title: Single cell miRNA-seq of BJ cell_BJ_SC1

description:
BJ_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

value: healthy

tag: sample type

value: single cell

tag: replicate

tag: protocol


title: 409

status: Public on Jun 05 2021

type: SRA

city: Barcelona

first: Carlota

last: Dobaño

address: Rosselló 153

country: Spain

institute: ISGlobal, Hospital Clínic - Universitat de Barcelona

library_source: transcriptomic

data_processing:
reads were aligned using BWA Aln version 0.7.10 using UCSC RefSeq (Human 19) with mitochondrial genes added
Quantified samples were then quality controlled using mapping summary statistics to remove low quality samples based on predetermined minimum values for the total number of mapped reads, percent of mapped reads mapped to the human genome, etc.
Downstream analysis was applied only to reads that mapped uniquely to a UMI and only mapped to isoforms of the same gene (UMI.unq).
The TMM normalization method was applied to account for differing number of read counts and to address unwanted technical variation. The voom transformation from the limma R package  was applied to transform the data into a form appropriate for linear models.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated_unique_refseq_umi_counts.tsv contains the count matrix for all samples/cells

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA was extracted at the Center for Infectious Disease Research (CIDR, Seattle) using the Promega SV 96 RNA Isolation kit following the manufacturer’s protocol. Samples kept in RNAprotect were centrifuged at 4,000g for 7 minutes at 4°C, cell pellets were resuspended in 150 μL RLT Buffer, and 150 μL of 70% ethanol was added prior to processing with Promega SV 96 RNA Isolation kit. RNAs were eluted with 100 μL nuclease free water. Each 96-well extraction batch was spot checked by Bioanalyzer using Agilent RNA 6000 Pico chip and had an average RIN score of 7.4. RNA samples were distributed in 384 well plates for library preparation. Samples from the same individuals were in the same plate and key study variables (vaccine, site and cases-controls) were checked for balance across plates to avoid batch effects.
An optimized version of Digital Gene Expression (DGE) was used, further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from antigen-stimulated PBMCs was linked to unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Then, cDNA from multiple cells were pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3′ ends and preserving strand information. Nextera XT library preparation and sequence paired-ends were employed on an Illumina NextSeq instrument at the Broad Institute.
SCRB-Seq

tag: cell type

value: PBMC

tag: plate

tag: pid

tag: stimulation

value: hbs

tag: visit

tag: site

value: BAGAMOYO

tag: age

value: old

tag: vaccine

value: rtss

tag: case

value: control

tag: match

tag: sid

tag: waz

tag: haz

tag: hb

tag: Sex

value: F

value: Low


title: 407

value: M


title: 401

value: dmso


title: Single cell miRNA-seq of BJ cell_BJ_SC3

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

description:
BJ_SC3
cell_lines_mirna_expr_dedup_counts.txt

data_processing:
Basecalls performed with bcl2fastq (2.20.0.422)
Adapter trimming and quality trimming was performed with cutadapt 2.10. Reads were trimmed at the 3’ end with a quality cutoff of 20. In addition to the 3’ adapter, polyA tails, polyG tails, and PCR primers were removed. Trimming was performed up to 3 times per read while allowing an error rate of 10%, at most 2 N bases and requiring a minimum length of 18 bases to keep the read.
The remaining reads were mapped against the primary assembly of the human genome GRCh38 using STAR (2.7.5b) with parameters: “--outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1 --outSAMstrandField intronMotif”.
For the samples containing miRExplore an additional mapping was performed with RazerS 3 (3.5.3) with parameters: “--forward -so 1 -dr 0 -rr 100 --percent-identity 80”
Reads were quantified with featureCounts (1.5.2) with parameters -F SAF -O -M -f –fracOverlap 0 -s 0
MiRNAs were quantified with miRMaster 1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: mirxplore_counts.txt: tab-delimited text file containing the raw counts of all miRExplore sequences for each sample.
Supplementary_files_format_and_content: sce_counts.txt: tab-delimited text file containing the raw counts of all RNAs of all single cell equivalent samples.
Supplementary_files_format_and_content: sce_mirna_expr_rpmmm_norm.txt: tab-delimited text file containing the RPMMM normalized miRNA counts for all single cell equivalent samples.
Supplementary_files_format_and_content: cell_lines_mirna_expr_dedup_counts.txt: tab-delimited text file containing the UMI deduplicated miRNA counts for all cell line samples.

molecule: total RNA

source_name: fibroblast from healthy foreskin

extract_protocol: Single cell miRNA-Seq /w 19 protocols, miRExplore spike-in, single cell equivalents and 67 circulating tumor cells

tag: cell line

value: BJ

value: fibroblast from healthy foreskin

tag: culture collection

tag: disease

tag: sample type

tag: replicate

tag: genotype

value: not applicable


title: Single cell miRNA-seq of A549 cell_A549_SC5

description:
A549_SC5
cell_lines_mirna_expr_dedup_counts.txt

source_name: epithelial lung cell from carcinoma

tag: cell type

value: epithelial lung cell from carcinoma

value: carcinoma

tag: protocol


title: 403

tag: plate

tag: pid

tag: stimulation

tag: visit

tag: site

tag: age


title: Single cell miRNA-seq of A549 cell_A549_SC3

description:
A549_SC3
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of BJ cell_BJ_SC6

description:
BJ_SC6
cell_lines_mirna_expr_dedup_counts.txt

value: healthy


title: 414

tag: vaccine

tag: case

tag: match

tag: sid

tag: waz

tag: haz


title: 413

value: case

tag: hb

tag: Sex


title: Single cell miRNA-seq of MCF7 cell_CL_6_SCE

description:
CL_6_SCE
sce_counts.txt

source_name: mammary gland/breast epithelial cell

tag: cell line

value: mammary gland/breast epithelial cell

tag: culture collection

tag: disease

value: adenocarcinoma

tag: sample type

value: single cell

tag: replicate

value: CL

tag: genotype

value: Single cell equivalent


title: 408

tag: cell type

value: PBMC

tag: plate

tag: pid

tag: stimulation

value: hbs

tag: visit

value: BAGAMOYO

value: old

value: rtss


title: 397

value: csp

tag: site

tag: age

tag: vaccine

tag: case

value: control

tag: match

value: F

value: Low


title: Single cell miRNA-seq of MCF7 cell_4N_CL_5_SCE

description:
4N_CL_5_SCE
sce_counts.txt

tag: protocol


title: 396

tag: sid

tag: waz

tag: haz

tag: hb

tag: Sex


title: Single cell miRNA-seq of MCF7 cell_CL_5_SCE

description:
CL_5_SCE
sce_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type

tag: replicate

tag: genotype


title: 398

tag: cell type

tag: plate

tag: pid

tag: stimulation

tag: visit

tag: site

value: M


title: Single cell miRNA-seq of MCF7 cell_4N_CL_6_SCE

description:
4N_CL_6_SCE
sce_counts.txt

tag: protocol


title: Single cell miRNA-seq of MCF7 cell_4N_CL_4_SCE

description:
4N_CL_4_SCE
sce_counts.txt


title: 399

value: dmso

tag: age

tag: vaccine

tag: case

tag: match

tag: sid

tag: waz

value: High


title: Single cell miRNA-seq of MCF7 cell_CL_4_SCE

description:
CL_4_SCE
sce_counts.txt

tag: cell line

value: mammary gland/breast epithelial cell

tag: culture collection

tag: disease


title: 394

tag: haz

tag: hb

tag: Sex


title: PD_rep3

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre – University Health Network

data_processing:
Illumina bcl2fastq v2.20.0.422 software was used for basecalling.
Alignment of the reads to a reference genome (human HG19) was performed using HISAT2 (version 2.1.0).
Transcripts and frequencies were determined from the aligned reads using HTSeq (version 0.10.0).
Differential gene expression analysis was performed using the Voom–limma workflow.
Genome_build: Human HG19

growth_protocol: Immortalized human dermal microvascular blood endothelial cells (ECs, XSEB113C1, Lonza) were incubated in endothelial serum-free medium-2D (ESFM-2D) at 37 ºC in 5% CO2 and 5% O2 for 5 days.

extract_protocol:
RNeasy Plus Mini Kit, QIAGEN
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen, Vienna, Austria, #015.96

treatment_protocol: XSEB113C1 cells were treated with bevacizumab or palivizumab plus DMSO or BET inhibitor (I-BET762, 1000 nM; JQ1, 300 nM).

tag: treatment

value: Palivizumab + DMSO

tag: biological replicate


title: BI_rep3

source_name: Immortalized human dermal microvascular blood endothelial cells

value: Bevavizumab + I-BET762


title: Single cell miRNA-seq of MCF7 cell_4N_5_SCE

description:
4N_5_SCE
sce_counts.txt

tag: cell type

value: adenocarcinoma

tag: sample type

value: single cell

tag: replicate

tag: genotype


title: BJQ_rep3

value: Bevavizumab + JQ1


title: 393

value: PBMC

tag: plate

tag: pid

tag: stimulation

tag: visit

tag: site

tag: age

tag: vaccine


title: Single cell miRNA-seq of MCF7 cell_4N_C3_6_SCE

description:
4N_C3_6_SCE
sce_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: protocol

value: Single cell equivalent


title: PJQ_rep2

tag: treatment

value: Palivizumab + JQ1


title: Single cell miRNA-seq of MCF7 cell_4N_C3_5_SCE

description:
4N_C3_5_SCE
sce_counts.txt


title: Single cell miRNA-seq of MCF7 cell_SBN_6_SCE

description:
SBN_6_SCE
sce_counts.txt

value: SBN


title: PI_rep3

value: Palivizumab + I-BET762

tag: biological replicate


title: Single cell miRNA-seq of MCF7 cell_4N_4_SCE

description:
4N_4_SCE
sce_counts.txt

tag: cell type


title: Single cell miRNA-seq of MCF7 cell_SBN_CL_4_SCE

description:
SBN_CL_4_SCE
sce_counts.txt

tag: sample type


title: PD_rep2


title: Single cell miRNA-seq of MCF7 cell_4N_6_SCE

description:
4N_6_SCE
sce_counts.txt

tag: replicate


title: Single cell miRNA-seq of MCF7 cell_4N_C3_4_SCE

description:
4N_C3_4_SCE
sce_counts.txt

tag: genotype


title: BD_rep2

value: Bevavizumab + DMSO


title: BD_rep3


title: Single cell miRNA-seq of MCF7 cell_SB_4N_6_SCE

description:
SB_4N_6_SCE
sce_counts.txt


title: Single cell miRNA-seq of MCF7 cell_SBN_CL_6_SCE

description:
SBN_CL_6_SCE
sce_counts.txt


title: BJQ_rep2


title: Single cell miRNA-seq of MCF7 cell_SBN_CL_5_SCE

description:
SBN_CL_5_SCE
sce_counts.txt


title: PI_rep2


title: Single cell miRNA-seq of MCF7 cell_SBN_4_SCE

description:
SBN_4_SCE
sce_counts.txt


title: BI_rep2


title: Single cell miRNA-seq of MCF7 cell_SBN_5_SCE

description:
SBN_5_SCE
sce_counts.txt


title: Single cell miRNA-seq of MCF7 cell_SB_4N_5_SCE

description:
SB_4N_5_SCE
sce_counts.txt


title: PJQ_rep3


title: PJQ_rep1


title: Single cell miRNA-seq of MCF7 cell_SB_4N_4_SCE

description:
SB_4N_4_SCE
sce_counts.txt


title: BD_rep1


title: Single cell miRNA-seq of MCF7 cell with miRXplore_CL_6_ME

description:
CL_6_ME
mirxplore_counts.txt

value: CL

value: miRExplore spike-in


title: Single cell miRNA-seq of MCF7 cell with miRXplore_CL_4_ME

description:
CL_4_ME
mirxplore_counts.txt


title: miCLIP C643 WT rep2

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

description: Co-immunoprecipitated RNA fragments

data_processing:
Reads were mapped to the respective genome and its annotation (GENCODE release 31) using STAR (v2.7.3a). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999), soft-clipping was prohibited on the 5'end of reads (--alignEndsType Extend5pOfRead1) and only uniquely mapping reads were kept for further analysis (--outFilterMultimapNmax 1).
Following mapping, BAM files were sorted and indexed (SAMtools v1.9) and duplicate reads were removed (UMI-tools v1.0.0).
After removing duplicates, all mutations found in reads were extracted using the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK, v1.1.3). The list was filtered for C-to-T mutations using basic Bash commands and kept in BED file format. Based on the filtered list of C-to-T mutations, deduplicated reads were separated into two BAM files holding reads with and without C-to-T mutation, respectively, using SAMtools and basic Bash commands. The BAM file of reads without C-to-T mutation was transformed to a BED file using bedtools bamtobed (BEDTools v2.27.1) and considering only the 5' mapping position of each read. Afterwards, the BED file was sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream (since this nucleotide is considered as the crosslinked nucleotide) using bedtools genomecov (BEDTools v2.27.1). Similarly, the BED files of C-to-T mutations were also sorted and summarized to strand-specific bedGraph files using bedtools genomecov. Finally, all bedGraph files were transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: *.C2T.plus.bw, *.C2T.minus.bw: bigwig files of positions with C-to-T mutations and their counts. They were generated by filtering for C-to-T mutations in the list of all found mutations, which were output of the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK). The filtered list was in BED file format and was then sorted and summarized to strand-specific bedGraph files using bedtools genomecov, which were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.noC2T.plus.bw, *.noC2T.minus.bw: bigwig files of positions upstream of reads without C-to-T mutation and their counts. They were generated by first removing all reads with C-to-T mutation from the BAM files and then transforming the resulting BAM file to a BED file using bedtools bamtobed considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: Sample miCLIP_C643_WT_1 was sequenced in two technical replicates (miCLIP_C643_WT_1_1 + miCLIP_C643_WT_1_2), for which we provide separate raw data files (fastq.gz), but have merged their bigwig tracks after processing into miCLIP_C643_WT_1.merged....
Supplementary_files_format_and_content: *.bed: bed files with predicted m6A sites by m6Aboost. In brief, bam files with reads without C-to-T mutation were used for peak calling with PureCLIP (v1.3.1) individually on each replicate for each condition. PureCLIP significant sites per replicate were then filtered for presence in at least two out of three replicates for a given condition. m6Aboost was applied to the reproducible peaks to predict m6A sites.

source_name: C643 cells

growth_protocol: Anaplastic thyroid carcinoma-derived C643 cells (CLS, RRID:CVCL_5969) were cultured on 15 cm dishes in Dulbecco's Modified Eagle Medium (DMEM; Thermo Fisher Scientific) supplemented with GlutaMAX (Thermo Fisher Scientific) and 10 % fetal bovine serum (FBS) at 37°C and 5 % CO2.

extract_protocol:
C643 cells were grown on 15 cm dishes to approximately 90-95% confluence. Subsequently, the DMEM was discarded and the cells were washed twice with PBS. Total RNAs were extracted by using TRIzol reagent (Thermo Fisher Scientific), according to the manufacturer’s instructions. Prior to isolation of polyadenylated RNAs (polyA(+) RNA), the total RNA samples were treated with DNase I (NEB), according to the manufacturer’s protocol and subsequently cleaned up again by using TRIzol LS (Thermo Fisher Scientific). Approximately 5 µg of polyA(+) RNA was purified from 500 µg Total RNA by using the Dynabeads mRNA purification Kit (Thermo Fisher Scientific) for two rounds, according to the manufacturer’s protocol.
Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

treatment_protocol: Untreated

value: Human Thyroidea Carcinoma cell line

tag: miclip antibody

value: rabbit anti-m6A antibody (Synaptic Systems, order number 202 003)


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_CL_5_ME

description:
4N_CL_5_ME
mirxplore_counts.txt


title: miCLIP C643 WT rep1, technical rep1

description:
Co-immunoprecipitated RNA fragments
miCLIP_C643_WT_1.merged.v2uniqMD.duprm.noC2T.plus.bw
miCLIP_C643_WT_1.merged.v2uniqMD.duprm.noC2T.minus.bw
miCLIP_C643_WT_1.merged.v2uniqMD.duprm.C2T.plus.bw
miCLIP_C643_WT_1.merged.v2uniqMD.duprm.C2T.minus.bw


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_CL_4_ME

description:
4N_CL_4_ME
mirxplore_counts.txt


title: PD_rep1


title: Single cell miRNA-seq of MCF7 cell_SB_6_SCE

description:
SB_6_SCE
sce_counts.txt

value: SB


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_C3_6_ME

description:
4N_C3_6_ME
mirxplore_counts.txt

value: mammary gland/breast epithelial cell


title: BJQ_rep1


title: Single cell miRNA-seq of MCF7 cell_SB_4_SCE

description:
SB_4_SCE
sce_counts.txt


title: BI_rep1


title: Single cell miRNA-seq of MCF7 cell with miRXplore_CL_5_ME

description:
CL_5_ME
mirxplore_counts.txt


title: miCLIP C643 WT rep3

description: Co-immunoprecipitated RNA fragments


title: HD3

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

country: China

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the G. biloba genome database downloaded from GigaDB using TopHat2 software with default parameters.
Gene abundances were quantified by RSEM, and the gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcriptper Million mapped reads) method.
Genome_build: GigaDB (http://gigadb.org/dataset/100209).
Supplementary_files_format_and_content: The tab-delimited text file include FPKM vaules of genes for each sample (gene_id, CK1_fpkm, CK2_fpkm, CK3_fpkm, MD1_fpkm, MD2_fpkm, MD3_fpkm, HD1_fpkm, HD2_fpkm, HD3_fpkm)

organism: Ginkgo biloba

source_name: High density leaves

growth_protocol: The 2-years-old G. biloba trees (‘Fozhi’ cultivar) grown at the leaf-harvesting G. biloba nursery were used in this study, with sufficient light, well-drained and fertile soil.

extract_protocol:
The leaves of different planting densities were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The ginkgo seedlings were planted at three planting densities (CK, 20; MD, 40; and HD, 80 plants/m2)

value: leaves at high density  (80 plants/m2)

tag: tissue

value: leaves


title: PI_rep1


title: miCLIP HEK293T cells rep2

description: Co-immunoprecipitated RNA fragments

data_processing:
miCLIP data processing:
Reads were mapped to the respective genome and its annotation (GENCODE release 31 for all human samples, GENCODE release M23 for all mouse samples) using STAR (v2.7.3a). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999), soft-clipping was prohibited on the 5'end of reads (--alignEndsType Extend5pOfRead1) and only uniquely mapping reads were kept for further analysis (--outFilterMultimapNmax 1).
Following mapping, BAM files were sorted and indexed (SAMtools v1.9) and duplicate reads were removed (UMI-tools v1.0.0).
After removing duplicates, all mutations found in reads were extracted using the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK, v1.1.3). The list was filtered for C-to-T mutations using basic Bash commands and kept in BED file format. Based on the filtered list of C-to-T mutations, deduplicated reads were separated into two BAM files holding reads with and without C-to-T mutation, respectively, using SAMtools and basic Bash commands. The BAM file of reads without C-to-T mutation was transformed to a BED file using bedtools bamtobed (BEDTools v2.27.1) and considering only the 5' mapping position of each read. Afterwards, the BED file was sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream (since this nucleotide is considered as the crosslinked nucleotide) using bedtools genomecov (BEDTools v2.27.1). Similarly, the BED files of C-to-T mutations were also sorted and summarized to strand-specific bedGraph files using bedtools genomecov. Finally, all bedGraph files were transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
RNAseq data processing:
Reads were mapped to the mouse genome and its annotation based on GENCODE release M23 using STAR (v2.6.1b). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999). SAMtools was used to remove secondary alignments and keep only one location for multimapping reads (-F 256).
For differential expression analysis, mapped reads were counted with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Genome_build: mm10 (GRCm38.p6), hg38 (GRCh38.p12)
Supplementary_files_format_and_content: *.C2T.plus.bw, *.C2T.minus.bw: bigwig files of positions with C-to-T mutations and their counts. They were generated by filtering for C-to-T mutations in the list of all found mutations, which were output of the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK). The filtered list was in BED file format and was then sorted and summarized to strand-specific bedGraph files using bedtools genomecov, which were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.noC2T.plus.bw, *.noC2T.minus.bw: bigwig files of positions upstream of reads without C-to-T mutation and their counts. They were generated by first removing all reads with C-to-T mutation from the BAM files and then transforming the resulting BAM file to a BED file using bedtools bamtobed considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: The samples miCLIP_mESC_WT_1 and miCLIP_mESC_Mettl3_KO_1 were sequenced in two technical replicates (miCLIP_mESC_WT_1_1 + miCLIP_mESC_WT_1_2 and miCLIP_mESC_Mettl3_KO_1_1 + miCLIP_mESC_Mettl3_KO_1_2), for which we provide separate raw data files (fastq.gz), but have merged their bigwig tracks after processing into miCLIP_mESC_WT_1.merged... and miCLIP_mESC_Mettl3_KO_1.merged...
Supplementary_files_format_and_content: *.txt: count tables of reads mapping to genes generated by counting reads with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Supplementary_files_format_and_content: *.bed: bed files with predicted m6A sites by m6Aboost. In brief, bam files with reads without C-to-T mutation were used for peak calling with PureCLIP (v1.3.1) individually on each replicate for each condition. PureCLIP significant sites per replicate were then filtered for presence in at least two replicates for a given condition. m6Aboost was applied to the reproducible peaks to predict m6A sites.

source_name: HEK293T cells

growth_protocol: Mouse embryonic stem cells (mESC) with wildtype and Mettl3 knockout genotype were taken from a previous publication (PMID: 25569111) and cultured as described therein. The HEK293T cell line was cultured in DMEM (Life Technologies) containing 10% FBS (Life Technologies), 1% L-glutamine (Life Technologies) and 1% penicillin-streptomycin (Life Technologies) at 37°C with 5% CO2.

extract_protocol:
For RNA extraction from HEK293T cells and mESCs, cells were washed in ice-cold PBS and collected on ice for the isolation of total RNA using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommended protocol. Poly(A)+ RNA was extracted using Oligo d(T)25 Magnetic Beads using the manufacturer’s recommended protocol. Poly(A)+ concentration was measured using Qubit™ RNA HS Assay Kit (ThermoFisher Scientific). The quality of poly(A)+ RNA was ensured using High sensitivity RNA screen tapes for the 2200 Tape station system (Agilent). If a predominant peak for ribosomal RNA was still detectable an additional round of poly(A) selection was performed. Mouse heart RNA was purchased from Takara Clontech (order number 636202): RNA isolated by a modified guanidinium thiocyanate method followed by poly A+ RNA selection with two rounds of oligo(dT)-cellulose columns.
RNA-seq: NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol beginning with fragmentation step (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 73ng for imb_koenig_2019_21 and amplified in 10 PCR cycles.Libraries were profiled in a DNA 1000 on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).  All 6 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput Flowcell, SR for 1x 84 cycles plus 1x 7 cycles for the index read.
miCLIP2: Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

treatment_protocol: In the case of mESCs, Mettl3 knockout (KO) cells were taken from a previous publication (PMID: 25569111).

value: HEK293T cells


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_C3_4_ME

description:
4N_C3_4_ME
mirxplore_counts.txt

value: adenocarcinoma

value: single cell


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_CL_3_ME

description:
4N_CL_3_ME
mirxplore_counts.txt


title: HD1


title: HT4

city: SAO PAULO

first: Robson

middle: José de

last: Almeida

state: SAO PAULO

address: RUA VERGUEIRO 235 249

department: Pós Graduação Stricto Sensu em Medicina

country: Brazil

institute: Universidade Nove de Julho

data_processing:
The alignment was made by ION S5 default protocol.
We made a conversion from .bam to fastq through 'samtools fastq'
The compression to bz2 was made through bzip2.
Genome_build: Hg19
Supplementary_files_format_and_content: xlsx file containing the reads of each sample

source_name: whole blood

extract_protocol:
The venous blood was collected in the PAXgene Blood RNA tube and extracted with the PAXgene Blood RNA Kit.
Ion AmpliSeq Transcriptome Human Gene Expression Kit  Catalog Number A26325, A26326, and A26327

value: whole blood

tag: disease state

value: hypothyroidism

tag: gender

value: female

tag: tsh


title: miCLIP HEK293T cells rep1

description: Co-immunoprecipitated RNA fragments


title: miCLIP HEK293T cells rep4

description: Co-immunoprecipitated RNA fragments


title: MD3

source_name: Moderate density leaves

value: leaves at moderate density (40 plants/m2)


title: Single cell miRNA-seq of MCF7 cell_SB_5_SCE

description:
SB_5_SCE
sce_counts.txt

value: Single cell equivalent


title: 404

value: PBMC

tag: plate

tag: pid

tag: stimulation

value: dmso

tag: visit

tag: site

value: BAGAMOYO

tag: age

value: old

value: rtss

tag: case

value: control

tag: match

tag: sid

tag: waz

tag: haz

tag: hb

tag: Sex

value: M

value: Low


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_C3_5_ME

description:
4N_C3_5_ME
mirxplore_counts.txt

tag: cell line

tag: cell type

value: mammary gland/breast epithelial cell

tag: culture collection

tag: disease

tag: sample type

tag: replicate

tag: protocol

tag: genotype

value: miRExplore spike-in


title: F112-1

city: Cambridge

first: Lucas

last: Pantaleao

address: 11A Glisson Road

country: United Kingdom

institute: University of Cambridge

description:
SLX-9052.A014
raw_count.txt (column12)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v1.2.3.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: raw_count.txt: Tab-delimited text file includes raw read counts for each Sample.

organism: Mus musculus

source_name: Heart

extract_protocol:
Cardiac RNA from male offspring was extracted using a Qiazol/miRNeasy mini kit protocol (Qiagen, Hilden, Germany).
High quality RNA samples from each group were randomly selected and subjected to a cDNA library preparation using TruSeq RNALibrary Preparation kit, following the manufacturer’s protocol.

treatment_protocol: Female C57BL/6J mice received either commercial standard (RM1) or a high-fat diet [20% lipids (Special Dietary Services)] plus sweetened condensed milk [55% simple carbohydrates/8% lipids (Nestle, UK)] from weaning. After around 6 weeks on their respective diets, mice were mated with male counterparts and went through a first pregnancy and lactation to ensure their breeding competence. Mice were mated a second time, and first day of pregnancy was marked by the detection of a vaginal plug. On day 18.5 of gestation, pregnant mice were killed by raising CO2 concentrations or cervical dislocation.

tag: strain

value: Wild Type

value: Male

tag: tissue

value: Heart

tag: maternal diet

value: Obesogenic


title: HD2

tag: treatment

value: leaves at high density  (80 plants/m2)

value: leaves


title: F120-2

description:
SLX-9052.A013
raw_count.txt (column11)


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_6_ME

description:
4N_6_ME
mirxplore_counts.txt

value: adenocarcinoma

value: single cell


title: miCLIP C643 WT rep1, technical rep2

value: Human Thyroidea Carcinoma cell line

tag: miclip antibody

value: rabbit anti-m6A antibody (Synaptic Systems, order number 202 003)


title: HT2

value: whole blood

tag: disease state

value: hypothyroidism

tag: gender

value: male

tag: age

tag: tsh


title: F117-1

description:
SLX-9052.A007
raw_count.txt (column9)

tag: Sex


title: miCLIP HEK293T cells rep3

description: Co-immunoprecipitated RNA fragments

tag: cell line

value: HEK293T cells


title: HT1

value: female


title: F105-1

description:
SLX-9052.A012
raw_count.txt (column10)


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_CL_5_ME

description:
SBN_CL_5_ME
mirxplore_counts.txt

tag: cell type

value: mammary gland/breast epithelial cell

tag: culture collection


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_5_ME

description:
4N_5_ME
mirxplore_counts.txt

tag: disease

tag: sample type

value: miRExplore spike-in


title: RC74-2A

description:
SLX-9052.A006
raw_count.txt (column8)

value: Wild Type

value: Control


title: CTL4

value: control


title: HT3


title: Single cell miRNA-seq of MCF7 cell with miRXplore_4N_4_ME

description:
4N_4_ME
mirxplore_counts.txt

tag: replicate

tag: protocol


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_CL_6_ME

description:
SBN_CL_6_ME
mirxplore_counts.txt

tag: genotype


title: RC73-2A

description:
SLX-9052.A005
raw_count.txt (column7)

tag: strain

value: Male

tag: tissue

value: Heart


title: CTL3


title: Control_CK1

source_name: Control leaves

tag: treatment

value: leaves at control density (20 plants/m2)

value: leaves


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_6_ME

description:
SBN_6_ME
mirxplore_counts.txt

value: adenocarcinoma

value: single cell

value: SBN


title: MD1

value: leaves at moderate density (40 plants/m2)


title: VH02001710_S2

first: Daniel

last: Ho

address: 250 Massachusetts Avenue

country: USA

institute: Novartis Institutes for Biomedical Research

data_processing:
Aligned raw data using Star with reference genome GRCh38
Custom scripts to perform UMI counting and filtering out UMI duplicates
Performed differential expression using limma trend
Genome_build: ensembl human GRch38
Supplementary_files_format_and_content: Rdata object containing UMI counts data; Tab-delimited UMI counts data

growth_protocol: Cells were plated down at 5000 cells per well in 384-well plates in DMEM  + 10% FBS + 1% penicillin/streptomycin the day prior to compound treatment

extract_protocol:
direct cell lysis was performed using custom-made 1x DRUGseq lysis buffer (containing 1M Tris-HCl, 2M KCl, 20% of 20% Ficoll PM-400, Triton-100, RNase Inhibitor)
DRUGseq library construction protocol using reagents from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit and Illumina Nextera XT DNA Library Preparation Kit

value: osteosarcoma cell line


title: Control_CK3


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_4_ME

description:
SBN_4_ME
mirxplore_counts.txt


title: VH02001708_S3


title: RC72-2A

description:
SLX-9052.A004
raw_count.txt (column6)

tag: maternal diet


title: CTL1

value: whole blood

tag: disease state


title: Young Fruiting body, replicate3

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

data_processing:
Reads were quality and adaptor trimmed using bbduk.sh and overlapping read pairs were merged with bbmerge.sh tools (part of BBMap/BBTools; http://sourceforge.net/projects/bbmap/) with the following parameters: qtrim=rl trimq=25 minlen=40.
A two-pass STAR alignment (Veeneman et al., 2015) was performed against reference genomes PleosPC15_2.
Counts were calculated using FeatureCounts (Liao et al 2014) with the following parameters: isGTFAnnotationFile=F,                         nthreads=ncpu, isPairedEnd=T, minFragLength=40, maxFragLength=600, strandSpecific=2,                         countChimericFragments=F,countMultiMappingReads=T, fraction=T, byReadGroup=F
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: JGI Mycocosm: Pterula gracilis CBS309.79 v1.0 (Ptegra1), Ptegra1_AssemblyScaffolds.fasta
Supplementary_files_format_and_content: Comma separated files containing raw count data

organism: Pterulicium gracile

source_name: Young Fruiting body

growth_protocol: Dikaryotic strain CBS 309.79  of Pterula gracilis was grownMalt Extract Agar  where growing conditions at 15 °C under 10/14h light/dark period.

extract_protocol:
Total RNA was extracted from the four tissue types in three biological replicates, using the Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol.
Strand-specific cDNA libraries were constructed from poly(A)-captured RNA, using the Illumina TruSeq Stranded RNA-Seq library preparation kit, and sequenced on the Illumina HiSeq 4000/x platform in PE 2x150 format with 40 million reads per sample at OmegaBioservices (USA)

treatment_protocol: VM samples were scraped off the cellophane after three days. We defined primordia (P) as small (<1mm) globose structures, young fruiting bodies as ~5 mm long awl-shaped structures, while structures longer than 10mm were considered mature fruiting bodies

tag: group

value: Pg-YFB

value: Young Fruiting body


title: RC65-3A

description:
SLX-9052.A002
raw_count.txt (column5)


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_4N_6_ME

description:
SBN_4N_6_ME
mirxplore_counts.txt

value: mammary gland/breast epithelial cell


title: Young Fruiting body, replicate1


title: VH02001704_S4


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_5_ME

description:
SBN_5_ME
mirxplore_counts.txt

value: miRExplore spike-in


title: Untreated Lgr5+ progenitor cells - H3K4me3_rep2

city: Nanjing

first: Xiangyu

last: Ma

address: Sipailou II

institute: Southeast University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
The initial QC was used to remove the duplicate reads and low-quality reads using fastx toolkit before mapping.
Then replicates of high-quality reads were matched to the mouse genome (mm10) by Bowtie2.
To identify the H3K4me3 peaks, MACS2 was used to call the peaks of enriched occupancy relative to a background input.
Peak annotation and enrichment analysis were performed using ChIPseeqer , ChIPpeakAnno and Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: Untreated Lgr5+ progenitor cells

growth_protocol: We here sacrificed postnatal day (P) 0-3 Lgr5-EGFP-creERT2 mice of either sex for each sample and dissected out their cochleae to were routinely culture in the DMEM/F12 medium supplemented by B27 (1:50 dilution, Invitrogen), N2 (1:100 dilution, Invitrogen), IGF-1 (50 ng/ml, Sigma), heparin sulfate (50 ng/ml, Sigma), bFGF (10 ng/ml, Sigma) and EGF (20 ng/ml, Sigma) (full medium).

extract_protocol:
Dissociated cells were classified on a BD FACS Aria III using the GFP channel. Lysates were clarified from  Nuclear Break Buffer mixed by gentle vertex and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). And libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Two replicates were neomycin treated for 12 hours.

value: Cochlea Lgr5+ progenitor cells

value: untreated

tag: chip antibody

value: Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam, United Kingdom)


title: CTL2

value: control

tag: gender

value: male

tag: age

tag: tsh


title: MD2


title: Young Fruiting body, replicate2


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_CL_4_ME

description:
SBN_CL_4_ME
mirxplore_counts.txt

tag: cell line

tag: cell type


title: VH02001712_S1


title: Untreated Lgr5+ progenitor cells - H3K4me3_rep1


title: Vegetative mycelium, replicate2

source_name: Vegetative mycelium

value: Pg-VM

value: Vegetative mycelium


title: Control_CK2

value: leaves at control density (20 plants/m2)

value: leaves


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_4N_5_ME

description:
SBN_4N_5_ME
mirxplore_counts.txt

tag: culture collection

tag: disease

value: adenocarcinoma

value: single cell


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SBN_4N_4_ME

description:
SBN_4N_4_ME
mirxplore_counts.txt

tag: sample type

tag: replicate


title: Vegetative mycelium, replicate1


title: VH02001702_S5

value: osteosarcoma cell line


title: VH02001700_S6


title: Neomycin-damaged Lgr5+ progenitor cells - H3K4me3_rep2

source_name: Neomycin-damaged Lgr5+ progenitor cells

value: treated with neomycin for 12 hours


title: VH02001618_S7


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SB_5_ME

description:
SB_5_ME
mirxplore_counts.txt

tag: protocol

value: SB

tag: genotype


title: Neomycin-damaged Lgr5+ progenitor cells - H3K4me3_rep1

tag: strain


title: Primordia, replicate3

source_name: Primordia

tag: tissue

value: Primordia


title: VH02001614_S8

tag: treatment


title: Primordia, replicate2


title: Primordia, replicate1


title: Neomycin-damaged Lgr5+ progenitor cells - input DNA


title: MHCC97H SR-2

city: Chongqing

first: yu

last: sha

address: No.1 Yi Xue Yuan Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

data_processing:
Rejected sequence reads are filtered using TrimMomatic
Hisat2 and Bowtie2 are used to compare the sequencing read length and reference genome of the filtered samples.
FPKM (Fragments Per Kilobase of Exon model Per Million mapped Fragments) method is used to standardize the gene expression in the samples
Genome_build: GENCODE and NCBI
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HCC cell line

extract_protocol:
RNA was harvested using Trizol reagent.  Direct-zol RNA Miniprep Kits(Cat#R2052)was used with all total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using EasyRNA-seq protocols

value: HCC cell line MHCC97H

tag: phenotype

value: sorafenib resistant


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SB_4_ME

description:
SB_4_ME
mirxplore_counts.txt

value: mammary gland/breast epithelial cell

value: miRExplore spike-in


title: VH02001612_S9


title: Fruiting body, replicate1

source_name: Fruiting body

tag: group

value: Pg-FB

value: Fruiting body


title: Untreated Lgr5+ progenitor cells - input DNA

value: Cochlea Lgr5+ progenitor cells

value: untreated

tag: chip antibody


title: MHCC97H SR-3


title: Fruiting body, replicate3


title: Young fruiting body stipe, replicate3

data_processing:
Reads were quality and adaptor trimmed using bbduk.sh and overlapping read pairs were merged with bbmerge.sh tools (part of BBMap/BBTools; http://sourceforge.net/projects/bbmap/) with the following parameters: qtrim=rl trimq=25 minlen=40.
A two-pass STAR alignment (Veeneman et al., 2015) was performed against reference genomes PleosPC15_2.
Counts were calculated using FeatureCounts (Liao et al 2014) with the following parameters: isGTFAnnotationFile=F,                         nthreads=ncpu, isPairedEnd=T, minFragLength=40, maxFragLength=600, strandSpecific=2,                         countChimericFragments=F,countMultiMappingReads=T, fraction=T, byReadGroup=F
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: JGI Mycocosm: Pleurotus ostreatus PC15 v2.0 (PleosPC15_2), PleosPC15_2_Assembly_scaffolds.fasta
Supplementary_files_format_and_content: Comma separated files containing raw count data

organism: Pleurotus ostreatus

source_name: Young fruiting body stipe

growth_protocol: Dikaryotic strain N001 (CECT-20600) of Pleurotus ostreatus was grown in spawn culture (in 3kg PE bags) where conditions were 18-19 °C, relative humidity 80-85% and 8/16h light/dark period.

treatment_protocol: We sampled vegetative mycelium (VM), six developmental stages and five tissue types, each in three biological replicates. Tissue from 3-8 individual fruiting bodies was pooled for each replicate of each sample type. Tissues were flash frozen in liquid nitrogen and kept at -80oC until futher extraction.

value: Po-YFB-S

value: Young fruiting body stipe


title: Single cell miRNA-seq of MCF7 cell with miRXplore_SB_6_ME

description:
SB_6_ME
mirxplore_counts.txt

source_name: mammary gland/breast epithelial cell


title: Fruiting body, replicate2


title: D28_r1_RNAseq

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

description:
FPKM_mat.txt
count_mat.txt

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina
Adaptors were removed using Cutadapt and Trimmomatic
For RNA-Seq samples reads were mapped to the human reference genome hg38 using TopHat v2.1.1 with default parameters. Assembly of mapped reads was performed with Cufflinks v2.2.1 and values of Fragments Per Kilobase of transcript per million Mapped reads (FPKM) were calculated for all annotated genes and transcripts.
For ATAC-Seq samples we used ENCODE ATAC-Seq pipeline (http://www.encodeproject.org/atac-seq/) . Paired-end reads were aligned to hg38 using Bowtie2. Next, we used SAMTools [PMID:19505943] to remove unmapped reads, fragments with unmapped mates, non-primary alignment reads, and reads failing platform quality checks. Low quality reads (MAPQ < 30) and reads which mapped to mitochondrial DNA were also excluded. Optical and PCR duplicates were also removed using Picard tools (http://broadinstitute.github.io/picard). To accurately locate the center of each transposon-binding event, the remaining reads were offset by +4 and -5 for positive and negative strands respectively . ATAC-Seq peak regions were called for each sample using MACS2 with parameters --shift 75 --extsize 150 --nomodel --keep-dup all --call-summits. Resulting peaks which overlapped with ENCODE blacklisted regions were filtered out.
For both RNA-Seq and ATAC-Seq we calculated raw read counts using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_mat and count_mat are tab-delimited files containing FPKM and raw counts. Each column represents a sample and each row represents a gene
Supplementary_files_format_and_content: Bigwig files were obtained with the bamCoverage function from deepTools. Values represent number of reads per bin. We used a bin size of 50.

source_name: H9 pluripotent stem cells

growth_protocol: The human embryonic stem cell line H9 (WA09)-GFP, which has constitutive expression of enhanced Green Fluorescent Protein (GPF), was used for all experiments. Prior to differentiation, cells were cultured in supplemented Knock Out (Gibco ®) medium, previously conditioned with mitotically inactivated mouse embryonic fibroblasts (MEFs) with fresh FGF-2 (10 ng/ml; Sigma), over a Matrigel (BD ®) matrix, until they reached 75% confluency.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
Approximately 150–300 ng of total RNA was used to construct each RNA-Seq library. Poly-A selected RNA samples were used for library construction with Illumina TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: The floor-plate dopaminergic differentiation procedure was described previously (Kriks et al., 2011) with minor modifications (Carballo-Molina et al., 2016).

tag: induction day


title: Young fruiting body stipe, replicate2


title: D14_r4_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: D14_r1_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: MHCC97H SR-1


title: MHCC97H control-3

value: sorafenib sensitive


title: Young fruiting body stipe, replicate1


title: D14_r3_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: Young fruiting body cap, replicate3

source_name: Young fruiting body cap

value: Po-YFB-H

value: Young fruiting body cap


title: BxPC3_dau_72h_rep2

type: RNA

city: Harbin

first: Yun

last: Bai

state: Hei Long Jiang

address: No.24 heping Street, XiangFang district

institute: Hei Long Jiang University of Chinese medicine

description: After the cells grew to 80% of the culture dish, add 24μmol dau for 72h.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: BxPC3 cells were cultured in RPMI-1640 (Hyclone, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin solution in an atmosphere of 95% air and 5% CO2 in a 37℃ incubator.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Human pancreatic adenocarcinoma cells

value: 24 μmol Dau for 72h


title: BxPC3_dau_72h_rep1

treatment_protocol: After the cells grew to 80% of the culture dish, add 24μmol dau for 72h.


title: BxPC3_dau_72h_rep3


title: BxPC3_72h_rep1

description: After the cells grew to 80% of the culture dish, they were cultured for 72 hours.

value: none; untreated


title: MHCC97H control-2


title: wildtype D20-3958

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Raw sequences were demultiplexed, aligned, filtered, barcode counting, unique molecular identifier (UMI) counting with Cell Ranger software v3.1 (10XGenomics) to digitalize the expression of each gene for each cell.
The outlier cells with very low number of gene features (<500), or high number of gene features as doublets (>5000),  or low total UMI (<1000) and high mitochondrial ratio (>10%) from each data set were removed.
Samples were combined based on the  identified anchors for the following integrated analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: retina

extract_protocol:
Single-cell suspensions of retinal cells taken from Igfbpl1-/- and age- and sex-matched B6 mice that were transcardially perfused with PBS. Immune cells were stained by PE anti- mouse CD45 and sorted by flow cytometry. Sorted cells were resuspended and washed in 0.05% RNase-free BSA in PBS for single-cell library preparation.
10x Chromium Next GEM Single Cell 3' Kit.
single cell RNA-Seq by NexSeq500

value: retina

value: single cell


title: Young fruiting body cap, replicate2


title: RF4

city: Dallas

first: Jessica

last: Cannavino

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern Medical center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3) (Langmead and Salzberg, 2012). STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
edgeR R Bioconductor package (Gentleman et al., 2004; Robinson et al., 2010; McCarthy et al., 2012) was used to normalize read counts and identify differentially expressed (DE) genes.
KEGG (Kanehisa et al., 2017) pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz).
The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package.
Genome_build: mm10
Supplementary_files_format_and_content: gene_count.txt, raw read count

source_name: Brown adipose tissue

extract_protocol:
After dissection BAT tissues were snap frozen in liquid nitrogen and pulverized with mortar and pestle. For RNA sequencing, (n = 3 mice per genotype) RNA was extracted using RNeasy Micro kit (74004, Qiagen) as per providerÕs instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FAM195A Knock out

tag: age

value: male

value: 12 weeks old

value: Brown adipose tissue


title: D14_r2_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: MHCC97H control-1

value: HCC cell line MHCC97H


title: BxPC3_72h_rep3


title: D28_r2_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: Primary tumor of case3

city: Kagoshima

first: Kengo

last: Tanigawa

address: 8-35-1 Sakuragaoka

department: Pulmonary Medicine

country: Japan

institute: Kagoshima university

data_processing:
Illumina CASAVA v1.8.2 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases. They were mapped to reference genome using bowtie v1.0.0 with parameters -p 4 -S -q -n 1 -e 80 -l 30 -a -m 5 --best --strata
The location information of mapping reads was compared with miRBase, Rfam and iGenomes. Annotations were added to reads and distribution of a variety of RNA reads was made up.
The reads mapped in the known miRNAs were counted with Htseq-count.
The expression levels of miRNAs among samples and groups were compared by edgeR.
Heatplus was used for clustering analysis and creating heatmaps.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each sample.

source_name: lung

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's protocol. Illumina TruSeq Small RNA Sample Preparation Kit was used for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary tumor of case3


title: Right hilar lymph node metastasis of case 2

source_name: lymph node


title: Primary tumor of case2

value: Primary tumor of case2


title: Igfbpl-/1 D20-3959


title: Right intrapulmonary metastasis of case 3


title: D0_r3_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: D0_r2_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: vegetative mycelium, replicate 2

source_name: vegetative mycelium

value: Po-VM

value: vegetative mycelium


title: ID-8, Control-IgG

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: cDNA

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: ID-8, mmu ovarian cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: C57BL/6 mice (aged 5 weeks) were purchased from CLEA Japan Inc. (Tokyo, Japan). A total of 2 × 10^6 ID-8 LUC2 cells were suspended as single cells in a volume of 0.2 mL PBS and injected intraperitoneally into the mice. Mice were assessed daily for general health.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: 14 days after the inoculation, the mice were intraperitoneally administered either control IgG 5 mg/kg (control group) or bevacizumab 5 mg/kg (bevacizumab group) twice a week, and finally the mice were sacrificed at day 42.

value: ovarian cancer


title: RE6

value: FAM195A heterozygous


title: RE9


title: D0_r1_RNAseq

description:
FPKM_mat.txt
count_mat.txt


title: Young fruiting body cap, replicate1

value: Po-YFB-H

value: Young fruiting body cap


title: RF3


title: Stable4 T1

city: Brest

first: Cristina

last: Bagacean

address: 2 Avenue Foch

country: France

institute: UBO

data_processing:
Fastq files were aligned to the reference Human genome hg38 with STAR
We removed reads mapping to multiple locations.
We quantified gene expression using the full Gencode v31 annotation.
We used also STAR to obtain the number of reads associated to each gene in the Gencode v31 database (restricted to protein-coding genes, antisense and lincRNAs).
We used the Bioconductor DESeq package to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
Bigwig visualization files were generated using STAR and the bam2wig python script.
Genome_build: hg38
Supplementary_files_format_and_content: For each sample, we quantified the number of reads per exon for each gene of the Gencode annotation. Using DEXseq, we compared these counts for Progressive_T0 versus Stable_T0, Stable T0 versus T1 and Progressive T0 versus T1, producing an excel file «SummaryDifferentialExonUsage_***_vs_***.xlsx» with all genes for which at least one exon is significantly differentially expressed (q<0.1) and with a minimum expression of 1 in one of the groups (fpkm > 1).

source_name: CLL B cells

extract_protocol:
Lymphocytes were isolated from peripheral blood mononuclear cells (PBMC) by Ficoll-Hypaque density gradient centrifugation (Eurobio, Courtaboeuf, France), and B cells were further enriched using the Pan B cell Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Cell purity was assessed by fluorescence-activated cell sorting analysis and was over 95% for B cells (CD19+). FACS antibodies used were purchased from Beckman Coulter (Brea, CA). RNA was extracted from purified B cells using the RNeasy Plus Micro Kit (Qiagen, Venlo, Netherlands). Quantification and purity were assessed using the NanoDrop 2000 Spectrophotometer. Next, RNA (300 ng) was reverse transcribed into cDNA using the Super Script III enzyme and random primers (Invitrogen Life Sciences, Carlsbad, CA).
Libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® NovaSeq™6000 protocol according to supplier recommendations. Briefly, the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1µg total RNA with the Magnetic mRNA Isolation Kit (NEB, Ipswich, MA), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing is then carried out on Paired End 100b reads of Illumina NovaSeq. Image analysis and base calling is performed using Illumina Real Time Analysis 3.4.4 with default parameters.

tag: individual

value: CLL stable4

tag: cll binet stage

value: A

value: untreated

value: B cells

tag: time


title: Stable4 T0

tag: cell type


title: ID-8, Bevacizumab

description: cDNA


title: Normal lung tissue (lower lobe of the right lung) of case 3


title: RF2

value: FAM195A Knock out


title: Stage 3 primordia stipe, replicate3

source_name: Stage 3 primordia stipe

value: Stage 3 primordia stipe


title: Liver metastasis of case 1

source_name: liver

value: Liver metastasis of case 1


title: vegetative mycelium, replicate 3


title: Para-aortic lymph node metastasis of case 1


title: BxPC3_72h_rep2

tag: cell line

value: Human pancreatic adenocarcinoma cells

value: none; untreated


title: Stable3 T1

value: CLL stable3


title: RF1

value: male

value: 12 weeks old

value: Brown adipose tissue


title: Mediastinal lymph node metastasis of case 1


title: Stage 3 primordia stipe, replicate2


title: vegetative mycelium, replicate 1

value: Po-VM

value: vegetative mycelium


title: Stable3 T0


title: Lesser curvature lymph node metastasis of case 1


title: KO-3

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GCF_000223135.1_CriGri_1.0_genomic
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

source_name: Osteoclasts

growth_protocol: Femurs were removed from 6-8 weeks old mice, flushed with sterile serum-free a-MEM and single cell suspensions were prepared using the 70mm cell strainer. Cells were spun down and cultured on petri dishes in a-MEM containing 10% FBS and 1% penicillin/streptomycin/glutamine at 37°C and 5% carbon dioxide for 16h. Suspension cells were collected and cultured on petri dishes as above with added 10% L929 cell conditioned media as a source of macrophage-colony stimulating factor and 50 ng/ml of GST-RANKL to obtain osteoclasts for an additional 7 days.

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

value: Global Elmo1-/-


title: Stable2 T1

value: CLL stable2


title: KO-4


title: Stage 3 primordia stipe, replicate1


title: Normal lung tissue (upper lobe of the right lung) of case 2


title: KO-2


title: Stage 3 primordia cap, replicate3

source_name: Stage 3 primordia cap

value: Stage 3 primordia cap


title: Stable2 T0

value: A


title: Stable1 T1

value: CLL stable1

value: untreated


title: Normal lung tissue (lower lobe of the left lung) of case 1


title: Stage 3 primordia cap, replicate2


title: WT-4


title: Stable1 T0

value: B cells


title: Normal lung tissue (upper lobe of the left lung) of case 1


title: KO-1


title: Stage 1 primordia, replicate3

source_name: Stage 1 primordia

value: Stage 1 primordia


title: Stage 3 primordia cap, replicate1


title: Control, CK10

city: jiaxing

first: yuxia

last: jin

address: East Zhong huan Road, 2468#

institute: Jiaxing University Affiliated Women and Children Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Serum exosomal miRNA_healthy

extract_protocol:
serum exosomes were isolated from serum using RiboTM Exosome Isolation Reagent according to the manufacturer's instructions (Guangzhou, China). total RNA was extracted and purified from exosomes using the Liquid miRNA Kit/HiPure Serum/Plasma miRNA Kit (Megan, China).  RNA  were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: serum

tag: gestational weeks

value: 16-18 weeks

tag: disease state

value: healthy individual in the fetus

tag: fraction

value: serum exosome miRNAs


title: WT-1

tag: genotype


title: Progressive3 T1

value: CLL Progressive3

value: B


title: Control, CK7


title: WT-3


title: Control, CK9


title: Stage 1 primordia, replicate2

tag: strain


title: Progressive4 T0

value: CLL Progressive4


title: Control, CK6

tag: tissue


title: Control, CK8


title: Stage 1 primordia, replicate1


title: Progressive3 T0

tag: treatment


title: Progressive2 T1

value: CLL Progressive2


title: Fruiting body skin, replicate2

source_name: Fruiting body skin

value: Po-FB-V

value: Fruiting body skin


title: Fruiting body skin, replicate3


title: Control, CK5


title: Fruiting body skin, replicate1


title: miCLIP2 macrophages replicate 2

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

institute: University Würzburg

description: Co-immunoprecipitated RNA fragments

data_processing:
miCLIP data processing:
Reads were mapped to the respective genome and its annotation (GENCODE release M23) using STAR (v2.7.3a). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999), soft-clipping was prohibited on the 5'end of reads (--alignEndsType Extend5pOfRead1) and only uniquely mapping reads were kept for further analysis (--outFilterMultimapNmax 1).
Following mapping, BAM files were sorted and indexed (SAMtools v1.9) and duplicate reads were removed (UMI-tools v1.0.0).
After removing duplicates, all mutations found in reads were extracted using the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK, v1.1.3). The list was filtered for C-to-T mutations using basic Bash commands and kept in BED file format. Based on the filtered list of C-to-T mutations, deduplicated reads were separated into two BAM files holding reads with and without C-to-T mutation, respectively, using SAMtools and basic Bash commands. The BAM file of reads without C-to-T mutation was transformed to a BED file using bedtools bamtobed (BEDTools v2.27.1) and considering only the 5' mapping position of each read. Afterwards, the BED file was sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream (since this nucleotide is considered as the crosslinked nucleotide) using bedtools genomecov (BEDTools v2.27.1). Similarly, the BED files of C-to-T mutations were also sorted and summarized to strand-specific bedGraph files using bedtools genomecov. Finally, all bedGraph files were transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: *.C2T.plus.bw, *.C2T.minus.bw: bigwig files of positions with C-to-T mutations and their counts. They were generated by filtering for C-to-T mutations in the list of all found mutations, which were output of the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK). The filtered list was in BED file format and was then sorted and summarized to strand-specific bedGraph files using bedtools genomecov, which were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.noC2T.plus.bw, *.noC2T.minus.bw: bigwig files of positions upstream of reads without C-to-T mutation and their counts. They were generated by first removing all reads with C-to-T mutation from the BAM files and then transforming the resulting BAM file to a BED file using bedtools bamtobed considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.bed: bed files with predicted m6A sites by m6Aboost. In brief, bam files with reads without C-to-T mutation were used for peak calling with PureCLIP (v1.3.1) individually on each replicate for each condition. PureCLIP significant sites per replicate were then filtered for presence in at least two out of three replicates for a given condition. m6Aboost was applied to the reproducible peaks to predict m6A sites.

source_name: RAW 264.7 cells

growth_protocol: RAW 264.7 cells (ATCC, Wesel, Germany, TIB-71) were cultured in DMEM (Thermo Fisher Scientific, 12430054) supplemented with 10% heat inactivated FBS (Biochrom, Berlin, Germany, S0613), 1x penicillin/streptomycin (Thermo Fisher Scientific, 15140-122).

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions. Poly(A)+ RNA was extracted by incubating 100 µg total RNA with 200 µl Dynabeads solution (Dynabeads mRNA Direct Purification Kit, Thermo Fisher Scientific, 61012) and purified following manufacturer’s protocols.
Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

value: macrophages

tag: miclip antibody

value: rabbit anti-m6A antibody (Synaptic Systems, order number 202 003)


title: miCLIP2 macrophages replicate 1

description: Co-immunoprecipitated RNA fragments


title: Control, CK4


title: Progressive4 T1


title: WT-2


title: Fruiting body stipe, replicate3

source_name: Fruiting body stipe

tag: group

value: Po-FB-S

value: Fruiting body stipe


title: RNAseq mESC Mettl3 KO rep3

description: poly(A)+ RNA

data_processing:
miCLIP data processing:
Reads were mapped to the respective genome and its annotation (GENCODE release 31 for all human samples, GENCODE release M23 for all mouse samples) using STAR (v2.7.3a). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999), soft-clipping was prohibited on the 5'end of reads (--alignEndsType Extend5pOfRead1) and only uniquely mapping reads were kept for further analysis (--outFilterMultimapNmax 1).
Following mapping, BAM files were sorted and indexed (SAMtools v1.9) and duplicate reads were removed (UMI-tools v1.0.0).
After removing duplicates, all mutations found in reads were extracted using the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK, v1.1.3). The list was filtered for C-to-T mutations using basic Bash commands and kept in BED file format. Based on the filtered list of C-to-T mutations, deduplicated reads were separated into two BAM files holding reads with and without C-to-T mutation, respectively, using SAMtools and basic Bash commands. The BAM file of reads without C-to-T mutation was transformed to a BED file using bedtools bamtobed (BEDTools v2.27.1) and considering only the 5' mapping position of each read. Afterwards, the BED file was sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream (since this nucleotide is considered as the crosslinked nucleotide) using bedtools genomecov (BEDTools v2.27.1). Similarly, the BED files of C-to-T mutations were also sorted and summarized to strand-specific bedGraph files using bedtools genomecov. Finally, all bedGraph files were transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
RNAseq data processing:
Reads were mapped to the mouse genome and its annotation based on GENCODE release M23 using STAR (v2.6.1b). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999). SAMtools was used to remove secondary alignments and keep only one location for multimapping reads (-F 256).
For differential expression analysis, mapped reads were counted with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Genome_build: mm10 (GRCm38.p6), hg38 (GRCh38.p12)
Supplementary_files_format_and_content: *.C2T.plus.bw, *.C2T.minus.bw: bigwig files of positions with C-to-T mutations and their counts. They were generated by filtering for C-to-T mutations in the list of all found mutations, which were output of the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK). The filtered list was in BED file format and was then sorted and summarized to strand-specific bedGraph files using bedtools genomecov, which were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.noC2T.plus.bw, *.noC2T.minus.bw: bigwig files of positions upstream of reads without C-to-T mutation and their counts. They were generated by first removing all reads with C-to-T mutation from the BAM files and then transforming the resulting BAM file to a BED file using bedtools bamtobed considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: The samples miCLIP_mESC_WT_1 and miCLIP_mESC_Mettl3_KO_1 were sequenced in two technical replicates (miCLIP_mESC_WT_1_1 + miCLIP_mESC_WT_1_2 and miCLIP_mESC_Mettl3_KO_1_1 + miCLIP_mESC_Mettl3_KO_1_2), for which we provide separate raw data files (fastq.gz), but have merged their bigwig tracks after processing into miCLIP_mESC_WT_1.merged... and miCLIP_mESC_Mettl3_KO_1.merged...
Supplementary_files_format_and_content: *.txt: count tables of reads mapping to genes generated by counting reads with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Supplementary_files_format_and_content: *.bed: bed files with predicted m6A sites by m6Aboost. In brief, bam files with reads without C-to-T mutation were used for peak calling with PureCLIP (v1.3.1) individually on each replicate for each condition. PureCLIP significant sites per replicate were then filtered for presence in at least two replicates for a given condition. m6Aboost was applied to the reproducible peaks to predict m6A sites.

source_name: Mettl3 KO mouse embryonic stem cells (mESC)

extract_protocol:
For RNA extraction from HEK293T cells and mESCs, cells were washed in ice-cold PBS and collected on ice for the isolation of total RNA using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommended protocol. Poly(A)+ RNA was extracted using Oligo d(T)25 Magnetic Beads using the manufacturer’s recommended protocol. Poly(A)+ concentration was measured using Qubit™ RNA HS Assay Kit (ThermoFisher Scientific). The quality of poly(A)+ RNA was ensured using High sensitivity RNA screen tapes for the 2200 Tape station system (Agilent). If a predominant peak for ribosomal RNA was still detectable an additional round of poly(A) selection was performed. Mouse heart RNA was purchased from Takara Clontech (order number 636202): RNA isolated by a modified guanidinium thiocyanate method followed by poly A+ RNA selection with two rounds of oligo(dT)-cellulose columns.
RNA-seq: NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol beginning with fragmentation step (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 73ng for imb_koenig_2019_21 and amplified in 10 PCR cycles.Libraries were profiled in a DNA 1000 on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).  All 6 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput Flowcell, SR for 1x 84 cycles plus 1x 7 cycles for the index read.
miCLIP2: Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

value: mouse embryonic stem cells (mESC)

value: mESC cells


title: Progressive2 T0

value: A

value: untreated

value: B cells


title: Control, CK2

value: serum

value: 16-18 weeks

value: healthy individual in the fetus


title: Fruiting body stipe, replicate2


title: Control, CK3

value: serum exosome miRNAs


title: miCLIP2 macrophages replicate 3

description: Co-immunoprecipitated RNA fragments


title: Fruiting body stipe, replicate1


title: Progressive1 T0

value: CLL Progressive1


title: Control, CK1


title: KMS-12-BM S63845 resistant

city: Vienna

first: Arnold

last: Bolomsky

address: Montleartstraße 37

country: Austria

institute: Wilhelminen Cancer Research Institute

data_processing:
Data processing was performed as described in Kumar A. et al., PMID 28818039
Illumina bcl2fastq Coversion Software versiota 2.20 was used for base calling
The differential expression analysis was perfomed using R packages edgeR (version 3.32.0) and limma (version 3.46.0). First, genes with low counts were filtered out using filterByExpr function. The count data was then transformed to log2 CPM with voom function. After that lmFit function was applied to the voom object to perform linear model fitting. The resulting object was then used to obtain further statisics via utilizing eBayes function.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: abundance measurements

source_name: Multiple myeloma

growth_protocol: Cells were kept in RPMI1640 medium supplemented with 10% heat-inactivated FBS, 1x Pen/Strep/Glut in the presence or absence of increasing S63845 doses for >1 year. Resistant S63845 cells were grown in the presence of 600 nM S63845.

extract_protocol:
Total RNA was extracted according to the manufacturers instructions using Qiagen AllPrep DNA/RNA/miRNA Universal Kit (cat#80224) - DNase treatment (Qiagen, cat# 79254) was included. Quality and quantity of the extracted RNA samples were analyzed with 2100 Bioanalyzer using RNA 6000 Nano Kit (cat# 5067-1511, Agilent, Santa Clara, CA, USA) and Qubit RNA BR kit ( cat# Q10211,Thermo Fisher Scientific, Waltham, MA, USA). For genomic DNA contamination measurement, Qubit dsDNA BR kit (cat# Q32850, Thermo Fisher Scientific, Waltham, MA, USA) was used.
Illumina TruSeq Stranded Total RNA Library Prep with Ribo-Zero Globin kit (Cat#20020612) was used with 800 ng of total RNA for the construction of sequencing libraries.
RNA-Seq. Sequencing was performed with Illumina NovaSeq 6000 system using v. 1.0 chemistry (Illumina, San Diego, CA, USA). Read length for paired-end run was 2x151 bp and target coverage minimum 80 M reads for each library.

treatment_protocol: Total RNA was isolated from untreated S63845 sensitive and resistant cell line variants. Continous S63845 exposure was stopped two weeks before sampling.

value: Multiple myeloma cel line

tag: status

value: S63845 resistant


title: RNAseq mESC Mettl3 KO rep1

description: poly(A)+ RNA


title: RNAseq mESC Mettl3 KO rep2

description: poly(A)+ RNA


title: RNAseq mESC WT rep3

description: poly(A)+ RNA

source_name: WT mouse embryonic stem cells (mESC)


title: KMS-12-BM S63845 sensitive

value: S63845 sensitive


title: Fetal Ventricular Septal Defect, A10

source_name: Serum exosomal miRNA_patient

value: Ventricular Septal Defect in the fetus


title: Fruiting body lamellae, replicate2

source_name: Fruiting body lamellae

value: Po-FB-L

value: Fruiting body lamellae


title: RNAseq mESC WT rep2

description: poly(A)+ RNA


title: Progressive1 T1

value: B


title: OPM-2 S63845 resistant


title: Fruiting body lamellae, replicate1


title: RNAseq mESC WT rep1

description: poly(A)+ RNA

value: mouse embryonic stem cells (mESC)


title: Fruiting body dedifferentiated cap, replicate2

source_name: Fruiting body dedifferentiated cap

value: Po-FB-D

value: Fruiting body dedifferentiated cap


title: OPM-2 S63845 sensitive


title: Fetal Ventricular Septal Defect, A8


title: miCLIP mouse heart 300ug RNA

description: Co-immunoprecipitated RNA fragments

source_name: purchased RNA from murine heart tissue (Takara Clontech, order number 636202)

value: mouse heart

value: rabbit anti-m6A antibody (Synaptic Systems, order number 202 003)


title: Fetal Ventricular Septal Defect, A7

value: serum


title: Fruiting body dedifferentiated cap, replicate1


title: CAF6-NIRA2

city: Wuhan

first: Tian

last: Fang

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp  paired-end reads, according to the manufacturer’ s instructions.
Raw data (raw reads) of fastq format were firstly processed through primary quality  control. In this step, clean data (clean reads) were obtained by removing read pairs that  contain N more than 3 or the proportion of base with quality value below 5 is more than 20%,  in any end,or adapter sequence was founded. All the downstream analyses were based on the  clean data with high quality.
Paired-end clean reads were aligned to the reference genome using TopHat. We selected  TopHat as the mapping tool for that TopHat can generate a database of splice junctions based  on the gene model annotation file and thus a better mapping result than other non-splice  mapping tools.
HTSeq was used to count the reads numbers mapped to each gene.
Differential expression analysis between two conditions was performed using the  DEGSeq R package (1.20.0). Differentially expressed genes were defined as those for which  the adjusted P-value below 0.05 and the log2(Fold change) more than 1.
Supplementary_files_format_and_content: fpkms

source_name: primary cancer-associated fibroblasts

growth_protocol: Primary cancer-associated fibroblasts were isolated from tumor specimens and cultured in DMEM/F-12 1:1 medium with 10% FBS and 1×PS in a humidified atmosphere incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells in a T75 culture flask were digested and washed with PBS, then dissoved in 1ml trizol and then stored in -80℃ for futher RNA isolation.
A total amount of 2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep  Kit for Illumina following manufacturer’ s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using  poly-T oligo-attached magnetic beads. Fragmentation was carried out using fragmentation buffer. First strand cDNA was synthesized and second strand cDNA synthesis was  subsequently performed. Remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated.  Then the PCR was performed. At last, Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 350bp.

treatment_protocol: When the confluence reach 60-70%, the medium were replaced with new complete medium containing 20uM niraparib or 30uM olaparib and incubated for 72h.

value: ovarian cancer

value: primary cancer-associated fibroblasts (CAFs)

value: niraparib 20um for 72h


title: miCLIP mouse heart 100ug RNA

city: Würzburg

description: Co-immunoprecipitated RNA fragments


title: Fruiting body lamellae, replicate3


title: CAF6-NIRA1


title: CAF6-NIRA3


title: Fruiting body cap, replicate3

source_name: Fruiting body cap

value: Po-FB-C

value: Fruiting body cap


title: miCLIP mouse heart 1ug RNA

description: Co-immunoprecipitated RNA fragments


title: Fetal Ventricular Septal Defect, A4

value: 16-18 weeks

value: serum exosome miRNAs


title: Fetal Ventricular Septal Defect, A5

value: Ventricular Septal Defect in the fetus


title: Fetal Ventricular Septal Defect, A6


title: CAF6-CON2

value: DMSO for 72h


title: miCLIP mESC Mettl3 KO rep3

description: Co-immunoprecipitated RNA fragments


title: CAF6-CON3


title: Fetal Ventricular Septal Defect, A3


title: Fetal Ventricular Septal Defect, A9


title: Fruiting body cap, replicate1


title: miCLIP mESC Mettl3 KO rep2

description: Co-immunoprecipitated RNA fragments


title: BxPC3_dau_72h_2 [miRNA]

hyb_protocol: 1. Kits and Reagents: 2×Hybridization buffer; Phalanx Hyb. Assembly  miRCURYTM Array, Wash buffer kit (Cat #208021, Exiqon):Buffer A, Buffer B,Buffer C  2. Prepare the hybridization mix in a PCR tube  3. Incubate at 95°C for 2 min. During the incubation the target preparation should be protected from light.  4. Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation.  5. Take cover slide out of the package.  6. Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label.  7. Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side).  8. Clip the bag with a clipper securely from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly.  9. Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes.  10. Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim.  11. Cut the second Hyb. Bag to approximately one-half of its original length.  12. Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag.  13. Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position.  14. Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight.  15. After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A.  16. Wash briefly at room temperature in Wash buffer B.  17. Wash for 2min. at room temperature in Wash buffer B.  18. Wash for 2min. at room temperature in Wash buffer C.  19. Wash briefly in water.  20. Dry the slides by centrifugation for 5 min. at 200* g(1000rpm). Scan slides immediately.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain Normalized Data, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.  d) Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.   e) You can find the detail information in miRNA Expression Profiling Data.
nomalized_data.txt contains Normalized signal intensity data

label_protocol: Briefly, total RNA from each sample was labeled with Hy3 according to miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) manufactor

value: Human pancreatic adenocarcinoma cells

value: 24 μmol Dau for 72h

tag: tag


title: Fetal Ventricular Septal Defect, A2


title: CAF6-CON1


title: miCLIP mESC Mettl3 KO rep1, technical rep2

description:
Co-immunoprecipitated RNA fragments
miCLIP_mESC_Mettl3_KO_1.merged.v2uniqMD.duprm.noC2T.minus.bw
miCLIP_mESC_Mettl3_KO_1.merged.v2uniqMD.duprm.C2T.plus.bw
miCLIP_mESC_Mettl3_KO_1.merged.v2uniqMD.duprm.C2T.minus.bw

value: mouse embryonic stem cells (mESC)


title: CAF3-OLA3

value: olaparib 30um for 72h


title: BxPC3_dau_72h_1 [miRNA]


title: miCLIP mESC Mettl3 KO rep1, technical rep1


title: miCLIP mouse heart 50ug RNA

description: Co-immunoprecipitated RNA fragments


title: CAF3-OLA2


title: BxPC3_72h_3 [miRNA]

value: none; untreated


title: Fruiting body cap, replicate2


title: miCLIP mESC WT rep3

description: Co-immunoprecipitated RNA fragments


title: BxPC3_dau_72h_3 [miRNA]


title: CAF3-OLA1


title: D28_r3_RNAseq

description:
FPKM_mat.txt
count_mat.txt

source_name: H9 pluripotent stem cells

tag: induction day


title: BxPC3_72h_2 [miRNA]


title: CAF3-CON3


title: miCLIP mESC WT rep2

description: Co-immunoprecipitated RNA fragments


title: BxPC3_72h_1 [miRNA]


title: miCLIP mESC WT rep1, technical rep2

description:
Co-immunoprecipitated RNA fragments
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.noC2T.plus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.noC2T.minus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.C2T.plus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.C2T.minus.bw


title: D28_ATACseq

extract_protocol:
Briefly, 50,000 cells were detached from each induction plate at the previously defined time-points and washed with cold PBS. Next 50 μl of cold lysis buffer was added to the cell pellet.
The Tn5-mediated tagmentation and adapter incorporation were performed with the Nextera DNA Library Prep Kit (Illumina) following manufacturer’s protocol at 37ºC for 30 min. The transposed DNA was purified using Qiagen MinElute PCR Purification Kit (Qiagen). To amplify DNA fragments, we used NEBNext High-Fidelity PCR Master Mix (New England Biolabs).


title: D14_ATACseq


title: Fetal Ventricular Septal Defect, A1


title: CAF3-CON2