title: coli_delta3dus_R_2

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

institute: Namur University

data_processing:
Library strategy: Rho-seq
Reads were quality- and adaptor-trimmed using trimmomatic 0.36 with options PE ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 HEADCROP:1 SLIDINGWINDOW:4:15 MINLEN:20
The filtered reads were mapped on the spike-in sequence with bowtie2 (options --no-discordant --no-mixed --phred33 -p 4 --un-conc) then on the genome using also bowtie2 for the E.coli libraries or tophat2 for the S. pombe libraries (options--mate-std-dev 150 -N 2 --read-edit-dist 2 --min-intron-length 5 --max-intron-length 3000 --no-discordant --no-coverage-search -p 4 --library-type fr-firststrand).
Properly paired mapped reads were split by strand. Then bedtools (options genomecov -ibam -d -5)  was used to calculate the number of RT termination events for each strand-specific position as the number of 5'end of R2 reads that map at this position. In parallel, the paired reads were computationally extended/merged into fragments that covered the genome from the left end of the left-most read to the right end of the right-most reads with the notable exeption that the fragments were not extended in identified introns. Those spliced fragments where then used to compute a fragment coverage reflecting the number of time a reverse transcriptase passed through a specific position. Then the ratio between the number of RT termination events and fragment coverage at each position (the D-ratio) was calculated.
After independent pre-filtering of the positions unlikely to have significant differences in D-ratio accross conditions (see manuscrit), the number of RT termination events out of the number of RT readthrough were modelised in generalized linear model of the binomial family (function glm in R) according to the effect of the treatment (R+ vs R-), the effect of the strain (wild-type vs delta4dus), and their interaction. The positions were the interaction between the wild-type and the delta4dus lead to a statistically  significant (FDR<0.1) increase of the proportion of RT termination events were retained as putative dihydrouridilation sites.
Genome_build: ASM294v2.26 (pombe) or ASM584v2.38 (coli)
Supplementary_files_format_and_content: Rho-seq_supplementary.xlsx is a spreadsheet describing the dihydrouridilated sites (D-sites) uncovered in our study. The first two sheets describe the D-sites found respectively on the S. pombe and the E. coli transcriptome, while the third sheet contains a legend explaining the column names in the first two sheets.

organism: Escherichia coli

source_name: E. coli cells

extract_protocol:
The cell pellets were resuspended in 750μL of TES buffer (10mM Tris pH 7.5, 10mM EDTA pH 8, 0.5% SDS) and the total RNA was isolated by hot phenol extraction.
Rhodamine labeling was performed as described in our manuscript. Briefly, 30μg of total RNA were resuspended in 1% sodium borohydride for 60min at 25°C. Mock samples (R-) were treated similarly but without sodium borohydride. The reduced RNA was then precipitated and the dried pellet was resuspended in 0.1M sodium formate pH 4. Rhodamine labeling was performed for 90min at 37°C in dark with 2.2mM of rhodamine chlorine. Labeled RNA was purified by phenol extraction. A synthetic dihydrouridilated RNA spike-in was added to the samples (1:1000) before ribodepletion of 5 μg of the RNA samples. Zinc-mediated fragmentation was performed at 70°C for 15min with 90-125 ng of ribodepleted RNA. Simultaneous DNA digestion and RNA extremities dephosphorylation were performed at 37°C for 30min with 2U of TURBO DNase and 3U of FastAP Thermosensitive Alkaline Phosphatase. 3'-end ligation of the RNA adapter was performed for 90min at 25°C with 39U of T4 RNA ligase. After ligation, 10pmol of DNA primer were added, the sample was denatured for 2min at 70°C and the reverse transcription was performed with Superscript III. The excess of DNA primer was subsequently digested with 4min incubation with 2μL of ExoSAP-IT. The 3'-end ligation of the cDNA with DNA adapter was performed overnight at 25°C with 48U of T4 RNA ligase. Nucleic acid clean-ups were performed between each step by using MyOne SILANE magnetic beads. 13 cycles od PCR amplification was performed in a 50μL-reaction by mixing cDNA, 1μM of barcoded PCR primer, 1μM of universal PCR primer and 25μL of NEBNext High- Fidelity 2X PCR Master Mix (NEB M0541). Finally, two successive rounds of DNA polymer size selection were performed by mixing PCR products with 1.2 and 1.1 volume of AMPure XP beads. The DNA library was quantified, examined on a DNA microchip and sequenced on Illumina HiSeq 2500.

tag: replicate

tag: percentage of d in spike-in

value: R+


title: coli_delta3dus_noR_2

status: Public on Oct 26 2021

type: SRA

city: Namur

department: Medecine

country: Belgium

library_source: transcriptomic

molecule: total RNA

growth_protocol: 50 mL of S. pombe grown in YES at 32°C (OD595nm ~ 0.5) or E. coli grown in LB at 37°C (OD595nm ~ 0.6) were harvested by centrifugation and washed in DEPC water.

tag: genotype

tag: treatment

value: R-


title: Methylome capture of HG003 using TruSeq [TruSeq_HG003_LAB01_REP02]

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

description: Whole Genome Bisulfite

library_source: genomic

data_processing:
Base-calling software: RTA v3.4.4
Adapter trimming: fastp v0.20.1
Alignment: bwa-meth v02.1
Sorting and indexing: sambamba
Duplicate marking: Picard MarkDuplicates v2.10.10-SNAPSHOT
Methylation calling: MethylDackel v0.3.0-3-g084d926
Genome_build: genome build: GRCh38
Supplementary_files_format_and_content: Bedgraph

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

extract_protocol:
Illumina TruSeq DNA Methylation
DNA (gDNA) was purchased from the Coriell Institute for Medical Research

tag: cell line


title: Cell from adult ovary follicle, S_4E

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Read QC with Cutadapt v2.10
Read alignment with STAR v2.7.5a
Read counting with HTSeq v012.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Adult ovary follicle

extract_protocol:
For single-cell RNA-sequencing, the small antral follicles (1-8 mm) were collected in saline solution (0.9% NaCl, Fresenius Kabi, Bad Homburg, Germany). The follicles were mechanically ruptured with tungsten needles and the region with the cumulus GCs and oocyte was trimmed and transferred into a clean dish. Individual follicular cells were manually picked up using a pulled glass-capillary under a stereo microscope (Zeiss). Oocytes were denuded by pipetting up and down. None of the collected oocytes contained a polar body. Each cell was transferred into a cold PCR tube contain 1.9 ml 0.2% TritonX-100 in DEPC water and 0.1 ml Recombinant RNase inhibitor (2313A, 40U/ml, TaKaRa), snap-frozen on dry ice and stored at -80°C.
Sequencing libraries were prepared according to the user guide of the Nextera XT (illumina)

tag: cell type

value: Follicular cell

tag: follicle id

tag: batch

tag: patient id


title: Cell from adult ovary follicle, S_4G


title: coli_WT_noR_2

value: wild-type


title: Cell from adult ovary follicle, S_4F


title: Methylome capture of HG004 using TruSeq [TruSeq_HG004_LAB01_REP01]

description: Whole Genome Bisulfite


title: input-CD4-rep1

city: Wuhan

first: jiwei

last: chang

state: Hubei

address: No.185, East Lake Road, Wuchang District,

department: Medical Research Institute,  School of Medicine,

country: China

institute: Wuhan University

data_processing:
fastp/trimmomatic trimming raw fastq files
kallisto mapping to GRCm38 cDNA sequences
SLAM-seq mapping NextGenMap
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized gene counts or raw gene counts:
Sample-IP-gene-counts-16cell_types.tsv (raw counts)
normalized-Sample-input-counts-gene-16cell_type.tsv (normalized counts)
Mettl3-normalized-gene-counts-input.tsv (normalized counts)
Mettl3-gene-counts-IP.tsv (raw counts)
Igf2bp2-LT.HSC-gene-counts.tsv (raw counts)
RNA-Ratio-T2C-6cell_type.tsv (T>C transition ratio)
RNA-T2C-ratio-average-LT.HSC.tsv (T>C transition ratio)
RNA-T2C-ratio-average-MkP.tsv (T>C transition ratio)

organism: Mus musculus

source_name: CD4 cell

extract_protocol:
Total RNA was isolated using Tirzol reagent (Takara). Anti-m6A antibody (0.5 μg per sample) (ab15320, Abcam) was pre-bound to Protein A magnetic beads (Thermo Fisher Scientific) in IP buffer (10mM Tris-HCl pH 7.4, 100mM NaCl,0.1% NP40, , 0.4 U/μl RNasin) with head-to-tail mixing at 4 °C for 2 h. Total RNA (100 ng per sample) was added and incubated at 4°C for another 2 h. Beads were washed twice with 200 μl IP buffer, twice with 200 μl low-salt buffer (10mM Tris-HCl pH 7.4, 50 mM NaCl, 0.1% NP-40, 0.4 U/μl RNasin), twice with 200 μl high-salt buffer (10mM Tris-HCl pH 7.4, 500mM NaCl, 0.1% NP40, 0.4 U/μl RNasin) and once with 200 μl 1× IP buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: CD4 cell

tag: rip antibody

value: untreated


title: Methylome capture of HG004 using TruSeq [TruSeq_HG004_LAB01_REP02]

description: Whole Genome Bisulfite


title: coli_WT_R_2


title: D10_lowSDS_FLAG_65C_eluted_ChIP-Seq

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

country: USA

institute: Gladstone Institute of Cardiovascular Disease

data_processing:
Libraries were sequenced on Illumina Novaseq
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using Bowtie2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

growth_protocol: mouse ESCs were maintained in DMEM media supplemented with LIF and serum

extract_protocol:
Cells were lysed, lysates were clarified and incubated with anti-FLAG antibody(Sigma, F1806) for O/N, captured with IgG coated magnetic beads, washed, and ChIPed DNA eluted. Protein-DNA complexes were reverse crosslinked, proteinase digested and ampure bead purified
To prepare libraries DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP  and ligated of Illumina adapters. Adapter ligated DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 200 - 500bp bp were band isolated from an agarose e-gel (invitrogen).  The purified libraries were quantified, and libraries were pooled before sequencing on Illumina NextSeq 500 system

treatment_protocol: mouse ESC lines were differentiated to cardiomyocytes using the Kattman et al 2011 Cardiomyocyte Differentiation protocol.

value: mouse ES cell derived cardiac myocytes

tag: timepoint

value: Day 10


title: Methylome capture of HG003 using TruSeq [TruSeq_HG003_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_4B


title: D10_highSDS_FLAG_eluted_ChIP-Seq


title: coli_delta3dus_noR_1


title: Cell from adult ovary follicle, S_4C


title: Cell from adult ovary follicle, S_4A


title: D6_highSDS_FLAG_65C_eluted_ChIP-Seq

value: mouse ES cell derived cardiac precursors

value: Day 6


title: Methylome capture of HG005 using TruSeq [TruSeq_HG005_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, OVA87_D


title: D6_highSDS_FLAG_eluted_ChIP-Seq


title: D6_lowSDS_FLAG_65C_eluted_ChIP-Seq


title: coli_WT_R_1


title: coli_WT_noR_1


title: Methylome capture of HG006 using TruSeq [TruSeq_HG006_LAB01_REP02]

description: Whole Genome Bisulfite


title: Neuron with ApoE reconstituted particle treatment 2

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

institute: University of Science and Technology of China

description: ApoE reconstituted particle  treatment

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized abundance measurements for each group

source_name: primary neurons

growth_protocol: Standard protocol for primary neuron culture for RNA-seq

extract_protocol:
Total RNA from neurons was extracted by Trizol.A total amount of 2 μg RNA per sample was used as input material for the RNA   sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library  Prep  Kit  for  Illumina®  (#E7530L, NEB, USA) following the manufacturer’s   recommendations  and  index  codes  were  added  to  attribute  sequences  to  each  sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: brain


title: Cell from adult ovary follicle, OVA87_G


title: Methylome capture of HG007 using TruSeq [TruSeq_HG007_LAB01_REP01]

description: Whole Genome Bisulfite


title: D4_highSDS_FLAG_65C_eluted_ChIP-Seq

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: Methylome capture of HG005 using TruSeq [TruSeq_HG005_LAB01_REP01]

description: Whole Genome Bisulfite


title: Methylome capture of HG007 using TruSeq [TruSeq_HG007_LAB01_REP02]

description: Whole Genome Bisulfite


title: D4_highSDS_FLAG_eluted_ChIP-Seq


title: coli_delta3dus_R_1


title: D10_lowSDS_FLAG_eluted_ChIP-Seq


title: Cell from adult ovary follicle, OVA87_F


title: Cell from adult ovary follicle, OVA87_A


title: Neuron with ApoE particle treatment 2

description: ApoE particle treatment


title: Methylome capture of HG006 using TruSeq [TruSeq_HG006_LAB01_REP01]

description: Whole Genome Bisulfite


title: Neuron with ApoE particle treatment 1

description: ApoE particle treatment


title: Cell from adult ovary follicle, OVA87_B


title: D4_lowSDS_FLAG_eluted_ChIP-Seq


title: Cell from adult ovary follicle, OVA87_C


title: Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG001_LAB01_REP02]

description: Whole Genome Bisulfite

extract_protocol:
NuGEN TrueMethyl oxBS-Seq
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: D4_lowSDS_FLAG_65C_eluted_ChIP-Seq


title: D6_lowSDS_FLAG_eluted_ChIP-Seq


title: Cell from adult ovary follicle, OVA87_E


title: CIML NK 2 mixture + OCI-AML3

city: Cambridge

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.
Cell subpopulations were defined as described in the manuscriipt
Genome_build: hg19
Supplementary_files_format_and_content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: CIML NK

extract_protocol:
Single-cell suspensions of cultured CIML NK 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 NovaSeq S4

treatment_protocol: CIML NK cells were induced by IL12 + IL15 + IL18 in vitro

value: PBMC


title: D10_Input


title: Neuron with ApoE reconstituted particle treatment 1

description: ApoE reconstituted particle  treatment


title: CIML NK 2 mixture


title: Neuron with control treatment 1

description: ApoE particle treatment control


title: Neuron with control treatment 2

description: ApoE particle treatment control


title: D6_Input


title: Cell from adult ovary follicle, S_L1

value: Oocyte


title: T3

city: Rozzano (MI)

first: Daniele

last: Braga

address: Via Manzoni 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Reads were processed using the 10XGenomics workflow (v4.0). Briefly, demultiplexing, assignment of barcodes and quantification of Unique Molecular Identifiers (UMIs) were performed with cellranger using default parameters. Reads were aligned to the reference genome mm10, already pre-built by 10XGenomics (http://software.10xgenomics.com/single-cell/overview/welcome). Cells with less than 500 UMIs, 200 detected genes and more than 30% of UMIs corresponding to mitochondrial reads were removed in order to keep just high-quality cells. Further downstream analyses were performed using the Seurat (v3) pipeline based on the function SCTransform. The Pearson residuals of the top 3000 most variable genes were used to calculate the first 15 principal components, which were used as input for the function FindNeighbors, together with a k.param of 25. Clusters were determined with the function FindClusters with a resolution parameter of 0.2. Finally, clusters were manually curated and annotated based on markers available in the literature. Marker genes for each cluster were defined with the function FindAllMarkers with parameters min.pct=0.25 and test.use=wilcox.
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized (SCTransform) single-cell gene expression. UMAP coordinates and single-cell metadata (cluster, cell cycle phase, sample of origin).

source_name: Choroid plexus

growth_protocol: Newly purchased 10/12 weeks old C57BL/6J male mice were randomized into 5 mice/cage and housed for one week to normalize gut microbiome. We induced acute colitis using two different protocols: Short and Long. During the short treatment, colitis was induced by administration of 3% Dextran Sulphate Sodium (DSS) (MP Biomedicals, molecular weight 36–50kDa) in drinking water for 1 (T1) and 3 days (T3).

extract_protocol:
Lateral ventricles CP of five adult mice were rapidly microdissected and pooled together in ice cold dissecting medium (HBSS supplemented with 0.6% glucose). Dissected CPs were settle down by gravity to aspirate the dissection medium and replace with fresh dissection media supplemented with 3 mM CaCl2 and 100 µg/ml collagenase D (Sigma-Roche, # 11088858001) and incubate at 37°C in 20% O2 and 5% CO2 on orbital shaker for 15 min. After the incubation, collagenase containing medium was aspirated and CPs were further incubate in papain using papain dissosciation system kit (Worthington, cat#LK003150) following the manufactured instructions. Dissociated CPs were finally centrifuged at 280 g for 5 min and resuspended in PBS. Next, 10 µl of single cells suspension was mixed with 10 µl of 0.4% trypan blue and automatically counted using Countess 3 automated cell counter (Invitrogen, cat#AMQAX2000). Approximately 7000 cells from each sample were loaded into Single Cell Chip B (10X Genomics,#PN-1000092) using the Single Cell 3’ v3 reagent kit (10X Genomics, # PN-1000074) for gel bead emulsion generation in the Chromium system.
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3
PE sequencing, standard 10XGenomics RNA-seq

value: Choroid plexus

value: DSS (72h)


title: Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG001_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_L2


title: T0

value: baseline


title: CIML NK 1 mixture


title: Cell from adult ovary follicle, OVA87_H

value: Follicular cell


title: D4_Input


title: T1

value: DSS (24h)


title: BrmKO_D10_highBMP4_Rep1_ATAC-seq

data_processing:
Libraries were sequenced on Nextseq 500
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using the bowtie
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

growth_protocol: Es cell were differentiated following Katman et al., 2011 and Wamstad et al., 2012 papers

extract_protocol:
We followed Corces et al., 2017 paper to perform ATACSeq
Lysed nuclei were tagmented at 37C for 45 mins for D4, and  D6 samples and 3hrs for D10 samples, before purified and PCR amplified with Ad1 and Ad2 primers (corces et al., 2017)

treatment_protocol: ES cells were differentiated to cardiac precursor or cardiomyocytes before harvested for ATACseq

value: Brg1-3xFLAG; Brm::Puro


title: CIML NK 1 mixture + OCI-AML3


title: human_delta4dus_noR_2

data_processing:
Library strategy: Rho-seq
Reads were quality- and adaptor-trimmed using trimmomatic 0.36 with options PE ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 HEADCROP:1 SLIDINGWINDOW:4:15 MINLEN:20
The filtered reads were mapped on the spike-in sequence with bowtie2 (options --no-discordant --no-mixed --phred33 -p 4 --un-conc) then on the genome using also bowtie2 for the E.coli libraries or tophat2 for the S. pombe libraries (options--mate-std-dev 150 -N 2 --read-edit-dist 2 --min-intron-length 5 --max-intron-length 3000 --no-discordant --no-coverage-search -p 4 --library-type fr-firststrand).
Properly paired mapped reads were split by strand. Then bedtools (options genomecov -ibam -d -5) was used to calculate the number of RT termination events for each strand-specific position as the number of 5'end of R2 reads that map at this position. In parallel, the paired reads were computationally extended/merged into fragments that covered the genome from the left end of the left-most read to the right end of the right-most reads with the notable exeption that the fragments were not extended in identified introns. Those spliced fragments where then used to compute a fragment coverage reflecting the number of time a reverse transcriptase passed through a specific position. Then the ratio between the number of RT termination events and fragment coverage at each position (the D-ratio) was calculated.
After independent pre-filtering of the positions unlikely to have significant differences in D-ratio accross conditions (see manuscrit), the number of RT termination events out of the number of RT readthrough were modelised in generalized linear model of the binomial family (function glm in R) according to the effect of the treatment (R+ vs R-), the effect of the strain (wild-type vs delta4dus), and their interaction. The positions were the interaction between the wild-type and the delta4dus lead to a statistically significant (FDR<0.1) increase of the proportion of RT termination events were retained as putative dihydrouridilation sites.
Genome_build: ASM294v2.26 (pombe), ASM584v2.38 (coli), hg38 (human)
Supplementary_files_format_and_content: Rho-seq_supplementary.xlsx is a spreadsheet describing the dihydrouridilated sites (D-sites) uncovered in our study. The first three sheets describe the D-sites found respectively on the S. pombe, the E. coli and human transcriptome, while the third sheet contains a legend explaining the column names in the first three sheets.

source_name: HCT116 cells

growth_protocol: 50 mL of S. pombe grown in YES at 32°C (OD595nm ~ 0.5) or E. coli grown in LB at 37°C (OD595nm ~ 0.6) or HCT116 human cells were harvested by centrifugation and washed in DEPC water.

extract_protocol:
The cell pellets were resuspended in 750μL of TES buffer (10mM Tris pH 7.5, 10mM EDTA pH 8, 0.5% SDS) and the total RNA was isolated by hot phenol extraction. Rhodamine labeling was performed as described in our manuscript. Briefly, 30μg of total RNA were resuspended in 1% sodium borohydride for 60min at 25°C. Mock samples (R-) were treated similarly but without sodium borohydride. The reduced RNA was then precipitated and the dried pellet was resuspended in 0.1M sodium formate pH 4. Rhodamine labeling was performed for 90min at 37°C in dark with 2.2mM of rhodamine chlorine. Labeled RNA was purified by phenol extraction.
A synthetic dihydrouridilated RNA spike-in was added to the samples (1:1000) before ribodepletion of 5 μg of the RNA samples. Zinc-mediated fragmentation was performed at 70°C for 15min with 90-125 ng of ribodepleted RNA. Simultaneous DNA digestion and RNA extremities dephosphorylation were performed at 37°C for 30min with 2U of TURBO DNase and 3U of FastAP Thermosensitive Alkaline Phosphatase. 3'-end ligation of the RNA adapter was performed for 90min at 25°C with 39U of T4 RNA ligase. After ligation, 10pmol of DNA primer were added, the sample was denatured for 2min at 70°C and the reverse transcription was performed with Superscript III. The excess of DNA primer was subsequently digested with 4min incubation with 2μL of ExoSAP-IT. The 3'-end ligation of the cDNA with DNA adapter was performed overnight at 25°C with 48U of T4 RNA ligase. Nucleic acid clean-ups were performed between each step by using MyOne SILANE magnetic beads. 13 cycles od PCR amplification was performed in a 50μL-reaction by mixing cDNA, 1μM of barcoded PCR primer, 1μM of universal PCR primer and 25μL of NEBNext High- Fidelity 2X PCR Master Mix (NEB M0541). Finally, two successive rounds of DNA polymer size selection were performed by mixing PCR products with 1.2 and 1.1 volume of AMPure XP beads. The DNA library was quantified, examined on a DNA microchip and sequenced on Illumina HiSeq 2500 or Novaseq.

value: R-


title: Cell from adult ovary follicle, S_L3


title: RNA_decay-MkP-3h

data_processing:
Library strategy: Slam-seq
fastp/trimmomatic trimming raw fastq files
kallisto mapping to GRCm38 cDNA sequences
SLAM-seq mapping NextGenMap
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized gene counts or raw gene counts:
Sample-IP-gene-counts-16cell_types.tsv (raw counts)
normalized-Sample-input-counts-gene-16cell_type.tsv (normalized counts)
Mettl3-normalized-gene-counts-input.tsv (normalized counts)
Mettl3-gene-counts-IP.tsv (raw counts)
Igf2bp2-LT.HSC-gene-counts.tsv (raw counts)
RNA-Ratio-T2C-6cell_type.tsv (T>C transition ratio)
RNA-T2C-ratio-average-LT.HSC.tsv (T>C transition ratio)
RNA-T2C-ratio-average-MkP.tsv (T>C transition ratio)

source_name: MkP

value: wild type

value: MkP

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 3h. Cells were collected at indicated time points 3h through FACS sorted.


title: RNA_decay-MkP-6h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 6h. Cells were collected at indicated time points 6h through FACS sorted.


title: BrmKO_D10_highBMP4_Rep2_ATAC-seq

value: mouse ES cell derived cardiac myocytes

value: Day 10


title: WT_D10_highBMP4_Rep2_ATAC-seq


title: Cell from adult ovary follicle, S_L7


title: human_delta4dus_R_2

value: R+


title: RNA_decay-MkP-9h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 9h. Cells were collected at indicated time points 9h through FACS sorted.


title: human_delta4dus_noR_1


title: RNA_decay-MkP-24h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 24h. Cells were collected at indicated time points 24h through FACS sorted.


title: human_WT_R_2

value: WT


title: Cell from adult ovary follicle, S_L5


title: human_WT_noR_2


title: RNA_decay-MkP-1h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 1h. Cells were collected at indicated time points 1h through FACS sorted.


title: RNA_decay-MkP-12h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 12h. Cells were collected at indicated time points 12h through FACS sorted.


title: BrmKO_D10_normalBMP4_Rep3_ATAC-seq


title: BrmKO_D10_normalBMP4_Rep2_ATAC-seq


title: human_WT_R_1


title: WT_D10_highBMP4_Rep3_ATAC-seq

value: Day 11


title: Cell from adult ovary follicle, S_E1

value: Oocyte


title: Cell from adult ovary follicle, S_L6

value: Follicular cell


title: RNA_decay-MkP-0.5h

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 0.5h. Cells were collected at indicated time points 0.5h through FACS sorted.


title: UPP_94 PWS UPD +ASD Neurons

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
Alignment performed with STAR 2.7, Count table generated using HTSeq, data normalized with CPM.
Genome_build: Hg38
Supplementary_files_format_and_content: Count matrix

source_name: Human Dental Pulp Stem Cells

growth_protocol: Control teeth were obtained through the Department of Pediatric Dentistry at the University of Tennessee Health Science Center (UTHSC). The UTHSC Institutional Review Board (IRB) approved this study and informed consent was obtained in accordance with IRB policy. Immediately following extraction, the teeth were placed in transportation media (DMEM/F12 with HEPES and 100 U/ml penicillin, 100μg/ml streptomycin). DPSC were isolated and culture as previously described in (Kiraly et al (2009) Neurochemistry International 55: 323-332) with slight modifications. Briefly, the pulp was minced and digested in a solution of 3 mg/ml Collagenase type I and 4 mg/ml Dispase II for 1 h at 37°C. Cells were seeded in poly-D-Lysine 12-well dishes and maintained under standard conditions (37°C, 5% CO2) in DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS) and 100 U/ml penicillin, 100μg/ml streptomycin. Sub-confluent cultures were passaged regularly with 0.1μM HyQTase (HyClone).   Neuronal Differentiation: 20,000 cells/cm2 were seeded in poly-D-lysine coated 12 well plates in DMEM/F12 (1:1), 2.5% FCS, 100 U/ml penicillin and 100 μg streptomycin, and culture for 24 hours. Epigenetic reprogramming was performed by exposing the DPSCs to 10 μM 5-azacytidine in DMEM/F12 containing 2.5% FCS and 10 ng/ml bFGF for 48 hours. Neural differentiation was induced by exposing the cells to 250μM IBMX, 50μM forskolin, 200 nM TPA, 1mM dbcAMP, 10ng/ml bFGF, 10 ng/ml NGF, 30 ng/ml NT-3, and 1% insulin-transferrin-sodium selenite premix (ITS) in DMEM/F12 for 3 days. At the end of the neural induction treatment, the cells were washed with 1X PBS. Neuronal maturation was performed by maintaining the cells in Neurobasal A media supplemented with 1mM dbcAMP, 1% N2, 1% B27, and 30 ng/ml NT-3 and 1X Glutamax for 3 days.

extract_protocol:
Total RNA was extracted from ~3 week cultured Neurons using the Zymo Direct-zol RNA purification kit.
Total RNA was checked for quantity and quality on an Agilent Bioanalyzer 6000 pico chip and determined to have an RNA Integrity Number (RIN) of >9.0. For eukaryotic organisms, mature mRNAs, processed and equipped with a poly(A) tail at the 3’end, are captured via oligo(dT) beads. For prokaryotic samples, rRNAs are removed by specialized kits, maintaining mRNA molecules. According to different demands, the mRNAs can be constructed into regular library and strand specific library.    Construction of regular RNA library (non-stranded, non-directional):  After enrichment, mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization(1). In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.

value: Neurons

value: Prader-Willi syndrome - uniparental disomy class

tag: autism diagnostic

value: Possible ASD


title: RNA_decay-LT.HSC-9h-rep1

value: wild type


title: UPP_228 PWS UPD +ASD Neurons


title: human_delta4dus_R_1


title: Cell from adult ovary follicle, S_L4


title: Cell from adult ovary follicle, S_L8


title: BrmKO_D10_normalBMP4_Rep1_ATAC-seq

value: Brg1-3xFLAG; Brm::Puro


title: Cell from adult ovary follicle, S_E6


title: Cell from adult ovary follicle, S_E3


title: Cell from adult ovary follicle, S_E7


title: UPP_250 PWS UPD +ASD Neurons


title: Cell from adult ovary follicle, S_E5


title: RNA_decay-LT.HSC-9h-rep2


title: WT_D10_highBMP4_Rep1_ATAC-seq

value: mouse ES cell derived cardiac myocytes


title: RNA_decay-LT.HSC-6h-rep2

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 6h. Cells were collected at indicated time points 6h through FACS sorted.


title: WT_D10_normalBMP4_Rep2_ATAC-seq

value: Day 10


title: WT_D10_normalBMP4_Rep1_ATAC-seq


title: WT_D10_normalBMP4_Rep4_ATAC-seq


title: Cell from adult ovary follicle, S_E4


title: Cell from adult ovary follicle, S_E2


title: RNA_decay-LT.HSC-6h-rep1


title: WT_D10_normalBMP4_Rep3_ATAC-seq


title: BrmKO_D6_highBMP4_Rep2_ATAC-seq

value: mouse ES cell derived cardiac precursor

value: Day 6


title: UPN_171 PWS UPD -ASD Neurons

value: Normal


title: RNA_decay-LT.HSC-3h-rep2

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 3h. Cells were collected at indicated time points 3h through FACS sorted.


title: UPN_249 PWS UPD -ASD Neurons


title: BrmKO_D6_highBMP4_Rep1_ATAC-seq


title: RNA_decay-LT.HSC-3h-rep1


title: Cell from adult ovary follicle, S_E8


title: human_WT_noR_1

value: WT

value: R-


title: UPN_162 PWS UPD -ASD Neurons


title: UPP_268 PWS UPD +ASD Neurons


title: Cell from adult ovary follicle, S_A4


title: RNA_decay-LT.HSC-24h-rep2

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 24h. Cells were collected at indicated time points 24h through FACS sorted.


title: UPN_156 PWS UPD -ASD Neurons


title: WT_D6_highBMP4_Rep1_ATAC-seq


title: Cell from adult ovary follicle, S_A8

value: Follicular cell


title: RNA_decay-LT.HSC-24h-rep1


title: WT_D6_highBMP4_Rep2_ATAC-seq


title: Del_152 PWS Deletion Neurons

value: Prader-Willi syndrome - deletion class


title: RNA_decay-LT.HSC-1h-rep2

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 1h. Cells were collected at indicated time points 1h through FACS sorted.


title: BrmKO_D6_normalBMP4_Rep3_ATAC-seq


title: Cell from adult ovary follicle, S_A6


title: RNA_decay-LT.HSC-1h-rep1


title: Del_192 PWS Deletion Neurons

value: Neurons


title: BrmKO_D6_normalBMP4_Rep2_ATAC-seq


title: RNA_decay-LT.HSC-12h-rep2

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 12h. Cells were collected at indicated time points 12h through FACS sorted.


title: Del_225 PWS Deletion Neurons


title: Cell from adult ovary follicle, S_A2


title: Cell from adult ovary follicle, S_A5


title: WT_D6_normalBMP4_Rep2_ATAC-seq


title: Cell from adult ovary follicle, S_A7


title: Con_38 Control Neurons

value: Neurotypical Control

value: Unknown


title: Del_258 PWS Deletion Neurons


title: Cell from adult ovary follicle, S_A1

value: Oocyte


title: RNA_decay-LT.HSC-0.5h-rep2

value: wild type

value: Cells were labeled with 10uM 4sU (Sigma) for 24h. The culture medium was changed every 3 hours for duration of the pulse and then washed twice with PBS and incubated with standard medium supplemented with 10mM uridine (Sigma) after 0.5h. Cells were collected at indicated time points 0.5h through FACS sorted.


title: BrmKO_D6_normalBMP4_Rep1_ATAC-seq

value: mouse ES cell derived cardiac precursor

value: Brg1-3xFLAG; Brm::Puro


title: RNA_decay-LT.HSC-0.5h-rep1


title: RNA_decay-LT.HSC-12h-rep1


title: Con_189 Control Neurons


title: BrmKO_D4_highBMP4_Rep4_ATAC-seq

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: Con_238 Control Neurons

value: Normal


title: BrmKO_D4_highBMP4_Rep3_ATAC-seq


title: Cell from adult ovary follicle, S_A3


title: WT_D6_normalBMP4_Rep1_ATAC-seq

value: Day 6


title: BrmKO_D4_highBMP4_Rep2_ATAC-seq


title: RNA_ratio-ST.HSC-rep1

value: treated with 100 mM 4 s U (Sigma) for 3 h


title: BrmKO_D4_highBMP4_Rep1_ATAC-seq


title: RNA_ratio-MPP-rep1

source_name: MPP

value: MPP


title: P9-J1

city: Boston

first: Richard

last: Li

address: 90 Canal St, Suite 120

department: GAIRI

institute: Genuity Science

data_processing:
Raw sequencing data was trimmed with Skewer v0.2.1 and alignment was performed with  STAR v2.5.3a, using SAMtools v0.1.19 for sorting/indexing
Quantification of gene expression was performed using RSEM (v1.3.0) with GENCODE annotation v25
TMM normalization with edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: log2 normalized TMM counts, with samples as columns and genes as rows

source_name: Whole Blood

extract_protocol:
PAXgene Blood RNA Kit (Qiagen)
TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina)
151bp paired-end

tag: disease state

value: Critical

tag: disease


title: V1PAKI_d16D

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

institute: Tongji University

data_processing:
Illumina HiSeq-PE150 System was used for basecalling.
Sequenced reads were trimed for adaptor and low-quality sequence using cutadapt v1.18 and then mapped to GRCh38 whole genome using HISAT2 v2.1.0 with parameters "--dta-cufflinks --no-discordant"
Differences in expression were determined using gfold V1.1.4 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

source_name: hESC-derived NP cell

growth_protocol: The hESCs were incubated with dispase (Gibco) at 37°C. Then, colonies were cultured in suspension as embryoid bodies (EBs) in hESC culture medium without FGF-2. On day 4, EBs were followed cultured with neural differentiation medium (DMEM/F12 (Gibco), 1% N2 supplement (Gibco), 1% NEAA (Gibco) and 2 μg/ml heparin (Sigma)). On day 7, the EBs were attached to plastic substrate and cultured with neural differentiation medium for 6-8 days, and the columnar neuroepithelia organized into rosette structures. The rosette were physically resuspended and cultured in neural differentiation medium. On day 28, neural spheres were attached to plastic substrate or coverslips treated with polyornithine (Sigma) and Matrigel (BD Biosciences) to promote neuron formation. For ventral telencephalon differentiation, we treated neuroepithelial cells with 200 ng/ml Shh (R&D Systems) and 1.5 μM SAG (Selleck) at days 10–25 as previously described.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived NP cell

value: SOX1-OT V1 PAKI


title: RNA_ratio-MPP-rep2


title: V1PAKI_d10


title: V1PAKI_d16V


title: Con_182 Control Neurons

value: Neurons


title: P8-J0


title: WT_D4_highBMP4_Rep3_ATAC-seq


title: RNA_ratio-ST.HSC-rep2


title: P7-J1


title: WT_D4_highBMP4_Rep2_ATAC-seq


title: RNA_ratio-MEP-rep2

source_name: MEP

value: MEP


title: P6-J13


title: P5-J10


title: Ctrl_d16V


title: WT_D4_highBMP4_Rep1_ATAC-seq


title: RNA_ratio-MEP-rep1


title: V1PAKI_d0

source_name: hESC

value: hESC


title: Ctrl_d16D


title: RNA_ratio-LT.HSC-rep2


title: BrmKO_D4_normalBMP4_Rep4_ATAC-seq


title: P4-J1


title: RNA_ratio-LT.HSC-rep1


title: Ctrl_d10


title: V1PAKI_d4


title: WT_D4_highBMP4_Rep4_ATAC-seq


title: RNA_ratio-GMP-rep2

source_name: GMP

value: GMP


title: P46-J1


title: BrmKO_D4_normalBMP4_Rep3_ATAC-seq


title: P44-J10


title: Ctrl_d4

value: wild type


title: RNA_ratio-GMP-rep1


title: BrmKO_D4_normalBMP4_Rep2_ATAC-seq


title: Ctrl_d0


title: WT_D4_normalBMP4_Rep4_ATAC-seq


title: P43-J0


title: RNA_ratio-CMP-rep1

source_name: CMP

value: CMP


title: RNA_ratio-CMP-rep2


title: XMU-MP-1_2

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

institute: Xinxiang Medical University

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
Mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI-1640 with 10% FBS.

extract_protocol:
Cellular RNA was extracted using Qiagen RNA extraction kit (Qiagen; Cat: 74104) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cells were treated with vehicle or 3 μM XMU-MP-1 for 6 hours.


title: BrmKO_D4_normalBMP4_Rep1_ATAC-seq


title: WT_D4_normalBMP4_Rep3_ATAC-seq


title: P47-J1


title: WT_D4_normalBMP4_Rep2_ATAC-seq


title: XMU-MP-1_3


title: Igf2bp2-LT-WT-rep2

value: untreated


title: P41-J1


title: XMU-MP-1_1


title: Igf2bp2-LT-KO-rep2

value: Igf2bp2 -/-


title: P40-J0


title: NC_2

value: control


title: WT_D4_normalBMP4_Rep1_ATAC-seq

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: P3-J9


title: NC_3


title: Igf2bp2-LT-KO-rep1


title: P42-J0


title: Igf2bp2-LT-WT-rep1


title: SH-SY5Y siMINCR sample 4

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using GRCh38 (Gencode release 27) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: counts,FPKM,TPM

source_name: Neuroblastoma cell line (SH-SY5Y)

growth_protocol: The human neuroblastoma cell line SH-SY5Y (ATCC) was grown in DMEM supplemented with 15% fetal bovine serum, 1% L-Glutammine and 1% penicillin/streptomycin, at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
SENSE Total RNA-Seq Library Prep Kit (Lexogen) using 500 ng total RNA and sequenced by Illumina NextSeq 550 sequencer.

treatment_protocol: Cells were transfected with a pCMV6-AC-GFP construct. Silencing of MINCR was obtained through siRNA-mediated silencing.

value: Neuroblastoma cell line (SH-SY5Y)

value: Downregulation of MINCR


title: ESC day 4 differentiation RAP-seq - Xist probes

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

data_processing:
Library strategy: RAP-seq
Reads were trimmed using trim_galore (v0.4.1) with default parameters to remove the standard Illumina adaptor sequence
Bowtie2 (v2.2.9) was used to align reads to the mouse genome (mm9) with the default parameters.
Reads with mapping quality less than 30 were removed using samtools (v1.2).
Picard MarkDuplicates (v2.1.0) was used to remove PCR duplicates.
Bedtools intersect (v2.26.0) was used to count reads in sliding windows (100Kb every 25Kb) along the X chromosome.
Xist localization across the X-chromosome was defined by calculating the Xist enrichment scores (pulldown/input). Unmappable regions were masked.
Genome_build: mm9
Supplementary_files_format_and_content: Xist enrichment bedgraph. Enrichment values are in column 4. Masked windows are indicated in column 5 (1=masked).

source_name: ESC

growth_protocol: ESCs were grown in 2i + LIF medium

extract_protocol: Biotinylated antisense probes were hybridized to the Xist lncRNA and pulled down from crosslinked cell lysate with its associated genomic DNA. The DNA was then sequenced.

treatment_protocol: ESCs were differentiated in EpiLC differentiation medium for 2 or 4 days

value: ESC (EpiLC)

value: Differentiation for 4 days


title: P38-J0

value: Critical


title: SH-SY5Y siMINCR sample 3


title: SH-SY5Y siMINCR sample 2


title: MDA-MB-231 Xenograft Tissue, Rep 3

city: Chapel Hill

first: Ian

middle: Jonathan

last: Davis

state: NC

address: 450 West Drive

institute: University of North Carolina-Chapel Hill

data_processing:
Basecalls performed using Illumina
Reads quality assessed using fastqc/0.11.5
Adapter sequences removed using cutadapt/1.12
Reads of poor base quality removed using fastx_toolkit/0.0.14 (-Q 33 -p 90 -q 20)
Duplicate reads removed
Reads aligned to hg19 genome using star/2.5.2b (--outFilterScoreMin 1 --outFilterMultimapNmax 1 --alignMatesGapMax 1000 --outFilterMismatchNmax 2 --chimJunctionOverhangMin 15 --chimSegmentMin 15)
Multimapping reads removed (samtools view -f 256) and reads aligning to blacklisted regions of genome removed
Bam files converted to bed files using bedtools/2.26 bamtobed
Reads shift extended to 150bp
Genome_build: hg19/mm9
Supplementary_files_format_and_content: Bed files converted to bedgraphs using bedtools/2.26 genomecov, scaling by the total number of reads aligned
Supplementary_files_format_and_content: Bedgraphs converted to bigwigs using bedGraphToBigWig

source_name: MDA-MB-231 tissue

growth_protocol: Cells were cultured in standard conditions at 37˚C with 5% CO2

extract_protocol:
FOR CELLS: 5 million cells (EWS894, UM-RC-2, MCF-7, HUVEC) were crosslinked in 1% formaldehyde   in biological triplicate and nuclei were prepared using the Active Motif Chromatin Preparation kit (53046) according to manufacturer’s instructions. 0.25 million formaldehyde crosslinked Drosophila S2 cells were mixed with the human tumor cells just prior to nuclei preparation   . Nuclei were resuspended at a concentration of 1 million nuclei per 90 µL of Lysis Buffer A (7) and 10 µL of nanodroplets (prepared as described in Kasoji et al. (23), available from Triangle Biotechnology, Inc.) was added to each tube prior to sonication. Sonication was performed in a Covaris E110 instrument using conditions described in (22) with nanodroplets (EWS89445 seconds; UM-RC-2 30 seconds; MCF-7 1.5 minutes; HUVEC 2 minutes) or without nanodroplets (EWS894and MCF-7 16 minutes; UM-RC-2 10 minutes, HUVEC sonicated with a probe sonicator as described in (51)). Following sonication, insoluble debris was removed by centrifugation and samples were digested with 200 µg RNase (Qiagen) at 37˚C for 30 minutes. Ten µL of sample was removed for input and digested with 40 mg Proteinase K (Worthington) for 1 hour at 55˚C, followed by 2 hours at 80˚C to reverse the crosslinks, then purified using a silica matrix column (Zymo Research, ChIP DNA Clean and Concentrate kit, D5201). FAIRE was performed on the remaining 90 µL of sonicated chromatin by purification on a silica matrix column as described in (51). DNA was quantified by fluorometry (Qubit dsDNA High Sensitivity Assay Kit, Invitrogen). Average peak fragment size of input and FAIRE DNA was confirmed using Agilent TapeStation. FOR TISSUE: FFPE tissue blocks were sectioned (UNC Translational Pathology Laboratory) to 10 µm thickness and each section was mounted on a charged glass slide. The top and bottom sections from the first sectioning of each block were stained with Haemotoxylin and Eosin (H&E), visualized on an Aperio ScanScope AT2 and nuclei counted using the Aperio ImageScope software. The slides were deparaffinized and hydrated in xylene, 100%,  85% and 70% ethanol followed by double deionized water. Tissue sections were scraped from the slide with a razor blade and transferred to a 100 µL glass borosilicate vial (Triangle Biotechnology, Inc.) containing 90 µL of Lysis Buffer A (7). Just prior to sonication, 10 µL of nanodroplets (Triangle Biotechnology, Inc. ) was added to each tube. Sonication and FAIRE were performed as described for fixed cells. For Fig. 3C, chromatin was extracted (Active Motif, 53045) from eight, 10 µm EWS894 FFPE tissue sections according to manufacturer instructions. For the nanodroplet extraction method, chromatin was extracted from one, 10 µm tissue section using protocol described above. Each FFPE FAIRE-seq sample consisted of FAIRE DNA extracted from 4 adjacent 10 µM tissue sections per tumor (see Supplemental Table 1 for nuclei count from FFPE tumors).
Sequencing libraries were prepared (Kapa HyperPrep) according to manufacturer instructions.

value: MDA-MB-231 tissue

tag: sonication method

value: + nanodroplets


title: NC_1


title: P37-J1


title: ESC day 2 differentiation RAP-seq - Xist probes

value: Differentiation for 2 days


title: SH-SY5Y WT sample 4

value: Wild-type


title: P36-J1


title: P35-J0


title: MDA-MB-231 Xenograft Tissue, Rep 1


title: SH-SY5Y siMINCR sample 1


title: SUM229 Xenograft Tissue, Rep 3

source_name: SUM229 tissue

value: SUM229 tissue


title: LH30_2

city: Stanford

first: Robert

middle: A

last: Saxton

address: 279 Campus Drive, Beckman Center, Room B173

department: Department of Molecular & Cellular Physiology

institute: Stanford University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5) (Dobin et. al., 2013).
The FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene and used to quantify relative gene expression levels (Mortazavi et. al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM and raw counts values for each Sample

source_name: mouse colon tissue

extract_protocol:
Colon tissues was isolated and flash frozen in liquid nitrogen. Tissues were disrupted with mortar and pestle in liquid nitrogen and 50 mg tissue was lysed in ice-cold RIPA lysis buffer (Thermo). Lysates were further homogenized via centrifugation through a QiaShredder column (Qiagen). RNA from each tissue was isolated using RNAeasy plus mini kit (Qiagen).
cDNA libraries were constructed using NEBnext® UltraTM II RNA Library Prep Kit for Illumina®, using 0.2 µg RNA input, and the mRNA enrichment method

treatment_protocol: 200 ug/mouse, 6 hour treatment.

value: colon


title: SH-SY5Y WT sample 3


title: P39-J1


title: ESC day 2 differentiation RAP-seq - Input DNA


title: P34-J0


title: LH5_2

value: WT IL-22


title: SUM229 Xenograft Tissue, Rep 2


title: P33-J0


title: LH5_1


title: SH-SY5Y WT sample 2


title: SUM229 Xenograft Tissue, Rep 1


title: MDA-MB-231 Xenograft Tissue, Rep 2


title: SH-SY5Y WT sample 1


title: SUM149 Xenograft Tissue, Rep 3

source_name: SUM149 tissue

value: SUM149 tissue


title: PBS_2

value: PBS


title: SUM149 Xenograft Tissue, Rep 2


title: SH-SY5Y MINCR sample 4

value: Overexpression of MINCR


title: SH-SY5Y MINCR sample 3


title: P31-J1


title: PBS_1


title: P30-J4


title: SUM149 Xenograft Tissue, Rep 1


title: LH30_1


title: ZR-75-1 Xenograft Tissue, Rep 1

source_name: ZR-75-1 tissue

value: ZR-75-1 tissue


title: P2-J3


title: P29-J9


title: D10_BrmKO_high_BMP4_scRNA-seq

data_processing:
Libraries were sequenced on Illumina Novaseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to mm9  using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WT and BRM KO cells at normal BMP4 concentration or combined with high BMP4 concentrations
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.
Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the ‘root’ cells. Next, all day 10 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.
Genome_build: mm9
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

source_name: mouse ES cell derived cardiomyocytes

extract_protocol:
Cells on day 4, day 6 and day 10 were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries

value: mouse ES cell derived cardiomyocytes

value: Brm-/-

value: Day 10


title: MCF-7 Xenograft Tissue, Rep 2

source_name: MCF-7 tissue

value: MCF-7 tissue


title: D10_WT_high_BMP4_scRNA-seq

value: wild type


title: SH-SY5Y MINCR sample 2

value: Neuroblastoma cell line (SH-SY5Y)


title: D10_WT_normal_BMP4_scRNA-seq


title: D10_BrmKO_normal_BMP4_scRNA-seq


title: P28-J5

value: Critical


title: MCF-7 Xenograft Tissue, Rep 1

value: + nanodroplets


title: Nanodroplet FAIRE in HUVEC cells - Rep 1

source_name: HUVEC cells

value: HUVEC cells


title: HAP1 haploid cells, TSZ

city: Dallas

first: Zhigao

last: Wang

state: TX

address: 5323 Harry Hines Blvd., NA8.202

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Bcl files were demultiplexed using bcl2fastq (v2.20)
sgRNA sequences were trimmed using an inhouse script
Enriched genes and normalized read counts were identified via MAGeCK (v0.5.1)
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO A & B)
Supplementary_files_format_and_content: tab-delimited text file that includes the normalized counts for each sgRNA

source_name: HAP1 haploid cells

growth_protocol: HAP1:RIPK3:MLKL cells were cultured in IMDM supplemented with 10% fetal bovie serum and penicilin/streptomycin. In addition, 0.5mg/ml G418 and 10mg/ml blasticidin were included to maintain transgene expression.

extract_protocol:
Cells were harvested and genomic DNA was extracted with a Blood & Cell Culture Midi kit (Qiagen).
Please refer to Shalem O, et al. Science. 2014;343:84–87 for detailed protocol. Two rounds of PCR were performed. For the first round, 100 µg of genomic DNA from Ctrl or TSZ samples was subjected to 18 cycles of amplification. For the second round, different Illumina adaptors were added to the primers to barcode samples, and 5µl of first PCR product was used as template for 24 cycels of amplification. PCR products were then gel purified and quantified, followed by sequencing.

treatment_protocol: Human GECKO v2 library (Addgene, 1000000048) which contains 122,411 unique sgRNAs targeting 19,050 genes was used. Briefly, 40 µg library DNA, together with viral packaging vectors 10 µg pMD2.G and 30 µg psPAX2, was transfected into 4x 15cm plates of 293T cells at a density of 6x10e6 cells/plate. Culture media containing viruses were harvested at 48 and 72 hours and viral titer was determined. Subsequently, 3x10e7 viruses were transduced into 1x10e8 of HAP1:RIPK3:MLKL cells in 16x 15cm plates at a MOI of 0.3. Two days later, the cells were split into 64 plates and selected with 1 µg/ml puromycin for 16 days. Genomic DNA was harvested from 16 plates as the pre-treatment sample. The other 48 plates were subjected to necroptosis-induction with T/S/Z for 2 days. The cells were then changed to fresh media and recovered for 5 days. Genomic DNA from the surviving cells was harvested. Two rounds of PCR were performed to amplify inserted sgRNA sequences. PCR products were then subjected to next generation sequencing.

tag: knockout strategy

value: GeCKO V2 library

value: Treated for 48 hrs with 20ng/ml TNF, 20nM Smac-mimetic, 20mM Z-VAD-FMK (T/S/Z)

value: HAP1 haploid cells


title: P32-J0

source_name: Whole Blood


title: Traditional FAIRE in HUVEC cells - Rep 1

value: - nanodroplets


title: D6_BrmKO_high_BMP4_scRNA-seq

source_name: mouse ES cell derived cardiac progenitors

value: Day 6


title: P26-J1


title: HAP1 haploid cells, ctrl

value: no treatment


title: SH-SY5Y MINCR sample 1

value: Overexpression of MINCR


title: D6_WT_high_BMP4_scRNA-seq

value: mouse ES cell derived cardiac progenitors


title: P25-J11


title: SK-NM-C Xenograft Tissue, Rep 1

source_name: SK-NM-C tissue

value: SK-NM-C tissue


title: MCF-7 Xenograft Tissue, Rep 3


title: D6_BrmKO_normal_BMP4_scRNA-seq

value: Brm-/-


title: D6_WT_normal_BMP4_scRNA-seq


title: hsLung116N_AO

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

description:
Bulk RNA sequencing of airway organoids in expansion medium
AOvsCilM_ndata.txt

data_processing:
After quality control, mapping and counting analyses were performed using our in-house RNA analysis pipeline v2.1.0 (https://github.com/UMCUGenetics/RNASeq), based on best practices guidelines (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). Differential gene expression analysis was performed using the DESeq2 package
Genome_build: hg38
Supplementary_files_format_and_content: The data are in txt format. The table contains UMI deduplicated counts normalized between samples.

source_name: Airway organoids in AO medium

growth_protocol: Airway organoids were passaged by mechanical disruption at 1:2 to 1:4 ratios after 10–14 days of culture. Airway organoid medium (Sachs et al., 2019)  was changed every 4 days.

extract_protocol:
Total RNA was isolated from organoids that were cultured in AO medium or cilia medium for 21 days after initial growth period in AO medium using the Qiagen RNeasy Mini Kit and used for library preparation and sequencing.
Library preparation was performed with 500 ng of total input RNA using the Truseq Stranded Total RNA Kit with Ribo-Zero Human/Mouse/Rat Sets A and B (Illumina; RS-122-2201 and RS-122-2202). Library quality was checked using the Agilent High-Sensitivity DNA Kit (5067-4626) and the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific; Q32854).  Libraries were pooled to a final concentration of 2 nM.

treatment_protocol: To obtain differentiated organoid-derived cultures, organoids were grown for at least 14 days in expansion medium (AO medium) until organoids had a cystic and fully grown morphology. Half of the wells were changed into CilM medium while the other half remained in AO medium. Differentiation was performed for 21 days while changing medium twice a week into the same medium.

value: Nasal airway

value: AO medium

value: Wildtype


title: hsLung116N_CilM

description:
Bulk RNA sequencing of airway organoids in differentiation medium
AOvsCilM_ndata.txt

source_name: Airway organoids in CilM medium

value: CilM medium


title: P24-J14

value: Critical


title: P23-J0


title: hsLung111-PCD6_CilM

value: Homozygous CCDC65 mutation


title: EWS894 Xenograft Tissue, Rep 3

source_name: EWS894 tissue

value: EWS894 tissue

value: + nanodroplets


title: SK-NM-C Xenograft Tissue, Rep 3


title: D4_BrmKO_high_BMP4_scRNA-seq

source_name: mouse ES cell derived cardiac mesoderm

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: P27-J1


title: P22-J0


title: hsLung111-PCD6_AO


title: EWS894 Xenograft Tissue, Rep 2


title: SK-NM-C Xenograft Tissue, Rep 2


title: D4_WT_high_BMP4_scRNA-seq

value: wild type


title: EWS894 Xenograft Tissue, Rep 1


title: D4_BrmKO_normal_BMP4_scRNA-seq


title: P21-J2


title: hsLung108-PCD4_AO

value: Homozygous LRRC6 mutation


title: A673 Xenograft Tissue, Rep 2

source_name: A673 tissue

value: A673 tissue


title: A673 Xenograft Tissue, Rep 1


title: D4_WT_normal_BMP4_scRNA-seq


title: P1-J0


title: P19-J0


title: hsLung108-PCD4_CilM


title: UMRC-2 Xenograft Tissue, Rep 2

source_name: UMRC-2 tissue

value: UMRC-2 tissue


title: P20-J3


title: PHH3

city: Leuven

first: RUBEN

last: BOON

state: Vlaams Brabant

address: Herestraat 49

institute: KU LEUVEN

description: Biological replicate 3

data_processing:
Cutadapt v1.14 was used for trimming sequences containing the adaptor sequence, bases with low Phred scores (<20), and ambiguous bases with following parameters -m 20 -q 20,20 --max-n=0.1 .
STAR v 020201 was used for the build of the human genome index GRCh38.92. Genome fasta and gtf files were downloaded from Ensembl.
STAR v 020201 was used for read alignment to the built genome (hg38).
The featureCounts function from the RSubRead R package was used to generate the raw count matrix.
Genome_build: hg38
Supplementary_files_format_and_content: format: txt ; content: raw read counts (output from featureCounts)

source_name: Primary human hepatocytes

extract_protocol:
Trizol extraction and RNA precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, Truseq library prep kit (Illumina) was used for library preparation. NextSeq High Output Kit (1X 75 cycles) (Illumina) was used for sequencing.

value: Primary human hepatocytes

tag: transcription factor overexpression


title: PHH2

description: Biological replicate 2


title: PHH1

description: Biological replicate 1


title: UMRC-2 Xenograft Tissue, Rep 3


title: P18-J4


title: MCF7_SCL-exo_TET2_mCD_E2_Rep3

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
Library strategy: SCL-exo-seq
All ChIP-seq and SCL-exo-seq sequencing reads were mapped to hg19 with using Bowtie (Langmead et al., Genome Biol. 2009). SAMtools (Li et al., Bioinformatics 2009) generated bam files which were processed with MACS (Zhang et al., Genome Biol. 2008) to generate wig files. Peak calling followed the procedure descibed in Sérandour et al (Nucleic Acids Res., 2012).
RNA-seq reads were mapped to hg19 with Bowtie (Langmead et al., Genome Biol. 2009) and transcripts were quantified with RSEM (Li and Dewey, Bioinformatics 2011). Differentially expressed genes were identified from RNA-seq data by the R package DESeq2 (Love et al., Genome Biol. 2014) after filtering of the raw data using the R package HTSFilter (Rau et al., Bioinformatics 2013).
SCL-exo-seq reads were treated as descibed (Sérandour et al., Bio-Protoc. 2018) using the python script available at https://mycore.core-cloud.net/index.php/s/4gyZ9dLTqgo86dt on SAM files.
Genome_build: hg19

source_name: TET2 mCD cells

growth_protocol: Cells were grown in high glucose and pyruvate containing DMEM (Gibco 41966) supplemented with 10% fetal calf serum (Eurobio S116365181H), non-essential amino acids (Gibco 11140035), Penicillin-Streptomycin (Gibco 15240) and Geneticin (Gibco 11811064) at 37°C and 5% CO2.

extract_protocol:
For ChIP-seq assays, cells were fixed in 1.5% formaldehyde (Sigma F8775) for 10 min at room temperature, the reaction was stopped by the addition of glycine (100 mM). Cells were lysed in lysis buffer (150 mM Tris-HCl pH 8.1, 10 mM EDTA, 0.5% Empigen BB, 1% SDS, protease inhibitor cocktail (Roche 5056489) and sonicated using a bioruptor (Diagenode, 15 min 30 sec ON /30 sec OFF). Sonicated chromatin was incubated at 4°C overnight with antibodies (ERa: mix of TE111.5D11 from Abcam and HC-20 from Santa Cruz Biotechnology, H3K4me3: 04-745 from Millipore, H3K27me3: 07-449 from Millipore) in IP buffer (2.8 ng/mL yeast tRNA, 20 mM Tris-HCl, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, proteases inhibitor cocktail). Complexes were recovered after 4h incubation with 45 mL protein A- and 15 mL protein G-conjugated sepharose beads slurry at 4°C. Beads were washed in washing buffers WB1 (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1 % Triton X-100), WB2 (20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1 % Triton X-100), WB3 (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 1 % deoxycholate, 1 % NP-40), WB4 (10 mM Tris-HCl pH 8, 1mM EDTA) and DNA fragments were eluted in extraction buffer (1% SDS, 0.1 M NaHCO3). For RNA-seq, total RNAs were extracted with the RNeasy Plus kit from QIAGEN including a DNase digestion step, and mRNA were enriched by selection with poly-dT beads. For SCL-exo-seq, genomic DNA was extracted using reagents from the DNeasy Blood and Tissue kit (QIAGEN).
ChIP-seq libraries (2 replicates) were generated with DNA fragments from 6 to 9 pooled individual ChIP experiments and the TruSeq kit from Illumina according to the manufacturer's protocol. For RNA-seq, three replicate libraries of each condition (TruSeq stranded mRNA, Illumina) were prepared and sequenced (single reads of 75 bases) at the Genomic Paris Center facility (Paris, France). For each SCL-exo experiment, 8 micrograms of gDNA were sonicated two times 7 min (30 sec ON /30 sec OFF) and two times 14 min (30 sec ON /30 sec OFF) with a bioruptor (Diagenode). Glucosylation and biotinylation of 5hmC were performed with the Hydroxymethyl Collector kit (Active Motif), followed by on beads-exonuclease digestion of the captured fragments and library preparation (TrueSeq library preparation kit, Ilumina). For normalization purpose, 400 pg of 5hmC Control DNA provided by the Hydroxymethyl Collector kit were added to each sample as spike-in. Libraries from 3 independent SCL-exo experiments were sequenced with a HiSeq 1500 (Illumina) by the GEH facility (Rennes, France).

treatment_protocol: For RNA-seq, ChIP-seq and SCL-exo-seq, cells were kept for 48h in phenol-red-free DMEM (Gibco 31052) supplemented with 2.5% dextran-charcoal-treated fetal calf serum (Eurobio S116365181W), glutamine, sodium pyruvate, non-essential amino acids, Penicillin-Streptomycin and Geneticin at 37°C and 5% CO2 before treatment with 10 nM estradiol or 0.1% EtOH.

value: MCF-7-derived breast cancer cells

tag: genotype/variation

value: TET2 mCD

value: 10 nM estradiol for 50 minutes


title: MCF7_SCL-exo_TET2_mCD_EtOH_Rep3

tag: treatment

value: 0.1% EtOH for 50 minutes


title: P15-J1


title: MCF7_SCL-exo_TET2_mCD_EtOH_Rep2

tag: cell line


title: 786-O Xenograft Tissue, Rep 2

source_name: 786-O tissue

tag: cell type

value: 786-O tissue


title: MCF7_SCL-exo_TET2_mCD_EtOH_Rep1


title: UMRC-2 Xenograft Tissue, Rep 1


title: MCF7_SCL-exo_TET2_mCD_E2_Rep1


title: HC6X_3

description: Biological replicate 3

source_name: Stem cell derived hepatocytes

value: HNF1A, FOXA3, PROX1, SIRT1, PGC1A, AMPK


title: P14-J1

value: Critical


title: HLC_3

description: Biological replicate 3


title: P17-J4


title: 786-O Xenograft Tissue, Rep 3


title: P13-J1


title: MCF7_SCL-exo_TET2_CD_EtOH_Rep3

source_name: TET2 CD cells

value: TET2 CD


title: 786-O Xenograft Tissue, Rep 1


title: MCF7_SCL-exo_TET2_CD_EtOH_Rep1


title: HLC_1

description: Biological replicate 1


title: HC6X_MED5_4

description: Biological replicate 4


title: P16-J1


title: MCF7_SCL-exo_TET2_CD_EtOH_Rep2


title: MCF7_SCL-exo_TET2_CD_E2_Rep2


title: C9-R

value: Non-critical


title: HC6X_2

description: Biological replicate 2


title: P12-J4


title: HC6X_1

description: Biological replicate 1


title: HC6X_MED5_1

description: Biological replicate 1


title: MCF7_SCL-exo_TET2_mCD_E2_Rep2


title: HC6X_MED5_3

description: Biological replicate 3


title: HLC_2

description: Biological replicate 2


title: AID_deficient_patient_P4

first: Brice

last: Laffleur

address: 2 avenue du professeur Léon Bernard

institute: INSERM

data_processing:
Library strategy: DNA-seq
Data were processed as previously described (PMID: 28416601) / parameters for analysis by the Csreport algorithm are provided in the Material and Methods section of the manuscript

source_name: Tonsil

extract_protocol:
DNA was extracted using GenElute Mammalian Genomic DNA miniprep Kit (Sigma Aldrich)
Ion Xpress plus Fragment Library Kit (Thermo Fisher Scientific); Chip 540 on the Ion S5 sequencer (Life Technologies)

value: Primary B cells

value: AID-deficient


title: MCF7_SCL-exo_EV_EtOH_Rep3

source_name: EV cells

value: EV


title: MCF7_SCL-exo_TET2_CD_E2_Rep3


title: P10-J8


title: HC6X_MED5_2

description: Biological replicate 2


title: HC3X_2

description: Biological replicate 2

value: HNF1A, FOXA3, PROX1


title: C7-R


title: MCF7_SCL-exo_TET2_CD_E2_Rep1


title: P11-J1


title: AP_24h

type: RNA

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Mouse whole genome 44K, Agilent Technologies) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: 24hr after AP treatement

label_protocol: The isolated RNA was amplified and labeled using a Low RNA Input Linear Amplification kit PLUS following manufacturer’s instructions (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Human primary bronchial epithelial cells were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA). The cells were grown in bronchial epithelial growth medium (ATCC) at 37°C under a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was purified from primary bronchial epithelial cells using TRIzol according to the manufacturer’s instructions (Thermo Fisher Scientific, Rockford, IL, USA). RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA integrity >7.0 were included in microarray analysis.

treatment_protocol: Aspergillus oryzae protease solution purchased from Sigma-Aldrich was diluted in serum-free medium at a concentration of 50 ng/mL. Primary bronchial epithelial cells were grown in 60-mm dishes and treated with AP. After 1 h of stimulation, the cells were washed using Phosphate-buffered saline with the detergent Tween 20 (PBS-T) and then incubated for 1, 6, 12, 18, and 24 h.

value: primary bronchial epithelial cells


title: MCF7_SCL-exo_EV_EtOH_Rep1


title: AID_deficient_patient_BE-MI P5

source_name: PBMC


title: HC3X_1

description: Biological replicate 1


title: C27-R

source_name: Whole Blood


title: 18-HepG2-MED5-S12

description: Biological replicate 3

source_name: HepG2 hepatoma cells


title: MCF7_SCL-exo_EV_EtOH_Rep2


title: C25-R


title: MCF7_SCL-exo_EV_E2_Rep2


title: AID_deficient_patient_EL P3


title: C6-R


title: C26-R


title: HC3X_3

description: Biological replicate 3


title: human_healthy-control2

value: healthy


title: AP_con

source_name: control


title: C8-R


title: AP_12h

source_name: 12hr after AP treatement


title: AP_6h

source_name: 6hr after AP treatement


title: AP_1h

source_name: 1hr after AP treatement


title: AID_deficient_patient_LE


title: 17-HepG2-MED5-S11

description: Biological replicate 2


title: Colletotrichum orbiculare in vitro rep 3 [Co_VH-3]

city: Yokohama

first: Pamela

last: Gan

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Plant Sciences

country: Japan

institute: RIKEN

data_processing:
Base calling was performed using Illumina's CASAVA v1.8 software.
Raw fastq reads were mapped to the C. orbiculare genome using STAR version 2.6.0a with the setting --alignIntronMax 1000.
Read counts were obtained using Rsubread (v1.32.2) with the settings: isGTFAnnotationFile = TRUE, GTF.featureType = “exon”, GTF.attrType = “Parent”
Genome_build: Colletotrichum orbiuclare version 2 (accession number AMCV02000000)
Supplementary_files_format_and_content: Matrix table with raw counts for every transcript and every sample
Supplementary_files_format_and_content: Matrix table with RPKM for every transcript and every sample

organism: Colletotrichum orbiculare

source_name: Colletotrichum orbiculare hyphae grown in vitro in potato dextrose broth

growth_protocol: Colletotrichum conidia at were inoculated onto Nicotiana benthamiana

extract_protocol:
RNA was extracted using QIAgen RNeasy plant mini kit.
RNAseq libraries were prepared using Illumina's TruSeq Sample Prep kit according to the manufacturer's protocol. PolyA+RNA was extracted from total RNA, reverse transcribed and ligated with Illumina adapters. Libraries were sequenced on an Illumina HiSeq 2000 machine to 50 bp in single-read mode.

treatment_protocol: Three biological replicates each were prepared of Colletotrichum orbiculare infecting Nicotiana benthamiana at 1, 3 and 7 days post-inoculation of conidia on leaf by brush inoculation at a concentration of 1E6 conidia/ml. In vitro grown hyphae grown in potato dextrose broth maintained at 25 degrees C and ungerminated conidia were collected as negative controls.

tag: developmental stage

value: In vitro

tag: tissue type

value: Hyphae


title: C23-R


title: human_healthy-control1


title: 16-HepG2-MED5-S10

description: Biological replicate 1


title: MCF7_SCL-exo_EV_E2_Rep1

value: MCF-7-derived breast cancer cells


title: MCF7_ER_TET2_mCD_EtOH_Rep1

data_processing:
All ChIP-seq and SCL-exo-seq sequencing reads were mapped to hg19 with using Bowtie (Langmead et al., Genome Biol. 2009). SAMtools (Li et al., Bioinformatics 2009) generated bam files which were processed with MACS (Zhang et al., Genome Biol. 2008) to generate wig files. Peak calling followed the procedure descibed in Sérandour et al (Nucleic Acids Res., 2012).
RNA-seq reads were mapped to hg19 with Bowtie (Langmead et al., Genome Biol. 2009) and transcripts were quantified with RSEM (Li and Dewey, Bioinformatics 2011). Differentially expressed genes were identified from RNA-seq data by the R package DESeq2 (Love et al., Genome Biol. 2014) after filtering of the raw data using the R package HTSFilter (Rau et al., Bioinformatics 2013).
SCL-exo-seq reads were treated as descibed (Sérandour et al., Bio-Protoc. 2018) using the python script available at https://mycore.core-cloud.net/index.php/s/4gyZ9dLTqgo86dt on SAM files.
Genome_build: hg19

value: TET2 mCD


title: C22-R


title: MCF7_SCL-exo_EV_E2_Rep3

value: 10 nM estradiol for 50 minutes


title: MCF7_ER_TET2_mCD_E2_Rep2


title: C20-R


title: MCF7_ER_TET2_CD_EtOH_Rep2

value: 0.1% EtOH for 50 minutes


title: MCF7_ER_TET2_mCD_E2_Rep1


title: C24-R


title: Colletotrichum orbiculare in vitro rep 1  [Co_VH-1]


title: C21-R


title: Colletotrichum orbiculare conidia rep 2 [Co_C-2]

source_name: Colletotrichum orbiculare conidia

value: Conidia


title: Colletotrichum orbiculare in vitro rep 2 [Co_VH-2]


title: MCF7_ER_TET2_mCD_EtOH_Rep2


title: Colletotrichum orbiculare conidia rep 3 [Co_C-3]


title: 14-HepG2-CTL-S8

description: Biological replicate 2


title: 6XMED3_3

description: Biological replicate 3

value: HNF1A, FOXA3, PROX1, SIRT1, PGC1A, AMPK


title: C1-R


title: 6XMED3_2

description: Biological replicate 2


title: 6XMED3_1

description: Biological replicate 1


title: MCF7_ER_TET2_CD_E2_Rep2


title: 13-HepG2-CTL-S7

description: Biological replicate 1


title: C18-R


title: 3XMED3_3

description: Biological replicate 3


title: Colletotrichum orbiculare conidia rep 1 [Co_C-1]


title: 15-HepG2 CTL-S9

description: Biological replicate 3


title: C19-R


title: MCF7_ER_TET2_CD_E2_Rep1


title: AP_18h

source_name: 18hr after AP treatement


title: Colletotrichum orbiculare in planta at 7 DPI rep 3 [Co_7DPI-3]

source_name: Colletotrichum orbiculare infecting Nicotinana benthamiana at 7 DPI

value: 7 dpi in planta

value: Nicotiana benthamiana infected leaf


title: Colletotrichum orbiculare in planta at 7 DPI rep 1 [Co_7DPI-1]


title: 3XMED3_1

description: Biological replicate 1


title: C17-R

value: Non-critical


title: Colletotrichum orbiculare in planta at 7 DPI rep 2 [Co_7DPI-2]


title: VAT3

first: Zuoyou

last: Ding

state: Shanghai

address: 180, Fenglin Road

institute: ZhongShan  Hospital affiliated Fudan University

data_processing:
Illumina Casava1.8 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
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: visceral adipose tissues

extract_protocol:
Adipose tissues were removed, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: visceral adipose tissues

tag: subject status

value: cancer-associated cachexia patient


title: 3XMED3_2

description: Biological replicate 2

source_name: Stem cell derived hepatocytes


title: MCF7_ER_EV_EtOH_Rep2

value: EV


title: MCF7_ER_EV_E2_Rep1


title: C16-R

data_processing:
Raw sequencing data was trimmed with Skewer v0.2.1 and alignment was performed with  STAR v2.5.3a, using SAMtools v0.1.19 for sorting/indexing
Quantification of gene expression was performed using RSEM (v1.3.0) with GENCODE annotation v25
TMM normalization with edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: log2 normalized TMM counts, with samples as columns and genes as rows


title: C15-R


title: MCF7_ER_EV_EtOH_Rep1


title: Colletotrichum orbiculare in planta at 3 DPI rep 3 [Co_3DPI-3]

source_name: Colletotrichum orbiculare infecting Nicotinana benthamiana at 3 DPI

value: 3 dpi in planta

value: Nicotiana benthamiana infected epidermal peel


title: MCF7_ER_TET2_CD_EtOH_Rep1

source_name: TET2 CD cells

value: TET2 CD


title: Colletotrichum orbiculare in planta at 3 DPI rep 2 [Co_3DPI-2]


title: Colletotrichum orbiculare in planta at 1 DPI rep 3 [Co_1DPI-3]

source_name: Colletotrichum orbiculare infecting Nicotinana benthamiana at 1 DPI

value: 1 dpi in planta


title: MCF7_Input_TET2_mCD

source_name: TET2 mCD cells


title: C12-R


title: C13-R


title: MCF7_Input_TET2_CD


title: Colletotrichum orbiculare in planta at 3 DPI rep 1 [Co_3DPI-1]


title: VAT1


title: SAT2

source_name: subcutaneous adipose tissues

value: subcutaneous adipose tissues


title: Colletotrichum orbiculare in planta at 1 DPI rep 1 [Co_1DPI-1]


title: MCF7_ER_EV_E2_Rep2

source_name: EV cells

value: MCF-7-derived breast cancer cells


title: Colletotrichum orbiculare in planta at 1 DPI rep 2 [Co_1DPI-2]


title: C10-R

source_name: Whole Blood


title: SAT1


title: SAT3


title: MCF7_Input_EV


title: SPC-RPM-548

status: Public on Oct 25 2021

city: Melbourne

middle: James

last: Gough

state: Victoria

address: 27-31 Wright Street, Clayton

department: Centre for Cancer Research

country: Australia

institute: Hudson Institute of Medical Research

description: Primary cell line derived from primary lung tumour mass

data_processing:
Quality of raw sequencing data confirmed by FastQC
Sequenced reads were mapped to mm10 using HISAT2
Counts per million reads mapped was determined from BAM files by featurecounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Primary lung cancer cell line

growth_protocol: Cells were extracted from mouse lungs at ethical endpoint by enzymatic digest and cultured in advanced RPMI+1%FCS until tumour spheroids formed. Cells were validated by flow cytometry.

extract_protocol:
Total RNA was extracted using Bioline kit.
RNA quality was verified by Agilent 2100 and 1ug of RNA was used in library construction by BGI.

tag: strain/genotype

tag: ad5-cre innoculum


title: VAT2


title: C14-R

extract_protocol:
PAXgene Blood RNA Kit (Qiagen)
TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina)
151bp paired-end


title: SPC-RPM-561


title: SPC-RPM-554


title: SPC-RPM-545


title: RPM-429


title: CGRP-RPM-386


title: CGRP-RPM-393


title: RPM-305


title: CGRP-RPM-419


title: CC10-RPM-563


title: C11-R


title: CGRP-RPM-381


title: CC10-RPM-555


title: CC10-RPM-553


title: MFA_shC-9

city: Kunming

first: Tianqing

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: Kunming University of Science and Technology

data_processing:
The sequencing qualities of 166 scRNA-seq profiles were examined with the FASTQC.
The scRNA-seq data were aligned to Macaca fascicularis genome (macFas5) with HISAT2 (v 2.1.0).
The alignment results of HISAT2 in the SAM format were converted to BAM format and sorted with SAMTools (v 1.1).
Quantified transposable element (TEs) and gene expression of single-cell sequencing data using scTE software.And annoted wtih http://ftp.ensembl.org/pub/release-102/gtf/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_5.0.102.gtf.gz  http://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/rmsk.txt.gz
Single cell dimensionality reduction and visualization use R package seurat (v4.0.1)
Genome_build: macFas5
Supplementary_files_format_and_content: transposable element (TEs) and gene expression (Counts) of single-cell sequencing data were stored in seurat object cymonkeyshRNAdim15r3dim15TrBEPIPrE.rds.

organism: Macaca fascicularis

source_name: embryo

growth_protocol: Oocytes were collected by laparoscopic follicular aspiration approximately 32–35 h after rhCG administration. Follicular contents were added to HEPES-buffered Tyrode’s albumin lactate pyruvate (TALP) medium containing 0.3% bovine serum albumin (BSA) (Sigma-Aldrich, USA) at 37°C. Oocytes were stripped of cumulus cells by pipetting after a brief exposure (< 1 min) to hyaluronidase (0.5 mg/mL) in TALP-HEPES to visually select nuclear-based mature metaphase II (MII; first polar body present) oocytes. The mature oocytes were immediately subjected to intracytoplasmic sperm injection and then cultured in  Connaught Medical Research Laboratories (CMRL) -1066 media (Thermo Fisher Scientific, USA) containing 10\% fetal bovine serum (FBS, Gibco, USA) at 37°C in 5% CO2. Fertilization was confirmed by the presence of a second polar body and two pronuclei. Zygotes were then cultured in chemically defined hamster embryo culture medium-9 containing 10% FBS at 37°C in 5% CO2 to allow embryo development. The culture medium was replaced every other day until the blastocyst stage.

extract_protocol:
Isolation of single cells. The embryos were washed in PBS for 3 times, washed in 0.25% trypsin (T4799; SigmaAldrich) 2 times, incubated with 0.25% trypsin for around 15 min at 37 °C, and terminated by DFBS. Embryo was dissociated into single cells by repeated pipetting and dispersed in 1% DFBS/PBS. A single cell was pipetted into a PCR tube. All operations above were performed under the Nikon SMZ645 microscopy.
The synthesis and amplification of full-length cDNAs were performed following Smart-seq2 protocol4. Briefly, single cells were washed in DPBS (Gibco 14190-144) and picked into lysis buffer using Pasteur pipettes under a dissecting microscope. Reversetranscription reactions and pre-amplification were performed using SuperScript II (Invitrogen 18064-014) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), respectively. The quality of the cDNAs were evaluated by Bioanalyzer 2100. Library construction and sequencing were performed by Annoroad Gene Technology (http://www.annoroad.com/). Pair-end sequencing was performed on Illumina X-ten platform.

tag: day

value: embryo invitro day 7

tag: shRNA

value: shscramble

tag: embryotag

tag: celltype

value: EPI


title: MFA_shC-89

value: TrB


title: MFA_shC-96


title: MFA_shC-8


title: MFA_shC-7


title: MFA_shC-6


title: MFA_shC-75


title: MFA_shC-53


title: MFA_shC-73

value: PrE


title: MFA_shC-57


title: MFA_shC-4


title: MFA_shC-47


title: MFA_shC-5


title: MFA_shC-43


title: RPM-309

first: Daniel


title: MFA_shC-40


title: MFA_shC-41


title: MFA_shC-3


title: MFA_shC-33


title: MFA_shC-34


title: MFA_shC-35


title: MFA_shC-38


title: MFA_shC-32


title: MFA_shC-36


title: MFA_shC-31


title: MFA_shC-30


title: MFA_shC-28


title: MFA_shC-2


title: MFA_shC-29


title: MFA_shC-27


title: MFA_shC-21


title: MFA_shC-26


title: MFA_shC-20


title: MFA_shC-24


title: MFA_shC-23


title: MFA_shC-22


title: MFA_shC-12


title: MFA_shC-14


title: MFA_shC-19


title: MFA_shC-18


title: MFA_shC-113


title: MFA_shC-11


title: MFA_shC-15


title: MFA_shC-13


title: MFA_shC-111


title: MFA_shC-105


title: MFA_shC-10


title: MFA_shC-109


title: MFA_sh346-9


title: MFA_shC-100


title: MFA_sh346-7


title: MFA_sh346-76


title: MFA_sh346-70


title: MFA_sh346-6


title: MFA_sh346-69


title: MFA_sh346-62


title: MFA_sh346-60


title: MFA_sh346-5


title: MFA_sh346-61


title: MFA_sh346-56


title: MFA_sh346-58


title: MFA_sh346-53


title: MFA_sh346-54


title: MFA_sh346-55


title: MFA_sh346-52


title: MFA_sh346-47


title: MFA_sh346-48


title: MFA_sh346-4


title: MFA_sh346-79


title: MFA_sh346-44


title: MFA_sh346-39


title: MFA_sh346-41


title: MFA_sh346-40


title: MFA_sh346-38


title: MFA_sh346-37


title: MFA_sh346-46


title: MFA_sh346-31


title: MFA_sh346-30


title: MFA_sh346-33


title: MFA_sh346-2


title: MFA_sh346-34


title: MFA_sh346-25


title: MFA_sh346-24


title: MFA_sh346-23


title: MFA_sh346-22


title: MFA_sh346-21


title: MFA_sh346-1


title: MFA_sh346-3


title: MFA_sh346-20


title: MFA_sh346-19


title: MFA_sh346-18


title: MFA_sh346-15


title: MFA_sh346-17


title: MFA_sh346-16


title: MFA_sh346-13


title: MFA_sh346-14


title: MFA_sh346-10


title: MFA_sh346-11


title: MFA_sh346-12


title: MFA_GE727


title: MFA_GE725


title: MFA_GE724


title: MFA_GE723


title: MFA_GE715


title: MFA_GE713


title: MFA_GE711


title: MFA_GE709


title: MFA_GE707


title: MFA_GE706


title: MFA_GE703


title: MFA_GE708


title: MFA_G82


title: MFA_GE702


title: MFA_GE728


title: Cortical neurons, KO_1 (RNA-Seq)

city: Rochester

first: Tatsuaki

last: Kurosaki

state: NY

address: 601 Elmwood Avenue, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using FastP version 0.20.1 with parameters "–length_required 35 –cut_front_window_size 1 –cut_front_mean_quality 13 –cut_front –cut_tail_window_size 1 –cut_tail_mean_quality 13 –cut_tail -w 8 -y –r -j".
Cleaned reads were mapped to the Mus musculus reference genome (GRCm38.p6 + Gencode-M25 Annotation) using STAR_2.7.6a and parameters "–twopass Mode Basic –runMode alignReads –outSAMtype BAM SortedByCoordinate –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical".
Gene-level read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (Gencode M22) and parameters "-s 2 -t exon -g gene_name".
Differential expression analysis was performed using DESeq2-1.22.1 with an adjusted P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Genome_build: GRCm38.p6 + Gencode-M25 Annotation
Supplementary_files_format_and_content: text file with raw gene counts for all reference genes

source_name: cerebral cortex

growth_protocol: Cerebral cortical tissues were removed from WT or Fmr1-KO P1 pups and dissociated using papain protease (Worthington) and mechanical trituration. Dissociated cells were plated on 5ng/ml laminin/poly-L lysine substrate (Thermo Fisher Scientific) at 4.2×104 cells/cm2 and cultured for 2 days in Neurobasal/B27 Plus Medium (Thermo Fisher Scientific) supplemented with 1× Penicillin-Streptomycin Solution (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted and purified using TRIzol reagent following manufacturer’s instructions (Thermo Fisher Scientific).
For RNA-seq library preparation using RNA from P1 cortical cells after culturing for 2 days, RNA concentration and quality were evaluated using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer 2100 (Agilent), respectively. RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and 200 ng of RNA following manufacturer’s instructions. The quantity and quality of libraries were measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific) and a 5300 Fragment Analyzer System (Agilent), respectively.

value: Cortical neurons

tag: tissue

value: cerebral cortex

tag: strain

tag: genotype

value: mouse one-day old (P1) cortical neurons cultured two-days in vitro (2DIV)


title: Cortical neurons, KO_2 (RNA-Seq)


title: Cortical neurons, KO_3 (RNA-Seq)


title: MFA_G79

last: Li


title: MFA_GE712


title: MFA_G74


title: MFA_G77


title: Cortical neurons, WT_2 (RNA-Seq)

value: wild type


title: Cortical neurons, WT_1 (RNA-Seq)


title: Cortical neurons, WT_3 (RNA-Seq)


title: Neuro-2A cells, p_UPF1_IP_3 (RIP-Seq)

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using FastP version 0.20.0 with parameters "–length_required 35 –cut_front_window_size 1 –cut_front_mean_quality 13 –cut_front –cut_tail_window_size 1 –cut_tail_mean_quality 13 –cut_tail -w 8 -y –r -j".
Cleaned reads were mapped to the Mus musculus reference genome (GRCm38.p6 + Gencode-M22 Annotation) using STAR_2.7.0f and parameters "–twopass Mode Basic –runMode alignReads –outSAMtype BAM Unsorted –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical".  Transcript-level reads were quantified with Salmon-0.13.1 using default parameters.
Differential expression analysis was performed using DESeq2-1.22.1 with an adjusted P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Genome_build: GRCm38.p6 + Gencode-M22 Annotation
Supplementary_files_format_and_content: text file with raw gene counts for all reference genes

source_name: Mouse Neuro-2A neuroblastoma cells

growth_protocol: N2A mouse neuroblastoma cells  were cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12, Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (VWR).

extract_protocol:
Cellular RNAs bound by p-UPF1 were immunoprecipitated using anti-p-UPF1 and Dynabeads Protein A magnetic beads (Thermo Fisher Scientific). The RNAs in bead-bound RNA p-UPF1 complexes were digested to be primarily 100 nts by incubation for 30 min at 4°C with RNase I (1U/l; Thermo Fisher Scientific). After extensive washing, bound complexes were eluted using IP elution buffer, and RNA fragments were purified using TRIzol Reagent (Thermo Fisher Scientific) and then separated in 6M urea 6% polyacrylamide in parallel with a DynaMarker Prestain Marker for Small RNA (BioDynamics Laboratory). Small-range RNAs (~25-50 nts) were excised from 6M urea 6% polyacrylamide and agitated overnight at 4°C in RNA extraction buffer (20 mM Tris, 300mM sodium acetate, 2 mM EDTA, 0.2 % v/v SDS). RNAs were eluted from 6M urea 15% polyacrylamide gel using a Coaster Spin-X column (Corning) and further purified using TRIzol Reagent followed by ethanol precipitation. In parallel, control IPs using rabbit IgG were performed. Additional control samples were prepared without IP. Purified 25-50-nt RNA fragments were treated with recombinant shrimp alkaline phosphatase (New England Biolabs) to remove 3'-phosphates and subsequently phosphorylated at 5'-hydroxyl groups using T4 polynucleotide kinase (New England Biolabs).
Sequencing libraries were generated using the NEBNext Small RNA Library Prep Kit (New England Biolabs) and 100 ng of fragmented total or immunoprecipitated N2A-cell RNA, which was ligated to 3'- and 5'-adaptors as specified by manufacturer. cDNA was synthesized, and libraries were generated using 12 PCR cycles. Library quantity and quality were assessed as described above for RNA-seq. Library fragments between 125−200 basepairs (considering that the adaptors added 120 basepairs) were size-selected using PippinHT (Sage Science) after electrophoresis in a 3% agarose gel.

treatment_protocol: Cells were treated with 200 nM okadaic acid (Sigma) for 2 hr.

value: Neuro-2A (ATCC, CCL-131)

value: Mouse neuroblastoma

tag: rip antibody


title: MFA_G72


title: MFA_G73


title: MFA_G69


title: Neuro-2A cells, p_UPF1_IP_2 (RIP-Seq)


title: MFA_GE704


title: Neuro-2A cells, p_UPF1_IP_1 (RIP-Seq)


title: Neuro-2A cells, rIgG_IP_3 (RIP-Seq)

value: rabbit IgG


title: Neuro-2A cells, rIgG_IP_2 (RIP-Seq)


title: Neuro-2A cells, rIgG_IP_1 (RIP-Seq)


title: MFA_G80


title: MFA_G42


title: Neuro-2A cells, Input_3 (RIP-Seq)


title: Neuro-2A cells, Input_2 (RIP-Seq)


title: MFA_G25


title: MFA_G32


title: MFA_G1P7


title: MFA_G65


title: Neuro-2A cells, Input_1 (RIP-Seq)


title: MFA_G1P6


title: mexR*-Stationary

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: mexR*. Early stationary growth phase in LB liquid cultures.

data_processing:
The quality of sequences were analyzed and trimmed using FastQC software.
The alignment of sequences and gene expression quantification were carried out using the "CLC Genomics Workbench" software (QIAGEN) using default parameters for reverse strand specificity. Only reads from “forward” fastq files were used in this step.
The numeric value of gene expression was normalized to Reads Per Kilobase of gene per million Mapped reads (RPKM). Subsequently, a cut-off value of 1 was added to each RPKM (RPKM + 1) in order to minimize the misleading fold change values caused by RPKMs close to 0 (Charles D. Warden et al., 2013).
Genome_build: NC_002516
Supplementary_files_format_and_content: Processed_RPKM.xlsx: Excel file containing RPKM values for all genes, calculated as described. Several IDs, synonyms and annotations per gene are included.

organism: Pseudomonas aeruginosa

growth_protocol: All strains were carried out in 100 ml glass-flasks containing 25 ml of Lysogeny Broth (LB) Lennox (Pronadisa) and routinely cultured at 37 °C with shaking. Overnight cultures of P. aeruginosa were washed and diluted in LB to an OD600 of 0.01. They were incubated up to exponential phase of growth (OD600 = 0.6) and diluted again to an OD600 of 0.01. Then, the cultures were grown to reach the exponential (OD600 = 0.6) or early stationary phase of growth (OD600 = 2.5).

extract_protocol:
Total RNA was obtained as describedm in Schuster et al. (2003) using the RNeasy mini kit (QIAGEN).
RNA samples were sequenced at the "Centro Nacional de Análisis Genómico" (CNAG), Barcelona (Spain). Ribosomal RNA was removed using "RiboZero rRNA Removal kit for Bacteria" (CNAG). To generate the libraries, 2 μg of RNA were treated with "TruSeq RNA sample preparation kit" (Illumina) combined with a specific strand labelling using dUTPs (Sultan, M., et al., 2012). The sequencing in 2 x 75 pair-end format with Illumina technology was performed.

treatment_protocol: The samples for RNA sequencing were treated with “RNAProtect Bacteria Reagent” (QIAGEN) following the manufacturer's instructions.

value: JFL30 (mexR*)

tag: genotype/variation

value: MexAB-OprM overexpressing mutant

tag: type of culture

value: Planktonic

tag: medium of culture

value: Lysogeny broth

tag: growth phase

value: Early stationary


title: mexR*-Exponential

description: mexR*. Exponential growth phase in LB liquid cultures.

value: Exponential


title: MFA_G49

value: embryo invitro day 7

value: shscramble


title: WT(PAO1)-Stationary

description: Wild Type. Early stationary growth phase in LB liquid cultures.

value: Wild Type


title: MFA_G18

value: TrB


title: MFA_G16

value: EPI


title: MFA_G11


title: WT(PAO1)-Exponential

description: Wild Type. Exponential growth phase in LB liquid cultures.


title: MFA_G1P4