title: MDA-MB-231 siJag1 cells, 3D Matrigel culture, biol rep 3

city: Turku

first: Marjaana

last: Parikainen

address: Tykistökatu 6

country: Finland

institute: Åbo Akademi University

description: Library name: siJag1_C

data_processing:
Sequencing read quality was checked using FastQ (v.0.11.14) and MultiQC(v.1.5)
Reads were aligned against the human reference genome hg38 using R(v.3.6.1) /Bioconductor(v.3.9) ::Rsubread(v.2.0.0) ::align
Uniquely mapped reads were used to generate gene-wise read counts using R(v.3.6.1) /Bioconductor(v.3.9) ::Rsubread(v.2.0.0) ::featureCount
The TMM normalization was used to normalize the filtered gene counts between the samples using R(v.3.6.1) /Bioconductor(v.3.9) ::edgeR(v.3.28.0) ::calcNormFactors.
Assembly: hg38
Supplementary files format and content: csv file containing raw counts for each sample
Supplementary files format and content: csv file containing CPM values for each sample
Supplementary files format and content: csv file containing RPKM values for each sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM high glucose supplemented with 10 % fetal bovine serum (FBS), 2 mM glutamine, penicillin (100 units/mL), and streptomycin (100 µg/mL) in humidified athmosphere with 5 % CO2 at 37C

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (MACHEREY-NAGEL #740955). 300 ng of total RNA was used for the construction of the sequencing libraries.
The sequencing libraries were prepared using Illumina TruSeq Stranded mRNA HT Sample Preparation kit according to manufacturer's instructions.

treatment_protocol: Cell culture plates were first coated with a thin layer of 4 mg/mL Matrigel (Corning #356231). 50 000 cells were seeded in 600 µL of 2 mg/mL Matrigel on a 6-well plate well. siRNA transfections were performed 7 hours prior to cell seeding. Matrigel was allowed to solidify o/n, after which pre-warmed cell culture medium was added on top of the 3D cultures. Spheroids were allowed to grow for 7 days. Fresh medium was changed once on day 4. Spheroids were extracted from Matrigel for further analysis with 5 mM EDTA in PBS. Briefly, 3D cultures were washed three times with ice-cold PBS before adding ice-cold EDTA/PBS and transferring the cultures to falcon tubes on ice. Matrigel was allowed to dissolve for 15 min before collecting the spheroids by centrifugation.

value: breast cancer cells

value: JAG1 knockdown

value: 3D Matrigel culture

value: Day 7


title: MDA-MB-231 siJag1 cells, 3D Matrigel culture, biol rep 1

status: Public on Feb 09 2026

type: SRA

description: Library name: siJag1_A

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time


title: 8077, plasma sample, pegIFNβ-1a, 0.33days

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

country: USA

institute: U.S. FDA

description: Library name: F14850524

library_source: other

data_processing:
CLC Genomics Workbench v21.0.1
Samples were processed using Toolbox "Ready to use workflow" for "Small RNA sequencing" and "Qiaseq miRNAquantification"
Sequence reads were trimmed for adapters and size, UMI reads are generated from grouping greads with the same or similar UMI and similar sequence.
Mature miRNA reads are considered as expression counts.
Raw data was normalized using Deseq2 R package
Assembly: mirBase v22
Supplementary files format and content: csv file includes raw counts for each sample

molecule: other

source_name: plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol:
EDTA plasma from whole blood. RNA was extracted using miRNeasy® Serum/Plasma Kit (Cat. 217184, Qiagen LLC).
Library preparations were carried out using the QIAseq miRNA Library Kit [96] (# 331505) together with QIAseq miRNA [96] Index IL (#331565), and an automated liquid handling method developed for preparation of 96 cDNA using the Biomek i7 Automated Liquid Handler (Beckman).

treatment_protocol: Subjects were randomized between IFNβ-1a, pegIFNβ-1a and placebo groups

tag: tissue

value: plasma

tag: disease state

value: Healthy


title: 8077, plasma sample, pegIFNβ-1a, 4days

description: Library name: F14851063


title: MDA-MB-231 siCtrl cells, 3D Matrigel culture, biol rep 2

description: Library name: siCtrl_B

value: WT


title: MDA-MB-231 siJag1 cells, 3D Matrigel culture, biol rep 2

description: Library name: siJag1_B


title: 8077, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F14850605


title: 8077, plasma sample, pegIFNβ-1a, 2days

description: Library name: F14850817


title: 8077, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F14850508


title: 8077, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F14850306


title: 8077, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F14850430


title: MDA-MB-231 siCtrl cells, 3D Matrigel culture, biol rep 3

description: Library name: siCtrl_C


title: MDA-MB-231 Jag1KO+ctrl cells, 3D Matrigel culture, biol rep 1

description: Library name: VectorCtrl_A

value: JAG1 knockout transfected with empty vector plasmid


title: MDA-MB-231 Jag1KO+rescue cells, 3D Matrigel culture, biol rep 3

description: Library name: Jag1rescue_C

value: JAG1 knockout transfected with JAG1-containing plasmid (rescued expression of JAG1)


title: 8073, plasma sample, IFNβ-1a, 6days

description: Library name: F14843118


title: MDA-MB-231 siCtrl cells, 3D Matrigel culture, biol rep 1

description: Library name: siCtrl_A


title: 8073, plasma sample, IFNβ-1a, 5days

description: Library name: F14842943


title: 8073, plasma sample, IFNβ-1a, 4days

description: Library name: F14842828


title: MDA-MB-231 Jag1KO+ctrl cells, 3D Matrigel culture, biol rep 2

description: Library name: VectorCtrl_B


title: MDA-MB-231 Jag1KO+ctrl cells, 3D Matrigel culture, biol rep 3

description: Library name: VectorCtrl_C


title: MDA-MB-231 Jag1KO cells, 3D Matrigel culture, biol rep 3

description: Library name: Jag1KO_C

value: JAG1 knockout


title: 8073, plasma sample, IFNβ-1a, 1.33days

description: Library name: F14842520


title: MDA-MB-231 Jag1KO+rescue cells, 3D Matrigel culture, biol rep 2

description: Library name: Jag1rescue_B


title: 8073, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14842289


title: MDA-MB-231 Jag1KO+rescue cells, 3D Matrigel culture, biol rep 1

description: Library name: Jag1rescue_A


title: MDA-MB-231 Jag1KO cells, 3D Matrigel culture, biol rep 1

description: Library name: Jag1KO_A


title: 8073, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14842273


title: 8073, plasma sample, IFNβ-1a, 2days

description: Library name: F14842582


title: 8073, plasma sample, IFNβ-1a, Baseline

description: Library name: F14842071


title: 8073, plasma sample, IFNβ-1a, 0.67days

description: Library name: F14842370


title: MDA-MB-231 Jag1KO cells, 3D Matrigel culture, biol rep 2

description: Library name: Jag1KO_B


title: 8072, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F14841789


title: MDA-MB-231 WT cells, 3D Matrigel culture,  biol rep 1

description: Library name: WT_A


title: 8072, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F14841517


title: MDA-MB-231 WT cells, 3D Matrigel culture, biol rep 2

description: Library name: WT_B


title: MDA-MB-231 WT cells, 3D Matrigel culture, biol rep 3

description: Library name: WT_C


title: TIGK infected with coculture (XH001+TM7x), biological replicate 2

city: Seattle

first: Jeffrey

middle: S

last: McLean

state: WA

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

description: Library name: 1906_2

data_processing:
Geneious 2024.0.7
Geneious 2024.0.7 RNA mapping tool was used with default paramaters which included a trimming step (parameter error probibility quality limit 0.05)
trimmed read were mapped to Homo_sapiens.GRCh38.dna_rm.primary_assembly using Geneious 2024.0.7 RNA mapping using default parameters
read count extraction was performed in Geneious 2024.0.7
Assembly: Homo_sapiens.GRCh38.dna_rm.primary_assembly
Supplementary files format and content: csv file incles raw counts for each sample

source_name: TIGK CRL-3397

growth_protocol: Human keratinocytes cells (TIGK) was grown in keratinocyte serum-free medium, supplemented with 0.4 mM calcium chloride, 25 mg/mL bovine pituitary extract (BPE), 0.2 ng/mL epidermal growth factor (EGF), and a PSG antibiotic cocktail (Penicillin-Streptomycin-Glutamine). Cells were incubated at 37°C in 5% CO₂.

extract_protocol:
RNA was harvested using total RNA mini prep kit (NEB-NEB#T2110). A total of 500ng RNA was used to construct sequencing library.
RNA library for RNA seq was prepared using Zymo-Seq RiboFree, Total RNA Library Kit (R3000, Zymo Research, Irvine, CA) following manufracturer's protocol.

treatment_protocol: Confluent TIGK cells were treated with bacteria (XH001, TM7x and coculture) for 8 hours.

value: TIGK CRL-3397

value: Gingival epithelial cells

value: Bacteria coculture

value: 8 h


title: 8072, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F14841070


title: 8072, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F14840778


title: TIGK infected with coculture (XH001+TM7x), biological replicate 3

description: Library name: 1906_3


title: 8072, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F14840532


title: 8072, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F14840470


title: TIGK infected with TM7x, biological replicate 1

description: Library name: TM7x_1

value: Bacteria TM7x


title: 8072, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F14840893


title: TIGK infected with coculture (XH001+TM7x), biological replicate 1

description: Library name: 1906_1


title: 8073, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14842195


title: TIGK infected with TM7x, biological replicate 3

description: Library name: TM7x_3


title: TIGK infected with TM7x, biological replicate 2

description: Library name: TM7x_2


title: TIGK non infected sample, biological replicate 2

description: Library name: Ctrl_2

value: No treatment


title: TIGK non infected sample, biological replicate 1

description: Library name: Ctrl_1


title: 8072, plasma sample, IFNβ-1a_placebo, 0.33days

description: Library name: F14840239


title: 8070, plasma sample, pegIFNβ-1a, 13days

description: Library name: F14837689


title: TIGK non infected sample, biological replicate 3

description: Library name: Ctrl_3


title: 8072, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F14840223


title: 8070, plasma sample, pegIFNβ-1a, 9days

description: Library name: F14837417


title: 8072, plasma sample, IFNβ-1a_placebo, 0.67days

description: Library name: F14840320


title: TIGK infected with XH001, biological replicate 3

description: Library name: XH001_3

value: Bacteria XH001


title: 8072, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F14840145


title: CUT&RUN in MCF-7 cells for CTCF after control GapmeR uptake, replicate 3

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

description: Library name: CUT_RUN_MCF7_CTCF_NT_3

library_source: genomic

data_processing:
RNA-seq: RNA-seq reads were mapped to the human genome (hg19 or hg38 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples.
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
SLAM-seq: estimation of half-lives and synthesis rates was performed using GRAND-SLAM/grandR (Jürges et al., 2018).
Assembly: hg19 and hg38
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, MACS2/epic2-called peaks are provided for the CUT&RUN data, and GRAND-SLAM kinetics parameters are provided for the SLAM-seq data.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid, siRNAs (final concentration 25 µM) and GapmeRs (50 µM) transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA/siRNAs/GapmeRs concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.

extract_protocol:
Metabolic labeling and SLAM-seq were then performed as previously described (Herzog et al., 2017; Zuckerman et al., 2020), with minor modifications. All steps were performed in the dark until the chemical conversion with iodoacetamide (IAA). After 48h hours, the growth medium was replaced with fresh media supplemented with 500 µM 4-Thiouridine (4sU, Sigma), and replaced again with fresh 4sU after every time point. In total, we collected RNA from cells at time 0 (unlabeled), and after 4, 8 and 24h hours post-4sU addition. RNA extraction was carried out as described above with the addition of DTT (0.1 mM final concentration) to keep the samples under reducing conditions, and IAA conversion was performed as described previously (Zuckerman et al., 2020).
UMI-4C was performed as previously described (Schwartzman et al., 2016)
CUT&RUN reactions were performed as previously described (Meers et al., 2019).
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. SLAM-seq libraries were prepared using the NEBNext Ultra II Directional Library Kit (NEB), according to the manufacturer's protocol. SLAM-seq libraries were generated as described before (Schwartzman et al., 2016). CUT&RUN libraries were prepared as described previously (Meers et al., 2019).

value: MCF-7 cells

tag: cut&run antibody

value: untreated


title: CUT&RUN in MCF-7 cells for CTCF after EPB41L4A-AS1 GapmeR uptake, replicate 1

description: Library name: CUT_RUN_MCF7_CTCF_EPB41L4A-AS1_KD_1


title: CUT&RUN in MCF-7 cells for CTCF after EPB41L4A-AS1 GapmeR uptake, replicate 2

description: Library name: CUT_RUN_MCF7_CTCF_EPB41L4A-AS1_KD_2


title: TIGK infected with XH001, biological replicate 2

description: Library name: XH001_2


title: 8070, plasma sample, pegIFNβ-1a, 5days

description: Library name: F14836793


title: 8072, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F14840021


title: 8070, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F14836220


title: 8070, plasma sample, pegIFNβ-1a, 6days

description: Library name: F14836970


title: 8070, plasma sample, pegIFNβ-1a, 4days

description: Library name: F14836678


title: 8070, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F14836370


title: TIGK infected with XH001, biological replicate 1

description: Library name: XH001_1


title: CUT&RUN in MCF-7 cells for CTCF after EPB41L4A-AS1 GapmeR uptake, replicate 3

description: Library name: CUT_RUN_MCF7_CTCF_EPB41L4A-AS1_KD_3


title: 8070, plasma sample, pegIFNβ-1a, 2days

description: Library name: F14836432


title: CUT&RUN in MCF-7 cells for CTCF after control GapmeR uptake, replicate 2

description: Library name: CUT_RUN_MCF7_CTCF_NT_2


title: CUT&RUN in MCF-7 cells for SUB1, replicate 2

description: Library name: CUT_RUN_MCF7_SUB1_2

value: SUB1/PC4 (Bethyl Laboratories, A301-161A)


title: CUT&RUN in MCF-7 cells for CTCF after control GapmeR uptake, replicate 1

description: Library name: CUT_RUN_MCF7_CTCF_NT_1


title: CUT&RUN in MCF-7 cells for SUB1, replicate 3

description: Library name: CUT_RUN_MCF7_SUB1_3


title: UMI-4C in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, replicate 2

description: Library name: UMI4C_MCF7_EPB41L4A-AS1_LNA2_2

data_processing:
RNA-seq: RNA-seq reads were mapped to the human genome (hg19 or hg38 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples.
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
SLAM-seq: estimation of half-lives and synthesis rates was performed using GRAND-SLAM/grandR (Jürges et al., 2018).
Assembly: hg19 and hg38
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, MACS2/epic2-called peaks are provided for the CUT&RUN data, and GRAND-SLAM kinetics parameters are provided for the SLAM-seq data.
Library strategy: 4C-Seq

tag: umi4c baits

value: EPB41L4A-AS1, EPB41L4A, STARD4


title: 8070, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F14836139

value: plasma


title: CUT&RUN in MCF-7 cells for SUB1, replicate 1

description: Library name: CUT_RUN_MCF7_SUB1_1


title: 8070, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F14835921

value: Healthy


title: 8070, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F14836045


title: UMI-4C in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, replicate 2

description: Library name: UMI4C_MCF7_EPB41L4A-AS1_LNA1_2


title: 8070, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F14836123


title: UMI-4C in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, replicate 1

description: Library name: UMI4C_MCF7_EPB41L4A-AS1_LNA2_1


title: 8069, plasma sample, IFNβ-1a, 2days

description: Library name: F14834382


title: UMI-4C in MCF-7 cells after control GapmeR uptake, replicate 1

description: Library name: UMI4C_MCF7_NT_1


title: UMI-4C in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, replicate 1

description: Library name: UMI4C_MCF7_EPB41L4A-AS1_LNA1_1


title: 8069, plasma sample, IFNβ-1a, 4days

description: Library name: F14834628


title: UMI-4C in MCF-7 cells after control GapmeR uptake, replicate 2

description: Library name: UMI4C_MCF7_NT_2


title: Ribodepleted RNA-seq in MCF-7 cells after GAS5 GapmeR uptake, replicate 3

description: Library name: RNA_MCF7_GAS5_KD_ribominus_3

data_processing:
RNA-seq: RNA-seq reads were mapped to the human genome (hg19 or hg38 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples.
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
SLAM-seq: estimation of half-lives and synthesis rates was performed using GRAND-SLAM/grandR (Jürges et al., 2018).
Assembly: hg19 and hg38
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, MACS2/epic2-called peaks are provided for the CUT&RUN data, and GRAND-SLAM kinetics parameters are provided for the SLAM-seq data.


title: 8069, plasma sample, IFNβ-1a, 5days

description: Library name: F14834743


title: 8069, plasma sample, IFNβ-1a, 0.67days

description: Library name: F14834170


title: 8069, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14834089


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (GAS5 control), replicate 3

description: Library name: RNA_MCF7_GAS5_control_ribominus_3


title: 8069, plasma sample, IFNβ-1a, Baseline

description: Library name: F14833871


title: 8069, plasma sample, IFNβ-1a, 6days

description: Library name: F14834918


title: 8069, plasma sample, IFNβ-1a, 1.33days

description: Library name: F14834320


title: 8069, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14833995


title: 8067, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F14446748

value: pegIFNβ-1a _placebo


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (GAS5 control), replicate 1

description: Library name: RNA_MCF7_GAS5_control_ribominus_1


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with siRNAs against SUB1, replicate 3

description: Library name: RNA_MCF7_siSUB1_3


title: 8069, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14834073


title: 8067, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F14445852


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with control siRNAs, replicate 3

description: Library name: RNA_MCF7_siNT_3


title: Ribodepleted RNA-seq in MCF-7 cells after GAS5 GapmeR uptake, replicate 1

description: Library name: RNA_MCF7_GAS5_KD_ribominus_1


title: 8067, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F14446476


title: Ribodepleted RNA-seq in MCF-7 cells after GAS5 GapmeR uptake, replicate 2

description: Library name: RNA_MCF7_GAS5_KD_ribominus_2


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (GAS5 control), replicate 2

description: Library name: RNA_MCF7_GAS5_control_ribominus_2


title: 8067, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F14446029


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with siRNAs against SUB1, replicate 2

description: Library name: RNA_MCF7_siSUB1_2


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with control siRNAs, replicate 2

description: Library name: RNA_MCF7_siNT_2


title: 8067, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F14445737


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with siRNAs against SUB1, replicate 1

description: Library name: RNA_MCF7_siSUB1_1


title: 8067, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F14445491


title: Ribodepleted RNA-seq in MCF-7 cells after transfection with control siRNAs, replicate 1

description: Library name: RNA_MCF7_siNT_1


title: 8067, plasma sample, pegIFNβ-1a _placebo, 1.33days

description: Library name: F14445429


title: 8067, plasma sample, pegIFNβ-1a _placebo, 0.33days

description: Library name: F14445198


title: PolyA+ RNA-seq in MCF-7 cells, SUB1 RIP, sample 2

description: Library name: RNA_MCF7_SUB1_RIP_2

molecule: polyA RNA

tag: rip antibody


title: 8067, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F14445182


title: PolyA+ RNA-seq in MCF-7 cells, SUB1 RIP, sample 1

description: Library name: RNA_MCF7_SUB1_RIP_1


title: PolyA+ RNA-seq in MCF-7 cells, Input, sample 1

description: Library name: RNA_MCF7_Input_RIP_1


title: 8067, plasma sample, pegIFNβ-1a _placebo, 0.125days

description: Library name: F14445104


title: 8067, plasma sample, pegIFNβ-1a _placebo, 0.67days

description: Library name: F14445279


title: 8067, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F14444980


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 2

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_ribominus_2


title: 8066, plasma sample, pegIFNβ-1a, 13days

description: Library name: F14444698


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 1

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_ribominus_1


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (EPB41L4A-AS1 control), replicate 3

description: Library name: RNA_MCF7_EPB41L4A-AS1_control_ribominus_3


title: 8066, plasma sample, pegIFNβ-1a, 6days

description: Library name: F14443979


title: 8066, plasma sample, pegIFNβ-1a, 9days

description: Library name: F14444426


title: PolyA+ RNA-seq in MCF-7 cells, Input, sample 2

description: Library name: RNA_MCF7_Input_RIP_2


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (EPB41L4A-AS1 control), replicate 1

description: Library name: RNA_MCF7_EPB41L4A-AS1_control_ribominus_1


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 3

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_ribominus_3


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake (EPB41L4A-AS1 control), replicate 2

description: Library name: RNA_MCF7_EPB41L4A-AS1_control_ribominus_2


title: 8066, plasma sample, pegIFNβ-1a, 4days

description: Library name: F14443687


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 3

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_polyA_3


title: 8066, plasma sample, pegIFNβ-1a, 5days

description: Library name: F14443802


title: 8066, plasma sample, pegIFNβ-1a, 2days

description: Library name: F14443441


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 1

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_polyA_1


title: 8066, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F14443379


title: 8066, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F14443229


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A GapmeR uptake, replicate 3

description: Library name: RNA_MCF7_EPB41L4A_KD_polyA_3


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A GapmeR uptake, replicate 1

description: Library name: RNA_MCF7_EPB41L4A_KD_polyA_1


title: 8066, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F14443132


title: 8066, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F14443054


title: PolyA+ RNA-seq in MCF-7 cells after control GapmeR uptake, replicate 3

description: Library name: RNA_MCF7_NT_polyA_3


title: 8066, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F14442930


title: PolyA+ RNA-seq in MCF-7 cells after control GapmeR uptake, replicate 1

description: Library name: RNA_MCF7_NT_polyA_1


title: siMETTL3 JURKAT (6h) rep1-resequenced

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

country: China

institute: Peking University

description:
Library name: JURKAT-K61-resequenced
JKKD6h-1

data_processing:
The quality control, adapter cutting and low quality sequence removal were performed by FastQC, fastp and FASTX toolkits.
The clean reads were mapped to human genome (hg38) by HISAT2 software (v2.2.1) and the expression values were calculated by featureCounts command with suggested parameter of the software.
The mRNA half-life was estimated following the method modified from (Wang et al., Nature, 2014, 505: s117–120).
The alternative splicing events were analyzed by rMATS turbo software (v4.1.0, default parameter), focusing on exon skipping and intron retention events.
Assembly: hg38
Supplementary files format and content:
Matrix table with raw gene counts for every gene and every sample
*exonskipping.txt: detected exon skipping event
*intronretention.txt: detected intron retention event
*estimatedhalflife.txt: estimated transcript half-life

source_name: JURKAT

growth_protocol: HEK293T and A549 cells were maintained in high-glucose Dulbecco's modified Eagle's medium (DMEM, Gibco, Cat# C11995500BT) supplemented with 10% fetal bovine serum (FBS, Gemini, Cat# 900-108). JURKAT cells were cultured in RPMI 1640 medium (Gibco, Cat# C22400500BT). H9 cells were maintained in TeSR-E8 Kit for hESC/hiPSC Maintenance (StemCell, Cat# 05990). HUVEC cells were cultured in ECM (HARVEYBIO, Cat# 1001).

extract_protocol:
Cells from each group and time points were collected and total RNA was harvested with Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7770)and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7760) were used with 400 ng of total RNA for the construction of sequencing libraries.
ERCC spike-in were added to total RNA before library construction, following the protocol recommended by ERCC spike-in kit manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: shRNA targeting sequences against METTL3 and control were designed, synthesized and subcloned into the GV307 vector. Then lentivirus was made by co-transfection of every GV307 shRNA vector with pHelper 1.0 and pHelper 2.0 in a 5:3:2 ratio into HEK293T cells. And each cell line was infected with siControl and siMETTL3 concentrated lentivirus supernatant.

value: JURKAT

value: siMETTL3 JURKAT (6h)


title: 8064, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F14440320


title: siMETTL3 JURKAT (3h) rep2-resequenced

description:
Library name: JURKAT-K32-resequenced
JKKD3h-2

value: siMETTL3 JURKAT (3h)


title: siMETTL3 JURKAT (3h) rep1-resequenced

description:
Library name: JURKAT-K31-resequenced
JKKD3h-1


title: siMETTL3 JURKAT (6h) rep2-resequenced

description:
Library name: JURKAT-K62-resequenced
JKKD6h-2


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A GapmeR uptake, replicate 2

description: Library name: RNA_MCF7_EPB41L4A_KD_polyA_2


title: 8064, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F14439873


title: 8064, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F14439335


title: 8066, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F14443148


title: 8064, plasma sample, pegIFNβ-1a _placebo, 0.67days

description: Library name: F14439123


title: 8064, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F14440592


title: 8064, plasma sample, pegIFNβ-1a _placebo, 1.33days

description: Library name: F14439273


title: 8064, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F14439696


title: siMETTL3 JURKAT (1h) rep2-resequenced

description:
Library name: JURKAT-K12-resequenced
JKKD1h-2

value: siMETTL3 JURKAT (1h)


title: PolyA+ RNA-seq in MCF-7 cells after control GapmeR uptake, replicate 2

description: Library name: RNA_MCF7_NT_polyA_2


title: siControl JURKAT (6h) rep1-resequenced

description:
Library name: JURKAT-C61-resequenced
JKCTL6h-1

value: siControl JURKAT (6h)


title: PolyA+ RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR uptake, replicate 2

description: Library name: RNA_MCF7_EPB41L4A-AS1_KD_polyA_2


title: siMETTL3 JURKAT (1h) rep1-resequenced

description:
Library name: JURKAT-K11-resequenced
JKKD1h-1


title: 8064, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F14439581


title: siControl JURKAT (3h) rep2-resequenced

description:
Library name: JURKAT-C32-resequenced
JKCTL3h-2

value: siControl JURKAT (3h)


title: siControl JURKAT (6h) rep2-resequenced

description:
Library name: JURKAT-C62-resequenced
JKCTL6h-2


title: 8064, plasma sample, pegIFNβ-1a _placebo, 0.125days

description: Library name: F14438948


title: 8064, plasma sample, pegIFNβ-1a _placebo, 0.33days

description: Library name: F14439042


title: 8064, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F14439026


title: siControl JURKAT (3h) rep1-resequenced

description:
Library name: JURKAT-C31-resequenced
JKCTL3h-1


title: 8064, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F14438824


title: siControl JURKAT (1h) rep2-resequenced

description:
Library name: JURKAT-C12-resequenced
JKCTL1h-2

value: siControl JURKAT (1h)


title: siControl JURKAT (1h) rep1-resequenced

description:
Library name: JURKAT-C11-resequenced
JKCTL1h-1


title: JURKAT, WT, rep2

address: 38 college road

description:
Library name: JURKAT-2
JURKAT-2

data_processing:
After sequencing, image analysis, base identification and QC, raw reads (Raw Data) are generated. QC was first performed using Q30.
Then cutadapt software (v1.9.3) was used to de-join and remove low quality reads to obtain clean reads.
Clean reads were aligned to the reference genome (hg38) and BAM files were obtained using STAR (v.2.7) and bowtie2 (v.2.2.4) software.
GLORI-tools took cleaned reads as input and finally reported the conversion rate (A-to-G) of GLORI and single-base loci of m6A sites with corresponding “A” rate as modification level.
Assembly: hg38
Supplementary files format and content: Files show the m6A modified sites identified by GLORI-Seq in A549, hESCs and JURKAT cells.
Library strategy: m6A-Seq

source_name: lymphocyte

growth_protocol: HEK293T and A549 cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum and antibiotics. Jurkat cell line was maintained in RPMI 1640 medium with 10% FBS and antibiotics. Human embryonic stem cells (hESCs) were cultivated in serum-free, defined mTeSR1 medium and grown on plates coated with growth-factor-reduced Matrigel. Human umbilical vein endothelial cells (HUVECs) were isolated as described. The clean vein of the umbilical cord was first lavaged with 0.25% trypsin at 37°C for 15 min. HUVECs were collected and suspended in Endothelial Cell Medium. Isolated HUVECs were cultured between passage 4–6 in ECM for experiment. Cells were grown at 37°C with 5% CO2.

extract_protocol:
Total RNA from the samples was extracted using TRIzol, and RNA was purified according to the MEGA clear transcription purification kit. RNA was incubated with fragmentation buffer for 4 min at 94°C and glyoxal solution and DMSO were added, and the mixture was incubated for 30 min at 50°C in a preheated thermal cycler.
Minutes, and at the end of the incubation, the tubes were brought to room temperature, and then saturated H3BO3 solution was added. The incubation was continued at 50 °C for 30 min. Then add to the pre-configured deamination buffer (750 mM NaNO2, 40 mM MES (pH 6.0), and 10 μl of glyoxal solution) for a total of 8 h of incubation.
Finally, RNA was purified by ethanol precipitation, and sequencing libraries were constructed by GenSeq® Low Input RNA Library Prep Kit following the process of the instructions provided by the manufacturer. The constructed sequencing libraries were subjected to quality control and quantification by BioAnalyzer 2100 system, followed by 150 bp double-end sequencing.

treatment_protocol: hESCs were passaged with non-enzymatic dissociation by 0.5 mM EDTA. Other cells were digested with 0.25% trypsin at 37°C for 2-5 min.

value: lymphocyte

value: acute T-cell lymphoblastic leukemia

value: Experimental group


title: 8060, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F14319136


title: 8060, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F14318844


title: 8060, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F14318959


title: JURKAT, WT, rep1

description:
Library name: JURKAT-1
JURKAT-1


title: hESC, WT, rep1

description:
Library name: hESC-1
hESC-1

source_name: early embryo

value: early embryo

value: hESC

value: human embryonic stem cell


title: hESC, WT, rep2

description:
Library name: hESC-2
hESC-2


title: 8060, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F14318598


title: 8060, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F14319855


title: ORM1-siRNA 2#-3

city: weifang

first: Jiaqiu

last: Li

address: Baotong west street No.7166

institute: shandong second medical university

description:
Library name: siRNA 2-3
Column name in raw count siRNA2#

data_processing:
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA).
After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.
The average insert size for the final cDNA librarys were 300±50 bp.
At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Assembly: HG19
Supplementary files format and content: The Excel file contains raw counts for each gene and each sample.

source_name: HCT116 cell

growth_protocol: HCT116 was cultured in McCOY’s 5A medium supplemented with 10% bovine serum at 37ºC with 5% CO2.

extract_protocol:
After ORM1 knockdown, total RNA was isolated using Trizol reagent. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cell was transfected with ORM1 specific small interfering RNA (siRNA) using Lipofectamine RNAiMax (Invitrogen).

value: HCT116 cell

value: colorectal cancer cell

value: ORM1 knockdown

value: ORM1 siRNA2#

tag: batch

value: Day 3


title: 8060, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F14318536

value: plasma

value: Healthy


title: A549, WT, rep2

description:
Library name: A549-2
A549-2

source_name: lung

value: lung

value: human lung adenocarcinoma cell


title: A549, WT, rep1

description:
Library name: A549-1
A549-1


title: 8060, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F14318289


title: 8055, plasma sample, pegIFNβ-1a, 9days

description: Library name: F14309333


title: ORM1-siRNA 2#-2

description:
Library name: siRNA 2-2
Column name in raw count siRNA2#


title: 8060, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F14319583


title: ORM1-siRNA 1#-2

description:
Library name: siRNA 1-2
Column name in raw count siRNA1#

value: ORM1 siRNA1#


title: 8060, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F14318211


title: control siRNA-3

description:
Library name: NC-3
Column name in raw count NC

value: Control

value: control siRNA


title: ORM1-siRNA 1#-3

description:
Library name: siRNA 1-3
Column name in raw count siRNA1#


title: 8055, plasma sample, pegIFNβ-1a, 13days

description: Library name: F14309605


title: 8060, plasma sample, IFNβ-1a_placebo, 0.67days

description: Library name: F14318386


title: 8055, plasma sample, pegIFNβ-1a, 5days

description: Library name: F14308709


title: 8060, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F14318087


title: control siRNA-2

description:
Library name: NC-2
Column name in raw count NC


title: ORM1-siRNA 2#-1

description:
Library name: siRNA 2-1
Column name in raw count siRNA2#


title: ORM1-siRNA 1#-1

description:
Library name: siRNA 1-1
Column name in raw count siRNA1#


title: 8055, plasma sample, pegIFNβ-1a, 6days

description: Library name: F14308886


title: control siRNA-1

description:
Library name: NC-1
Column name in raw count NC


title: hESC, L1TD1, rep3

description: Library name: L1TD1-3

data_processing:
Firstly, use cutadapt (v3.7) to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using STAR software (v2.7.8a).
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
Next, run Picard to remove duplicates and sort the output BAM files. To identify editing sites, we used Bullseye (https://github.com/mflamand/Bullseye) .
Assembly: hg38
Supplementary files format and content: Files show the target sites of DDX6, FUBP3, FXR2 and L1TD1 identified by TRIBE in hESCs.

growth_protocol: Human embryonic stem cells (hESCs) were cultivated in serum-free, defined mTeSR1 medium (STEMCELL, catalog#85850) and grown on plates coated with growth-factor-reduced Matrigel.

extract_protocol:
Sanger sequencing was used to conﬁrm proper insertion and then control and RBP-ADAR plasmids were infected into hESCs by transfection reagent jetOPTIMUS (Polyplus, catalog#101000051). After transient transfection into target cells for 24 h, the cells containing RBP-ADAR fusion proteins or mCherry-ADAR proteins were sorted by GFP and mCherry ﬂuorescence and using TRIzol reagent to extract the mRNA from the sorted cells.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
After library quality control, quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 with paired-end 150-bp reads, providing sequencing data at 40 Gb per library.

treatment_protocol: hESCs were passaged with non-enzymatic dissociation by 0.5 mM EDTA (Beyotime, catalog#C0196-100ml).


title: 8055, plasma sample, pegIFNβ-1a, 2days

description: Library name: F14308348


title: hESC, L1TD1, rep2

description: Library name: L1TD1-2


title: 8055, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F14308286


title: 8055, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F14308136


title: hESC, L1TD1, rep1

description: Library name: L1TD1-1


title: 8055, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F14308055


title: hESC, FXR2, rep3

description: Library name: FXR2-3


title: 8055, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F14307961


title: 8055, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F14307837


title: 8055, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F14308039


title: 8055, plasma sample, pegIFNβ-1a, 4days

description: Library name: F14308594


title: 8054, plasma sample, IFNβ-1a, 6days

description: Library name: F14306834


title: hESC, FXR2, rep1

description: Library name: FXR2-1


title: hESC, FXR2, rep2

description: Library name: FXR2-2


title: hESC, DDX6, rep3

description: Library name: DDX6-3


title: hESC, FUBP3, rep3

description: Library name: FUBP3-3


title: 8054, plasma sample, IFNβ-1a, 5days

description: Library name: F14306659


title: 8054, plasma sample, IFNβ-1a, 2days

description: Library name: F14306298


title: hESC, FUBP3, rep1

description: Library name: FUBP3-1


title: 8054, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14306005


title: 8054, plasma sample, IFNβ-1a, 4days

description: Library name: F14306544


title: hESC, CTL, rep2

description: Library name: ADAR-2

value: Control group


title: hESC, DDX6, rep1

description: Library name: DDX6-1

value: Experimental group


title: hESC, FUBP3, rep2

description: Library name: FUBP3-2

value: early embryo


title: 8054, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14305989


title: hESC, CTL, rep1

description: Library name: ADAR-1

value: hESC


title: 8054, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14305911


title: HEK293T, YTHDF1, rep3

description:
Library name: YTHDF1-3
YTHDF1-3

data_processing:
Firstly, use cutadapt (v3.7) to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using STAR software (v2.7.8a).
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
Next, run Picard to remove duplicates and sort the output BAM files. To identify editing sites, we used Bullseye (https://github.com/mflamand/Bullseye), a set of Perl scripts adapted from the HyperTRIBE pipeline.
Assembly: hg38
Supplementary files format and content: Text file shows the target sites of YTHDF1 identified by TRIBE.

source_name: embryonic kidney

growth_protocol: HEK293T cell lines were cultured in DMEM medium (Gibco, catalog#C11995500BT) supplemented with 10% fetal bovine serum (FBS, Gemini, catalog#900-108) and antibiotics.

extract_protocol:
Sanger sequencing was used to conﬁrm proper insertion and then control and YTHDF1-ADAR plasmids were infected into HEK293T cells by transfection reagent lipo3000. After transient transfection into target cells for 24 h, the cells containing RBP-ADAR fusion proteins or mCherry-ADAR proteins were sorted by GFP and mCherry ﬂuorescence and using TRIzol reagent to extract the mRNA from the sorted cells.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
After library quality control, quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 with paired-end 150-bp reads, providing sequencing data at 40 Gb per library.

treatment_protocol: The control plasmid, mammalian expression plasmid, containing mCherry ADAR control and p2A GFP reporter can be obtained from Addgene (Plasmid #154786). As for RBP-TRIBE plasmid, using standard restriction enzyme-based cloning to clone YTHDF1 into TRIBE plasmid.

value: embryonic kidney

value: Human embryonic kidney


title: hESC, CTL, rep3

description: Library name: ADAR-3

value: human embryonic stem cell


title: 8054, plasma sample, IFNβ-1a, 1.33days

description: Library name: F14306236


title: 8054, plasma sample, IFNβ-1a, 0.67days

description: Library name: F14306086


title: hESC, DDX6, rep2

description: Library name: DDX6-2


title: 8050, plasma sample, IFNβ-1a, 5days

description: Library name: F14298459


title: 8054, plasma sample, IFNβ-1a, Baseline

description: Library name: F14305787


title: HEK293T, YTHDF1, rep2

description:
Library name: YTHDF1-2
YTHDF1-2


title: HEK293T, YTHDF1, rep1

description:
Library name: YTHDF1-1
YTHDF1-1


title: 8050, plasma sample, IFNβ-1a, 2days

description: Library name: F14298098


title: 8050, plasma sample, IFNβ-1a, 1.33days

description: Library name: F14298036


title: 8050, plasma sample, IFNβ-1a, 4days

description: Library name: F14298344


title: HEK293T, CTL, rep3

description:
Library name: ADAR-3
ADAR-3


title: 8050, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14297805


title: HEK293T, CTL, rep2

description:
Library name: ADAR-2
ADAR-2


title: 8050, plasma sample, IFNβ-1a, 0.67days

description: Library name: F14297886


title: 8050, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14297789


title: 8050, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14297711


title: THP-1 derived macrophages, siControl, LPS 48H, bio rep 2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Fastq files were generated using bcl2fastq. Fastq files were mapped to hg38 human genome using STAR aligner.
Assembly: hg38
Supplementary files format and content: bedGraph files of mapped reads.

growth_protocol: THP-1 cells were cultured in RPMI 1640 with 10% (vol/vol) of fetal bovine serum (FBS) and 1% penicillin-streptomycin. THP-1 cells were cultured at 37℃, 5% CO2 in the fully humidified air. The cells were passaged after 3-4 days.

extract_protocol:
RNA was harvested and purified using RNeasy Mini kits (Qiagen). 500ng of total RNA was used for the constrction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

treatment_protocol:
Macrophages differentiation was induced by 100 ng/mL phorbol-12-myristate-13-acetate (PMA) for 48 hours, and they were then cultured in fresh medium to rest for 24 hours prior to further treatment.
To induce the inflammation response, the cells were treated with LPS (100 ng/mL) for different hours.

value: monocytes

value: WT

value: PMA differentiation

value: LPS stimulation


title: THP-1 derived macrophages, siControl, LPS 48H, bio rep 1


title: 8050, plasma sample, IFNβ-1a, Baseline

description: Library name: F14297587

value: plasma

value: Healthy


title: THP-1 derived macrophages, siMALAT1, LPS 48H, bio rep 2

value: MALAT1 knockdown


title: THP-1 derived macrophages, siMALAT1, LPS 48H, bio rep 1


title: THP-1 derived macrophages, siControl, LPS 48H, bio rep 3


title: 8047, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F14102325

value: pegIFNβ-1a _placebo


title: HEK293T, CTL, rep1

description:
Library name: ADAR-1
ADAR-1


title: 8047, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F14101878


title: 8047, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F14102597


title: 8047, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F14101586


title: THP-1 derived macrophages, siMALAT1, LPS 24H, bio rep 1


title: 8047, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F14101701


title: THP-1 derived macrophages, siControl, LPS 24H, bio rep 3


title: 8047, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F14101340


title: THP-1 derived macrophages, siControl, LPS 24H, bio rep 2


title: THP-1 derived macrophages, siMALAT1, LPS 24H, bio rep 2


title: THP-1 derived macrophages, siMALAT1, LPS 48H, bio rep 3


title: 8047, plasma sample, pegIFNβ-1a _placebo, 0.67days

description: Library name: F14101128


title: THP-1 derived macrophages, siMALAT1, LPS 24H, bio rep 3


title: 8047, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F14101031


title: THP-1 derived macrophages, siMALAT1, LPS 12H, bio rep 1


title: 8047, plasma sample, pegIFNβ-1a _placebo, 0.33days

description: Library name: F14101047


title: THP-1 derived macrophages, siMALAT1, LPS 12H, bio rep 3


title: THP-1 derived macrophages, siControl, LPS 12H, bio rep 3


title: 8042, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F14092075


title: THP-1 derived macrophages, siControl, LPS 12H, bio rep 1


title: 8042, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F14091451


title: THP-1 derived macrophages, siControl, LPS 24H, bio rep 1


title: THP-1 derived macrophages, siControl, LPS 12H, bio rep 2


title: 8042, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F14092347


title: THP-1 derived macrophages, siMALAT1, LPS 0H, bio rep 2


title: 8047, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F14100829


title: 8047, plasma sample, pegIFNβ-1a _placebo, 1.33days

description: Library name: F14101278


title: THP-1 derived macrophages, siMALAT1, LPS 12H, bio rep 2


title: 8042, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F14091628


title: 8042, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F14091336


title: THP-1 derived macrophages, siMALAT1, LPS 0H, bio rep 1


title: THP-1 derived macrophages, siControl, LPS 0H, bio rep 2


title: 8042, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F14091028


title: THP-1 derived macrophages, siControl, LPS 0H, bio rep 3


title: 8042, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F14090781


title: 8042, plasma sample, IFNβ-1a_placebo, 0.67days

description: Library name: F14090878


title: WT_45_3

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 600 West Campus Dr

department: Chemistry

institute: Yale University

data_processing:
Read files were trimmed to deplete adapter sequences using the following bash script, which invokes bbduk.sh, part of the BBMap (V38) array of tools $ module load Java/17.0.4 $ for i in `ls -1 reads/*R1_001.fastq.gz | sed 's/R1_001.fastq.gz//'` $ do     bbmap/bbduk.sh \     in1=$i\R1_001.fastq.gz \     in2=$i\R2_001.fastq.gz \     out1=$i\R1_trimmed.fastq.gz \     out2=$i\R2_trimmed.fastq.gz \     ref=/home/mgm67/project/bbmap/resources/adapters.fa \     ktrim=r k=23 mink=11 hdist=1 tpe tbo minlen=40 $ done
The resulting trimmed read files were then assessed for quality control with FastQC (v0.11.9) using the following bash script:  $ fastqc -t 12 -o qc *.fastq.gz
Subsequently, the reads were mapped to the E. coli str. K-12 substr. MG1665 genome using STAR (2.7.11b) and the following bash script:  $ for i in `ls -1 reads2/*R1_trimmed.fastq.gz | sed \     's/R1_trimmed.fastq.gz//'` $ do     STAR-master/source/STAR --readFilesCommand zcat \     --runThreadN 20 \     --genomeDir genome \     --readFilesIn $i\R1_trimmed.fastq.gz $i\R2_trimmed.fastq.gz \     --outSAMtype BAM SortedByCoordinate \     --outFileNamePrefix $i \     --limitBAMsortRAM 1368240413 $ done
The resulting alignment files (.BAM) were analyzed using featureCounts (Subread-2.0.6) with the following bash script:  $ featureCounts \ $ -p --countReadPairs -g gene -t gene \ $ -a ncbi_dataset/data/GCF_000005845.2/genomic.gtf \ $ -o feature_counts.tsv -T 6 reads/*.bam
The featureCounts program outputs a tab-separated column (.tsv) file. Microsoft Excel was used for downstream analysis. To normalize for gene length, reads per kilobase (RPK) values were calculated for each replicate by dividing the reads for each gene by the length of the gene in kilobases. To normalize for read depth, first the scaling factor for each replicate was calculated by summing up all RPK values and dividing by 106. Then, transcripts per million (TPM) values were calculated by dividing the RPK value for each gene by the scaling factor for the replicate.
Assembly: GCF_000005845.2_ASM584v2_genomic.fna
Supplementary files format and content: Excel sheet tabulating the TPM values for each sample type (three replicates) associated with each gene

organism: Escherichia coli

source_name: WT

extract_protocol:
RNeasy Protect Bacteria kit (Qiagen catalog #74524)
KAPA Hyper Kit (KK8504, 07962363001)

value: heat shock


title: 8042, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F14090579


title: 8040, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F14088247


title: 8042, plasma sample, IFNβ-1a_placebo, 0.33days

description: Library name: F14090797


title: THP-1 derived macrophages, siMALAT1, LPS 0H, bio rep 3


title: WT_45_1


title: aKO-Rescue_45_2

source_name: aKO-Rescue

value: aKO-Rescue


title: 8040, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F14087975


title: THP-1 derived macrophages, siControl, LPS 0H, bio rep 1


title: COs, PD1/PEM

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: hg38
Supplementary files format and content: Cellranger output files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: iPSC-CM, iPSC-EC, iPSC-CF

extract_protocol:
The COs were digested as per published protocol (DOI:10.3791/61879). The single cell suspension was neutralized, labelled with hashing antibodies on ice for 30 mins. Cells were washed and resuspended in  2% BSA and processed for 10X capture.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics).

value: iPSC-CM, iPSC-EC, iPSC-CF

value: Pembrolizumab


title: aKO-6PGDf_45_3


title: aKO-Rescue_45_1


title: aKO-Rescue_45_3


title: 8042, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F14090703


title: 8042, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F14091090


title: 8040, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F14086990


title: WT_45_2


title: 8040, plasma sample, pegIFNβ-1a _placebo, 0.33days

description: Library name: F14086697


title: 8040, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F14087528


title: shNSUN5-3 input

city: Zhengzhou

first: xue

last: chen

address: NO.101 Kexue Road High-Tech Development Zone Of States Zhengzhou

institute: Zhengzhou University

description:
Methylated_RNA_sites.mRNA
Methylated_RNA_sites.LncRNA
Methylated_RNA_sites.circRNA

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC hg19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: HG38
Supplementary files format and content: The excel table contains m5C methylation site identification information for each sample
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA was extracted using Trizol reagent
m5C RNA immunoprecipitation was performed with the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m5C IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq instrument with 150bp paired-end reads..

tag: antibody


title: shNSUN5-3


title: 8040, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F14087351


title: 8040, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F14087236


title: 8040, plasma sample, pegIFNβ-1a _placebo, 0.67days

description: Library name: F14086778


title: COs, Control

value: Isotype


title: aKO-6PGDf_45_2


title: 8040, plasma sample, pegIFNβ-1a _placebo, 1.33days

description: Library name: F14086928


title: aKO-6PGDf_45_1


title: shNSUN5-2 input


title: 8040, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F14086681


title: COs, PDL1/ATZ

value: Atezolizumab


title: 8040, plasma sample, pegIFNβ-1a _placebo, 0.125days

description: Library name: F14086603


title: gKO_45_3

source_name: gKO

value: gKO


title: 8039, plasma sample, IFNβ-1a, 6days

description: Library name: F14085476


title: 8039, plasma sample, IFNβ-1a, 4days

description: Library name: F14085186


title: 8040, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F14086479


title: gKO_45_1


title: 8039, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14084647


title: shNSUN5-2


title: 8038, plasma sample, pegIFNβ-1a, 9days

description: Library name: F13942756


title: shNC-3

value: shNC


title: 8038, plasma sample, pegIFNβ-1a, 6days

description: Library name: F13942309


title: D10_polydactyl_brachial_1

city: Basel

first: Patrick

last: Tschopp

state: Basel-Stadt

address: Vesalgasse 1

department: Umweltwissenschaften

country: Switzerland

institute: Universität Basel

description: Library name: 10x_NeuralTube_Poly_1_0420

data_processing:
Cellranger v3.1.0 (day 10 samples), v5.0.1 (day 5 and 7 samples)
Assembly: GRCg6a chicken genome assembly and its extended annotation, published in Feregrino et al. 2021
Supplementary files format and content: barcodes.tsv.gz contains barcode sequences corresponding to column indices
Supplementary files format and content: features.tsv.gz contains features corresponding to row indices
Supplementary files format and content: matrix.mtx.gz contains the sparse count matrix

organism: Gallus gallus

source_name: spinal cord

growth_protocol: Fertilized embryos were incubated at 38°C and 60% humidity.

extract_protocol:
Dissected caudal LMCs were transferred into 3ml preheated dissociation media (FACSmax™ media, Amsibio with 0,375 mg/ml Papain, Millipore Sigma) and incubated for 5 minutes in a water bath at 37°C. First and second trituration were performed with a P1000 pipette tip cut 5mm from the tip and quickly burnt with a Bunsen burner to eliminate sharp edges. The last two triturations were carried out with an uncut P1000 pipette tip. Each trituration was followed by 5 mins of incubation at 37°C. Cell suspensions were centrifugated at 300g for 7 min at 4°C. The supernatantwas discarded, cell pellets were resuspended in 1ml HBSS 5% FBS (ThermoFisher), passed through a cell strainer (Flowmi®, Millipore Sigma) into a 1,5 ml Eppendorf tube and cen-trifuged again at 300g for 7 mins at 4°C. Cell pellets were resuspended in 100μl HBSS 5% FBS and cell number and viability were assessed with an automated cell counter (Cellome-ter®, AOPI ViaStain™). Only samples above 80% viability were processed for sequencing.
Chromium Next GEM Single-cell 3 Reagent Kits v3.1 (Dual Index)

treatment_protocol: Resinbeads (AG1-X2, Biorad) were formatted in formic acid for an hour, washed with clean water until the pH stabilized around 4.5. The beads can be stored in water at 4°C for a month. Before implantation, beads were incubated in 1 mg/ml all-trans retinoic acid (RA) solution for at least 20 minutes, then incubated in DMEM media (Gibco) until they turned red. A small incision was made between the Apical Ectodermal Ridge and the mesenchyme at the anterior margin of the limb bud and RA-soaked beads were implanted. Eggs were closed with a tape and reincubated for 7 days after operation.

value: spinal cord

tag: age

value: embryonic day 10


title: gKO_45_2


title: shNC-3 input


title: D10_lumbar_1

description: Library name: 10x_NeuralTube_Lumbar_1_0420


title: 8038, plasma sample, pegIFNβ-1a, 4days

description: Library name: F13942017


title: shNSUN5-1 input


title: 8039, plasma sample, IFNβ-1a, 2days

description: Library name: F14084940


title: D10_brachial_1

description: Library name: 10x_NeuralTube_Control_1_0420


title: 8038, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F13941559


title: 8039, plasma sample, IFNβ-1a, 1.33days

description: Library name: F14084878


title: 8038, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F13941478


title: shNC-1


title: 8038, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F13941462


title: shNSUN5-1


title: D07_brachial

description: Library name: 10X_Gg_caudal_NT_WT_1121

value: embryonic day 7


title: 8038, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F13941384


title: D10_polydactyl_brachial_2

description: Library name: 10x_NeuralTube_Poly_2_0420


title: 8034, plasma sample, pegIFNβ-1a, 9days

description: Library name: F13934556


title: 8039, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14084631


title: murine retina,  full spectrum white light exposed, scRNA-seq

city: hangzhou

first: xuhong

last: zhang

address: qingchun road, no. 79. shangcheng strait, hangzhou

institute: the first affiliated hospital, school of medicine, Zhejiang university

description: Library name: sample2

data_processing:
Raw sequencing reads were quality-controlled and filtered using Fastp. The feature-barcode matrix was generated, and reads were aligned to the reference genome using the 10x Genomics Cell Ranger pipeline. Downstream analysis, including data normalization, dimensionality reduction (PCA), cell clustering (graph-based clustering with Seurat), and differential expression analysis (using edgeR), was performed. Marker genes were functionally annotated through GO, KEGG, Reactome, and PPI network analyses. Additional analyses included cell-cell communication (CellChat), transcription factor activity (SCENIC), and RNA velocity (scVelo).
Assembly: mm10
Supplementary files format and content: The primary processed data files are in the standard 10x Genomics Cell Ranger output format. This includes:barcodes.tsv.gz: A list of all cellular barcodes identified.features.tsv.gz (or genes.tsv.gz): A list of all gene identifiers (e.g., gene symbols).matrix.mtx.gz: A sparse matrix file in Matrix Market format containing the UMI count data for each gene (row) in each cell (column).

organism: Mus musculus

source_name: retina

extract_protocol:
Single-cell suspensions were prepared by mincing the retinal tissue into small pieces and digesting at 37°C for approximately 30 minutes. The cell pellet was collected by centrifugation, resuspended in 1640 medium containing 2% FBS, and filtered through a 30 μm cell strainer. Cell viability and concentration (700–1200 cells/μL) were assessed using AOPI staining, and samples were documented via microscopy with trypan blue staining.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium platform (3’ v3.1/v4 chemistry). Briefly, single cells were partitioned into Gel Bead-in-Emulsions (GEMs) using the Chromium Controller. Within each GEM, cell barcoding and reverse transcription were performed to generate barcoded cDNA. The cDNA was then purified with Dynabeads MyOne SILANE beads, amplified by PCR (cycles adjusted based on cell recovery), and enzymatically fragmented. The library was completed through end repair, A-tailing, and adapter ligation.

value: retina

value: all cells in retina

value: full spectrum white light exposed


title: 8039, plasma sample, IFNβ-1a, 5days

description: Library name: F14085301

value: plasma

value: Healthy


title: 8034, plasma sample, pegIFNβ-1a, 6days

description: Library name: F13934109


title: 8034, plasma sample, pegIFNβ-1a, 5days

description: Library name: F13933932


title: murine retina, short wavelength light exposed, scRNA-seq

description: Library name: sample1

value: short wavelength light exposed


title: 8039, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14084553


title: 8034, plasma sample, pegIFNβ-1a, 2days

description: Library name: F13933571


title: OTM 1d (mouse alveolar bone, right first molar, pooled 10)

city: Chongqing

first: miao

last: tan

address: 426 Songshi North Road, Yubei District, Chongqing, China

institute: College of Stomatology,Chongqing Medical University

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics, v8.0.1) with default parameters. Reads were aligned to the mouse reference genome (mm10). Filtered feature-barcode matrices were generated and used for downstream clustering, dimensionality reduction, and differential expression analysis in Seurat (R package).
Assembly: Mus musculus, GRCm39-2024-A
Supplementary files format and content: Processed data are provided as 10x Genomics HDF5 format (filtered_feature_bc_matrix.h5) for each sample. Files contain gene expression counts per cell barcode.

source_name: Alveolar bone within 1 mm of first molar extraction socket, gingiva removed

extract_protocol:
Alveolar bone tissues within 1 mm of the maxillary first molar (gingiva removed) were dissected, rinsed in ice-cold PBS with 1% FBS, minced into 1–2 mm fragments, and digested with 2 mL GEXSCOPE® Bone Tissue Dissociation Solution at 37 °C for 60 min. Cell suspensions were filtered, centrifuged, and red blood cells were removed with GEXSCOPE® RBC lysis buffer
Single-cell suspensions (700–1200 cells/μL) were loaded onto the 10x Genomics Chromium Next GEM system, and libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (PN-1000268) according to the manufacturer’s protocol. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: Mixed cell population from alveolar bone (single-cell suspension)

value: Orthodontic tooth movement (OTM, 1 day)


title: Ribo-seq_siMETTL3 HUVEC rep2

data_processing:
Library strategy: Ribo-Seq
The quality control, adapter cutting and low quality sequence removal were performed by FastQC, fastp and FASTX toolkits.
The clean reads were mapped to human genome (hg38) by HISAT2 software (v2.2.1) and the expression values were calculated by featureCounts command with suggested parameter of the software.
The translation efficiency was evaluated by the xtail software (version 1.1.5) using the suggested analysis pipeline.
Genome_build: hg38
Supplementary_files_format_and_content:
Matrix table with raw gene counts for every gene and every sample
*translation.txt: Translation efficiency analysis results

source_name: HUVEC

extract_protocol:
To digest the RNA other than RPFs, cell  lysate was treated with unspecific endoribonuclease RNase ǀ. Isolation of monosomes was performed by size-exclusion chromatography with MicroSpin S-400 HR columns.
The RNA samples were treated with rRNA depletion kit to deplete the samples of as much rRNA contamination as possible before PAGE purification of the relatively short (20~38 nt) RPFs. Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR (Ingolia et al., Nat Protoc., 20127(8):1534-1550).

value: HUVEC

tag: molecule subtype

value: ribosome footprints


title: 8039, plasma sample, IFNβ-1a, Baseline

description: Library name: F14084429

data_processing:
CLC Genomics Workbench v21.0.1
Samples were processed using Toolbox "Ready to use workflow" for "Small RNA sequencing" and "Qiaseq miRNAquantification"
Sequence reads were trimmed for adapters and size, UMI reads are generated from grouping greads with the same or similar UMI and similar sequence.
Mature miRNA reads are considered as expression counts.
Raw data was normalized using Deseq2 R package
Assembly: mirBase v22
Supplementary files format and content: csv file includes raw counts for each sample

source_name: plasma


title: 8034, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F13933509


title: Control (mouse alveolar bone, left first molar, pooled 10

description:
Library name: Sample 1
10x Genomics

value: Alveolar bone within 1 mm of first molar extraction socket, gingiva removed

value: Control


title: 8034, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F13933359


title: shNC-2 input


title: 8034, plasma sample, pegIFNβ-1a, 4days

description: Library name: F13933817


title: D10_lumbar_2

description: Library name: 10x_NeuralTube_Lumbar_2_0420


title: 8034, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F13933262


title: 8034, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F13933184


title: 8034, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F13933278


title: 8038, plasma sample, pegIFNβ-1a, 13days

description: Library name: F13943028


title: D10_brachial_2

description: Library name: 10x_NeuralTube_Control_2_0420


title: 8038, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F13941709


title: shNC-2


title: 8038, plasma sample, pegIFNβ-1a, 5days

description: Library name: F13942132


title: 8028, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F13713113


title: shNC-1 input


title: 8034, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F13933060


title: Ribo-seq_siControl HUVEC rep1

value: siControl


title: 8038, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F13941260


title: 8034, plasma sample, pegIFNβ-1a, 13days

description: Library name: F13934828


title: 8028, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F13712394


title: Ribo-seq_siMETTL3 JURKAT rep1

value: JURKAT


title: Ribo-seq_siMETTL3 JURKAT rep2


title: Isotype Control

description: Library name: Cnt_R

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Heart

extract_protocol:
The mouse hearts were digested as per published protocol (DOI:10.3791/4205) and processed for 10X capture.
Library was performed according to the manufacturer's instructions (Single Cell 3ʹ Reagent Kits v3.1 protocol, 10x Genomics).

value: Heart

value: NOD/SCID

value: Isotype


title: 8028, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F13712841

extract_protocol:
EDTA plasma from whole blood. RNA was extracted using miRNeasy® Serum/Plasma Kit (Cat. 217184, Qiagen LLC).
Library preparations were carried out using the QIAseq miRNA Library Kit [96] (# 331505) together with QIAseq miRNA [96] Index IL (#331565), and an automated liquid handling method developed for preparation of 96 cDNA using the Biomek i7 Automated Liquid Handler (Beckman).


title: D05_brachial

description: Library name: 10X_Gg_NT_D5_ctrl_0322

value: spinal cord

value: embryonic day 5


title: 8028, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F13712217


title: Ribo-seq_siControl JURKAT rep2


title: Ribo-seq_siControl JURKAT rep1


title: 8028, plasma sample, IFNβ-1a_placebo, 0.33days

description: Library name: F13711563


title: Ribo-seq_siMETTL3 HUVEC rep1


title: 8028, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F13711794


title: 8028, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F13711547


title: 8028, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F13711469


title: S34F_DOX_VEHICLE_3

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

description: Library name: Sample_09

data_processing:
Illumina Novaseq 6000 using paired reads extending 150 bases
Mouse: The reads were then mapped using STAR (v2.7.0) against the GRCm38.95 version of the mouse genome from the Ensembl consortium. Human: The reads were then mapped using STAR (v2.7.0) against the GRCh38.95 version of the human genome from the Ensembl consortium
Gene counts were determined by  processing the resulting reads using using kallisto v0.43.1
Assembly: mm10/hg38
Supplementary files format and content: tab seperated text file that includes raw counts for each sample

source_name: Bone marrow hematopoietic cells

extract_protocol:
RNA was isolated from sorted GFP+ mouse MLL::AF9 BM cells after SMG1i-63 or vehicle treatment using the Quick-RNA MicroPrep Kit (Fisher-Zymo, No. R1050). Quality of isolated RNA was determined using Agilent RNA 6000 Nano chip using the Agilent 4200 TapeStation platform. Quantification was performed using Qubit Fluorometer (Thermo-Fisher Scientific). Total RNA samples with RNA integrity number (RIN) >9 were selected for Illumina sequencing library preparation. For K562 same protocol was used for library preparation.
The RNA-sequencing libraries were constructed using KAPA RNA HyperPrep Kit with RiboErase (Roche, Catalog # KK8560/61), per the manufacturer’s protocol. After amplification, final libraries (~360 bp mean size) were sequenced on Illumina NovaSeq 6000, generating 2 x 150bp paired-end reads.

value: Bone marrow hematopoietic cells

value: 7 doses

value: Vehicle


title: Ribo-seq_siControl HEK293T rep1


title: Ribo-seq_siControl HUVEC rep2


title: PDL1/ATZ

description: Library name: ATZ_R

value: Pembrolizumab


title: S34F_DOX_VEHICLE_2

description: Library name: Sample_08


title: S34F_DOX_VEHICLE_1

description: Library name: Sample_07


title: 8026, plasma sample, IFNβ-1a, 2days

description: Library name: F13421873

value: plasma

value: Healthy


title: Ribo-seq_siControl H9 rep2


title: 8026, plasma sample, IFNβ-1a, 1.33days

description: Library name: F13421811


title: PD1/PEM_3

description:
DT4772
CheckPoint_TPM_02252024.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Raw read counts were counted by using FeatureCounts
Assembly: hg38
Supplementary files format and content: CheckPoint_TPM_02252024.csv

source_name: iPSC-CM

extract_protocol:
RNeasy Plus Micro kit (Qiagen, 74004). RNA quantity and quality were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies). All samples passed a quality-control threshold (RIN ≥ 9) to proceed to library preparation and RNA-seq on
Standard poly-A mRNA enrichment followed by construction of double-stranded cDNA library through size selection and PCR enrichment.

tag: cell line_source

value: healthy iPSC line 3

value: iPSC-CM


title: Ribo-seq_siMETTL3 HEK293T rep2

value: ribosome footprints


title: PD1/PEM

description: Library name: PEM_R

value: Atezolizumab


title: S34F_DOX_SMG1_3

description: Library name: Sample_12


title: 8026, plasma sample, IFNβ-1a, 0.67days

description: Library name: F13421661


title: 8028, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F13712102


title: 8026, plasma sample, IFNβ-1a, 0.33days

description: Library name: F13421580


title: Ribo-seq_siMETTL3 HEK293T rep1


title: Ribo-seq_siControl A549 rep2

value: siControl


title: S34F_NO_DOX_VEHICLE_2

description: Library name: Sample_02


title: S34F_DOX_SMG1_2

description: Library name: Sample_11


title: 8028, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F13711856


title: 8026, plasma sample, IFNβ-1a, Baseline

description: Library name: F13421362


title: Isotype Control_2

description:
DT1420
CheckPoint_TPM_02252024.csv

value: healthy iPSC line 2


title: Ribo-seq_siControl HEK293T rep2


title: S34F_DOX_SMG1_1

description: Library name: Sample_10


title: 8026, plasma sample, IFNβ-1a, 0.125days

description: Library name: F13421486


title: 8028, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F13711345


title: 8026, plasma sample, IFNβ-1a, 5days

description: Library name: F13422234


title: 8026, plasma sample, IFNβ-1a, 6days

description: Library name: F13422409


title: Ribo-seq_siMETTL3 H9 rep1


title: Ribo-seq_siMETTL3 H9 rep2


title: PD1/PEM_1

description:
DT202
CheckPoint_TPM_02252024.csv

value: healthy iPSC line 1


title: siMETTL3 JURKAT (6h) rep1

data_processing:
The quality control, adapter cutting and low quality sequence removal were performed by FastQC, fastp and FASTX toolkits.
The clean reads were mapped to human genome (hg38) by HISAT2 software (v2.2.1) and the expression values were calculated by featureCounts command with suggested parameter of the software.
The mRNA half-life was estimated following the method modified from (Wang et al., Nature, 2014, 505: s117–120).
The alternative splicing events were analyzed by rMATS turbo software (v4.1.0, default parameter), focusing on exon skipping and intron retention events.
Assembly: hg38
Supplementary files format and content:
Matrix table with raw gene counts for every gene and every sample
*exonskipping.txt: detected exon skipping event
*intronretention.txt: detected intron retention event
*estimatedhalflife.txt: estimated transcript half-life

source_name: JURKAT

extract_protocol:
Cells from each group and time points were collected and total RNA was harvested with Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7770)and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7760) were used with 400 ng of total RNA for the construction of sequencing libraries.
ERCC spike-in were added to total RNA before library construction, following the protocol recommended by ERCC spike-in kit manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: JURKAT


title: KFN3

city: Grand Forks

first: Takako

last: Ishida-Takaku

state: ND

address: 1301 North Columbia Road

department: Department of Biomedical Sciences

institute: University of North Dakota

description:
Library name: APP.NL-G-F.Female.Normal.rep3
19-027-141KIKI.Female.Normal

data_processing:
Adapter sequences were removed using trimmomatic, and the reads were subsequently mapped to the mm10 genome using HISAT2 aligner. Read counts for each gene were collected by featureCounts. Differentially expressed genes were identified with DESeq2 using filtering thresholds of FDR < 0.05. Differential gene expression analysis and pathway enrichment analysis was performed by iDEP2.0 online tool.
Assembly: mm10
Supplementary files format and content: featureCounts
Supplementary files format and content: DESeq2

source_name: Colon

extract_protocol:
Total RNAs were purified using Qiazol RNA Isolation Reagent (QIAGEN).
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). Fragmented mRNAs were reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies) and random hexamers. Illumina sequencing adapters were ligated to the cDNAs. Ligated fragments were then amplified for 12-15 cycles and sequenced on an Illumina NovaSeq 6000.

value: Colon

value: APP knock-in transgenic mice (App NL-G-F, KI:RBRC06344)

tag: strain

tag: Sex

value: Female

value: Non-treatment


title: 8026, plasma sample, IFNβ-1a, 4days

description: Library name: F13422119


title: S34F_NO_DOX_SMG1_3

description: Library name: Sample_06

value: Bone marrow hematopoietic cells

value: 7 doses


title: KFN2

description:
Library name: APP.NL-G-F.Female.Normal.rep2
19-027-140KIKI.Female.Normal


title: PDL1/ATZ_1

description:
DT201
CheckPoint_TPM_02252024.csv


title: Ribo-seq_siControl H9 rep1

tag: cell line


title: 8025, plasma sample, pegIFNβ-1a, 6days

description: Library name: F13420361


title: S34F_NO_DOX_SMG1_2

description: Library name: Sample_05


title: Ribo-seq_siMETTL3 A549 rep1


title: PDL1/ATZ_3

description:
DT4771
CheckPoint_TPM_02252024.csv

tag: cell type


title: Isotype Control_3

description:
DT4770
CheckPoint_TPM_02252024.csv

value: Isotype


title: KFN1

description:
Library name: APP.NL-G-F.Female.Normal.rep1
19-027-138KIKI.Female.Normal

tag: genotype


title: S34F_NO_DOX_VEHICLE_3

description: Library name: Sample_03

tag: treatment

value: Vehicle


title: S34F_NO_DOX_SMG1_1

description: Library name: Sample_04

tag: time


title: 8026, plasma sample, IFNβ-1a, 0.25days

description: Library name: F13421564

tag: tissue

value: plasma

value: Healthy


title: Isotype Control_1

description:
DT200
CheckPoint_TPM_02252024.csv

value: iPSC-CM


title: WFT3

description:
Library name: WT.Female.Tumor.rep3
19-027-153 WT.Female.Tumor

value: wild-type

value: AOM/DSS


title: siMETTL3 JURKAT (1h) rep2


title: Ribo-seq_siMETTL3 A549 rep2

value: ribosome footprints


title: Ribo-seq_siControl A549 rep1

value: siControl


title: PD1/PEM_2

description:
DT1422
CheckPoint_TPM_02252024.csv

value: healthy iPSC line 2

value: Pembrolizumab


title: 8025, plasma sample, pegIFNβ-1a, 4days

description: Library name: F13420069

tag: disease state


title: siMETTL3 JURKAT (1h) rep1

value: JURKAT


title: THP-1 derived macrophages, IgG, LPS 24H, RIP, bio rep 1

extract_protocol:
RNA was purified using RNeasy Mini kits (Qiagen). 10ng of RNAs was used for the constrction of sequencing libraries.
RNA libraries for RIP-seq were prepared using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

treatment_protocol:
Macrophages differentiation was induced by 100 ng/mL phorbol-12-myristate-13-acetate (PMA) for 48 hours, and they were then cultured in fresh medium to rest for 24 hours prior to further treatment.
To induce the inflammation response, the cells were treated with LPS (100 ng/mL) for 24 hours.

value: monocytes

value: IgG (Millipore, #17-701)

value: PMA differentiation

value: LPS stimulation


title: 8025, plasma sample, pegIFNβ-1a, 2days

description: Library name: F13419823


title: 8025, plasma sample, pegIFNβ-1a, 5days

description: Library name: F13420184


title: PDL1/ATZ_2

description:
DT1421
CheckPoint_TPM_02252024.csv

value: Atezolizumab


title: WFT1

description:
Library name: WT.Female.Tumor.rep1
19-027-105 WT.Female.Tumor

value: Colon

value: Female


title: siMETTL3 JURKAT (6h) rep2


title: siMETTL3 JURKAT (0h) rep2


title: 8025, plasma sample, pegIFNβ-1a, 13days

description: Library name: F13421080

value: plasma


title: siMETTL3 JURKAT (3h) rep2


title: S34F_NO_DOX_VEHICLE_1

description: Library name: Sample_01

value: Bone marrow hematopoietic cells

value: 7 doses

value: Vehicle


title: WFT2

description:
Library name: WT.Female.Tumor.rep2
19-027-152 WT.Female.Tumor

value: wild-type

value: AOM/DSS


title: 8025, plasma sample, pegIFNβ-1a, 9days

description: Library name: F13420808

value: Healthy


title: THP-1 derived macrophages, IgG, LPS 24H, RIP, bio rep 2


title: siMETTL3 JURKAT (3h) rep1


title: 8025, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F13419611


title: 8025, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F13419530


title: THP-1 derived macrophages, HADHB, LPS 24H, RIP

value: HADHB (LS-B4668, LifeSpan)


title: siControl JURKAT (6h) rep2


title: siControl JURKAT (6h) rep1

value: siControl


title: 8025, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F13419761


title: KMT3

description:
Library name: APP.NL-G-F.Male.Tumor.rep3
19-027-154KIKI.Male.Tumor

value: APP knock-in transgenic mice (App NL-G-F, KI:RBRC06344)

value: Male


title: WFN3

description:
Library name: WT.Female.Normal.rep3
19-027-101WT.Female.Normal

value: Non-treatment


title: Control_replicate_22

type: RNA

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: Sample name: K48

data_processing:
Cycle of quantification values (Cq-values) were determined using the second derivative method as provided by the Roche LC480 software. RT-qPCR miRNA data were normalized to the Cq-value of the RNA Spike-In (UniSp4) to account for analytical variability (CqUniSp4 – CqmiRNA = normalized deltaCq). Missing miRNA data below the detection limit were not imputed.
Matrix normalized worksheet reports normalized signal (against RNA spike-in control).
Fold Change file reports T1D/control ratios.

label: SYBR green

source_name: EDTA Plasma

label_protocol: Reverse transcription (RT) quantitative PCR (qPCR) analysis of 23 distinct miRNAs and 5 controls was performed as previously described [11-14]. In brief, cDNA was synthesized using the miRCURY RT kit (Qiagen, Germany, catalog number 339340) where 2 µL of total RNA were used as input per 10 µL RT reaction mix. Cel-miR-39-3p was added to each RT reaction to monitor RT efficiency. PCR amplification was performed in a 384-well plate format using custom Pick&Mix plates (Qiagen, Germany) in a Roche LC480 II instrument (Roche, Germany) and miRCURY SYBR(R) Green Mix (Qiagen, Germany, catalog number 339347) with the following settings: 95 °C for 10 min, 45 cycles of 95 °C for 10 s and 60 °C for 60 s, followed by melting curve analysis. miRCURY LNA miRNA PCR Assay (Qiagen, catalog number 339306).

extract_protocol: For sample lysis, 200 µL of plasma were mixed with 1000 µL Qiazol to which 1 µL spike-in controls had been added (Qiagen, Germany). Following incubation at room temperature for 10 min, 200 µL chloroform were added to the lysates. After centrifugation at 12,000×g for 15 min at 4 °C, 650 µL of the upper aqueous phase were obtained and mixed with 7 µL glycogen (50 mg/mL) to enhance precipitation. RNA washing and clean-up was performed using the miRNeasy mini kit (Qiagen, Germany): the aqueous phase was transferred to a column, and RNA was precipitated by adding 750 µL ethanol. Washing with RPE and RWT buffer was performed in a QiaCube liquid handling robot (Qiagen, Germany). In the last step, total RNA was eluted in 30 µL nuclease free water and stored at −80 °C until further analysis.

value: Control

tag: gender

value: F


title: Control_replicate_23

description: Sample name: K47

value: M


title: Control_replicate_24

description: Sample name: K33


title: siMETTL3 JURKAT (0h) rep1

value: JURKAT


title: T1D_replicate_23

description: Sample name: D43


title: siControl JURKAT (3h) rep2


title: siControl JURKAT (3h) rep1


title: 8025, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F13419436


title: T1D_replicate_24

description: Sample name: D48


title: 8025, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F13419514


title: KMT2

description:
Library name: APP.NL-G-F.Male.Tumor.rep2
19-027-136KIKI.Male.Tumor

value: Colon


title: WFN1

description:
Library name: WT.Female.Normal.rep1
19-027-099WT.Female.Normal

value: Female


title: Control_replicate_21

description: Sample name: K31

value: plasma


title: T1D_replicate_22

description: Sample name: D27


title: WFN2

description:
Library name: WT.Female.Normal.rep2
19-027-100WT.Female.Normal


title: T1D_replicate_21

description: Sample name: D46


title: 8024, plasma sample, IFNβ-1a, 5days

description: Library name: F11650579


title: 8024, plasma sample, IFNβ-1a, 6days

description: Library name: F11650754


title: 8025, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F13419312


title: KMT1

description:
Library name: APP.NL-G-F.Male.Tumor.rep1
19-027-133KIKI.Male.Tumor


title: KMN3

description:
Library name: APP.NL-G-F.Male.Normal.rep3
19-027-132KIKI.Male.Normal


title: siControl JURKAT (1h) rep2


title: Control_replicate_20

description: Sample name: K32


title: 8024, plasma sample, IFNβ-1a, 4days

description: Library name: F11650464


title: KMN2

description:
Library name: APP.NL-G-F.Male.Normal.rep2
19-027-130KIKI.Male.Normal


title: siControl JURKAT (0h) rep1


title: KMN1

description:
Library name: APP.NL-G-F.Male.Normal.rep1
19-027-129KIKI.Male.Normal


title: 8024, plasma sample, IFNβ-1a, 1.33days

description: Library name: F11650181


title: Control_replicate_19

description: Sample name: K28


title: siControl JURKAT (0h) rep2


title: WMT3

description:
Library name: WT.Male.Tumor.rep3
19-027-117WT.Male.Tumor


title: T1D_replicate_20

description: Sample name: D33


title: siControl JURKAT (1h) rep1


title: 8024, plasma sample, IFNβ-1a, 0.67days

description: Library name: F11650031


title: T1D_replicate_19

description: Sample name: D31


title: siMETTL3 HUVEC (6h) rep2

value: HUVEC


title: siMETTL3 HUVEC (6h) rep1


title: siMETTL3 HUVEC (3h) rep2


title: 8024, plasma sample, IFNβ-1a, 0.33days

description: Library name: F11649950


title: WMN3

description:
Library name: WT.Male.Normal.rep3
19-027-110WT.Male.Normal


title: siMETTL3 HUVEC (3h) rep1


title: 8024, plasma sample, IFNβ-1a, 2days

description: Library name: F11650218


title: T1D_replicate_18

description: Sample name: D28


title: WMN2

description:
Library name: WT.Male.Normal.rep2
19-027-109WT.Male.Normal


title: WMT2

description:
Library name: WT.Male.Tumor.rep2
19-027-116WT.Male.Tumor


title: 8024, plasma sample, IFNβ-1a, 0.25days

description: Library name: F11649934


title: WMT1

description:
Library name: WT.Male.Tumor.rep1
19-027-113WT.Male.Tumor


title: 8024, plasma sample, IFNβ-1a, 0.125days

description: Library name: F11649856


title: siMETTL3 HUVEC (1h) rep2


title: WMN1

description:
Library name: WT.Male.Normal.rep1
19-027-108WT.Male.Normal


title: T1D_replicate_17

description: Sample name: D26


title: Control_replicate_18

description: Sample name: K25


title: 8024, plasma sample, IFNβ-1a, Baseline

description: Library name: F11649732


title: siMETTL3 HUVEC (1h) rep1


title: siMETTL3 HUVEC (0h) rep2


title: 8021, plasma sample, pegIFNβ-1a, 13days

description: Library name: F11645585


title: siMETTL3 HUVEC (0h) rep1


title: Control_replicate_16

description: Sample name: K43


title: P14 Rnu11 mutant testis 2

city: Storrs

first: Rahul

middle: N

last: Kanadia

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

description:
Library name: Sample 5
Included in control-mutant-DE files in "C2 average TPM"

data_processing:
Paired-end reads were mapped to GRCm38.Ens99 using Hisat2 with end-to-end alignment, disallowing discordant and mixed alignments, and using the "sensitive" preset for improved alignment accuracy.
Gene and transcript abundance per sample were estimated from HISAT2-generated alignments using IsoEM2 with a 95% confidence threshold.
Differential gene and transcript expression was analyzed from IsoEM2 outputs using IsoDE2, comparing the bootstrap estimates from control and mutant conditions. A p-value threshold of 0.01 was applied to determine significance.
Assembly: GRCm38.Ens99
Supplementary files format and content: {sample}_gene_tpm_estimates.txt and {sample}_iso_tpm_estimates.txt are text files containing the IsoEM2 abundances (TPM) for each sample.
Supplementary files format and content: control-mutant-DE_geneTPM.txt and control-mutant-DE_isoTPM.txt are text files containing the IsoDE2 outputs for control versus mutant abundances (TPM).

source_name: Whole testis

extract_protocol:
Whole testes were dissected from postnatal day 14 mice and total RNA was extracted using the Zymo DirectZOL RNA MiniPrep kit
Library preparation was carried out using the Illumina TruSeq Stranded Total RNA Library Sample Prep Kit with RiboZero for ribosomal RNA depletion

value: Whole testis

value: Rnu11 cKO


title: Control_replicate_17

description: Sample name: K39


title: 8021, plasma sample, pegIFNβ-1a, 9days

address: 10903 New Hampshire Avenue

description: Library name: F11645483


title: P14 Rnu11 mutant testis 1

description:
Library name: Sample 4
Included in control-mutant-DE files in "C2 average TPM"


title: T1D_replicate_16

description: Sample name: D44


title: siControl HUVEC (6h) rep2


title: 8021, plasma sample, pegIFNβ-1a, 6days

description: Library name: F11645020


title: P14 control testis 3

description:
Library name: Sample 3
Included in control-mutant-DE files in "C1 average TPM"


title: Control_replicate_15

description: Sample name: K23


title: P14 Rnu11 mutant testis 3

description:
Library name: Sample 6
Included in control-mutant-DE files in "C2 average TPM"


title: siControl HUVEC (6h) rep1


title: Control_replicate_14

description: Sample name: K38


title: siControl HUVEC (3h) rep2


title: T1D_replicate_15

description: Sample name: D23


title: 8021, plasma sample, pegIFNβ-1a, 5days

description: Library name: F11644843


title: 8021, plasma sample, pegIFNβ-1a, 4days

description: Library name: F11644728


title: P14 control testis 1

description:
Library name: Sample 1
Included in control-mutant-DE files in "C1 average TPM"


title: T1D_replicate_14

description: Sample name: D30


title: 8021, plasma sample, pegIFNβ-1a, 2days

description: Library name: F11644482


title: siControl HUVEC (3h) rep1


title: naïve non-parenchymal liver cells, SNp1 [scRNA-seq]

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

description:
Library name: SN
10x Genomics

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings
10x 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GRCm38 - mm10 genome to obtain gene expression matrices
Assembly: GRCm38 - mm10
Supplementary files format and content: _filtered_feature_bc_matrix.h5: Feature barcode matrices file in the HDF5 format

source_name: Liver

extract_protocol:
Livers were digested with Collagenase and Dnase and passed through a 33% Percoll gradient to retain non-parenchymal cells
Manufacturer's instructions (10x Visium) were followed to prepare sequencing libraries

value: Liver

value: C57BL/6J wild type

value: no treatment


title: 8021, plasma sample, pegIFNβ-1a, 1.33days

city: Silver Spring

first: Lakshmi Manasa

last: Chekka

institute: U.S. FDA

description: Library name: F11644445

value: Healthy


title: Control_replicate_13

description: Sample name: K45


title: siControl HUVEC (1h) rep1

value: siControl


title: P14 control testis 2

description:
Library name: Sample 2
Included in control-mutant-DE files in "C1 average TPM"


title: T1D_replicate_13

description: Sample name: D38


title: L. donovani infected non-parenchymal liver cells, SC1 [scRNA-seq]

description:
Library name: SC1
10x Genomics

value: L. donovani infected


title: Control_replicate_12

description: Sample name: K34


title: 8021, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F11644198


title: siControl HUVEC (0h) rep2


title: 8021, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F11644295


title: T1D_replicate_12

description: Sample name: D49


title: siControl HUVEC (1h) rep2


title: naïve non-parenchymal liver cells, SNp2, [scRNA-seq]

description:
Library name: SNp
10x Genomics


title: siMETTL3 HEK293T (6h) rep2


title: L. donovani infected non-parenchymal liver cells, SC2 [scRNA-seq]

description:
Library name: SC2
10x Genomics


title: L. donovani infected liver cells, SC4 [scRNA-seq]

description:
Library name: SC4
10x Genomics


title: L. donovani infected non-parenchymal liver cells, SI4 [scRNA-seq]

description:
Library name: SI4
10x Genomics


title: siMETTL3 HEK293T (3h) rep2


title: siMETTL3 HEK293T (6h) rep1


title: T1D_replicate_11

description: Sample name: D47


title: 8021, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F11644214


title: 8021, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F11643996


title: siMETTL3 HEK293T (3h) rep1


title: 8018, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F11639849