title: DE_HiC_Rep1

description: Hi-C

value: DE stage

value: H9 hESCs

value: in vitro differentiated DE cells

value: WT

value: Pancreatic differentiation


title: DE_HiC_Rep2

status: Public on Sep 19 2023

type: SRA

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

country: China

institute: XIAMEN UNIVERSITY

description: Hi-C

library_source: genomic

data_processing:
Hi-C data processing.   Paired-end reads from Hi-C experiments were aligned to the human hg38 reference genome using HiC-Pro v2.10.0. After PCR duplicates and low-quality reads were removed, high-quality reads were assigned to DpnII restriction fragments, filtered for valid interaction PETs, and used to generate binned contact matrix hic files. For visualization and further analysis of Hi-C contact maps, Knight-Ruiz (KR) normalized signal for the interaction matrices were derived using the Juicebox tools dump command. HiCCUPS (https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS) and SIP v1.3.3 (https://github.com/PouletAxel/SIP/releases) were used to call CTCF loops in the Hi-C interaction matrix. Fit-Hi-C (https://github.com/ay-lab/fithic) was used to call significant interaction at 5,10 and 25kb resolution with a q value cutoff of > 0.001 and merged together for all the rest analysis.
Assembly: hg38
Supplementary files format and content: .hic; matrix showing long-range contacts in Hi-C data, visible in Juicebox browser

molecule: genomic DNA

organism: Homo sapiens

source_name: H9 hESCs

extract_protocol:
For in-situ Hi-C, H9 cells and their in vitro differentiated organoids were collected, fixed with 1% formaldehyde for 10 min at room temperature and quenched with glycine, washed with PBS and stored frozen at -80°C. For library preparation, fixed organoids were gently homogenized in Hi-C lysis buffer with pestle A to release nuclei. To derive the proximity ligation products of chromatin, DpnII digestion, biotin-dCTP fill in and re-ligation were applied to released nuclei sequentially. To extract and purify re-ligated DNA, samples were digested by Proteinase K, reverse-crosslinked at 65°C overnight, and then precipitated by ethanol to get pure DNA. Purified DNA were further sheared by sonication to 200-500 bp in length. After that, streptavidin dynal beads were incubated with sheared DNA to pull down biotin-labeled proximity ligation products for library preparation on beads. After end-repair, A-tailing and Truseq adapter ligation, PCR amplification was finally performed by using Truseq barcoded primers to generate libraries for Illumina sequencing.
Truseq libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

tag: developmental stage

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: PBS replicate 3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single Cell Software Suite v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and 3’ gene counting using 10X Genomics custom annotation of murine genome assembly mm10.
After mapping with CellRanger (with parameters force = 15000) on the mouse reference refdata-gex-mm10-2020-A, cells were considered for further processing using Seurat (4.1.1).
Using Seurat (4.1.1), cells with more than 20% mitochondrial content were removed to exclude dying cells; only cells in which at least 200 genes were expressed were retained; and only genes detected in at least 10 cells were retained, for a final set of 1524 cells and 17901 genes.
Samples were independently log normalized and integrated using 4000 most variable features.
Unsupervised clustering was performed by applying the graph-based clustering approach and Louvain algorithm and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction was performed based on the previously computed neighbor graph using the top 30 PCs.
assembly: mm10
tab separated log normalized counts

molecule: total RNA

organism: Mus musculus

source_name: B16F10 melanoma

extract_protocol:
Subcutaneous B16F10 tumors were enzymatically digested by tumor dissociation kit (Miltenyi Biotec; Cat. No. 130-096-730) in gentleMACS™ Octo Dissociator machine (Miltenyi Biotec; Cat No.130-096-427)
Single-cell tumors were then washed twice in PBS containing 0.04% BSA. After filtration through a 40 um Flowmi strainer (Bel-Art, Wayne, NJ), cells were resuspended in PBS with 0.04% BSA, checked for absence of significant doublets or aggregates, and loaded into a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA) in a chip together with beads, master mix reagents (containing RT enzyme and poly-dt RT primers) and oil to generate single-cell-containing droplets.
Single-cell gene expression libraries were then prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000268) following the manufacturer's instruction (protocol CG000315 Rev C). Quality control was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA high sensitivity assay (Thermo) following manufacturer instructions.
The sequencing libraries were loaded onto an Illumina HiSeq 4000 paired-end Flow Cell and sequenced using read lengths of 28 nt for read1 and 91 nt for read2, at a depth of ca 35k reads/cell.

treatment_protocol: We inoculated B16F10 melanoma cells subcutaneously in mice. Then, we injected the mice i.v. with a mixture of 2 x 10^6 DCP-FLT3L and 10^6 DCP-IL-12 (termed DCP-IL-12/FLT3L) on both day 3 and 5 post-tumor challenge. Control mice received PBS. We terminated the experiment 6 days after the second DCP (or PBS) administration to harvest tumors for single-cell RNA sequencing (scRNA-Seq). Tumor-associated cells were analyzed without prior enrichment or exclusion of specific cell types.

tag: tissue

value: tumor

value: PBS

tag: replicate


title: DeltaD4

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

country: USA

institute: SUNY Upstate Medical Univ

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample96

library_source: transcriptomic

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were quantified to hg38 Ensembl transcripts release 105 using Salmon, using minimum assigned fragments of 10, minimum score fraction of 0.65, match value 2, mismatch value -4, gap opening value 6 and gap extension value of 2
Quantified features were filtered to eliminate those with less than 1 count in 80% or more of the samples
Normalization performed on filtered features using TPM followed by quantile and log2 transformation
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated values matrix file containing raw Salmon feature counts
Supplementary files format and content: Tab-separated matrix file containing filtered and normalized feature abundances

source_name: saliva

extract_protocol:
RNA was purified from saliva swabs used for clinical PCR COVID-19 testing, using Zymo Quick-RNA Viral 96 Kit or the KingFisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
RNA-seq libraries were synthesized using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) according to manufacturer protocol

value: saliva

tag: group

value: Infected-Unvax

tag: Sex

value: Female

tag: race

value: White or Caucasian

tag: ethnicity

value: Not Hispanic

tag: age


title: C5aR KO-TAM1

city: Chongqing

first: Xiaojin

last: Luan

address: yuzhong road

institute: Chongqing medical university

data_processing:
Illumia Casva 1.7 software used for base-calling.
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2  software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs between two different samples, the expression level of each transcript was  calculated  according  to  the  transcripts per million  reads method.  RSEM was used to quantify  gene  abundances.  Essentially,  differential  expression  analysis  was  performed  using  the  DESeq2 or DEGseq .
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000.
RNA purification,  reverse  transcription,  library  construction  and  sequencing  were performed  at  Shanghai Majorbio  Bio-pharm  Biotechnology  Co.,  Ltd.  (Shanghai,  China)  according  to  the  manufacturer’s  instructions (Illumina, San Diego, CA).

value: ID8 cells injected into C5aR knockout mice

value: tumor associated macrophages


title: MEF-IGF2BP1-KO-Wnt3a, Biol rep 2

city: Hershey

first: Vonn

last: Walter

state: PA

address: 500 University Drive

department: Public Health Sciences

institute: Penn State College of Medicine

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12, Illumina), allowing no mismatches in the index read. After the quality and polyA trimming by BBDuk and alignment by HISAT2 (version 2.1.0), read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Assembly: GRCm38
Supplementary files format and content: raw read counts are provided in txt file

source_name: Embryonic

growth_protocol: Cells were cultured in DMEM Medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit from Qiagen (74104)
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment close to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for their size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: 90% confluent cells were treated/untreated with Wnt3a(100ng/ml) for 24hrs to induce the Wnt signaling

value: Embryonic

value: Mouse Embryonic Fibroblast Cells-IGF2BP1 knockout

tag: biological repeats

value: Biol rep 2

value: Fibroblast


title: MEF-WT-UT, Biol rep 1

value: Mouse Embryonic Fibroblast Cells

value: Biol rep 1

value: Untreated


title: DeltaE2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample97

value: Infected-Vax


title: WT-TAM2

value: tumor

value: ID8 cells injected into WT mice


title: DeltaC3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample91

value: saliva

value: Male

value: Unknown/Other


title: hESCs_HiC_Rep2

description: Hi-C

value: undifferentiated hESCs

value: H9 hESCs

value: H9 human embryonic stem cells

value: WT

value: undifferentiated state


title: hESCs_HiC_Rep1

description: Hi-C


title: PP_HiC_Rep2

description: Hi-C

value: PP stage

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: 0.5hr Gln_rep2

city: Taipei City

first: Yi-Jie

last: Hung

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: IPMB

country: Taiwan

institute: Academia Sinica

data_processing:
Low quality reads, which are shorter than 35 base pairs or have an error probability greater than 0.05, were filtered out.
Mapping reads to the Arabidopsis reference genome TAIR10 by using BLAT method.
R1 BAM file of each sample under SAMtools.
For each sample, pick up R1 BAM file for reads per kilo-base-pair gene model per million mapped reads (RPKM) computation.
TMM normalization is applied to normalize all RPKM files.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text file include normalized RPKM values for each sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis seeds were surface sterilized and grown on a hydroponic solution box containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) adjusted to pH 5.7 with 1 N KOH. The box was kept at 4℃ for 2 days and then transferred to a growth chamber on a 16-h-light/8-h-dark cycle at 22°C for 14 days.

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

treatment_protocol: Arabidopsis were be transferred to treatment which containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) plus 2.5 mM Gln, adjusted to pH 5.7 with 1 N KOH.

tag: ecotype

value: Columbia (Col)

value: 14-day-old seedlings

value: whole seedlings


title: DeltaC4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample92

value: Infected-Unvax

value: Female

value: White or Caucasian

value: Not Hispanic


title: 0.5hr Gln_rep1


title: PP_HiC_Rep1

description: Hi-C


title: PBS replicate 1

value: tumor

value: PBS


title: DCP-IL-12/FLT3L replicate 3


title: PGT_HiC_Rep2

description: Hi-C

value: PGT stage

value: in vitro differentiated PGT cells


title: DeltaC2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample90

value: saliva

value: Infected-Vax


title: 0hr Gln_rep2


title: DCP-IL-12/FLT3L replicate 1


title: DeltaB3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample87

value: Male


title: DeltaB2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample86


title: 0hr Gln_rep1


title: PGT_HiC_Rep1

description: Hi-C

value: H9 hESCs

value: WT


title: LN-229-TRE-R132H cells, doxycycline+VSVΔ51, biol rep 2

city: Guangzhou

first: Xueqin

last: Chen

address: Huangpu West Road 601

institute: Jinan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (0.20.0 parameter -q 20)
Trimmed sequence reads were mapped to GRCh38 using HISAT2(2.1 parameters -p 8 -x Homo_sapiens.GRCh38 -1 S.1.fq.gz -2 S.2.fq.gz)
Read count extraction and normalization were performed using HTSeq(10.1 parameters -f bam -a 10 -m union -i gene_name S.bam Homo_sapiens.GRCh38.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

growth_protocol: LN-229-TRE-R132H cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: LN-229-TRE-R132H cells were infected with or without VSVΔ51 (MOI = 1) for 12 h in the presence or absence of IDH1 mutation induced by doxycycline (1 μg/ml) pretreatment for 48 h.

value: glioblastoma cells

value: with doxycycline

value: with VSVΔ51 infection


title: DeltaB1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample85


title: LN-229-TRE-R132H cells, doxycycline+VSVΔ51, biol rep 3


title: DeltaB4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample88


title: MEFs-Wnt3a-3

data_processing:
We followed the pipeline detailed in Busch et al., Methods, 2022 178:49-62, PMID 31751605
Demultiplexing was performed with Flexbar 3.5.0 to produce the fastq files in this submission. Adapter trimming was also performed. No mismatches for barcode matching were allowed, and only 1 nucleotide of overlap between the read 3’ end and the beginning of the adapter was required.  Trimmed reads with length at least 15 were retained for further analyses.
The STAR 2.7.3a aligner was used to make index files based on the primary fasta file (GRCm38.primary_assembly.genome.fa) and gene annotation file (gencode.vM25.annotation.gtf). The alignment was then performed with STAR to produce bam files based on the parameters in Busch et al. and a maximum read length of 52.
UMI-tools 1.0.0 was applied to remove technical duplicate reads from the bam files that arise during PCR amplification.  Duplicate reads were identified based on their read ID using the --method unique option.
Next, the duplicate-removed bam files were converted to bed format using Bedtools 2.29.2.  These bed files were shifted by 1 nucleotide in the 5’ direction in order to correctly identify crosslinked nucleotides.  The shifted bed files were used to create bedgraph coverage files, a process that was performed separately for each strand.  Bigwig format coverage files were also created.
Using PureCLIP 1.3.1, the bam files were processed to make bed files containing sites that were associated with a significant crosslinked signal.  Post-processing steps were applied to these bed files with the goal of resizing the binding sites to have uniform width 9 nucleotides, as was done in the Busch et al. manuscript. These bed files were the basis of numerous downstream analyses.
Assembly: mm10
Supplementary files format and content: As described in Busch et al., filtered bed files were created that contain information about cross-linking sites (sampleID_bs_clean.bed, where sampleID is a sample identifier).  The sampleID_coverage_20210708.txt files contain informationa above coverage.

organism: Mus

extract_protocol: We followed the iCLIP protocol detailed in Huppertz et al., Methods, 2014 65(3):274–287, PMID 24184353

value: Embryonic

value: Biol repe 3

value: Mouse Embryonic Fibroblast Cells

value: Fibroblast


title: MEFs-Wnt3a-2

value: Biol repe 2


title: DeltaA4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample84

value: Infected-Unvax

value: Female

value: White or Caucasian

value: Not Hispanic


title: PBS replicate 2

value: tumor

value: PBS


title: WT-TAM1

value: ID8 cells injected into WT mice

value: tumor associated macrophages


title: LN-229-TRE-R132H cells, doxycycline+VSVΔ51, biol rep 1


title: DCP-IL-12/FLT3L replicate 2


title: MEFs-Wnt3a-1

value: Biol repe 1


title: DeltaA3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample83

value: saliva

value: Male


title: LN-229-TRE-R132H cells, VSVΔ51, biol rep 3

value: glioblastoma cells

value: without doxycycline

value: with VSVΔ51 infection


title: MEFs-Untreated-3

value: Embryonic

value: Biol rep 3

value: Mouse Embryonic Fibroblast Cells

value: Untreated


title: DeltaC1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample89

value: Infected-Unvax


title: DeltaA1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample81

value: Infected-Vax

value: White or Caucasian


title: LN-229-TRE-R132H cells, VSVΔ51, biol rep 2


title: MEFs-Untreated-2

value: Biol rep 2

value: Fibroblast


title: LN-229-TRE-R132H cells, doxycycline, biol rep 2

value: with doxycycline

value: without VSVΔ51 infection


title: MEFs-Untreated-1

value: Biol rep 1


title: LN-229-TRE-R132H cells, doxycycline, biol rep 1


title: PL1, rep1

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode M18 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: prefrontal cortex

extract_protocol:
Frontal cortex were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 16-18 months

tag: cognitive test

value: poor learner or impaired


title: LN-229-TRE-R132H cells, doxycycline, biol rep 3

value: glioblastoma cells


title: GL2, rep2

value: good learner or resilient


title: LN-229-TRE-R132H cells, control, biol rep 3

value: without doxycycline


title: GL1, rep1


title: LN-229-TRE-R132H cells, control, biol rep 1


title: DeltaA2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample82

value: saliva

value: Female

value: Not Hispanic


title: LN-229-TRE-R132H cells, VSVΔ51, biol rep 1

value: with VSVΔ51 infection


title: Lm biofilm cells in 0.5X TSB, biolog rep 3, technical rep 2

status: Public on Sep 18 2023

city: College Park

first: Jie

last: Zheng

state: MD

address: 5001 Campus Drive

institute: FDA

data_processing:
FastQC was used to check the quality of the sequence reads.
Read counts were generated using Salmon v1.9.0.
Supplementary files format and content: tab-delimited .sf files including raw counts and tpm values for each sample

organism: Listeria monocytogenes

source_name: biofilm cell

growth_protocol: Listeria monocytogenes FS2025 (serotype 1/2b, ST5, CC5) was grown in cantaloupe juice or TSB at 24C statically.

extract_protocol:
RNA was harvested using Invitrogen RiboPure™ Bacteria Kit (ThermoFisher Scientific).
RNA libraries for RNA Seq were prepared using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus kit following manufacturer's instructions.

treatment_protocol: Planktonic cells were collected after 48h incubation and biofilm cells were harvested from stainless steel coupons after 3 days incubation via sonication.

tag: agent

value: TSB

value: biofilm cell

value: WT


title: H1299, NC3, rep3

city: Shanghai

first: Wanxin

last: Guo

address: West Huaihai Road No.241

institute: Shanghai Chest Hospital

description:
N3
RNA-seq-proccessed.txt

data_processing:
The sequencing data was filtered with SOAPnuke
Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [8].
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: The file includes gene symbol and gene id for each sample. "N" means NC for DMSO treated and  "T" means test for RSL3 treated.
Supplementary files format and content: The file includes fpkm, tpm, readcounts and fold change for each sample.

extract_protocol:
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2.2 Sample Purification 2.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS)

value: tumor

value: LUAD

value: DMSO


title: Lm biofilm cells in 0.5X TSB, biolog rep 3, technical rep 3


title: H1299, RSL3_1, rep1

description:
T1
RNA-seq-proccessed.txt


title: H1299, NC2, rep 2

description:
N2
RNA-seq-proccessed.txt


title: H1299, NC1, rep 1

description:
N1
RNA-seq-proccessed.txt


title: H1299, RSL3_2, rep2

description:
T2
RNA-seq-proccessed.txt


title: PL3, rep2


title: PL4, rep3


title: Lm biofilm cells in 0.5X TSB, biolog rep 2, technical rep 3


title: Lm biofilm cells in 0.5X TSB, biolog rep 2, technical rep 1


title: H1299, RSL3_3, rep3

description:
T3
RNA-seq-proccessed.txt


title: Lm biofilm cells in 0.5X TSB, biolog rep 3, technical rep 1


title: Lm biofilm cells in 0.5X TSB, biolog rep 1, technical rep 3


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 3, technical rep 2

value: cantaloupe juice


title: Lm biofilm cells in 0.5X TSB, biolog rep 2, technical rep 2


title: LN-229-TRE-R132H cells, control, biol rep 2

value: without VSVΔ51 infection


title: GL3, rep3

value: 16-18 months


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 2, technical rep 2


title: Lm biofilm cells in 0.5X TSB, biolog rep 1, technical rep 1


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 2, technical rep 3


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 3, technical rep 1


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 3, technical rep 3


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 1, technical rep 3


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 1, technical rep 2


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 1, technical rep 1


title: N2ApOC2△HOX 1, RNA-seq

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

description:
Cells overexpressing pOC2△HOX, infected with HSV-1 for 5 hours
OC2dHB1
Processed data file_FPKMs.txt

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2) [1] by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.1.0)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) . The expression level of genes was calculated by RSEM.
Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors
Within-group differential gene analysis was performed using DESeq [6] under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and classifications, the differentially expressed genes were functionally classified, the phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of ≤ 0.05 as the threshold, candidate genes that met this condition were defined as significantly enriched.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

source_name: N2ApOC2△HOX1 cells derived from Neuro-2a cells infected with HSV-1

extract_protocol:
Total RNA  was extracted according to promega.ls1040 Eastep Super total RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For infection, cells were infected with ICP0-null HSV-1 (strain 7134) for 5 hpi (MOI = 1) before RNA-seq

value: Brain

value: overexpressing pOC2{delta}HOX2

tag: infection


title: Lm biofilm cells in 0.5X TSB, biolog rep 1, technical rep 2


title: N2ApOC2△HOX 2, RNA-seq

description:
Cells overexpressing pOC2△HOX, infected with HSV-1 for 5 hours
OC2dHB2
Processed data file_FPKMs.txt

source_name: N2ApOC2△HOX2 cells derived from Neuro-2a cells infected with HSV-1

tag: cell line


title: N2ApcDNA 3, RNA-seq

description:
Cells overexpressing pcDNA, infected with HSV-1 for 5 hours
pcDNA3
Processed data file_FPKMs.txt

source_name: N2ApcDNA3 control cells derived from Neuro-2a cells infected with HSV-1

value: overexpressing pcDNA


title: N2ApOC2△HOX 3, RNA-seq

description:
Cells overexpressing pOC2△HOX, infected with HSV-1 for 5 hours
OC2dHB3
Processed data file_FPKMs.txt

source_name: N2ApOC2△HOX3 cells derived from Neuro-2a cells infected with HSV-1


title: N2ApcDNA 1, RNA-seq

description:
Cells overexpressing pcDNA, infected with HSV-1 for 5 hours
pcDNA1
Processed data file_FPKMs.txt

source_name: N2ApcDNA1 control cells derived from Neuro-2a cells infected with HSV-1


title: N2ApcDNA 2, RNA-seq

description:
Cells overexpressing pcDNA, infected with HSV-1 for 5 hours
pcDNA2
Processed data file_FPKMs.txt

source_name: N2ApcDNA2 control cells derived from Neuro-2a cells infected with HSV-1


title: C4-2 cells with YTHDF2 knockdown inhibited by actinomycin D for 2 hours

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
RNA-Seq reads were mapped to human reference genome version hg19 using TopHat (version v2.0.12)  with default parameters. Next, Cuffdiff (version 2.2.1) was used to generate read count matrix. Normalized gene expression values in FPKM (fragments per kilobases per million mapped reads) was further calculated using UCSC knownGene as the reference genes. Genes with FPKM value larger than one were retained for further analysis. Differential expression test was performed using edgeR.
MeRIP-Seq data was filtered by Trimmomatic to remove low-quality bases and then mapped to human genome (version hg19) by Tophat (version v2.0.12) using default parameters. The read coverage calculation and normalization were conducted by deepTools. The distribution of m6A signal across gene body (5’UTR, CDS and 3’UTR) was measured by FPKM values in bins by deepTools. The normalized IP signal per bin was subtracted by normalized input signal to generate m6A signal coverage plot. Enrichment peaks of m6A signal were called by MACS2 and exomePeak2 using default parameters (parameter and p-value). M6A peaks called by MACS2 required q-value less than 0.05, and by exomePeak2 q-value less than 0.1. Differential methylation sites were identified by exomePeak2.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized gene expression (FPKM values) for all the RNA-seq samples.
bigWig for all the MeRIP-seq samples.

molecule: polyA RNA

source_name: human prostate cancer cell line C4-2

extract_protocol:
PrEC and C4-2 cells were treated with transcription inhibitor actinomycin D (ActD, Sigma) at a concentration of 5 μg/ml for 0, 15 minutes, 1 hour and 2 hours. RNA samples were then isolated using RNeasy Plus Mini Kit (Qiagen) and sent to BGI for library preparation and follow-up sequencing.
Samples were sent to BGI for library preparation and follow-up sequencing

tag: cell type

value: prostate cancer cells

value: YTHDF2 knockdown

value: actinomycin D

tag: time point

value: 2 hours


title: 4T1_Malat1_KO2-1

city: Houston

first: Dhiraj

last: Kumar

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
After reads filtering, we map clean reads to reference genome using HISAT according to Kime et al. Nat. Methods 12, 357-360 (2015).
Gene expression level was calculated for each sample with RSEM using protocol from Li et al. BMC Bioinformatics 12, 323 (2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.gene.fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: 4T1-TGL Cells either with/without Malat1 were grown in DMEM/F12 medium.

extract_protocol:
Total RNA isolated using Maxwell RNA isolation kit from 4T1-TGL Malat1 WT or KO cells.
Libraries were prepared according to BGISEQ-500. Paired-end 100 bp. 40 million reads per sample.

value: Breast cancer cell line

value: BALBC

tag: genotype

value: Malat1 KO


title: 4T1_Malat1_KO1-2


title: 4T1_Malat1_KO2-3


title: C4-2 cells with YTHDF2 knockdown inhibited by actinomycin D for 0 hour

tag: treatment

value: 0 hour


title: C4-2 cells with YTHDF2 knockdown inhibited by actinomycin D for 1 hour

value: 1 hour


title: 4T1_Malat1_KO1-3


title: 4T1_Ctrl-3

value: WT


title: 4T1_Ctrl-1


title: Lm biofilm cells in 0.5X cantaloupe juice, biolog rep 2, technical rep 1

value: biofilm cell


title: C4-2 cells (knockdown control) inhibited by actinomycin D for 1 hour

value: knockdown control


title: C4-2 cells with YTHDF2 knockdown inhibited by actinomycin D for 15 minutes

value: 15 minutes


title: C4-2 cells with METTL3 knockdown inhibited by actinomycin D for 1 hour

value: METTL3 knockdown


title: 4T1_Malat1_KO2-2


title: C4-2 cells with METTL3 knockdown inhibited by actinomycin D for 15 minutes


title: 4T1_Malat1_KO1-1


title: C4-2 cells (knockdown control) inhibited by actinomycin D for 2 hours


title: 4T1_Ctrl-2


title: C4-2 cells (knockdown control) inhibited by actinomycin D for 15 minutes


title: C4-2 cells with METTL3 knockdown inhibited by actinomycin D for 2 hours


title: C4-2 cells inhibited by actinomycin D for 2 hours

value: control


title: C4-2 cells (knockdown control) inhibited by actinomycin D for 0 hour


title: C4-2 cells inhibited by actinomycin D for 0 hour


title: C4-2 cells inhibited by actinomycin D for 15 minutes


title: C4-2 cells inhibited by actinomycin D for 1 hour


title: PrEC cells inhibited by actinomycin D for 2 hours

source_name: human prostate primary epithelial cells

value: prostate primary epithelial cells (PrEC)


title: PrEC cells inhibited by actinomycin D for 1 hour


title: PrEC cells inhibited by actinomycin D for 0 hour


title: C4-2 cells with METTL3 knockdown inhibited by actinomycin D for 0 hour


title: EMA2 KO cross2 small RNAs @8 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012; Noto et al. 2015). Briefly, following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed, and reads that perfectly match the MIC genome were used.
Sequenced 26 to 32 nt RNAs that map uniquely to Type-A IESs (described in Noto et al. 2015), or 10 kb fragments of MDSs from the MAC genome assembly released in 2020 (Sheng et al. 2020) are counted, and normalized numbers (reads per kb per million reads [RPKM]) are shown.
Assembly: Tetrahymena thermophila MAC genome assembly released in 2020 (Sheng et al. 2020, https://tet.ciliate.org/common/downloads/tet/latest/Tetrahymena_thermophila_coding_sequences_v5.fasta)  and Type-A IES sequences descrived by Noto et al. 2015 were used foe mapping.
Supplementary files format and content: Text files containing normalized read numbers (reads per kb per million reads [RPKM]) that mapped uniquely to 4,691 Type-A IESs ("TypeA_Ind_Uni.txt") or 10,235 10 kb fragments of MDSs ("MDS2020_Ind_Uni.txt").

organism: Tetrahymena thermophila

source_name: EMA2 KO

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight.

extract_protocol:
Total RNA was extracted with TRIzol reagent . 1 mL of Trizol reagent was used to lyse1x10e6 cells.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

treatment_protocol: To induce conjugation, exponentially growing cells (~3-5x 10e5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for overnight and mixed for conjugation (5x 10e5/ml) at 30°C.

value: EMA2 KO


title: EMA2 KO cross1 small RNAs @8 hpm


title: AAN mice with Paquinimod treatment

type: RNA

city: Cardiff

first: Anne-Catherine

last: Raby

state: Cardiff

address: Heath Park, Academic Avenue

country: United Kingdom

institute: Cardiff University

description: AAN + Paquinimod

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software: https://geneglobe.qiagen.com/us/analyze
For the normalization, average of a combination of automatically selected housekeeping genes (out of 5 tested Actb,B2m, Gapdh, Gusb, Hsp90ab1) were used
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-changes are 2^-ΔΔCt, where ΔΔCt = (ΔCt_Test Group - ΔCt_Control group)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports AAN/PBS or AAN+ Paquinimod/PBS ratios.

label: SYBR green

source_name: aortas

label_protocol: RT: Qiagen RT2 first strand kit, qPCR on QuantStudio12 flex

extract_protocol: Total RNA extracted with RNeasy Fibrous Tissue Mini Kit

value: repeated i.p. AA + Paquinimod (x4)

value: female

tag: time

value: day 21


title: EMA2 KO cross1 small RNAs @3 hpm


title: Control mice.

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software: https://geneglobe.qiagen.com/us/analyze
For the normalization, average of a combination of automatically selected housekeeping genes (out of 5 tested Actb,B2m, Gapdh, Gusb, Hsp90ab1) were used
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-changes are 2^-ΔΔCt, where ΔΔCt = (ΔCt_Test Group - ΔCt_Control group)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports AAN/PBS or AAN+ soluble TLR2/PBS ratios.

value: repeated PBS i.p. (x4)


title: Aristolochic Acid -induced Nephropathic (ANN) mice.

description: AAN

value: repeated i.p. Aristolochic Acid (AA, x4)


title: EMA2 KO cross2 small RNAs @3 hpm


title: AAN mice with soluble TLR2 treatment

description: AAN+ soluble TLR2

value: repeated i.p. AA + soluble TLR2 (x4)


title: Control mice

description: Control


title: Aristolochic Acid -induced Nephropathic (ANN) mice

description: AAN


title: GR mutant betamethasone-treated 24

city: Sheffield

first: Dheemanth

last: Subramanya

address: Firth Court, Western Bank

department: Department of Biomedical Science

institute: University of Sheffield

data_processing:
Sequence quality was determined using FastQC
Sequence data was demultiplexed using QIIME 1
Primers were trimmed using cutadapt
Data was aligned to the reference genome (Danio rerio, GRCz10 release 85) and methylation levels were called using BSseeker2
Genome_build: GRCz10 release 85
Supplementary_files_format_and_content: Processed data files are in .tsv format. They represent differential methylated sites or regions, as analyzed by BSseeker2.

organism: Danio rerio

source_name: Dissected larval head

extract_protocol:
Heads were dissected from 5dpf zebrafish larvae and genomic DNA was extracted using the Qiagen DNAeasy kit. Each DNA sample was bisulfite treated using the Qiagen Epitect kit, according to the kit instructions, and quantified using an Agilent Tapestation with High-sensitivity tape.
100pg bisulfite-converted DNA was amplified for 40 cycles in PCR round 1, using KAPA Hifi Uracil+ Readymix with 300nM primer. The optimum annealing temperature and MgCl2 concentration for each primer pair were determined by analysing PCR products on a 2% agarose gel. The PCR round 1 primers included a 25-30 bp amplicon-specific sequence, designed using MethPrimer (Bernstein et al., 2015) plus an 18 bp overhang to allow the annealing of PCR round 2 primers. All PCR round 1 amplicons were pooled for each individual sample at 10 ng/amplicon based on quantification via the Agilent Tapestation. Excess primers and dNTPs were removed using the Qiagen PCR clean-up kit. Individual samples were then barcoded via a second round of PCR. PCR round 2 reactions were 20ul, using the KAPA Hifi Uracil+ mastermix, with 300 nM primer and 1 ng of pooled PCR round 1 product for each sample. The PCR round 2 forward primer was identical to the 5’ overhang on the PCR round 1 amplicons, whilst the reverse primer included a region to anneal to the 3’ overhang on the PCR round 1 amplicons, plus a 6 bp sample-specific barcode. The final barcoded amplicons ranged from 199-270 bp. Excess primers and dNTPs were removed using the Qiagen PCR clean-up kit. Sample quantity and size was determined using the Agilent Tapestation. Products outside of the expected range were removed using AMPure XP beads. Samples were then pooled in an equimolar manner, and a 500 ng pool was shipped to GATC Biotech for sequencing. Illumina adapters were ligated by GATC Biotech and the samples were sequenced on the Illumina Hiseq for 150 bp paired end reads.

tag: Stage

value: GR mutant

value: 100uM betamethasone


title: GR mutant betamethasone-treated 21


title: GR mutant betamethasone-treated 15


title: GR mutant betamethasone-treated 16


title: GR mutant betamethasone-treated 17


title: GR mutant betamethasone-treated 23


title: GR mutant betamethasone-treated 14


title: GR mutant betamethasone-treated 13


title: PrEC cells inhibited by actinomycin D for 15 minutes

value: actinomycin D


title: GR mutant betamethasone-treated 12


title: GR mutant betamethasone-treated 11


title: GR mutant betamethasone-treated 9


title: GR mutant betamethasone-treated 10


title: GR mutant betamethasone-treated 8


title: GR mutant betamethasone-treated 22


title: GR mutant betamethasone-treated 6


title: GR mutant betamethasone-treated 7


title: AAN mice with soluble TLR2 treatment

description: AAN + soluble TLR2

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software: https://geneglobe.qiagen.com/us/analyze
For the normalization, average of a combination of automatically selected housekeeping genes (out of 5 tested Actb,B2m, Gapdh, Gusb, Hsp90ab1) were used
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-changes are 2^-ΔΔCt, where ΔΔCt = (ΔCt_Test Group - ΔCt_Control group)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports AAN/PBS or AAN+ treatment/PBS ratios.

source_name: Blood

extract_protocol: Total RNA extracted with QIAamp RNA Blood Mini Kit

tag: Sex


description: AAN


title: GR mutant betamethasone-treated 19


title: GR mutant betamethasone-treated 20


title: GR mutant betamethasone-treated 18


title: AAN mice with Paquinimod treatment

description: AAN + Paquinimod


title: GR mutant betamethasone-treated 3


title: GR mutant betamethasone-treated 2


title: GR mutant betamethasone-treated 4


title: GR mutant control 23

value: Control:0.2% ethanol


title: GR mutant betamethasone-treated 1


title: GR mutant betamethasone-treated 5


title: GR mutant control 24


title: GR mutant control 20


title: GR mutant control 19


title: GR mutant control 21


title: Pancreatic stellate cells, pH7.4, 120h, biol. replicate B

city: Münster

first: Zoltan

last: Pethö

state: NRW

address: Robert-Koch Str. 27B

department: Physiology II

country: Germany

institute: University of Münster

data_processing:
Data processing and analysis was primarily carried out on the Galaxy platform (usegalaxy.eu)
Raw fastq files were aligned and mapped against the murine reference genome (mm10) with the HISAT2 v2.2.1 algorithm
Counts were subsequently extracted using featureCounts 2.0.1(53)
Differential expression of genes was analyzed using limma 3.50.1
Assembly: mm10
Supplementary files format and content: Excel file PSC_pH_RNAseq_counts includes raw count values for each Sample. Excel file PSC_pH_RNAseq_processed contains the DE output of limma 3.50.1 that was used to obtain study conclusions.

source_name: pancreas

growth_protocol: Cells were grown in DMEM/Ham F12 1:1, supplemented with 10% FCS and 1% penicillin/streptomycin on plastic tissue culture dishes.

extract_protocol:
The Rneasy Mini Kit was used to extract RNA from PSCs cultured 120 h at pHe6.6 or pHe7.4. Quality and quantity of isolated RNA were evaluated using the NanoDrop 2000. A total of 800 ng RNA was used per sample.
RNA libraries for RNA-seq were prepared using NEBNext RNA Ultra II directional library prep kit plus NEBNext Poly(A) enrichment kit following manufacturer's protocols.

treatment_protocol: Medium of  DMEM/Ham F12 was set to pH6.6 or pH7.4 using differential amount of sodium bicarbonate.

tag: tissue

value: pancreas

value: Pancreatic stellate cells

value: C57BL6/J WT


title: Control mice

description: Control


title: Pancreatic stellate cells, pH7.4, 120h, biol. replicate C


title: Pancreatic stellate cells, pH7.4, 120h, biol. replicate A


title: GR mutant control 18


title: Pancreatic stellate cells, pH6.6, 120h, biol. replicate C


title: GR mutant control 17


title: Pancreatic stellate cells, pH6.6, 120h, biol. replicate A


title: Pancreatic stellate cells, pH6.6, 120h, biol. replicate B


title: GR mutant control 16


title: GR mutant control 15


title: GR mutant control 14


title: GR mutant control 13


title: GR mutant control 11


title: GR mutant control 9


title: GR mutant control 8


title: GR mutant control 22


title: GR mutant control 10


title: GR mutant control 12


title: GR mutant control 6


title: GR mutant control 4


title: GR mutant control 3


title: GR mutant control 2


title: GR mutant control 1


title: GR wild-type betamethasone-treated 24

value: Wild-type


title: GR wild-type betamethasone-treated 23


title: GR mutant control 5


title: GR wild-type betamethasone-treated 21


title: GR wild-type betamethasone-treated 22


title: female, PFC, single housed water,  replicate 3

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

hyb_protocol: Labeled cDNA was hybridized to GeneChip Mouse Transcriptome Arrays (ClariomS)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Each array was processed through quality control, normalization using Expression Console and the Transcriptome Analysis Center (TAC, Affymetrix)

label: biotin

source_name: brain tissue harvested on PND 57 after single or neighbor housing +/- 2BC

label_protocol: Biotinylated cRNA from PFC and NAc was reverse transcribed and labeled for microarray hybridization using standard kits and protocols from Affymetrix

growth_protocol: Male and females C57BL/6J mice (n = 4-5/group) were single or neighbor housed on PND 26. Half of the mice were given ethanol 2-BC drinking and half the mice were given two bottles of water from PND 29-52, as above. PFC and NAc were collected on PND 57 (n = 4-5/group) and flash frozen.

extract_protocol: Total RNA was isolated using STAT 60 Reagent (Tel-Test, Friendswood, TX, United States) and RNeasy mini kit (Qiagen, Valencia, CA, United States) according to the manufacturer’s protocol.

treatment_protocol: Prefrontal cortex (PFC) and Nucleus Accumbens (NAC) were collected on PND 57 and flsh frozen

value: brain

tag: brain region

value: PFC

tag: group

value: single housed water


title: GR mutant control 7


title: female, PFC, single housed water,  replicate 4


title: female, PFC, single housed ethanol,  replicate 3

value: single housed ethanol


title: female, PFC, neighbor housed water,  replicate 4

value: female

value: neighbor housed water


title: female, PFC, single housed ethanol,  replicate 5


title: GR wild-type betamethasone-treated 20


title: female, PFC, neighbor housed ethanol,  replicate 5

value: neighbor housed ethanol


title: female, PFC, neighbor housed water,  replicate 5


title: female, PFC, single housed water,  replicate 1


title: female, PFC, neighbor housed ethanol,  replicate 3


title: female, PFC, neighbor housed water,  replicate 3


title: female, PFC, neighbor housed ethanol,  replicate 4


title: female, PFC, neighbor housed ethanol,  replicate 2


title: GR wild-type betamethasone-treated 19


title: female, PFC, single housed water,  replicate 2


title: female, PFC, neighbor housed water,  replicate 2


title: GR wild-type betamethasone-treated 17


title: GR wild-type betamethasone-treated 16


title: GR wild-type betamethasone-treated 15


title: GR wild-type betamethasone-treated 13


title: GR wild-type betamethasone-treated 12


title: female, PFC, single housed ethanol,  replicate 2


title: female, NAC, neighbor housed water,  replicate 5

value: NAC


title: female, PFC, single housed ethanol,  replicate 1


title: female, PFC, neighbor housed ethanol,  replicate 1


title: female, PFC, neighbor housed water,  replicate 1


title: GR wild-type betamethasone-treated 11


title: female, NAC, neighbor housed water,  replicate 3


title: GR wild-type betamethasone-treated 18


title: female, NAC, single housed ethanol,  replicate 5


title: GR wild-type betamethasone-treated 10


title: GR wild-type betamethasone-treated 9


title: GR wild-type betamethasone-treated 8


title: GR wild-type betamethasone-treated 14


title: GR wild-type betamethasone-treated 6


title: GR wild-type betamethasone-treated 7


title: female, NAC, single housed ethanol,  replicate 3


title: GR wild-type betamethasone-treated 5


title: female, PFC, single housed water,  replicate 5


title: female, NAC, single housed ethanol,  replicate 4


title: RVOT cardiac specimen, cyanotic TOF patient9

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

description: Gene expression data of cardiac muscle from the RV outflow tract of a paediatric patient with TOF cardiac defects and cyanosis

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: Cardiac specimen of Right Ventricular Outflow Tract

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: Cardiac specimens (muscle bundles that are routinely resected from the RV outflow tract as part of surgery) were recovered from 11 pediatric patients with sporadic TOF cardiac defects and cyanosis (repeated oxygen saturation measurements of ≤ 91.0 % on room air, and episodes of spells; 4 males, 7 females; age 23.2 ± 5.0 months).

extract_protocol: Total RNA was isolated from heart tissue with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: All pediatric patients had sporadic TOF without any other malformation.

value: Heart muscle of Right Ventricular Outflow Tract (RVOT)

tag: gender

value: Female

tag: age

value: Paediatric patient

tag: diagnosis

value: Sporadic TOF cardiac defects and cyanosis


title: RVOT cardiac specimen, cyanotic TOF patient10


title: female, NAC, single housed water,  replicate 4

tag: strain


title: female, NAC, single housed water,  replicate 3


title: RVOT cardiac specimen, cyanotic TOF patient11


title: female, NAC, single housed water,  replicate 5


title: RVOT cardiac specimen, cyanotic TOF patient8

value: Male


title: GR wild-type betamethasone-treated 2

value: 100uM betamethasone


title: GR wild-type betamethasone-treated 3


title: female, NAC, single housed water,  replicate 2


title: GR wild-type betamethasone-treated 1


title: GR wild-type betamethasone-treated 4


title: GR wild-type control 24

value: Control:0.2% ethanol


title: GR wild-type control 23


title: RVOT cardiac specimen, cyanotic TOF patient7


title: GR wild-type control 21


title: GR wild-type control 22


title: female, NAC, single housed water,  replicate 1


title: female, NAC, neighbor housed ethanol,  replicate 4


title: GR wild-type control 19


title: female, NAC, neighbor housed ethanol,  replicate 3


title: RVOT cardiac specimen, cyanotic TOF patient5


title: female, NAC, neighbor housed water,  replicate 2


title: GR wild-type control 17


title: female, NAC, neighbor housed ethanol,  replicate 5


title: RVOT cardiac specimen, cyanotic TOF patient4


title: RVOT cardiac specimen, cyanotic TOF patient6


title: RVOT cardiac specimen, cyanotic TOF patient3


title: female, NAC, neighbor housed ethanol,  replicate 2


title: RVOT cardiac specimen, cyanotic TOF patient2


title: female, NAC, neighbor housed water,  replicate 4


title: GR wild-type control 16


title: GR wild-type control 14


title: GR wild-type control 20


title: GR wild-type control 12


title: GR wild-type control 13


title: cyclophosphamide induced mice urinary bladder isolated cells-1

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

data_processing:
Quality control to asses, the need for trimming of the adaptor sequence or bad segments,  Fastqc v0.11.7 and Trim Galore!v04.2.
Aligned to the reference mouse genome version mm10 with program STAR v2.6.le
miRNA level expression was assessed by counting each miRNA defined in the NCBI database.
Raw counts were normalized as transcript per million
Differential miRNA expression between groups of samples was assessed with R package DESeq2 vl. 26.0
miRNAs with log1.5fold change ( 1.5) and FDR 0.05 are selected for analysis using miRNAs gene ontology.
Assembly: mm10
Supplementary files format and content: 189441.all_samples.summary, QIAseq-miRNA-NGS_data analysis_20211105111505

source_name: microRNAs data from urinary bladder cells  8 days after cyclophosphamide induction

growth_protocol: Urinary bladder cells were isolated from bladder tissue of both  naïve as well as cyclophosphamide treated  mice by standard protocol in our laboratory.

extract_protocol:
Trizol extraction of total RNA was performed according to manufacturer's instruction from Qiagen
Libraries were prepared from 100ng total RNA, using the Qiagen miRNA library prep kit (p/n 331509), following manufactuer's instructions

treatment_protocol: At 8 weeks of age, one group of  naïve animals that will serve as the control group, while the other half were  treated with four doses of intraperitoneal (i.p.) injection of cyclophosphamide 80 mg/kg body weight of mouse were given to the CYP group on alternate days (days 2, 4, 6, 8) and i.p. injections of saline were given to the control group.

value: Urinary bladder cells

value: CYP induced


title: cyclophosphamide induced mice urinary bladder isolated cells-3


title: GR wild-type control 10

value: Wild-type


title: GR wild-type control 11


title: GR wild-type control 15


title: GR wild-type control 18


title: Control mice isolated urinary bladder cells-3

source_name: microRNAs data from urinary bladder cells  without induction

value: Control


title: GR wild-type control 9


title: female, NAC, single housed ethanol,  replicate 2

value: brain


title: Control mice isolated urinary bladder cells-2


title: female, NAC, neighbor housed water,  replicate 1


title: Control mice isolated urinary bladder cells-1


title: GR wild-type control 8


title: GR wild-type control 6


title: GR wild-type control 7


title: GR wild-type control 5


title: RVOT cardiac specimen, cyanotic TOF patient1


title: female, NAC, single housed ethanol,  replicate 1

value: single housed ethanol


title: female, NAC, neighbor housed ethanol,  replicate 1

value: female


title: FVB rep4

description: FVB_rep4 (TPM)

data_processing:
Trimmed RNA-Seq reads in FASTQ format were generated by GATC Biotech AG. RNA-Seq reads in FASTQ format were imported into the program CLC Genomics workbench 20 version 20.0.4 (QIAGEN Bioinformatics, QIAGEN Aarhus A/S) and aligned to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20.
The trimmed RNA-Seq reads in FASTQ format were mapped to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20. The following mapping settings were used: Mismatch count: 2; Insertion cost: 3; Deletion cost: 3; Length fraction: 0.8; Similarity fraction: 0.8; Maximum number of hits for a read: 10; Expression value: TPM. Gene and transcript annotations of the reference genome were added to the mapped reads. With these settings, read tracks and reports were generated. The processed data files show transcripts per million (TPM) for every transcript and every sample.
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated text (txt) files include TPM values for each sample and transcript. The following tab-separated columns are presented in the processed data files: Name; Chromosome; Region; TPM; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype.
Supplementary files format and content: The matrix table shows TPM values of every transcript and every sample. The following tab-separated columns are included in the matrix table (Matrix_table_total_heart.txt): Name; Chromosome; Region; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype; TPM values of 8 samples.

source_name: Total heart

growth_protocol: After weaning at an age of 3-4 weeks, Tg-BBLN mice and non-transgenic FVB/N control mice were housed until the end of the observation period at an age of 8 months in groups of 2-4 mice under SPF conditions with a 12 h dark cycle in individually ventilated cages. All the mice had free access to food and water and were fed a standard rodent diet.

extract_protocol:
Hearts were rapidly isolated from euthanized, male, eight-month-old Tg-BBLN mice and non-transgenic FVB/N mice, and rapidly frozen in liquid nitrogen. Hearts were pulverized under liquid nitrogen, and total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Discover protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina paired-end read sequencing (2 x 150 bp) with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.

value: Total heart

value: FVB/N

value: male

value: non-transgenic

value: 8 months


title: cyclophosphamide induced mice urinary bladder isolated cells-2


title: GR wild-type control 4


title: GR wild-type control 3


title: GR wild-type control 2


title: FVB rep3

description: FVB_rep3 (TPM)


title: GR wild-type control 1


title: FVB rep2

description: FVB_rep2 (TPM)


title: FVB rep1

description: FVB_rep1 (TPM)


title: glp-1_TU3401_mxl-2i-2

city: Suita

first: Tatsuya

last: Shioda

state: Osaka

address: Yamadaoka 1-1

country: Japan

institute: Osaka University

description: glp-1_TU3401_Luc vs glp.1_TU3401_mxl-2i.xlsx

data_processing:
Illumina package bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat (v2.1.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: text file includes raw conts for each sample
Supplementary files format and content: text file includes RPKM values for each sample

organism: Caenorhabditis elegans

growth_protocol: Nematodes were maintained at 20 °C using standard techniques on NGM plates with Escherichia coli

extract_protocol:
C. elegans samples were harvested in QIAZOL (QIAGEN) at various time points. Total RNA was extracted using the RNeasy® mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNAi was carried out by feeding worms with HT115 (DE3) bacteria transfcted with the L4440 vector, which induces the expression of dsRNA against the targeted gene.

value: Whole body

value: adult day 1


title: glp-1_TU3401_mxl-2i-4


title: glp-1_TU3401_mxl-2i-1


title: male, PFC, neighbor housed water,  replicate 5

value: PFC

value: neighbor housed water


title: male, PFC, neighbor housed water,  replicate 4


title: glp-1_TU3401_mml-1i-3

description: glp-1_TU3401_Luc vs glp.1_TU3401_mml-1i.xlsx


title: male, PFC, single housed ethanol,  replicate 2


title: glp-1_TU3401_mml-1i-4


title: glp-1_TU3401_mml-1i-2


title: Tg BBLN rep4

description: Tg_BBLN_rep4 (TPM)

value: FVB/N-TgMHCBBLN

value: BBLN


title: Tg BBLN rep3

description: Tg_BBLN_rep3 (TPM)


title: glp-1_TU3401_mml-1i-1


title: male, PFC, single housed ethanol,  replicate 1


title: male, PFC, single housed ethanol,  replicate 4


title: Tg BBLN rep2

description: Tg_BBLN_rep2 (TPM)


title: male, PFC, neighbor housed ethanol,  replicate 5

value: neighbor housed ethanol


title: glp-1_TU3401_Luc-3

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: glp-1_TU3401_mxl-2i-3


title: glp-1_TU3401_Luc-4

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: glp-1_TU3401_Luc-1

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: Tg BBLN rep1

description: Tg_BBLN_rep1 (TPM)


title: male, PFC, single housed ethanol,  replicate 3


title: TU3401_Luc-4

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: TU3401_Luc-3

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: male, PFC, neighbor housed ethanol,  replicate 4


title: FVB_left_rep4

description: FVB_left_rep4 (TPM)

data_processing:
Trimmed RNA-Seq reads in FASTQ format were generated by GATC Biotech AG. RNA-Seq reads in FASTQ format were imported into the program CLC Genomics workbench 20 version 20.0.4 (QIAGEN Bioinformatics, QIAGEN Aarhus A/S) and aligned to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20.
The trimmed RNA-Seq reads in FASTQ format were mapped to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20. The following mapping settings were used: Mismatch count: 2; Insertion cost: 3; Deletion cost: 3; Length fraction: 0.8; Similarity fraction: 0.8; Maximum number of hits for a read: 10; Expression value: TPM. Gene and transcript annotations of the reference genome were added to the mapped reads. With these settings, read tracks and reports were generated. The processed data files show transcripts per million (TPM) for every transcript and every sample.
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated text (txt) files show TPM values of each sample and transcript. The following tab-separated columns are presented in the processed data files: Name; Chromosome; Region; TPM; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype.
Supplementary files format and content: The matrix table shows TPM values of every transcript and every sample. The following tab-separated columns are included in the matrix table (Matrix_table_right_left_heart.txt): Name; Chromosome; Region; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype; TPM values of 16 samples.

source_name: left ventricular heart specimen

growth_protocol: After weaning at an age of 3-4 weeks, Tg-BBLN mice and non-transgenic FVB/N control mice were housed until the end of the observation period at an age of 3-4 months in groups of 2-4 mice under SPF conditions with a 12 h dark cycle in individually ventilated cages. All the mice had free access to food and water and were fed a standard rodent diet.

extract_protocol:
Right and left ventricular heart specimens were dissected from total hearts isolated from euthanized, male Tg-BBLN mice and non-transgenic FVB/N mice (age: 3-4 months). Dissected heart specimens were  rapidly frozen in liquid nitrogen. For RNA isolation, right and left heart specimens were pulverized under liquid nitrogen, and total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Discover protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina paired-end read sequencing (2 x 150 bp) with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.

value: left ventricular heart specimen

value: 3-4 months


title: FVB_left_rep3

description: FVB_left_rep3 (TPM)


title: TU3401_Luc-2

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: male, PFC, single housed water,  replicate 3

value: brain

value: single housed water


title: TU3401_Luc-1

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: FVB_left_rep2

description: FVB_left_rep2 (TPM)


title: 3_gTU_atg2i

description: gTU_luc vs gTU_atg2i.xlsx

source_name: glp-1 with neuronal atg-2i


title: 3_gTU_hlh30i

description: gTU_luc vs gTU_hlh-30i.xlsx

source_name: glp-1 with neuronal hlh-30i


title: 3_gTU_atg18i

description: gTU_luc vs gTU_atg18i.xlsx

source_name: glp-1 with neuronal atg-18i


title: glp-1_TU3401_Luc-2

description: TU3401_Luc vs glp.1_TU3401_Luc.xlsx


title: male, PFC, single housed water,  replicate 5


title: male, PFC, single housed water,  replicate 4


title: 3_TU_luc

description: TU_luc vs gTU_luc.xlsx

source_name: control


title: male, PFC, single housed water,  replicate 2


title: Tg_BBLN_left_rep4

description: Tg_BBLN_left_rep4 (TPM)


title: 2_gTU_hlh30i

description: gTU_luc vs gTU_hlh-30i.xlsx


title: 2_gTU_atg2i

description: gTU_luc vs gTU_atg2i.xlsx


title: 2_gTU_luc

description: TU_luc vs gTU_luc.xlsx

source_name: glp-1 control


title: male, PFC, neighbor housed ethanol,  replicate 3


title: male, PFC, neighbor housed ethanol,  replicate 2


title: Tg_BBLN_left_rep2

description: Tg_BBLN_left_rep2 (TPM)


title: Tg_BBLN_left_rep3

description: Tg_BBLN_left_rep3 (TPM)


title: 2_TU_luc

description: TU_luc vs gTU_luc.xlsx


title: 2_gTU_atg18i

description: gTU_luc vs gTU_atg18i.xlsx


title: 3_gTU_luc

description: TU_luc vs gTU_luc.xlsx


title: male, PFC, neighbor housed water,  replicate 3


title: 1_gTU_atg18i

description: gTU_luc vs gTU_atg18i.xlsx


title: FVB_right_rep3

description: FVB_right_rep3 (TPM)

source_name: right ventricular heart specimen

value: right ventricular heart specimen


title: male, PFC, neighbor housed water,  replicate 1


title: FVB_right_rep1

description: FVB_right_rep1 (TPM)


title: Tg_BBLN_right_rep3

description: Tg_BBLN_right_rep3 (TPM)


title: Tg_BBLN_right_rep4

description: Tg_BBLN_right_rep4 (TPM)


title: 1_gTU_luc

description: TU_luc vs gTU_luc.xlsx


title: 1_gTU_hlh30i

description: gTU_luc vs gTU_hlh-30i.xlsx


title: Tg_BBLN_left_rep1

description: Tg-BBLN_left_rep1 (TPM)


title: male, PFC, neighbor housed water,  replicate 2


title: Tg_BBLN_right_rep2

description: Tg_BBLN_right_rep2 (TPM)


title: WT tumors

first: Sebastian

last: Ouyang

address: 107 Yanjiangxi Road

department: Dept. of Urology

institute: Sun Yat-sen Memorial Hospital

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Ref) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted.
After that, we used STAR v2.6.1a (Ref) to map reads to the reference GRCm38 (ensembl version 92 annotation).
UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref) software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Matrix File

source_name: Sub-epithelial WT cancer tissues

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads

value: Sub-epithelial WT cancer tissues

value: Murine urothelial carcinoma cells

value: WT


title: mFgfr3 tumors

source_name: Sub-epithelial mFgfr3 cancer tissues

value: Sub-epithelial mFgfr3 cancer tissues

value: Fgfr3-mutant (S243C)


title: FVB_right_rep4

description: FVB_right_rep4 (TPM)

value: FVB/N

value: male

value: non-transgenic


title: 1_gTU_atg2i

description: gTU_luc vs gTU_atg2i.xlsx

value: Whole body

value: adult day 1


title: 1_TU_luc

description: TU_luc vs gTU_luc.xlsx


title: PF-04457845 treated 3

city: Nagoya

first: Masahisa

last: Katsuno

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology

institute: Nagoya University Graduate School of Medicine

data_processing:
The quality of the raw paired-end sequence reads was assessed with Fast QC (Version 0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome using RNA-Seq aligner HISAT2 (Version 2.1.0). The HISAT2-resultant .sam files were converted into .bam files with samtools and used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3). The raw counts were normalized with transcripts per million (TPM).
Supplementary files format and content: raw count data, tsv

source_name: spinal cord

extract_protocol:
Mice were deeply anesthetized, and the entire spinal cord were dissected and snap-frozen in powdered CO2 in acetone. We dissected the mice at the age of 16 weeks.Total RNA was extracted from the thoracic spinal cord using the InvitrogenTM TRIzolTM Plus RNA Purification Kit.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.)

treatment_protocol: SOD1*G93A transgenic mice were treated with PD-04457845(1mg/kg/day) or vehicle by chow from age of week 8 until endpoint

value: spinal cord


title: PF-04457845 treated 4


title: PF-04457845 treated 2


title: Tg_BBLN_right_rep1

description: Tg_BBLN_right_rep1 (TPM)

value: FVB/N-TgMHCBBLN

value: BBLN


title: FVB_right_rep2

description: FVB_right_rep2 (TPM)

value: 3-4 months


title: male, PFC, single housed water,  replicate 1

value: brain

value: PFC


title: PF-04457845 treated 1


title: male, NAC, neighbor housed water,  replicate 4

value: NAC

value: neighbor housed water


title: male, NAC, single housed ethanol,  replicate 4

value: single housed ethanol


title: male, NAC, neighbor housed water,  replicate 5


title: male, NAC, single housed ethanol,  replicate 3


title: male, NAC, single housed ethanol,  replicate 1


title: male, NAC, neighbor housed ethanol,  replicate 5

value: neighbor housed ethanol


title: Vehicle_treated 4

value: vehicle


title: male, NAC, single housed ethanol,  replicate 2


title: Vehicle_treated 1


title: Vehicle_treated 2


title: Vehicle_treated 3


title: 2-1-input

data_processing:
Real-Time Analysis(v3.4.4) and bcl2fastq(v2.19) softwares used for basecalling.
Reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide were discarded to obtain clean reads using fastp (version 0.23.1).
The clean reads were aligned to the reference genome using alignment algorithms Bowtie2 (version 2.3.4.3) with default parametres.
The virus and mouse reads were splited. DeepTools (verison 3.5.1) bamCoverage was used to calculated the read coverage, plotProfiles and computeMatrix were utilized to plot signals around the reference-point of TSS. Peak calling algorithms, MACS2 (version 2.2.7.1), were used to identify significant peaks representing protein-DNA binding sites for mouse and virus seperately.
The peaks were annotated to known genomic features using ChIPseeker (version 1.32.1). Homer2 (version 4.11.1) findMotifsGenome.pl was the used to enrich the known and de novo motifs. Integrative Genomics Viewer (IGV) was used to visualize the read coverage and the identified peaks.
Assembly: mm10

source_name: Brain

extract_protocol:
Cell monolayers in 100-mm plates were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 0.125 M of glycine for 5 min, washed twice with 5 ml of cold PBS. The cells were then scraped into 15 ml tubes with 8 ml of cold PBS and spinned at 2000 rpm for 5 min at 4°C. The supernatant was discarded and the cell pellet was store at -80C. On the day of sonication, the cells were lysed for 30 min on ice in 300 ul of 0.4% SDS lysis buffer (1% SDS, 10 mM of EDTA, 50 mM of Tris, pH 8.0) and transferred into 1.5 ml Eppendorf tubes. The cell lysate was sonicated on ice using a Ultrasonic Homogenizer SCIENTZ-IID for 10 cycles of 1 min each on the setting of 30 s ON, 30 s OFF and 80 watts.
the purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (catalogue no. E7645L; NEB) for ChIP-seq library preparation.

treatment_protocol: For infection, cells were infected with ICP0-null  HSV-1 (7134) for 5hpi (MOI = 3) before ChIP-seq

value: Brain

value: mouse neuroblastoma N2a cells


title: 2-1-ip


title: 2-2-input


title: N2ApOC2△HOX2, ATAC, rep1

description: N2ApOC2deltaHOX2 cells derived from Neuro-2a cells infected

data_processing:
For 10X Genomics ATAC-seq library, we integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ using Drop-seq tools
snaptools was used to pre-process the 10X Genomics ATAC data. Demultiplexed sequencing reads are aligned to the mouse reference (mm10 genome) and HSV-1 reference
Assembly: mm10 and KOS
Supplementary files format and content: bigwig

source_name: Cells overexpressing pOC2△HOX2, infected with HSV-1 for 2 hours

extract_protocol:
Genomic DNA  was extracted according to TruePrepTM DNA Library Prep Kit V2 for Illumina®（Vazyme TD501）
ATAC libraries were prepared for sequencing using TruePrepTM Index Kit V2 for Illumina® (Vazyme TD202)

treatment_protocol: For infection, cells were infected with ICP0-null HSV-1 (strain 7134) for 2 hpi (MOI = 1) before ATAC

value: overexpressing OC2{delta}HOX2


title: N2ApOC2△HOX2, ATAC, rep2


title: N2ApcDNA, ATAC, rep2

description: N2ApcDNA control cells derived from Neuro-2a cells infected

source_name: Cells overexpressing pcDNA, infected with HSV-1 for 2 hours

value: control


title: N2ApcDNA, ATAC, rep1


title: male, NAC, neighbor housed ethanol,  replicate 4

source_name: brain tissue harvested on PND 57 after single or neighbor housing +/- 2BC

value: male


title: 2-2-ip


title: male, NAC, single housed water,  replicate 4

value: single housed water


title: C4-2 cells with METTL3 knockdown MeRIP-seq m6A input (replicate 1)

data_processing:
RNA-Seq reads were mapped to human reference genome version hg19 using TopHat (version v2.0.12)  with default parameters. Next, Cuffdiff (version 2.2.1) was used to generate read count matrix. Normalized gene expression values in FPKM (fragments per kilobases per million mapped reads) was further calculated using UCSC knownGene as the reference genes. Genes with FPKM value larger than one were retained for further analysis. Differential expression test was performed using edgeR.
MeRIP-Seq data was filtered by Trimmomatic to remove low-quality bases and then mapped to human genome (version hg19) by Tophat (version v2.0.12) using default parameters. The read coverage calculation and normalization were conducted by deepTools. The distribution of m6A signal across gene body (5’UTR, CDS and 3’UTR) was measured by FPKM values in bins by deepTools. The normalized IP signal per bin was subtracted by normalized input signal to generate m6A signal coverage plot. Enrichment peaks of m6A signal were called by MACS2 and exomePeak2 using default parameters (parameter and p-value). M6A peaks called by MACS2 required q-value less than 0.05, and by exomePeak2 q-value less than 0.1. Differential methylation sites were identified by exomePeak2.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized gene expression (FPKM values) for all the RNA-seq samples.
bigWig for all the MeRIP-seq samples.

source_name: human prostate cancer cell line C4-2

extract_protocol:
MeRIP-seq was conducted in duplicates using Magna MeRIP™ m6A Kit (Millipore) with the procedure provided by the manufacturer. In brief, the total RNA from C4-2 and PrEC cells was extracted using RNeasy Plus Mini Kit (Qiagen), followed by mRNA isolation using PolyATtract mRNA Isolation System (Promega). The obtained mRNA was fragmented into ~100 nt in length and purified by miRNeasy Mini Kit (Qiagen). After incubation with anti-m6A antibody-magnetic beads mixture at 4 °C overnight, the m6A-modified mRNA fragments bound to beads were eluted and shipped to BGI for library preparation and sequencing using the DNBseq platform.
Samples were sent to BGI for library preparation and follow-up sequencing
MeRIP-seq

value: prostate cancer cells

value: METTL3 knockdown

tag: rip antibody

value: anti-m6A antibody


title: EEDKO_H3K27me3_rep2

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 203 Research Dr

department: Head and Neck Surgery & Communication Sciences

institute: Duke University

data_processing:
ChIP-Seq data was processed using the trimmomatic toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads and reserving reads 20nt or longer for further analysis
Reads were mapped to the GRCm38 mouse genome assembly (mm10) using the bowtie alignment tool, keeping those alignments mapping to a single genomic location in. Amplification artifacts were removed using the Picard toolkit.
Data was subsampled to target 7 million reads using Samtools. Bigwig files were generated using deepTools.
Supplementary files format and content: bigwig

source_name: Olfactory epithelium

extract_protocol:
Olfactory tissue was obtained from adult Krt5-CreERT2;Rosa-Ai9;Eed-fl/fl mice mice euthanized 7-10 days following methimazole lesion by decapitation after deep anesthesia, and olfactory mucosa was dissociated in an enzyme cocktail (collagenase, Dispase and DNase I in HBSS for 15 min, followed by 3 min with 0.125% trypsin with gentle trituration. Cells from 6-10 mice were pooled per ChIP replicte, and GBCs were purified from the cell suspension using APC-conjugated antibody to c-Kit for 15 minutes and then APC magnetic selection. Cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature.Cells were lysed and homogenized, and a Bioruptor Pico was used to shear chromatin. Chromatin was incubated with antibodies (30 μg chromatin and 4 μg of antibody) at 4°C overnight.
NEBNext Ultra II DNA Library Prep Kit for Illumina with at least 1 ng of ChIP genomic DNA was used as starting material for library prep following manufacturer instructions.

value: Olfactory epithelium

value: Globose basal cell

tag: chip antibody

value: Tamoxifen, Methimazole


title: C4-2 cells with METTL3 knockdown MeRIP-seq m6A IP (replicate 2)

tag: cell line


title: Biopsy_end.of.cold.ischemia_patient_16

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H19_0

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the oligo package. We used an alternative CDF probset description file from Brainarray (version 22) at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): pd.hgu133plus2.hs.entrezg_22.0.0.tar.gz

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: paired samples

value: patient 16

tag: timepoint

value: cit

value: lung


title: male, NAC, single housed water,  replicate 3

value: brain

value: NAC


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_17

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H20_6

value: patient 17


title: Biopsy_end.of.cold.ischemia_patient_17

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H20_0


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_15

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H18_6

value: patient 15


title: EEDKO_H3K27me3_rep1

tag: cell type

tag: genotype


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_16

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H19_6


title: Biopsy_end.of.cold.ischemia_patient_15

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H18_0


title: male, NAC, single housed water,  replicate 5


title: C4-2 cells with METTL3 knockdown MeRIP-seq m6A IP (replicate 1)


title: C4-2 cells with METTL3 knockdown  MeRIP-seq m6A input (replicate 2)


title: male, NAC, neighbor housed ethanol,  replicate 1

value: neighbor housed ethanol


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_14

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H17_6

value: patient 14


title: WC65

city: Bethesda

first: Francis

last: Collins

address: 50 South Dr

department: NHGRI

institute: NIH

data_processing:
Aligned the processed reads to the GRCm38 genome assembly using STAR v2.73a with default parameters
Quantified expression levels of gencode.vM24 genes using QoRTs (v1.3.6).
Generated a raw read count matrix of gene by library
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include read counts per gene per sample

source_name: 8-week femoral diaphysis

extract_protocol:
total RNA extracted using Trizol, then treated with 1U/ul Dnase I
Strand-specific
Poly-A enrichment, 80M clusters PE150 each

value: 8-week femoral diaphysis

value: female


title: Biopsy_end.of.cold.ischemia_patient_14

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H17_0


title: male, NAC, neighbor housed ethanol,  replicate 3

value: male


title: C4-2 cells (knockdown control)  MeRIP-seq m6A input (replicate 2)

value: prostate cancer cells

value: knockdown control


title: male, NAC, single housed water,  replicate 2

value: single housed water


title: male, NAC, neighbor housed ethanol,  replicate 2


title: male, NAC, neighbor housed water,  replicate 3

value: neighbor housed water


title: WC64


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_13

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H15_6

value: patient 13


title: male, NAC, neighbor housed water,  replicate 2


title: WC63


title: C4-2 cells (knockdown control) MeRIP-seq m6A input (replicate 1)

value: anti-m6A antibody


title: C4-2 cells (knockdown control) MeRIP-seq m6A IP (replicate 1)


title: WC62


title: PF-04457845 treated

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were deeply anesthetized, and the entire spinal cord were dissected and snap-frozen in powdered CO2 in acetone. We dissected the mice at the age of 16 weeks.Spinal cords from 4 mice for each condition were pooled for homogenization and nuclear isolation. Briefly, fresh frozen murine spinal cord was placed in a Dounce homogenizer (Kimble Chase 2 ml Tissue Grinder) containing ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal and 0.2 U/μl RNase inhibitor). After homogenizing with 5 strokes of pestle A and 5–10 strokes of pestle B, the lysate was diluted with 1.4 mL of lysis buffer and incubated for 5 minutes. The homogenate was passed over a 70 μm strainer (Fisher Scientific). The filtered lysate was centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the pellet was resuspended in 1.5 ml lysis buffer and incubated for 3 minutes on ice. Then, the pellet was centrifuged again at 500 × g for 5 minutes and resuspended in 1500 µl of wash buffer (1× PBS with 1% BSA and 0.2 U/µl SUPERase-InTM RNase Inhibitor (Thermo Fisher). The nuclei were washed and centrifuged at 500 × g for 5 minutes three times and filtered through a 40 µm cell strainer. The cell suspensions were processed according to the debris removal solution (Milteni Biotec) protocol, a density gradient method to remove dead cells and debris. Cells were resuspended in cold PBS with 0.04% BSA and stained with DAPI. The nuclei were sorted with a FACS Aria instrument (Becton Dickson) with a 100 nm nozzle and 405 nm excitation laser. The instrument was controlled by a PC running FACS DiVa™ software (Becton Dickson). These nuclei were centrifuged, inspected for appearance, and concentrated for the next step.
The nuclei per sample were run on the 10 × Chromium Single cell 3’ gene expression v3.1 platform. Sequencing libraries were constructed according to the manufacturer’s instructions, and cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip as quality control and determination of cDNA concentrations. The samples were run on an Illumina HiSeq2500 at Read 1 = 28 bp and Read 2 = 90 bp, with a minimum depth of 20,000 reads per nucleus. For alignment, introns and exons were included in the reference genome (mm10) using the CellRanger v6.1.2 pipeline (10X Genomics). Sequencing data were analyzed using the R package Seurat Version 4.1.3. The gene barcode matrices for each sample were imported into R using the Read10X function.

value: spinal cord

tag: treatment

value: 16 weeks


title: WC61


title: Vehicle_treated

value: vehicle


title: PrEC cells MeRIP-seq m6A input (replicate 2)

source_name: human prostate primary epithelial cells

value: prostate primary epithelial cells (PrEC)

value: control


title: Biopsy_end.of.cold.ischemia_patient_13

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H15_0

value: cit

value: lung


title: male, NAC, neighbor housed water,  replicate 1

value: brain

value: NAC


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_12

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H14_6

value: patient 12


title: Control_3

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Sequencing data were processed with RTA v1.18.66.3.
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing adapter contaminations were removed using Cutadapt.
Reads were mapped on transcriptome and gene expression quantified using RSEM.
RSEM-estimated raw gene counts were normalized with Limma-Voom.
Genome_build: GRCm38 assembly, Ensembl genebuild 70.
Supplementary_files_format_and_content: Matrix table contains raw expected_counts as obtained from RSEM aligner.

source_name: Embryo

extract_protocol:
RNA was isolated at E15.5 from ventricles of Control (Mib1flox/+; Tnnt2-Cre/+) and Mib1R530X/flox; Tnnt2-Cre/+, and WT and Mib1R530X/+ Asxl3M1361V/+ Apcdd1V150I/+ embryos. Samples were distributed in three pools of four pairs of ventricles per genotype. Tissue was homogenized with a pestle mechanical homogenizer and RNA was extracted using RNEasy Mini Kit (Qiagen, 74104).
cDNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit
Libraries were sequenced on a HiSeq 2500 system (Illumina) to generate 60 base single reads.

value: Mib1_flox/+; Tnnt2-Cre/+


title: WC60

value: 8-week femoral diaphysis

value: male


title: PrEC cells MeRIP-seq m6A input (replicate 1)


title: Control_2


title: WC59

value: Lmna+/+

value: female


title: WC58


title: PrEC cells MeRIP-seq m6A IP (replicate 2)


title: Biopsy_end.of.cold.ischemia_patient_12

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H14_0


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_11

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H13_6

value: patient 11


title: Control_1


title: male, NAC, single housed water,  replicate 1

value: single housed water


title: C4-2 cells (knockdown control) MeRIP-seq m6A IP (replicate 2)

value: prostate cancer cells

value: knockdown control

value: anti-m6A antibody


title: WC57


title: Biopsy_end.of.cold.ischemia_patient_10

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H12_0

value: patient 10


title: WT_3

value: WT


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_10

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H12_6


title: WC56


title: WT_2