX treatment

description: Library name: P15_Pre_TCR


title: TCR-seq, P04, after RTX treatment

description: Library name: P04_Post_TCR


title: scRNA-seq, P15, before RTX treatment

description: Library name: P15_Pre_GEX


title: scRNA-seq, P04, before RTX treatment

description: Library name: P04_Pre_GEX


title: TCR-seq, P04, before RTX treatment

description: Library name: P04_Pre_TCR


title: TCR-seq, P01, after RTX treatment

description: Library name: P01_Post_TCR


title: TCR-seq, P01, before RTX treatment

description: Library name: P01_Pre_TCR


title: scRNA-seq, P01, before RTX treatment

description: Library name: P01_Pre_GEX


title: ChIP-seq_sgHBG1_2

description: Library name: sgHBG1_2

data_processing:
Sequencing reads were processed using fastp (v0.23.2) with the following parameters: adapter auto-detection for paired-end reads, quality trimming (5' and 3' ends with window size 4 and mean quality 20), right-side trimming (window size 4, mean quality 20), quality filtering (Q15 threshold), unqualified percent limit (40%), base correction for overlapping regions, and length filter (30 bp).
Processed reads were then aligned to human genome assembly hg38 using Bowtie2 (v2.4.5) in local alignment mode with default parameters.
Alignment files were processed using samtools (v1.15.1) for sorting and indexing, followed by read group addition and duplicate marking using Picard tools (v3.0.0).
The bigWig files were generated using deepTools bamCoverage (v3.5.1) with the following arguments: bin size of 1 bp.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were fiex with 1% formaldehyde for 10min\ at RT with shaking.After quenching and cell lysis chromatin was sonicated.
For ChIP-seq analysis using the Illumina NovaSeq, 10-20 ng of ChIP DNA was processed for library generation using the TransNGS DNA Library Prep Kit according to the manufacturer's protocol(TransGen). Raw reads that aligned to exactly one location in the reference human genome (hg38) were retained for downstream data analysis.


title: ChIP-seq_Control

description: Library name: Control


title: MV4-11-ENO1-02

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description:
Library name: Sample 2
CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS2 (v2.0.10)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: AML cell line

tag: antibody

value: ENO1 (ABclonal,# A1033)


title: MV4-11_sh-ENO1-3

description:
Library name: Sample 6
MV4-11 sample with ENO1 knockdown

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ENO1 knockdown


title: MV4-11-ENO1-01

description:
Library name: Sample 1
CUT&Tag DNA


title: MV4-11_sh-ENO1-1

description:
Library name: Sample 4
MV4-11 sample with ENO1 knockdown


title: MV4-11_NC-3

description:
Library name: Sample 3
MV4-11 sample with no treatment


title: MV4-11_NC-2

description:
Library name: Sample 2
MV4-11 sample with no treatment


title: N206_dCeMM2_IC50_rep3

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description:
Library name: RNA019385
all_raw_counts_dCeMM2_Drugging.txt

data_processing:
Reads were quality checked with FastQC (v0.11.7) and aligned to the Homo sapiens reference genome (GRCh38.96) using STAR (v2.7.2b).
Post-alignment, read counts were generated and normalized with edgeR (v3.36.0).
After performing PCA plotting, certain replicates were removed from the analysis as they did not cluster with the other replicates, indicating potential outliers or inconsistencies.
Differential expression analysis was performed using the Limma-Voom pipeline (v3.50.3) with three or four replicates per condition.
Assembly: Homo sapiens GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts per experiment

source_name: neuroblastoma cell line

extract_protocol:
RNA was isolated as described in the ‘RNA isolation and RT-qPCR’ section. RNA quality was measured using the Fragment analyzer 12 capillary array prior to profiling
A total of 55ng of RNA was used as input for the library preparation with the Illumina Stranded mRNA prep (#20040534). During the library preparation 15 PCR cycles were used. qPCR quantification of the libraries was done using the Kapa Library Quantification Kit for the Illumina LightCycler 480 (Roche diagnostics #07960298001).

value: neuroblastoma cell line

value: neuroblast

value: GI50 dCeMM2


title: N206_dCeMM2_DMSO_rep3

description:
Library name: RNA019384
all_raw_counts_dCeMM2_Drugging.txt

value: DMSO in dCeMM2 experiment


title: SY5Y_dCeMM2_IC50_rep3

description:
Library name: RNA019383
all_raw_counts_dCeMM2_Drugging.txt

source_name: bone marrow

value: bone marrow


title: SY5Y_dCeMM2_DMSO_rep3

description:
Library name: RNA019382
all_raw_counts_dCeMM2_Drugging.txt


title: N206_dCeMM2_DMSO_rep2

description:
Library name: RNA019349
all_raw_counts_dCeMM2_Drugging.txt


title: SY5Y_dCeMM2_DMSO_rep2

description:
Library name: RNA019347
all_raw_counts_dCeMM2_Drugging.txt


title: N206_dCeMM2_IC50_rep1

description:
Library name: RNA019257
all_raw_counts_dCeMM2_Drugging.txt


title: N206_dCeMM2_DMSO_rep1

description:
Library name: RNA019256
all_raw_counts_dCeMM2_Drugging.txt


title: SY5Y_dCeMM2_IC50_rep1

description:
Library name: RNA019255
all_raw_counts_dCeMM2_Drugging.txt


title: SY5Y_dCeMM2_DMSO_rep1

description:
Library name: RNA019254
all_raw_counts_dCeMM2_Drugging.txt


title: N206_SR4835_rep3

description:
Library name: RNA019393
N206_SR4835_rep3

extract_protocol:
RNA was isolated as described in the ‘RNA isolation and RT-qPCR’ section. RNA quality was measured using the Fragment analyzer 12 capillary array prior to profiling
A total of 55ng of RNA was used as input for the library preparation with the Illumina Stranded mRNA prep (#20040534). During the library preparation 15 PCR cycles were used. qPCR quantification of the libraries was done using the Kapa Library Quantification Kit for the Illumina LightCycler 480 (Roche diagnostics #07960298001).
RNA-Seq libraries were sequenced on the Illumina NextSeq 2000 platform using the NextSeq 2000 P2 Reagents 100 Cycles single-end kit (Illumina #20100987).


title: N206_SR4835_DMSO_rep3

description:
Library name: RNA019392
N206_SR4835_DMSO_rep3

value: DMSO in SR-4835 experiment


title: SH-SY5Y_SR4835_rep3

description:
Library name: RNA019391
SH_SY5Y_SR4835_rep3


title: N206_SR4835_rep2

description:
Library name: RNA019358
N206_SR4835_rep2


title: SH-SY5Y_SR4835_rep2

description:
Library name: RNA019356
SH_SY5Y_SR4835_rep2


title: SH-SY5Y_SR4835_DMSO_rep2

description:
Library name: RNA019355
SH-SY5Y_SR4835_DMSO_rep2


title: N206_SR4835_rep1

description:
Library name: RNA019265
N206_SR4835_rep1