title: A_21_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 21 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: iPSC-EC_Untreated_48h_Sample1

status: Public on Jul 31 2025

type: SRA

city: Palo Alto

first: Joseph

middle: C

last: Wu

state: California

address: 240 Pasteur Drive

department: Cardiovascular Institute

country: USA

institute: Stanford University

library_source: transcriptomic

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: TPM_NicotineTreated.csv

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: EGM2 media supplemented with 25 ng/mL VEGF, 10 ng/mL bFGF and 5 µM SB431542

extract_protocol:
Trizol
Messenger RNA 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 using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: 1 uM nicotine for 48h

tag: tissue

value: cell line

tag: cell line

value: iPSC-derived endothelial cells

tag: cell type

value: Endothelial cells

tag: treatment

value: Untreated


title: iPSC-EC_Nicotine_48h_Sample19

value: Nicotine


title: iPSC-EC_Nicotine_48h_Sample17


title: iPSC-EC_Nicotine_48h_Sample16


title: iPSC-EC_Nicotine_48h_Sample15


title: A_20_tumor_INPUT

city: Guangzhou

first: Jian

last: Zhen

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

country: China

institute: Sun Yat-sen University Cancer Center

description: Input sample of MeRIP-seq

data_processing:
Reads were first mapped to the human reference genome (GRCh38) by BWA (v0.7.15) and the annotation file obtained from the GENCODE database (https://www.gencodegenes.org/). Circm6A was applied to detect the circRNAs and their m6A modifications from all our PDAC tissue and normal tissue samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count files of circRNAs for each sample

source_name: pancreas tissue

extract_protocol:
Total RNA from pancreatic cancer patient 20 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor

tag: disease

value: pancreatic cancer


title: wt strain, T60, repl. 2

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Library name: A10_BY_T60_2

data_processing:
Mapping was performed using STAR with default parameters except –alignIntronMax 1500 –alignMatesGapMax 1500 alignJSoverhangMin 5
For counting, we used featureCounts with a custom SAF file (saccharomyces20170228_corr_nochr.saf)
Assembly: Saccer3
Supplementary files format and content: raw_counts.txt contains raw number of counts for each sample and feature.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: cell culture

growth_protocol: Cells were grown in rich YPD medium to a A600nm of 0.6 to 0.8

extract_protocol:
Total RNA was extracted with hot phenol from yeast cells and precipitated in the presence of ammonium acetate and ethanol. After additional washes in 70% ethanol, RNA was recovered in pure water.
The Novogene company performed the sequencing, using poly(A) selection and strand specific RNA sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: IAA and beta-oestradiol were added to cultures that were incubated for 60 minutes at 30°C. Total RNA and proteins were extracted from the cultures without or with treatment.

value: cell culture

tag: genotype

value: WT

value: IAA (100 uM) + beta-oestradiol (1 uM)


title: iPSC-EC_Nicotine_48h_Sample14


title: A_22_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 22 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: lsm1-ideg strain T0, repl. 3

description: Library name: A15_LSM1_T0_3


title: iPSC-EC_Untreated_48h_Sample5


title: A_20_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 20 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: iPSC-EC_Nicotine_48h_Sample13


title: dcp2-ideg strain T0, repl. 2

description: Library name: A9_DCP2_T0_2


title: dcp2-ideg strain T60, repl. 2

description: Library name: A11_DCP2_T60_2


title: iPSC-EC_Nicotine_48h_Sample12


title: A_21_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 21 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: A_2_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 2 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor adjant


title: iPSC-EC_Nicotine_48h_Sample10


title: iPSC-EC_Nicotine_48h_Sample9


title: iPSC-EC_Nicotine_48h_Sample11


title: A_2_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 2 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: iPSC-EC_Nicotine_48h_Sample8


title: wt strain, T0, repl. 2

description: Library name: A7_BY_T0_2


title: sub_library4

city: Cambridge

first: Emma

last: Rawlins

address: Tennis court road

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic single cell

data_processing:
The sequencing data was initially processed with split-pipe (Version 1.1.1, Parse Biosciences) to demultiplex with the sample loading information for each sub-library, and then combine the results of sublibraries. The combined gene count matrix was used for downstream analysis in Seurat (Version 5).
Assembly: GRCh38.p14
Supplementary files format and content: An r object of scRNA-seq data in Seurat with cells clustered.

source_name: lung organoids

extract_protocol: Evercode Whole Transcriptome v2 kit

value: lung organoids


title: lsm1-ideg strain T60, repl. 2

description: Library name: A8_LSM1_T60_2


title: dcp2-ideg strain T60, repl. 1

description: Library name: A5_DCP2_T60_1


title: sub_library3


title: iPSC-EC_Nicotine_48h_Sample7


title: A_19_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 19 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: lsm1-ideg strain T60, repl. 1

description: Library name: A6_LSM1_T60_1


title: sub_library1


title: A_19_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 19 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: A_18_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 18 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: iPSC-EC_Nicotine_48h_Sample6


title: sub_library2


title: wt strain, T60, repl. 1

description: Library name: A4_BY_T60_1


title: A_18_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 18 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: lsm1-ideg strain T0, repl. 1

description: Library name: A3_LSM1_T0_1


title: A_18_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 18 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: iPSC-EC_Nicotine_48h_Sample5


title: iPSC-EC_Nicotine_48h_Sample3


title: Treated with CHIKV pseudotype 1

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

description:
Library name: CHIKV_psudotype_infection
Culumn name in all_samples_normalized_counts.txt: Time_1

library_source: genomic

data_processing:
MAGeCK-VISPR
Assembly: hg19
Supplementary files format and content: Normalized counts from MAGeCK-VISPR
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: A549 cells  were grown in DMEM supplemented with 10% FCS, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
RNA was extracted usin Trizol
Follwing instruction from Joung et al, Nature Protocols, 2017

treatment_protocol: Ceudovitox

value: lung carcinoma epithelial cells

value: Wilde Type

value: Pseudotype


title: Untreated Control 1

description:
Library name: Time_0
Culumn name in all_samples_normalized_counts.txt: CHIKV_psudotype_infection


title: wt strain, T0, repl. 1

description: Library name: A1_BY_T0_1


title: dcp2-ideg strain T0, repl. 1

description: Library name: A2_DCP2_T0_1


title: iPSC-EC_Nicotine_48h_Sample1


title: A_17_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 17 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: KO2

city: Zhanjiang

first: Ji-Xin

last: Tang

state: Guangdong

address: No.57, Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: KO2 FPPM', 'KO2 TPM' and ‘KO2 Read Count’

data_processing:
Transcriptome sequencing procedures include RNA extraction, RNA sample quality detection, library construction, library purification, li-brary detection, library quantification, generation of sequencing clusters, and comput-er sequencing. In order to ensure the accuracy and reliability of source data, we carried out strict quality control for each step of the experimental process.
Different libraries were mixed according to the requirements of effective concen-tration and target data volume and then sequencing by Illumina.
Bcl2fastq (v2.17.1.14) was used for image Base Calling for preliminary quality analysis to obtain the original sequencing Data (Pass Filter Data), and the results were stored in FASTQ file format. It contains sequencing sequence information and its corresponding sequencing quality information. The sequencing data quality was evaluated by FastQC (v0.10.1) software.
Raw data was preprocessed using Cutadapt (version 1.9.1) software and low quality data was filtered to remove contamination and joint sequences. The filtered sequenc-ing Clean Data was compared with the reference genome for analysis.
Hisat2(v2.0.1) software was used to compare short reads with the default parameters. Gene expres-sion was calculated using Cuffdiff software (v2.2.1), which calculated gene expression using TPM[38]. Genetic difference anal-ysis was performed using cuffdiff(v2.2.1), which was based on a negative binomial distribution model. The detection results were screened according to the differential significance criteria (differential gene expression changes of more than 2 times and qvalue(fdr, padj<=0.05), and the down-regulation of significant differential gene ex-pression was counted.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: matrix-CON-TAX1BP1 KO.xls contains the count value and TPM value of each sample, and the corresponding gene ID.
Supplementary files format and content: fastq.gz are the original sequencing data of the corresponding sample.

source_name: HK-2 cell

extract_protocol:
Total cellular RNA was extracted from cultured cells using RNAiso Plus (Takara, 9108, Japan) according to the manufacturer’s protocol.
The RNA concentra-tion and purity were quantified using NanoDrop 2000 ultrafine spectrophotometer (Thermo Scientific, Massachusetts, America). And then the genome DNA was elimi-nated with the RNase-free DNase H. The RNA was then reverse-transcribed with 5× FastKing-RT SuperMix kit (TIANGEN, KR118–01, Beijing, China) according to the manufacturer’s protocols. The reverse-transcribed cDNA was used as template for qPCR using Genious 2X SYBR Green Fast qPCR Mix (ABclonal, RK21204) according to the manufacturer’s protocol. LightCycler 480 II real-time fluorescence quantitative PCR instrument was used for PCR reaction. The primer sequences used for amplifying the target fragments and GAPDH as internal control were listed in Table1. Gene’s rela-tive expression levels were calculated by the 2-ΔΔCt (threshold cycle) method.

value: HK-2 cell

value: gene knock out cell


title: iPSC-EC_Nicotine_48h_Sample2

extract_protocol:
Trizol
Messenger RNA 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 using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: cell line


title: KO3

description: KO3 FPPM', 'KO3 TPM' and ‘KO3 Read Count’


title: A_17_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 17 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: CR_VSV_2

first: Fan

last: Xing

address: No. 106 Zhongshan 2nd Road, Guangzhou, Guangdong Province, China

institute: Guangdong Provincial People's Hospital

data_processing:
Raw fastq were quality-controlled using fastp(v0.23.4) with default parameters.
The clean fastqas were mapped to reference genome(GRCh38) by STAR(v2.7.11a) with parameter "--quantMode GeneCounts".
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file with expression counts matrix

extract_protocol: RNA libraries for RNA-seq were prepared using mRNA-seq library Prep Kit following manufacturer's protocols

value: CR23_B7H3_CAR_T cels

value: loading VSVΔ51


title: KO1

description: KO1 FPPM', 'KO1 TPM' and ‘KO1 Read Count’


title: A_17_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 17 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: CR_VSV_3


title: A_17_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 17 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: thiolutin,nc,wt,40-3

city: Kunming, Yunnan

first: fei

last: li

address: Dongwaihuan South Road, University Town, Chenggong District, Kunming City, Yunnan Province

institute: Yunnan university

description:
Library name: sample58
WT-40-3
featurecounts_nc_decay.txt

data_processing:
SLAM-Seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) data were processed using a custom computational pipeline. First, adapter trimming was performed using Trim Galore (v0.6.10) to remove sequencing adapters and low-quality bases. Cleaned reads were then aligned to the reference genome of either Homo sapiens (GRCh38) or the Neurospora crassa using STAR (v2.7.10a) with default parameters, allowing detection of mismatches such as T>C conversions.
Following alignment, SAMtools (v1.15.1) was used to convert, sort, and index the aligned SAM files into BAM format. A custom Python script was then employed to extract reads containing T>C mutations, which are indicative of 4-thiouridine incorporation and subsequent alkylation. This step produced a mutation-specific BAM file consisting only of T>C conversion-containing reads.
To quantify gene-level expression and mutation levels, featureCounts (Subread v2.0.3) was used to separately count:
(1) the number of T>C mutation reads, and
(2) the total reads (mutation-inclusive and -exclusive),
mapped to each gene based on the corresponding genome annotation (GTF file).
Finally, for each gene, a T>C mutation ratio (termed remaining reads percentage) was calculated by dividing the number of T>C mutation reads by the total number of reads, providing a quantitative measure of RNA stability and labeling retention.
Ribosome profiling data for Neurospora crassa (assembly NC12), Mus musculus(GRCm38), and Homo sapiens(GRCh38) were processed according to established pipelines. Raw sequencing reads underwent adapter trimming and size selection (retaining 25-40 nt fragments), followed by rRNA depletion. Filtered reads were aligned using Bowtie to custom genomic references containing the longest transcript per gene plus 100-nt flanking regions at both ends.  Ribosome-protected footprints (RPFs) were stratified by length, with A-site codon assignment to nucleotides 16-18 from the 5' end. Subsequently, the groups of RPFs with a high ratio of in-frame codons (e.g., >70% for N. crassa, >70% for H. sapiens, >80% for M. musculus) are selected for further analysis. These groups include RPFs in the 0 frame, as well as the +1 and -1 frames
Assembly: hg38?nc10
Supplementary files format and content: feature counts for each sample

organism: Neurospora crassa

source_name: fungal cell

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1×penicillin-streptomycin and incubated at 37℃ with 5% concentration of CO2. Neurospora crassa strains were grown in minimal mediu at 25℃ with constant light.

extract_protocol:
total RNA was extracted with Trizol reagent.
1.For SLAM-seq :After alkylation modification with iodoacetamide, 1ug total RNA (HCT116 cell) or 50 ng mRNA (N. crassa) was prepared for library. and library preperation was following the manufacturers protocal of VAHTS Universal V8 RNA-seq Library Prep Kit
2.For Ribo-seq in human cell : 2×10? HCT116 cells were lysed in 300 µL ice-cold lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl?, 1 mM DTT, 100 ?g/mL cycloheximide, 0.5% Triton X-100, 2 U/mL DNase I, 1× protease inhibitor cocktail). Lysates were centrifuged at 10,000 × g for 10 min at 4°C. Supernatants were treated with RNase I (1 U per OD??? unit) for 45 min at 25°C. Total RNA was extracted using TRIzol reagent, precipitated with glycogen, and washed with 80% ethanol. Ribosome-protected fragments (28-34 nt) were resolved on 16% TBE-urea PAGE, excised, and eluted in RNA Gel Extraction Buffer (300 mM NaOAc, 1mM EDTA, 0.25% SDS). RNA was precipitated with 1× volume isopropanol at -20°C overnight. For library preparation, 100-200 ng RNA fragments were adenylated using poly(A) polymerase and PNK (37°C, 30 min). Preadenylated 5' adapter were ligated to ribosome-protected fragments with T4 RNA Ligase 2, truncated KQ (25°C, 2 h). Then purifying the ligation product with Streptavidin magnetic bead. And template-switching primer was used in reverse transcription with SuperScript III reverse (50°C, 30 min), following the library amplification.

treatment_protocol: 100 nM 4sU was added to medium for 2 hours (N. crassa) or 24 hours (K562 cells) labeling. Then cultures were supplied with 10uM uridine to stop further labeling.

value: fungal cell


title: CR_VSV_1


title: thiolutin,nc,wt,60-1

description:
Library name: sample59
WT-60-1
featurecounts_nc_decay.txt


title: thiolutin,nc,wt,60-2

description:
Library name: sample60
WT-60-2
featurecounts_nc_decay.txt


title: thiolutin,nc,wt,60-3

description:
Library name: sample61
WT-60-3
featurecounts_nc_decay.txt


title: A_16_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 16 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: A_18_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 18 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: CON2

description: CON2 FPKM' , 'CON2 TPM' and ‘CON2 Read Count’

value: normal cell


title: CR23_3

value: control


title: CON1

description: CON1 FPKM' , 'CON1 TPM' and ‘CON1 Read Count’


title: iPSC-EC_Nicotine_48h_Sample4

value: iPSC-derived endothelial cells

value: Endothelial cells

value: Nicotine


title: CON3

description: CON3 FPKM' , 'CON3 TPM' and ‘CON3 Read Count’

value: WT


title: thiolutin,nc,wt,40-1

description:
Library name: sample56
WT-40-1
featurecounts_nc_decay.txt


title: A_15_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 15 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor

value: pancreatic cancer


title: thiolutin,nc,wt,20-3

description:
Library name: sample55
WT-20-3
featurecounts_nc_decay.txt


title: CR23_1


title: A_15_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 15 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: thiolutin,nc,wt,40-2

description:
Library name: sample57
WT-40-2
featurecounts_nc_decay.txt


title: B7_VSV_3

value: B7H3_CAR_T cels


title: A_16_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 16 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: thiolutin,nc,wt,20-2

description:
Library name: sample54
WT-20-2
featurecounts_nc_decay.txt


title: thiolutin,nc,wt,10-3

description:
Library name: sample52
WT-10-3
featurecounts_nc_decay.txt


title: RNA-seq of Vehicle-1

first: Wenjie

last: Zhang

address: Guangzhou Medical University, No.1 Xinzao Road, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

description: Library name: Sample 4

data_processing:
Raw data (FASTQ format) underwent base calling and quality control. Differentially expressed genes (DEGs) were identified (threshold: |log₂FC| > 0.58, adjusted P value < 0.05). DEG heatmaps were generated using the pheatmap package, and volcano plots were created with ggplot2. Downregulated DEGs were analyzed for GO enrichment using Metascape (Fisher’s exact test，P < 0.05).
Assembly: macrophages
Supplementary files format and content: .xlsx

organism: Mus musculus

source_name: plantar

extract_protocol:
Total RNA was isolated, treated with DNase, and purified using columns. RNA concentration was measured and adjusted. RNA quality was confirmed using a fragment analyzer.
Qualified samples were used for library preparation: mRNA was enriched with oligo-dT beads, fragmented, and cDNA was synthesized. Adapters were ligated and PCR-amplified. Libraries were sequenced (paired-end) on an Illumina platform.

value: plantar


title: RNA-seq of Vehicle-3

description: Library name: Sample 6


title: RNA-seq of Vehicle-2

description: Library name: Sample 5


title: RNA-seq of HSPA1A-2

description: Library name: Sample 2


title: B7_VSV_2


title: A_14_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 14 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor adjant


title: thiolutin,nc,wt,20-1

description:
Library name: sample53
WT-20-1
featurecounts_nc_decay.txt


title: B7_3


title: A_13_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 13 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: RNA-seq of HSPA1A-1

description: Library name: Sample 1


title: A_14_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 14 normal tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: CR23_2


title: B7_VSV_1


title: A_13_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 13 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: thiolutin,nc,wt,10-1

description:
Library name: sample50
WT-10-1
featurecounts_nc_decay.txt


title: B7_2


title: A_12_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 12 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: thiolutin,nc,wt,0-3

description:
Library name: sample49
WT-0-3
featurecounts_nc_decay.txt


title: B7_1


title: TCDD 2

city: Ann Arbor

first: Timothy

last: Frankel

state: MI

address: 1500 East Medical Center Dr

institute: University of Michigan

description: Library name: TCDD 2

data_processing:
The University of Michigan Advanced Genomics Core performed processing and alignment of the raw data using Cell Ranger (version 7.1.0) with default settings and an initial expected cell count of 10,000.
Assembly: mm10-2020-A
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: Orthotopic pancreas tumor

growth_protocol: Mice were orthotopically injected with 30k syngeneic KPC cells (cell line 7940b), and mice were treated with 10ug/Kg TCDD or vehicle control (DMSO) once a week for 2 weeks. Tumors were harvested on day 19

extract_protocol:
To prepare tissues for sequencing, samples were disrupted to single cell suspension by mechanically mincing the tissue, followed by enzymatic digestion with Collagenase V (1 mg/mL in RPMI, #C9263, Sigma-Aldrich) at 37°C for 30 min under constant shaking. After digestion, suspensions underwent serial filtration through 500 µm, 100 µm, and 40 µm mesh cell strainers. We then enriched for live cells using the MACS Dead Cell Removal Kit (#130-090-101, Miltenyi Biotec). The resulting single cell suspensions were brought to the University of Michigan Advanced Genomics Core for cDNA library preparation and sequencing.
Samples were run using 50-cycle paired-end reads on the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.

value: Orthotopic pancreas tumor

tag: strain

value: TCDD

tag: batch


title: thiolutin,nc,wt,10-2

description:
Library name: sample51
WT-10-2
featurecounts_nc_decay.txt


title: A_11_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: A_12_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 12 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: Hypoxia_HIF1a_rep6

data_processing:
Data was processed using the nf-core/rnaseq pipeline
Assembly: GRCh38.p13
Supplementary files format and content: raw gene counts in tsv format

extract_protocol:
RNeasy Mini Kit
Novogene RNA-seq library preparation

value: lung organoids

value: Hypoxia


title: thiolutin,nc,wt,0-2

description:
Library name: sample48
WT-0-2
featurecounts_nc_decay.txt


title: Hypoxia_HIF1a_rep5


title: Vehicle 2

description: Library name: Vehicle 2

value: Vehicle


title: thiolutin,nc,wt,0-1

description:
Library name: sample47
WT-0-1
featurecounts_nc_decay.txt

value: fungal cell


title: Hypoxia_HIF1a_rep3


title: A_11_normal_rep2_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 normal _rep2 tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: NC,UPF1,60-1

description:
Library name: sample28
slam-UPF1-60-1
featurecounts_nc.txt

extract_protocol:
total RNA was extracted with Trizol reagent.
1.For SLAM-seq :After alkylation modification with iodoacetamide, 1ug total RNA (HCT116 cell) or 50 ng mRNA (N. crassa) was prepared for library. and library preperation was following the manufacturers protocal of VAHTS Universal V8 RNA-seq Library Prep Kit
2.For Ribo-seq in human cell : 2×10? HCT116 cells were lysed in 300 µL ice-cold lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl?, 1 mM DTT, 100 ?g/mL cycloheximide, 0.5% Triton X-100, 2 U/mL DNase I, 1× protease inhibitor cocktail). Lysates were centrifuged at 10,000 × g for 10 min at 4°C. Supernatants were treated with RNase I (1 U per OD??? unit) for 45 min at 25°C. Total RNA was extracted using TRIzol reagent, precipitated with glycogen, and washed with 80% ethanol. Ribosome-protected fragments (28-34 nt) were resolved on 16% TBE-urea PAGE, excised, and eluted in RNA Gel Extraction Buffer (300 mM NaOAc, 1mM EDTA, 0.25% SDS). RNA was precipitated with 1× volume isopropanol at -20°C overnight. For library preparation, 100-200 ng RNA fragments were adenylated using poly(A) polymerase and PNK (37°C, 30 min). Preadenylated 5' adapter were ligated to ribosome-protected fragments with T4 RNA Ligase 2, truncated KQ (25°C, 2 h). Then purifying the ligation product with Streptavidin magnetic bead. And template-switching primer was used in reverse transcription with SuperScript III reverse (50°C, 30 min), following the library amplification.

value: UPF1 KD


title: Vehicle 1

description: Library name: Vehicle 1


title: NC,UPF1,60-2

description:
Library name: sample29
slam-UPF1-60-2
featurecounts_nc.txt


title: A_11_normal_rep2_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 normal _rep2 tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: pIR_P1_lung_rep2

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Library name: pIR_P1_lung_rep2

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matrices were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed using DESeq2 package. Only genes with adjusted P value (for cell lines) or P value (for organs) < 0.05, fold change > 2 and basemean > 12.5 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. To evaluate the transcription level of transposons, the clean data were mapped to mm10 using Hisat2 with the parameters -k 100 -no-unal -no-mixed -no-discordant. Then the TEcount function of TE transcritps (v2.2.1) was used to count reads from TE with the parameters -mode multi. Differentially expressed TE analysis was performed using DESeq2 package. Only TEs with a P value < 0.05 and fold change > 2 were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: comma or tab separated values file, raw counts for gene expression.

source_name: lung

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for following library preparation. RNA-Seq libraries were prepared with VAHTS mRNA-Seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 instrument. For Smart-Seq2 library preparation, the cDNA was synthesized and amplified using the Single Cell Full-Length mRNA-Amplification Kit (Vazyme, N712). The full-length cDNA was assessed for quality and quantity using QIAxcel Advanced (QIAGEN) and Qubit 3.0 (ThermoFisher). Then RNA-Seq libraries were constructed from 1 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Amplified libraries were purified with VAHTS DNA Clean Beads (Vazyme, N411) and sequenced on the Illumina NovaSeq 6000.

value: lung

value: pIR


title: Hypoxia_HIF1a_rep2


title: Hypoxia_HIF1a_rep4


title: A_11_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: pWT_P1_lung_rep3

description: Library name: pWT_P1_lung_rep3

value: pWT


title: A_11_normal_rep1_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 normal _rep1 tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: pIR_P1_lung_rep1

description: Library name: pIR_P1_lung_rep1


title: NC,UPF1,40-3

description:
Library name: sample27
slam-UPF1-40-3
featurecounts_nc.txt


title: TCDD 1

description: Library name: TCDD 1


title: Hypoxia_HIF1a_rep1


title: pWT_P1_lung_rep2

description: Library name: pWT_P1_lung_rep2


title: A_11_normal_rep1_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 11 normal _rep1 tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: NC,UPF1,60-3

description:
Library name: sample30
slam-UPF1-60-3
featurecounts_nc.txt


title: NC,UPF1,40-2

description:
Library name: sample26
slam-UPF1-40-2
featurecounts_nc.txt


title: pWT_P1_lung_rep1

description: Library name: pWT_P1_lung_rep1


title: Hypoxia_NTC_rep6


title: A_10_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 10 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: NC,UPF1,40-1

description:
Library name: sample25
slam-UPF1-40-1
featurecounts_nc.txt


title: Hypoxia_NTC_rep5


title: NC,UPF1,20-2

description:
Library name: sample23
slam-UPF1-20-2
featurecounts_nc.txt


title: NC,UPF1,20-3

description:
Library name: sample24
slam-UPF1-20-3
featurecounts_nc.txt


title: pIR_P1_liver_rep2

description: Library name: pIR_P1_liver_rep2

source_name: liver

value: liver


title: A_10_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 10 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: A_1_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 1 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP).
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.


title: pIR_P1_liver_rep1

description: Library name: pIR_P1_liver_rep1


title: pWT_P1_liver_rep3

description: Library name: pWT_P1_liver_rep3


title: NC,UPF1,20-1

description:
Library name: sample22
slam-UPF1-20-1
featurecounts_nc.txt


title: Hypoxia_NTC_rep2


title: NC,UPF1,10-3

description:
Library name: sample21
slam-UPF1-10-3
featurecounts_nc.txt


title: 7dpci 3

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell. Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Well numbers refer to the 384-well plate in the following ordre: A1 to A24 - B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
Assembly: zv9 (with improved 3' annotation, see Junker et al (2014) Cell)
Supplementary files format and content: .tsv, count table

organism: Danio rerio

source_name: cardiac ventricle

growth_protocol: standard fish husbandry protocols

extract_protocol:
Single cells of border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 1, 3 and 7 dpci into 384well plates
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates, each well containing 1 cell, containing Vapor-Lock oil with CEL-Seq2 barcoded primers, spike-in mRNA and dNTPs (Single Cell Discoveries). Plates were spun down and frozen at -80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT-seq protocol. In this protocol, the CEL-seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform.

treatment_protocol: Cryo-injury was induced on the tip of the ventricle using a copper probe pre-chilled in liquid nitrogen.

value: cardiac ventricle

value: border zone cardiomyocytes

value: TL


title: 7dpci 2


title: Hypoxia_NTC_rep1


title: pWT_P1_liver_rep1

description: Library name: pWT_P1_liver_rep1


title: pWT_P1_liver_rep2

description: Library name: pWT_P1_liver_rep2


title: NC,UPF1,10-2

description:
Library name: sample20
slam-UPF1-10-2
featurecounts_nc.txt


title: Normoxia_NTC_rep6

value: Normoxia


title: NC,UPF1,10-1

description:
Library name: sample19
slam-UPF1-10-1
featurecounts_nc.txt


title: 7dpci 1


title: pIR_P1_kidney_rep2

description: Library name: pIR_P1_kidney_rep2

source_name: kidney

value: kidney


title: Hypoxia_NTC_rep4


title: Normoxia_NTC_rep5


title: A_1_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 1 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor

value: pancreatic cancer


title: Hypoxia_NTC_rep3


title: Normoxia_NTC_rep4


title: pIR_P1_kidney_rep1

description: Library name: pIR_P1_kidney_rep1


title: 1dpci


title: NC,UPF1,0-2

description:
Library name: sample17
slam-UPF1-0-2
featurecounts_nc.txt


title: NC,UPF1,0-3

description:
Library name: sample18
slam-UPF1-0-3
featurecounts_nc.txt


title: Normoxia_NTC_rep3


title: pWT_P1_kidney_rep3

description: Library name: pWT_P1_kidney_rep3


title: pWT_P1_kidney_rep2

description: Library name: pWT_P1_kidney_rep2


title: NC,WT,60-3

description:
Library name: sample15
slam-WT-60-3
featurecounts_nc.txt

value: WT


title: Normoxia_NTC_rep2

value: lung organoids


title: pIR_P1_heart_rep2

description: Library name: pIR_P1_heart_rep2

source_name: heart

value: heart


title: NC,WT,60-2

description:
Library name: sample14
slam-WT-60-2
featurecounts_nc.txt


title: Subcutaneous Adipose Tissue (Backfat) Cow 2

city: Lubbock

first: Mollie

last: Green

state: TX

address: 1006 Canton Ave, Room 109

institute: Texas Tech University

description:
Library name: BF2
10x Genomics

data_processing:
Raw base call files were demultiplexed using cellranger mkfastq (v6.1.2) to generate FASTQ files.
Assembly: ARS-UCD1.2 (Bos taurus)
Supplementary files format and content: Processed data includes filtered feature-barcode matrices (MTX, TSV), normalized expression matrices (.csv), metadata with cell annotations (.csv), and UMAP coordinates (.csv).

molecule: nuclear RNA

organism: Bos taurus

source_name: Subcutaneous Adipose Tissue

growth_protocol: Cattle were raised under standard commercial feedlot conditions until slaughter. Diet, age, and breed  unkown

extract_protocol:
Fresh adipose tissue was dissected and minced on ice. Tissue was homogenized using a pre-chilled Dounce homogenizer in ice-cold lysis buffer. Nuclei were filtered through a 40 µm strainer, pelleted, washed, and resuspended for counting and quality assessment before loading onto the 10x Chromium platform.
Single-nucleus RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3' v3.1 kit, following the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: No experimental treatment was applied prior to tissue collection. Animals were managed identically under uniform feeding and handling protocols.

value: Subcutaneous Adipose Tissue


title: Intramuscular Adipose Tissue, Cow 2

description:
Library name: IM2
10x Genomics

source_name: Intramuscular Adipose Tissue

value: Intramuscular Adipose Tissue


title: HealthyControl_blood_sample13,control

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description: Ribosomes removed RNA

library_source: other

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, PCR duplicates were removed using seqkit v2.4.0. The 8-bp UMIs the 6-mer following the UMI were excised from the deduplication reads using UMI_tools v1.1.4. To enhance the accuracy of the mapping results, we trimmed the 6-mer sequence to minimize such errors.
All fastq files were aligned to the human reference genome hg38, using HISAT2 v2.2.1.
The following data analysis procedures for site identification are mainly referred to PRAISE
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: other

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
Five hundred nanogram fragmented total RNA was subjected to bisulfite treatment as previous references (PMID: 36997645; 36302989; 37968414). The BS treated RNA was labeled as ‘treat’ sample, while the BS untreated RNA was labeled as ‘Input’ sample. Ten nanogram ‘treated’ RNA sample and 10 ng ‘Input’ RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v3—Pico Input Mammalian (Takara Bio, 634485) according to the manufacturer’s protocol with several modifications as previous reference. All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).
PRAISE (PMID: 36997645), BID-seq (PMID: 36302989; PMID: 37968414)

value: Peripheral blood

value: untreated


title: pIR_P1_heart_rep1

description: Library name: pIR_P1_heart_rep1

value: pIR


title: NC,WT,60-1

description:
Library name: sample13
slam-WT-60-1
featurecounts_nc.txt

value: fungal cell


title: Subcutaneous Adipose Tissue (Backfat) Cow 1

description:
Library name: BF1
10x Genomics


title: HealthyControl_blood_sample12,control

description: Ribosomes removed RNA


title: 3dpci


title: pWT_P1_heart_rep3

description: Library name: pWT_P1_heart_rep3

value: pWT


title: E70-S1-62b-IVP: IVP Conceptus_Endometrium Co-culture_Rep 7

city: Knoxville

first: Daniel

last: Mathew

state: TN

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

description: Library name: Sample69

data_processing:
The RNA-Seg raw sequences (fastq) underwent adaptor removal and quality trimming using Trimmomatic and quality reads were aligned to the bovine reference genome (ARS-UCD1.2.103) using the STAR aligner program for the endometrial sequences and Hisat2 mapper program for conceptus sequences (Dobin et al., 2013; Kim et al., 2015). The sorted binary alignment maps and the NCBI gene annotation assembly were subjected to FeatureCounts to quantify read counts of genes for each sample (Liao et al., 2014).
Assembly: ARS-UCD1.2.103
Supplementary files format and content: Gene FeatureCounts in Excel

source_name: Conceptus

extract_protocol:
Briefly, endometrial and conceptus total RNA was extracted using bead homogenization (Beadmill 4; FisherScientific) and Trizol following kit on-column isolation (endometrium) or simply the latter (conceptus) with a DNase I digestion step (RNeasy; Qiagen). Eluted RNA was assessed for quantity and quality using a NanoDrop 1000 (ThermoFisher) and the 2100 Bioanalyzer (Agilent Technologies), respectively. Total RNA was extracted from endometrial tissue from the following cultures: Endo (n=13), Endo-IVD Conc (Endo-IVD Conc; n=15), and Endo-IVP Conc (Endo-IVP Conc; n=12) and total RNA was extracted from conceptus tissue from the following cultures: IVD Conc (n=7), IVP Conc (n=7), Endo-IVD Conc (Endo-IVD Conc; n=9), and Endo-IVP Conc (Endo-IVP Conc; n=7). Endometrial and conceptus tissue RNA integrity numbers (RIN) ranged from 5.2 to 9.3 and 6.5 to 10, respectively
Library preparation including poly (A) enrichment and RNA-Seq of the explant and conceptus total RNA was performed by the University of Missouri DNA Core facility (Columbia, MO). The cDNA libraries were prepared using the Stranded RNA Prep Ligation Kit (Illumina) as described by the manufacturer. The final amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads (Corning) and the final construct of each purified library was evaluated using a Fragment Analyzer automated electrophoresis system (Agilent), quantified using the Invitrogen Qubit HS dsDNA assay kit and Qubit fluorometer, and diluted according to Illumina’s standard protocol for sequencing on the NovaSeq 6000 (Illumina).

value: Conceptus

value: RPMI Medium + Endometrium


title: NC,WT,40-3

description:
Library name: sample12
slam-WT-40-3
featurecounts_nc.txt


title: HealthyControl_blood_sample11,control

description: Ribosomes removed RNA


title: NC,UPF1,0-1

description:
Library name: sample16
slam-UPF1-0-1
featurecounts_nc.txt

value: UPF1 KD


title: E69-S1-62b-IVP: IVP Conceptus_Endometrium Co-culture_Rep 6

description: Library name: Sample68


title: Intramuscular Adipose Tissue, Cow 1

description:
Library name: IM1
10x Genomics


title: Normoxia_NTC_rep1

value: Normoxia


title: pWT_P1_heart_rep2

description: Library name: pWT_P1_heart_rep2


title: HealthyControl_blood_sample10,control

description: Ribosomes removed RNA


title: NC,WT,40-2

description:
Library name: sample11
slam-WT-40-2
featurecounts_nc.txt


title: NC,WT,40-1

description:
Library name: sample10
slam-WT-40-1
featurecounts_nc.txt


title: pWT_P1_heart_rep1

description: Library name: pWT_P1_heart_rep1


title: E69-Q1-62a-IVP: IVP Conceptus_Endometrium Co-culture_Rep 5

description: Library name: Sample67


title: HealthyControl_blood_sample9,control

description: Ribosomes removed RNA


title: NC,WT,20-3

description:
Library name: sample9
slam-WT-20-3
featurecounts_nc.txt


title: pWT_P1_kidney_rep1

description: Library name: pWT_P1_kidney_rep1

value: kidney


title: E39-Q1-24-IVP: IVP Conceptus_Endometrium Co-culture_Rep 3

description: Library name: Sample65


title: NC,WT,20-2

description:
Library name: sample8
slam-WT-20-2
featurecounts_nc.txt


title: CHI 25 mg/mL

city: Suzhou

first: Mengyao

state: Jiangsu

address: No.899 Pinghai Road

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample 3

data_processing:
The raw sequencing data was processed by Fastp to trim primer sequence and low quality bases. And then cellranger was used to process sequence data and aligned to human GRCh38 in order to obtain gene expression matrix. We used Seurat (version 4.0.0) to filter low quality cells, cells with number of detected genes <200 or >5000 were omitted, and use MAD variance normal to remove cells affected by mitochondrial genes. After quality control and filtering, library-size normalization to each cell was performed by NormalizeData of Seurat. The variable genes were calculated by FindVariableGenes. Then, all libraries were combined together using FindIntegrationAnchors and IntegrateData with default parameters, and using ScaleData to regress out the variability of the numbers of UMIs. Then the RunPCA and RunUMAP was used to reduce dimensions. FindClusters was used to cluster cells using the 20 dims at a resolution of 0.8.
Assembly: mouse mm10
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output H5 file

source_name: subcutaneous cholangiocarcinoma

extract_protocol:
The tissue is washed with preconfigured PBS solution, sterilized mechanically spliced, and digested with preconfigured digestion solution for 30-60 minutes (depending on the type of tissue). After digestion is terminated, centrifugation, supernatant removal, and resuspension are performed. The suspension is collected by centrifugation through a 70 nm sieve and subjected to cell lysis red (depending on the type of tissue, lysis red treatment is selected). After lysis red is completed, centrifugation and resuspension are performed through a 40 nm sieve. Finally, counting cell number and viability to observe and judge whether the cell suspension was qualified. After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1x PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg.30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer). Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
After cell counts and viability were determined, cell suspensions were adjusted to a concentration of 1,000 cells/ml in PBS supplemented with 0.04% BSA. The 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 was used according to the manufacturer's instructions. Agilent 4200 TapeStation was used to detect the fragment length distribution of the library. Also, Qubit HS DNA Kit was used to accurately quantify the effective concentration of the library ( > 10nmol/L).The qualified library was sequenced on the DNBSEQ T7 platform at the illumina NovaSeq 6000 with PE150 read length.

value: subcutaneous cholangiocarcinoma


title: HealthyControl_blood_sample7,control

description: Ribosomes removed RNA


title: E14-S1-23-IVP: IVP Conceptus_Endometrium Co-culture_Rep 2

description: Library name: Sample64


title: NC,WT,20-1

description:
Library name: sample7
slam-WT-20-1
featurecounts_nc.txt


title: CHI 0 mg/mL

description: Library name: Sample 1


title: CHI 12.5 mg/mL

description: Library name: Sample 2


title: HealthyControl_blood_sample5,control

description: Ribosomes removed RNA


title: E38-U1-37-IVP: IVP Conceptus_Mono-culture_Rep 5

description: Library name: Sample62

value: RPMI Medium


title: HealthyControl_blood_sample6,control

description: Ribosomes removed RNA


title: E14-Q1-24-IVP: IVP Conceptus_Endometrium Co-culture_Rep 1

description: Library name: Sample63


title: NC,WT,10-3

description:
Library name: sample6
slam-WT-10-3
featurecounts_nc.txt

value: WT


title: NC,WT,10-2

description:
Library name: sample5
slam-WT-10-2
featurecounts_nc.txt


title: Bone marrow, mRNA vaccine, scRNA-seq, Biol rep 3

city: Seoul

first: Jae-Hun

last: Ahn

address: Daehak-ro 101, Jongro-gu

department: Biomedical Research Institute

country: South Korea

institute: Seoul National Universty Hospital

description: Library name: 84TIF034

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v8.0.1 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Briefly, raw BCL files from Illumina NovaSeq were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
Then, these raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the mouse reference genome (GRCm39), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: The reference genome sequence is Mus musculus (GRCm39) from the NCBI Genome assembly
Supplementary files format and content: ZIP file. Filtered UMI count matrix (barcode, features, matrix) from Cell Ranger

source_name: Bone marrow (Femur)

growth_protocol: Six-week-old CrlOri:CD1(ICR) female mice (Specific Pathogen Free condition) were used for this expermient.

extract_protocol:
bone marrow in the left femur of the mice was immediately harvested through cold PBS flushing followed by centrifuging at 300 RCF, 4 °C for 5 mins. The supernatant was discarded and the bone marrow pellet was dissolved with RBC lysis buffer (Cat#: 00-4333-57, Invitrogen). Five minutes after the RBC lysis reaction, cells were washed twice and suspended with cell freezing medium (Cat#: 12648010, Gibco, Waltham, MA, USA). Cells were gradually frozen using a controlled-rate freezing container before being stored in liquid nitrogen until use. Prior to sequencing, frozen cells were thawed and counted using the LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems). Cell preparation followed the recommendations provided in the 10x Genomics Single Cell Protocols Cell Preparation Guide (Document CG00053) and Guidelines for Optimal Sample Preparation (Document CG000126).
Single-cell libraries were prepared using the Chromium X platform with the Chromium GEM-X Single Cell 3' Reagent Kit v4 (10x Genomics, Document CG000731) according to the manufacturer’s protocol. Briefly, cell suspensions were diluted in PBS to achieve a target recovery of 10,000 cells. Cells were mixed with the master mix and loaded onto a Chromium GEM-X Single Cell 3’ Chip v4, along with gel beads and partitioning oil. Within the generated droplets, RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed. The resulting cDNA molecules were pooled and subjected to end repair, A-tailing, adaptor ligation, and PCR amplification to construct the final cDNA libraries. Purified libraries were quantified using qPCR following the KAPA qPCR Quantification Protocol Guide, and the quality was assessed using the Agilent 4200 TapeStation. Libraries were sequenced on an Illumina NovaSeq platform according to the read length parameters specified in the user guide.

treatment_protocol: A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, bone marrow tissue was harvested from the left side femur followed by RBC lysed and kept in Cell freezing media at liquid nitrogen

value: Bone marrow (Femur)

tag: Sex

value: female

value: mRNA vaccine


title: NC,WT,10-1

description:
Library name: sample4
slam-WT-10-1
featurecounts_nc.txt


title: E69-W1-62b-IVP: IVP Conceptus_Mono-culture_Rep 4

description: Library name: Sample61


title: E39-S1-23-IVP: IVP Conceptus_Endometrium Co-culture_Rep 4

description: Library name: Sample66