title: HUVEC,siSERPINB2-3

city: 广州

first: Min

last: Xie

state: 广东省

address: 广东省广州市天河区金穗路7号

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
The RNA sequencing reads were first trimmed to remove poly-A and unguallied reads were elminated using Cutadapt.
The remainina reads were then aligned to theHomo sapiens relerence aenome GRch38 usina HISAT2 (V2.1.0).
Gene expression values were calculaled from fraqments per kilobases per miion fragmenls (fPKlw) values.
Assembly: http://www.ensembl.org/Mus_musculus/Info/Annotation; http://asia.ensembl.org/Homo_sapiens/Info/Index

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were maintained in an ECM supplemented with 5% fetal bovine serum (FBS), 1% Endothelial Cell Growth Supplement（ECGS）and 1% antibiotics in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
The collected cells were lvsed withTrizoseacent dnvirooen l ifeTechnolodies) accordina to the manufacturer's protocol.
The cDNA libraries were constructed and sequenced using an lumina NovaSeg 6000 platomm (umina) Shanghai Personal Biotechnology Cp. Ltd.

treatment_protocol: (1)Laser-induced CNV model, and shSerpinb2 (1 µg/µl) injection in vitreous cavity immediately after CNV.(2)The siRNA was transfected into HUVEC using Escot(Sigma) Transfection Reagent, and samples were collected 48 hours later and sent for sequencing.

value: HUVEC

value: siSERPINB2 knock down


title: A_38_tumor_IP

status: Public on Jul 31 2025

type: SRA

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: IP sample of MeRIP-seq

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: pancreas tissue

extract_protocol:
Total RNA from pancreatic cancer patient 38 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.

tag: tissue

value: tumor

tag: disease

value: pancreatic cancer


title: A_40_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 40 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: HUVEC,siSERPINB2-1

address: 广东省广州市天河区金穗路7号

tag: cell line

tag: cell type

tag: genotype


title: HUVEC,siSERPINB2-2

address: 广东省广州市天河区金穗路7号


title: A_38_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 38 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_39_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 39 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: HUVEC,siNC-3

address: 广东省广州市天河区金穗路7号

value: siNC

value: siNC knock down


title: mix_CSF.MS_48h

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: normCount_GEOsubmission.rds rds object containing the normalized reads as sparse matrix
Supplementary files format and content: metadata_GEOsubmission.tsv Tab-separated values files and matrix files

source_name: Organoids IPS derived

extract_protocol:
For the enzymatic cellular dissociation, 30 organoids, for each experiment and for each donor, were first washed in Hank’s balanced salt solution (HBSS) and then, incubated with a freshly prepared dissociation solution (HBSS, papain and DNAase I)for 45 min at 37°C on an orbital shaker (90 rpm), and gently triturated using a P1000 pipette. Cells were incubated again for 15 min at 37°C on an orbital shaker (90 rpm) centrifuged and gently triturated using a P1000 pipette. After the single cell dissociation, the cell suspension was mixed (1:1) with 10 mg/mL ovomucoid protease inhibitor solution and centrifuged at 300g for 5 min. The pellet was resuspend ed in 1X PBS containing BSA (1:50). Cells were counted using trypan blue and a haemocytometer under bright field. A yield of 700-1,200 cells per μL per sample was targeted. For each condition, cell viability was assessed using Luna II Automated Cell Counter. Samples with more than 80% viable cells were processed for downstream analysis. For droplet-based scRNAseq, libraries were prepared using the Chromium Single Cell 3ʹ v3, according to the manufacturer's protocol (10x Genomics) without modifications, targeting 10,000 cells per sample. Using the Illumina Novaseq platform, all samples were sequenced at 50,000 reads per cells. Preparation of cDNA libraries and sequencing support were performed at the Center for Omics Sciences (San Raffaele Scientific Hospital, Milan).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Organoids IPS derived

tag: treatment

tag: clone

value: mix

tag: doxy

tag: exposure

tag: timepoint


title: A_38_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 38 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: A_4_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 4 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: A_38_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 38 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: HUVEC,siNC-2

address: 广东省广州市天河区金穗路7号


title: HUVEC,siNC-1

address: 广东省广州市天河区金穗路7号


title: LINC01929_knockdown_MDAMB231_rep3

city: Halifax

first: Marie-Claire

last: Wasson

state: NS

address: Rm 11-C1, 5850 College Street

country: Canada

institute: Dalhousie University

description: small RNA

data_processing:
The quality of the raw data was verified with FastQC and Cutadapt (v4.0) was used to trim NEBNext Small RNA library adaptors and retained reads between 12-51 nucleotides in length.
rRNA reads were removed with SortmeRNA Release (v4.3.7).
Bowtie2 (v2.5.1) was used to align reads to the reference genome (hg38 assembly).
Samtools was used to align and index files.
FeatureCount (v2.0.1) was used to annotate the .bam file based on annotation from the miRbase
edgeR (v4.0) was used to identify differentially expressed miRNAs across LINC01929 knockdown and control conditions.
Assembly: hg38
Supplementary files format and content: Numbers of reads determined by FeatureCounts
Supplementary files format and content: miRNA differential expression in MCF7 cells.csv
Supplementary files format and content: miRNA differential expression in MDA-MB-231.csv

growth_protocol: Cells were cultured in a humidified incubator at 37C, with 5% CO2 in culture media, supplemented with 10% FBS.

extract_protocol:
Small RNA was extracted from the cells with mirVana™ miRNA Isolation Kit (Invitrogen, Thermo Fisher Scientific) as per manufacturer’s instructions
NEBNext small RNA library prep for Illumina

treatment_protocol: Cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

value: LINC01929 ASO


title: A_37_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 37 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_37_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 37 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_36_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 36 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_36_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 36 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: LINC01929_knockdown_MDAMB231_rep1

description: small RNA


title: LINC01929_control_MDAMB231_rep3

description: small RNA

value: Control ASO


title: LINC01929_control_MDAMB231_rep2

description: small RNA


title: A_35_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 35 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_35_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 35 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_34_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 34 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: LINC01929_control_MDAMB231_rep1

description: small RNA


title: A_34_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 34 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: LINC01929_knockdown_MCF7_rep3

description: small RNA


title: LINC01929_knockdown_MCF7_rep2

description: small RNA


title: A_33_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 33 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_33_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 33 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: LINC01929_knockdown_MCF7_rep1

description: small RNA


title: A_33_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 33 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: A_33_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 33 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: LINC01929_knockdown_MDAMB231_rep2

description: small RNA


title: A_32_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 32 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: V14

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
*library strategy: Spatial Transcriptomic
raw sequencing data were processed using the 10X Genomics Spaceranger pipeline (v 1.3.1) to generate FASTQ files
Sequences were aligned to the reference transcriptome provided by 10X (refdata-gex-GRCh38-2020- A) to generate gene expression count
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz gene expression count data
Supplementary files format and content: aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: scalefactors_json.json scalefactors in json format
Supplementary files format and content: tissue_hires_image.png hi-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png low-res image of the tissue
Supplementary files format and content: tissue_positions_list.csv list of barcodes and the coordinates specifying spots

source_name: brain

extract_protocol:
Frozen samples were embedded in OCT and cryosectioned at −20 °C
Libraries were prepared according to the Visium Spatial Gene Expression User Guide CG000239 using slides and reagents recommended

value: brain

tag: case id

tag: case diagnosis

value: secondary progressive MS

tag: cause of_death

value: aspiration pneumonia

tag: ms treatment

tag: tissue pathology

value: NAWM+cortex

tag: brain tissue_bank

value: NBB

tag: Sex

value: M

tag: age

tag: pmi


title: A_32_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 32 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.

tag: tissue

tag: disease


title: V12

value: pneumonia; subdural haematoma

value: azatioprine 1988; IFN𝛽1b 1996-2001

value: F


title: V10

value: CI lesion


title: A_31_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 31 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: A_31_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 31 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: V09


title: A_31_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 31 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: LINC01929_control_MCF7_rep3

description: small RNA

extract_protocol:
Small RNA was extracted from the cells with mirVana™ miRNA Isolation Kit (Invitrogen, Thermo Fisher Scientific) as per manufacturer’s instructions
NEBNext small RNA library prep for Illumina

tag: cell line


title: LINC01929_control_MCF7_rep2

description: small RNA

tag: treatment


title: A_30_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 30 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: V05

value: coma

value: dymethil fumarate 2013; natalizumab 2014-2017

value: active lesion


title: V06

value: primary progressive MS

value: rupture of abdominal aorta aneurysm

value: CI lesion+cortex


title: A_32_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 32 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: A_30_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 30 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: LINC01929_control_MCF7_rep1

description: small RNA

value: Control ASO


title: A_30_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 30 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_32_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 32 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: V04

value: brain

value: progressive MS

value: pulmonary metastasis rectum carcinoma

value: NAWM


title: A_30_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 30 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: V02

value: secondary progressive MS

value: aspiration pneumonia

value: IFN𝛽1a 1998

value: CAL +cortex

value: NBB


title: A_3_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 3 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

value: pancreatic cancer


title: V11

value: pneumonia; subdural haematoma

value: azatioprine 1988; IFN𝛽1b 1996-2001

value: CI lesion

value: F


title: Cortex, s65

description: 10x Genomics

source_name: Cortex

extract_protocol:
Nuclei extraction from snap-frozen human brains was performed on wet ice. The frozen, dissected tissue was lysed using a Dounce homogenizer (10 strokes with the loose pestle followed by 20 strokes with the tight pestle) in 600 μl of freshly made cold lysis buffer (low-sucrose buffer, Triton X-100 20%, RNase inhibitor 40 U μl−1). The homogenate was filtered through a 40-μm cell strainer for nuclei extraction with 4 ml of low-sucrose buffer (0.64 M sucrose, HEPES pH8, CaCl2, MgAc, EDTA, DTT and nuclease-free water). Sonication of the homogenate was performed for 10 s. To remove cellular and myelin debris, a sucrose gradient (12 ml of high-sucrose buffer (2 M sucrose, HEPES pH 8, MgAc, DTT, nuclease-free water) underneath the low-sucrose buffer) was centrifuged at 3200g for 30 min, and the supernatant was discarded. Nuclei were resuspended in 1 ml resuspension solution (PBS, 5% BSA and RNase inhibitor 40 U μl−1) and centrifuged for 12 min at 3200g. Nuclei were again resuspended in 50 μl cold resuspension solution. Nuclei were counted using trypan blue and a haemocytometer under bright field.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
snRNA-seq

value: Cortex

value: Non-neurological control

value: Metastasized breast carcinoma

tag: tissue class

tag: disease status

tag: pathological stage

value: Normal cortex


title: V03

value: brain

value: progressive MS

value: pulmonary metastasis rectum carcinoma

value: remyelinated lesion


title: A_3_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 3 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: A_31_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 31 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


title: A_29_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 29 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: V01

extract_protocol:
Frozen samples were embedded in OCT and cryosectioned at −20 °C
Libraries were prepared according to the Visium Spatial Gene Expression User Guide CG000239 using slides and reagents recommended

value: secondary progressive MS

value: aspiration pneumonia

value: IFN𝛽1a 1998

value: CAL + cortex


title: Cortex, s60

description: 10x Genomics

value: Progressive MS

value: M

value: Aspiration pneumonia

value: NBB

value: MS

value: Myelinated cortex


title: A_29_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 29 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: pancreatic cancer


title: V08

value: infection

value: unknown

value: NAWM+cortex

value: F


title: Cortex, s57

description: 10x Genomics

value: Cortex

value: Non-neurological control

value: Breast carcinoma; Euthanasia

value: Normal cortex


title: A_28_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 28 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


title: Cortex, s69

description: 10x Genomics

value: NINDS/NIH


title: Cortex, s55

description: 10x Genomics

value: Progressive MS

value: Cardiac arrest after rupture of abdominal aorta aneurysm


title: A_28_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 28 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: Cortex, s53

description: 10x Genomics

value: Pneumonia; subdural haematoma

value: azatioprine 1988; IFN𝛽1b 1996-2001

value: Demyelinated cortex


title: Cortex, s54

description: 10x Genomics

value: Metastasized breast carcinoma

value: NBB


title: Mex3a_cKO-Early_Polysome-RNA_rep2

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

country: USA

institute: Columbia University

description: Library name: 11_KO2_Poly1

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
libraries were aligned with STAR, and bam files were used for DESeq2 data analysis
Assembly: mm10
Supplementary files format and content: csv with transcript per million data for each library

organism: Mus musculus

source_name: Main olfactory epithelium

growth_protocol: Mice were given food and water ad libitum

extract_protocol:
Tissue lysates were loaded on top of a sucrose gradient and subjected to ultracentrifugation. Approximately 42 350uL fractions were collected along the sucrose gradient where trop fractions were less dense and bottom fractions were more dense. Early polysomes were from fractions 27-34 and Late polysomes were from fractions 35-42. 50uL from each fraction was pooled and RNA was extracted using Trizol LS reagent and 1-Bromo-3-chloropropane. After ETOH was added to samples, the Zymo RNA Clean and Concentrator kit was used to finalize extraction protocol.
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara)

value: Main olfactory epithelium

tag: genotype

value: Mex3a flox/flox (Alvarez-Varela et al. 2022, PMID:35773527); Foxg1iresCre (Kawaguchi et al. 2016, PMID:26896590)

value: tissue was treated with 100ug/mL Cyclohexamide in PBS 1X upon dissection


title: A_28_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 28 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

value: pancreatic cancer


title: Cortex, s51

description: 10x Genomics

value: Cortex

tag: case id

value: F

value: Aspiration pneumonia

value: IFN𝛽1a 1998

value: MS


title: Cortex, s48

description: 10x Genomics

tag: case diagnosis

value: Progressive MS

value: Sepsis

value: IFN𝛽1a 2008; natalizumab 2011-2015

value: Myelinated cortex


title: Mex3a_WT-Late_Polysome-RNA_rep2

description: Library name: 10_WT2_Poly2

value: Mex3a flox/flox (Alvarez-Varela et al. 2022, PMID:35773527) or Mex3a flox/+


title: Mex3a_WT-Early_Polysome-RNA_rep2

description: Library name: 9_WT2_Poly1


title: A_28_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 28 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: Cortex, s47

description: 10x Genomics

value: Non-neurological control

tag: cause of_death

value: Chronic pain; Euthanasia

value: Normal cortex


title: Cortex, s46

description: 10x Genomics

value: Unknown

tag: ms treatment

value: Rocky Mountain Brain Bank


title: A_27_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 27 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


title: Mex3a_cKO-Late_Polysome-RNA_rep2

description: Library name: 12_KO2_Poly2

value: Main olfactory epithelium

value: Mex3a flox/flox (Alvarez-Varela et al. 2022, PMID:35773527); Foxg1iresCre (Kawaguchi et al. 2016, PMID:26896590)

value: tissue was treated with 100ug/mL Cyclohexamide in PBS 1X upon dissection


title: Cortex, s44

description: 10x Genomics

value: Cortex

value: M

value: Pneumonia by aspiration

value: NBB

value: Demyelinated cortex


title: Cortex, s45

description: 10x Genomics

value: Progressive MS

value: F

value: Respiratory failure with end stage multiple sclerosis

value: MS


title: Mex3a_cKO-Late_Polysome-RNA_rep1

description: Library name: 4_KO1_Poly2


title: Mex3a_cKO-Early_Polysome-RNA_rep1

description: Library name: 3_KO1_Poly1


title: Cortex, s43

description: 10x Genomics

value: Non-neurological control

value: Intestinal ischemia by thrombosis of the mesenteric superior artery


title: A_26_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 26 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: pancreatic cancer


title: Cortex, s42

description: 10x Genomics

value: End stage MS with urosepsis


title: Cortex, s41

description: 10x Genomics

value: Euthanasia; Hodgkin's lymphoma

value: Normal cortex


title: Mex3a_WT-Late_Polysome-RNA_rep1

description: Library name: 2_WT1_Poly2

value: Main olfactory epithelium

value: Mex3a flox/flox (Alvarez-Varela et al. 2022, PMID:35773527) or Mex3a flox/+


title: Cortex, s49

description: 10x Genomics

value: Cortex

value: Massive pulmonary embolisms or cardiac arrest

value: IFN𝛽-1a (between age 37-44)

value: Myelinated cortex


title: A_26_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 26 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


title: Cortex, s35

description: 10x Genomics

value: Progressive MS

value: Sepsis in cholecystitis

value: IFN𝛽 2002; autologous BMT 2003

value: NBB

value: Demyelinated cortex


title: Mex3a_WT-Early_Polysome-RNA_rep1

description: Library name: 1_WT1_Poly1

value: tissue was treated with 100ug/mL Cyclohexamide in PBS 1X upon dissection


title: WM, s31

description: 10x Genomics

source_name: WM

value: WM

value: Non-neurological control

value: M

value: Pancreas carcinoma

value: Normal White Matter


title: A_26_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 26 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

value: pancreatic cancer


title: WM, s27

description: 10x Genomics

value: F

value: Chronic pain; Euthanasia


title: A_27_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 27 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: WM, s26

description: 10x Genomics

value: Breast carcinoma; Euthanasia


title: A_26_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 26 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: WM, s25

description: 10x Genomics

extract_protocol:
Nuclei extraction from snap-frozen human brains was performed on wet ice. The frozen, dissected tissue was lysed using a Dounce homogenizer (10 strokes with the loose pestle followed by 20 strokes with the tight pestle) in 600 μl of freshly made cold lysis buffer (low-sucrose buffer, Triton X-100 20%, RNase inhibitor 40 U μl−1). The homogenate was filtered through a 40-μm cell strainer for nuclei extraction with 4 ml of low-sucrose buffer (0.64 M sucrose, HEPES pH8, CaCl2, MgAc, EDTA, DTT and nuclease-free water). Sonication of the homogenate was performed for 10 s. To remove cellular and myelin debris, a sucrose gradient (12 ml of high-sucrose buffer (2 M sucrose, HEPES pH 8, MgAc, DTT, nuclease-free water) underneath the low-sucrose buffer) was centrifuged at 3200g for 30 min, and the supernatant was discarded. Nuclei were resuspended in 1 ml resuspension solution (PBS, 5% BSA and RNase inhibitor 40 U μl−1) and centrifuged for 12 min at 3200g. Nuclei were again resuspended in 50 μl cold resuspension solution. Nuclei were counted using trypan blue and a haemocytometer under bright field.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
snRNA-seq

value: Mediastinum carcinoma


title: A_25_normal_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 25 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_Untreated_48h_Sample17

city: Palo Alto

first: Joseph

middle: C

last: Wu

state: California

address: 240 Pasteur Drive

department: Cardiovascular Institute

institute: Stanford University

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

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

value: cell line

value: iPSC-derived endothelial cells

tag: cell type

value: Endothelial cells

value: Untreated


title: iPSC-EC_Untreated_48h_Sample18


title: A_25_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 25 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


title: A_25_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 25 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_Sample20


title: iPSC-EC_Untreated_48h_Sample15


title: dcp2-ideg strain T60, repl. 4

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: A23_DCP2_T60_4

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

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


title: iPSC-EC_Untreated_48h_Sample19


title: lsm1-ideg strain T60, repl. 4

description: Library name: A24_LSM1_T60_4


title: iPSC-EC_Untreated_48h_Sample16


title: wt strain, T60, repl. 4

description: Library name: A22_BY_T60_4

value: WT


title: iPSC-EC_Untreated_48h_Sample14


title: lsm1-ideg strain T0, repl. 4

description: Library name: A21_LSM1_T0_4


title: dcp2-ideg strain T0, repl.4

description: Library name: A20_DCP2_T0_4


title: iPSC-EC_Untreated_48h_Sample13


title: wt strain, T0, repl. 4

description: Library name: A19_BY_T0_4


title: iPSC-EC_Untreated_48h_Sample12


title: A_24_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 24 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_Sample9


title: iPSC-EC_Untreated_48h_Sample11


title: lsm1-ideg strain T60, repl. 3

description: Library name: A18_LSM1_T60_3


title: iPSC-EC_Untreated_48h_Sample10


title: A_24_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 24 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_25_normal_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 25 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: dcp2-ideg strain T60, repl. 3

description: Library name: A17_DCP2_T60_3


title: Cortex, s39

description: 10x Genomics

value: Cortex

value: Progressive MS

value: M

value: Euthanasia

tag: brain tissue_bank

value: NBB

value: MS

value: Demyelinated cortex


title: A_23_tumor_IP

description: IP sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 23 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: pancreatic cancer


title: wt strain, T60, repl. 3

description: Library name: A16_BY_T60_3


title: iPSC-EC_Untreated_48h_Sample8


title: iPSC-EC_Untreated_48h_Sample7


title: A_23_tumor_INPUT

description: Input sample of MeRIP-seq

extract_protocol:
Total RNA from pancreatic cancer patient 23 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: iPSC-EC_Untreated_48h_Sample6


title: iPSC-EC_Untreated_48h_Sample2


title: A_22_tumor_INPUT

description: Input 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.
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_Sample18

value: Nicotine


title: iPSC-EC_Nicotine_48h_Sample20

value: cell line


title: iPSC-EC_Untreated_48h_Sample4

value: iPSC-derived endothelial cells


title: lsm1-ideg strain T0, repl. 2

description: Library name: A12_LSM1_T0_2


title: wt strain, T0, repl. 3

description: Library name: A14_BY_T0_3


title: iPSC-EC_Untreated_48h_Sample3

value: Endothelial cells


title: dcp2-ideg strain T0, repl. 3

description: Library name: A13_DCP2_T0_3