title: HDF

description: This sample is identical to GSM2308280.


title: p5 n/Entr

status: Public on Sep 20 2019

type: SRA

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer v.0.0.14), then mapped to hg19 whole genome using tophat2 v.2.0.9
Read count were calculated using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: dermal fibroblast cells

growth_protocol: HDF cells were cultured with DMEM including 10% FBS, and 1% penicillin/streptomycin at 37 oC in an atmosphere of 5% CO2. Culture of hNSC was suspension cultured in StemPro® NSC SFM (Gibco) supplemented with 2 mM GlutaMAX™-I Supplement (Gibco), 6 U/mL heparin (Sigma-Aldrich, St. Louis, MO, USA), and 200 µM ascorbic acid (Sigma) at 37 oC in an atmosphere of 5% CO2.  And n/Entr cells were cultured with ultrasound treated hNSC culture medium

extract_protocol:
RNA was isolated using Trizol reagent. The construction of library was performed using SENSE 3’ mRNA-Seq Library Prep Kit from 1 ug of total RNA.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit standard protocols.

treatment_protocol: The HDF cells were directly exposed to ultrasound stimulus (20 KHz, 1.0 W/cm2) for 5 sec. And then, 2 x 105 cells of ultrasound treated cells were cultured with ultrasound-treated media (20 KHz, 5.0 W/cm2, for 10min) on the 35mm petri dish.

tag: tissue

value: skin

tag: passage


title: EndoC-βH1 cells preparation 4 under cytokine treatment

city: Badalona

first: Mireia

last: Ramos-Rodríguez

address: Carretera de Can Ruti, camí de les escoles s/n

department: Division of Endocrinology

country: Spain

institute: Germans Trias i Pujol University Hospital and Research Institute

data_processing:
Sequencing reads were mapped to the Homo sapiens genome (version GRCh37/hg19) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options the GENCODE 18 annotation of genes transcripts. The Tophat mapper reports all mappings and split-mappings.
Aligned reads were assigned to Gencode version 18 gene annotation using htseq-count (version 0.6.1p1) with default parameters. The number of reads that mapped to each genes is provided.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard tab separated .txt format. For each sample the corresponding file contains the counts of the number of reads that mapped to each gene. The summary table (matrix.htse-count.txt) contains the count for each genes for all the sammples.

molecule: polyA RNA

source_name: EndoC-βH1 cells

growth_protocol: Human insulin-producing EndoC-βH1 cells (Scharfmann et al., 2014) were grown on matrigel/fibronectin (100 and 2 μg/mL, respectively) coated plates and cultured in DMEM medium as previously described

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides.
mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.

treatment_protocol: EndoC-βH1 cells where exposed or not to a cocktail of pro-inflammatory cytokines IFN-γ and IL-1β for 48 hours. The cytokine concentrations used were those described in previous dose-response experiments (see paper methods)

tag: cell line

tag: cell type

value: Human insulin producing cell line

tag: condition

value: pro-inflammatory cytokine exposure


title: EndoC-βH1 cells preparation 3 under cytokine treatment


title: EndoC-βH1 cells preparation 5 under cytokine treatment


title: EndoC-βH1 cells preparation 5 under control condition

value: control


title: EndoC-βH1 cells preparation 3 under control condition


title: SAM24342204 Intestine Small Normal KO

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

organism: Mus musculus

source_name: RNA from e16.5 mouse intestine

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen)
and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

tag: developmental stage

tag: primary tissue

value: Intestine Small

tag: tissue diagnosis

value: Normal

tag: group

value: Casp8 wildtype MLKL knockout (Casp8 WT MLKL KO)


title: HEK-293T_siHNRNPH1_rep2

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: HEK-293T cells treated with siHNRNPH1, replicate 2

data_processing:
RNA libraries were prepared and sequenced on a NextSeq 500 Sequencer
RNA-Seq reads were aligned to the hg19 reference genome using TopHat v2.0.13
FPKM values was calculated using Cufflinks and ucsc genome browser gene level coordinates.
RSEM tools were utilized for the analysis of the expression level of protein-coding EWSR1 transcript variants from targeted RNA-Seq data.
Reads counts across the signature junction of each transcript variant were extracted and calculated using an in-house splicing junction analysis tools developed in Python (v 3.6.0).
Genome_build: hg19

source_name: HEK-293T cells, 48h siHNRNPH1

growth_protocol: Both cell lines were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

extract_protocol:
RNA was extracted with Maxwell® 16 LEV simplyRNA Cells Kit. RNA quantity was measured using the Nanodrop.
Poly(A)-selected RNA from three biological replicates and sequencing libraries were created using TruSeq Stranded mRNA LT Sample Preparation Kit as described by manufacturer’s instructions (Illumina, San Diego, CA). Then, we incorporated a capture step using fosmid clones of full genomic coverage for EWSR1 (WIBR2-3436F12; GRCh37/hg19 chr22:29662533-29698996) or EWS-FLI1 (WIBR2-3436F12 and WIBR2-1520I3; GRCh37/hg19 chr11:128640224-128682737). Capture bait was prepared by Klenow extension of biotinylated random hexamers priming on purified fosmid DNA template. The prepared bait was bound to streptavidin-coated Dynabeads C1 (Invitrogen) and hybridized to denatured, pooled libraries for 48 hours. The enriched library was recovered after a series of stringency washes by PCR using primers homologous to library end-sequences (Forward: 5'-AATGATACGGCGACCACC-3’, Reverse: 5’-CAAGCAGAAGACGGCATA-3’). Libraries were quantified by qPCR (Kapa Biosystems, Wilmington, MA).

treatment_protocol: To generate enriched EWSR1 and EWS-FLI1 profiles for each cells, total RNA was purified from siRNA-transfected each cells. We transfected cells in six-well plates (1.35E-5 cells per well) using RNAi-max and 20 nM siRNA. Cells were harvested 48 hours post siRNA-transfection.

value: Human Embryonic Kidney

tag: treatment


title: EndoC-βH1 cells preparation 2 under cytokine treatment


title: wt_68h_sRNA_setB

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
Wild Type Gravid Adults
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel. WAGO class 22G-RNA annotation was based on (Phillips et al 2012).
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

organism: Caenorhabditis elegans

source_name: Whole worms, gravid adults (68h, 20 C)

growth_protocol: Animals were grown on NGM plates containing the E. coli strain OP50. Animals undergoing pos-1 RNAi were grown NGM RNAi plated containing the E. coli strain HT115 expressing dsRNA against the pos-1 locus.

extract_protocol:
Small RNAs (~16-28-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase or Tobacco Alkaline Phosphatase to facilitate capture of 22G-RNAs and/or oxidized with sodium periodate to distinguish methylated small RNAs (as indicated in the molecule section), followed by ligation of preadenylated 3’ adapters and non-adenylated 5’ adapters. Adapter-ligated small RNAs were size selected at each ligation step from 12-15% polyacrylamide gels. Adapter-bound small RNAs were reverse transcribed and then amplified using PCR. PCR products (~134-146 bp) were size selected from 10% polyacrylamide gels
Added to SAMPLES section.
Added to SAMPLES section.

treatment_protocol: Added to SAMPLES section.

tag: genotype


title: wt_52h_sRNA_setB

description:
Wild Type L4s
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx

source_name: Whole worms, L4 larvae (52h, 20 C)


title: henn-1_52h_sRNA_setB

description:
henn-1(pk2295) Mutant L4s
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx

value: henn-1(pk2295) III


title: EndoC-βH1 cells preparation 1 under cytokine treatment


title: HEK-293T_siNeg_rep1

description: HEK-293T cells treated with siNeg, replicate 1

source_name: HEK-293T cells, 48h siNeg

value: siNeg


title: EndoC-βH1 cells preparation 1 under control condition


title: Ligation_bias_test_input

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

data_processing:
Library strategy: m6ACE-sesq
Basecalls performed using FASTQ Generation v1.0.0.Fastq sequences were first trimmed of 5’ and 3’ adapter sequences and poly(A) tails using Cutadapt. The 8-mer ‘N7B’ (N=A/C/G/T, B=C/G/T) UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed. Reads were mapped to the methylated spike-in using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates. Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR<0.1, padj<0.05). Based on read-start patterns observed from m6ACE-seq of methylated spike-ins, we considered identified “sites” that were 1-4 nucleotides upstream of another identified significant Rm6AC site or “sites” found within clustered read-starts to be m6ACE-seq false-positives and filtered them out. To identify m6A or m6Am sites that were differentially methylated between sample conditions, we calculated the RML of each site in each sample: The read-start counts at positions -4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions -51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions -21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition. A site was denoted as differentially methylated if the average RML differs between sample conditions with a log2fold-change (LFC) cutoff of 2.0 (for methylase-KO or demethylase-OE induced RML reduction) or 1.0 (for demethylase-KO induced RML accumulation), as well as a one-tailed T-test p-value cutoff of <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of forward reads. Text files comparing RML of WT versus gene-KO/KD samples.

organism: synthetic construct

source_name: Synthetic oligonucleotide

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37oC, and in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin, and used within passage number 3-20.

extract_protocol:
Total RNA was isolated using Trizol-LS.
Poly(A) RNA was purified using Poly(A)Purist Mag kit (Thermofisher AM1922) according to manufacturer’s instructions. Poly(A) RNA was fragmented using RNA fragmentation buffer (Ambion AM8740) and dephosphorylated at its 3’ end with T4 PNK (NEB M0201) for 30min at 37oC. 5’ phosphorylation was then initiated by adding 1mM ATP and incubating for 30min at 37oC. 3’ ligation was then performed as previously described 2, where 5’-adenylated,3-dideoxyC DNA adapters were ligated with truncated T4 RNA ligase 2 (NEB M0242) in 1X ATP-free T4 RNA ligase buffer [50mM Tris pH 7.5, 60µg/ml BSA, 10mM MgCl2, 10mM DTT, 12.5% PEG8000] for 2hr at 25oC. 3’-ligated methylated RNA spike-in (Table S1) was added to ligated Poly(A) RNA and the mixture was denatured for 5min at 65oC before incubating for 2min on ice. This denatured RNA mixture was incubated overnight at 4oC with anti-m6A antibody (Synaptic Systems 202003) in 1X IP buffer [150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL CA-630 (Sigma I8896)] supplemented with RNasin Plus (Promega N2611). In parallel, Protein-A-dynabeads (Life Technologies 10002D) was blocked overnight at 4oC in 1X IP buffer supplemented with 0.5mg/ml BSA (Sigma A7906). The iced antibody-RNA mixture was crosslinked with 0.15J/cm2 254nm UV radiation six times. 1% of the antibody-RNA mixture was set aside as “input” and the rest (designated as “m6ACE”) was mixed with decanted BSA-blocked Protein-A-dynabeads for 1.5hr at 4oC. Beads bound with crosslinked RNA were then washed with the following cold buffers in this order: Wash buffer 1 [1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 2 [0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 3 [1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA], TE [10mM Tris pH 8, 1mM EDTA] and finally 10mM Tris pH 8. m6ACE RNA was subjected to 5’ to 3’ exonuclease treatment with XRN-1 (NEB M0338) for 1hr at 37oC. The m6ACE RNA-bead mixture was then washed with Wash buffer 1, Wash buffer 2, Wash buffer 3, TE and 10mM Tris pH 8. Both input and m6ACE RNAs were reverse crosslinked in elution buffer [1%SDS, 200mM NaCl, 25mM Tris pH 8, 2mM EDTA, 1mg/ml Proteinase K (Thermo Scientific EO0491)] for 1.5hr at 50oC. RNAs were ethanol-precipitated and ligated to 5’adapters (Table S1) with T4 RNA ligase (Ambion AM2140) for 16hr at 16oC. Reverse transcription primer (Table S1) was annealed (72oC 2min, ice 2min) and reverse transcription was performed with SuperscriptIII (Invitrogen 18080) for 1hr at 50oC, with the reaction stopped by incubating for 15min at 70oC. The cDNA was used for PCR amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and Truseq PCR primers. Finally, primer-dimer and adapter-dimers were removed with AMpure XP beads before undergoing PE75 sequencing on the Illumina Nextseq platforms.

tag: genotype/variation

tag: passage number

tag: antibody

value: none (input)


title: wt_embryos_sRNA_setB

description:
Wild Type Embryos
Polyphosphatase treated small RNAs
Embryos were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx

source_name: Embryos, egg preps (20 C)


title: Merged UMI-4C TNFSF10 cytokine-treated

state: Please Selec

library_source: genomic

data_processing:
Reads from biological replicates (different human islet samples) were merged before the analysis.
Data was processed using umi4cPackage (https://bitbucket.org/tanaylab/umi4cpackage) as described in their vignette, with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files (adj) are a 3 column tab-delimited table with headers: fragment end 1 coordinates (fend1), fragment end 2 coordinates (fend2), UMI count (count)

molecule: genomic DNA

source_name: Human pancreatic islets

extract_protocol:
Formaldehyde crosslinked human islets (estimated ~4 million individual cells) were treated with ice-cold lysis buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 1% TX-100, 0.5% IGEPAL-CA-630, Sigma; 5mM EDTA, AppliChem; 1X protease inhibitor cocktail, Millipore) and permeabilized with SDS (Millipore) and TX-100. Nuclei were digested with DpnII (New England Biolabs) for 16h at 37ºC. Afterwards, more DpnII was added for 4h and ligated with T4 DNA ligase (Promega) at 16ºC overnight. Cross-link was reversed by overnight incubation with Proteinase K at 65°C. Next, after 30 min incubation with 30 µl of 10 mg/ml RNase A at 37°C, DNA was purified by phenol/chloroform and ethanol precipitation. DNA was then resuspended in 10 mM Tris-HCl pH 8 and 5 ug aliquots were sonicated by Covaris S2 to fragment sizes in the range of 450-550 bp. Sonicated DNA was next incubated for 30 min at 20ºC with 20 µl 10× end-repair buffer and 10 µl end-repair mix (NEB E6050S). The reaction was next cleared by 2× AmpureXP beads (Agencourt AMPure XP, Beckman Coulter) and eluted in 75 µl EB (10 mM Tris-HCl pH 8). A-tailing was performed on the elute by adding 10 µl NEB buffer 2, 4 µl Klenow fragment (NEB M0212L) and 10 µl 10 nM dATP 20 min at 37 ºC and 20 min at 75ºC to inactivate the reaction. DNA was next dephosphorylated with 2 µl calf intestinal alkaline phosphatase (NEB M0290S) and incubated at 50°C for 60 min and immediately purified by 2x AmpureXP beads. Illumina forked adaptors were added (final concentration 0.4 µM) and incubated with 80 µl quick ligase buffer and 5 µl of Quick Ligase (NEB M2200S) for 20 min at 25°C. DNA was next denatured at 96ºC for 5 min, moved to ice for 5 min and then purified by 0,8x AmpureXP beads to release the non-ligated strand of the adaptor. Denatured DNA was quantified by Qubit (ssDNA HS Assay, Q32851, Invitrogen).
200 ng of DNA were used for library preparation by nested PCR. The first PCR reaction was performed with 10 µl GoTaq Flexi Buffer, 3 µl MgCl2 25mM, 1 µl dNTP 10 mM, 2 µl US bait primer and 2 µl Illumina universal primer 10 µM (0,4 µM final concentration each primer) and 1 µl GoTaq (Promega, M5005) with the following program: 2 min 95°C, 20 cycles of 30 s 95°C, 30 s 56°C and 60 s 72°C and final extension of 5 min 72°C. After the first PCR reaction, the DNA was purified with 1× AmpureXP beads, and 31 µl of the elute was used to perform a second PCR reaction following the same conditions as the first one but using the DS bait primer and 17 amplification cycles instead of 20. Finally, DNA was purified by 0,8x AmpureXP beads. To increase molecular complexity, each library was obtained by pooling 5-10 PCRs per viewpoint.
UMI-4C

value: IFN-γ + IL-1β 48h

tag: bait name

tag: bait coordinates


title: henn-1_embryos_2_sRNA_setH

description:
henn-1(pk2295) Mutant Embryos
Polyphosphatase treated small RNAs
Embryos were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setH_raw_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel. WAGO class 22G-RNA annotation was based on (Phillips et al 2012). piRNA annotation was based on WormBase release WS230.
Raw counts table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230


title: EndoC-βH1 cells preparation 4 under control condition


title: henn-1_embryos_3_sRNA_setH


title: henn-1_embryos_1_sRNA_setH


title: Merged UMI-4C rs78037977 cytokine-treated


title: LPS246 Vector-5

city: Philadelphia

first: M.

middle: Celeste

last: Simon

state: PA

address: 421 Curie Blvd

department: AFCRI

institute: University of Pennsylvania

data_processing:
Sequencer used was HiSeq 4000 with HCS (HiSeq Control Software) version 3.4.0.38 and RTA version 2.7.7
Basecalls (bcl files) were converted to fastq files using software bcl2fastq version v2.17.1.14
raw data was aligned to GRCh38 with STAR which was also used to count reads per gene in gencode 26
Genome_build: GRCh38.p10, gene models from genecode version 26
Supplementary_files_format_and_content: raw (non-normalized) counts per gene

source_name: liposarcoma

growth_protocol: Cells were cultured in DMEM medium, supplemented with 10% serum and 2 mM L-glutamine.

extract_protocol: Total RNA was isolated from cell lysates using RNeasy Mini Kit (Qiagen), followed by standard QC pipeline by Novogene Corporation.

treatment_protocol: LPS246 cells expressing TetO-FBP2 were evenly seeded on 9 wells. 5 wells were treated with vehicle and 4 wells were treated with doxycycline to induce FBP2 expression for 48 hours.

value: LPS246 liposarcoma cell line

tag: treatment 1

value: Constitutively express TetO-FBP2

tag: treatment 2

value: PBS


title: LPS246 Vector-3


title: wt_embryos_2_sRNA_setH

description:
Wild Type Embryos
Polyphosphatase treated small RNAs
Embryos were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setH_raw_counts_table.xlsx

extract_protocol:
Small RNAs (~16-28-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase to facilitate capture of 22G-RNAs and/or oxidized with sodium periodate to distinguish methylated small RNAs (as indicated in the molecule section). Libraries were then prepared according to the NEBNext® Multiplex Small RNA kit protocol. PCR products (~134-146 bp) were size selected from 10% polyacrylamide gels
Added to SAMPLES section.
Added to SAMPLES section.


title: Merged UMI-4C SOCS1 cytokine-treated


title: LPS246 Vector-4


title: wt_embryos_1_sRNA_setH


title: EndoC-βH1 cells preparation 2 under control condition


title: henn-1_pos-1_PolyP_sRNA_setE

description:
henn-1(pk2295) Gravid Adults Undergoing pos-1 RNAi
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setE_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from pos-1 were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel.
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

source_name: Whole worms, gravid adults (48h, 25 C)


title: wt_pos-1_PolyP_Ox_sRNA_setE

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setE_counts_table.xlsx


title: LPS246 Vector-2


title: henn-1_embryos_sRNA_setB

description:
henn-1(pk2295) Mutant Embryos
Polyphosphatase treated small RNAs
Embryos were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx


title: LPS246 Vector-1


title: Merged UMI-4C IRF1 cytokine-treated


title: wt_embryos_3_sRNA_setH


title: RDE-1_henn-1_IP_2_sRNA_setG

description:
henn-1(pk2295);GFP::rde-1 GFP IP Fraction, Rep 2
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were  incubated with anti-FLAG antibody (Sigma F1804-50UG) followed by protein G magnetic beads (BioRad 161-4023) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel. miRNA annotations were based on miRBase release 20.
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

value: henn-1(pk2295);rde-1(cmp133[(gfp + loxP + 3xFLAG)::rde-1]) V


title: wt_pos-1_PolyP_sRNA_setE

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setE_counts_table.xlsx


title: Merged UMI-4C LAMP3 cytokine-treated


title: RDE-1_henn-1_IP_1_sRNA_setG

description:
henn-1(pk2295);GFP::rde-1 GFP IP Fraction, Rep 1
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were  incubated with anti-FLAG antibody (Sigma F1804-50UG) followed by protein G magnetic beads (BioRad 161-4023) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: Ligation_bias_test

value: anti-M6A Synaptic Systems 202003


title: Merged UMI-4C IFIT1 cytokine-treated


title: RDE-1_henn-1_input_2_sRNA_setG

description:
henn-1(pk2295);GFP::rde-1 Input Fraction, Rep 2
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: LPS246 FBP2-5

value: doxycycline


title: LPS246 FBP2-4


title: RDE-1_henn-1_input_1_sRNA_setG

description:
henn-1(pk2295);GFP::rde-1 Input Fraction, Rep 1
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: Merged UMI-4C RSAD2 cytokine-treated


title: Merged UMI-4C IFIH1 cytokine-treated


title: RDE-1_input_2_sRNA_setG

description:
GFP::rde-1 Input Fraction, Rep 2
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx

value: rde-1(cmp133[(gfp + loxP + 3xFLAG)::rde-1]) V


title: henn-1_pos-1_PolyP_Ox_sRNA_setE

description:
henn-1(pk2295) Gravid Adults Undergoing pos-1 RNAi
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setE_counts_table.xlsx


title: Merged UMI-4C GBP1 cytokine-treated


title: LPS246 FBP2-1


title: WAGO-1_IP_sRNA_setC

description:
GFP::wago-1 GFP IP Fraction
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were incubated with anti-GFP mAb-agarose (MBL, D153-8) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setC_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel. WAGO class 22G-RNA annotation was based on (Phillips et al 2012). CSR-1 class 22G-RNA annotation was based on (Claycomb et al 2009).
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

value: USC988[mut-16(cmp41[mut-16::mCherry + loxP]) wago-1(cmp92[(GFP + loxP + 3xFLAG)::wago-1]) I] GFP IP


title: Merged UMI-4C DOCK9 cytokine-treated


title: RDE-1_input_1_sRNA_setG

description:
GFP::rde-1 Input Fraction, Rep 1
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: HRDE-1_IP_sRNA_setC

description:
FLAG::hrde-1 IP Fraction
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were  incubated with anti-FLAG antibody (Sigma F1804-50UG) followed by protein G magnetic beads (BioRad 161-4023) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setC_counts_table.xlsx

value: FLAG::hrde-1 II


title: RDE-1_IP_1_sRNA_setG

description:
GFP::rde-1 GFP IP Fraction, Rep 1
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were  incubated with anti-FLAG antibody (Sigma F1804-50UG) followed by protein G magnetic beads (BioRad 161-4023) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: WAGO-1_input_sRNA_setC

description:
GFP::wago-1 Input Fraction
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setC_counts_table.xlsx

value: mut-16(cmp41[mut-16::mCherry + loxP]) wago-1(cmp92[(GFP + loxP + 3xFLAG)::wago-1]) I


title: 130.1-24h

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

description:
epithelial culture
sample name:
RHP5615

data_processing:
FASTQ files were mapped using STAR to UCSC human genome build GRCh38
Gene counts were obtained using featureCounts on GENCODE V24 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: genecounts_final.txt

source_name: In vitro differentiated nasal epithelial cells

extract_protocol:
 All human RNAs were analyzed on the Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA) or the Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA) for quality assessment with RNA Integrity Number (RIN) or RNA Quality score range from 6.8–9.7 and median of 9.0.
 cDNA libraries were prepared using 2 ng of total RNA and 1 L of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion®  Thermo Fisher Scientific, Waltham, MA, USA) using SMARTSeq v2 protocol
 The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA). Sixteen samples were subjected to an indexed PE sequencing run of 2   51 cycles on an Illumina HiSeq 4000 (16 samples/ lane), and 65 samples to an

treatment_protocol: Treated with influenza over timepoints

tag: donor

tag: timepoint post influenza infection


title: 130.1-48h

description:
epithelial culture
sample name:
RHP5616

growth_protocol: In vitro differentiated nasal epithelial cells

tag: cell type


title: HRDE-1_input_sRNA_setC

description:
FLAG::hrde-1 Input Fraction
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were subjected to Trizol/chloroform extraction.
sRNA_setC_counts_table.xlsx


title: 130.1-8h

description:
epithelial culture
sample name:
RHP5613

value: In vitro differentiated nasal epithelial cells


title: Merged UMI-4C CXCL11 cytokine-treated


title: henn-1_gonads_2_mRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 2
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx

data_processing:
Adapters and low-quality bases were removed using Trimmomatic v. 0.35
Trimmed reads were mapped to the C. elegans genome (Wormbase release WS230) using Star v. 2.5.0a
Reads from specific features were counted using RSEM v. 1.3.0. Differential expression analysis was done using DESeq2 v. 1.18.1.
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

source_name: Dissected gonads, gravid adults (68-70h, 20 C)

extract_protocol:
RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. Libraries were then prepared according to the NEBNext® Ultra™ II Directional RNA kit protocol. Size selection and library purification was done using AMPure XP beads.
Added to SAMPLES section.
Added to SAMPLES section.


title: henn-1_gonads_3_mRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 3
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx


title: Merged UMI-4C CMPK2 cytokine-treated


title: wt_gonads_3_mRNA_setA

description:
Wild Type Dissected Gonads, Rep 3
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx


title: 130.1-0h

description:
epithelial culture
sample name:
RHP5612


title: Merged UMI-4C CIITA cytokine-treated

value: CIITA


title: henn-1_gonads_1_mRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 1
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx


title: RDE-1_IP_2_sRNA_setG

description:
GFP::rde-1 GFP IP Fraction, Rep 2
Polyphosphatase treated small RNAs
Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were  incubated with anti-FLAG antibody (Sigma F1804-50UG) followed by protein G magnetic beads (BioRad 161-4023) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to Trizol/chloroform extraction.
sRNA_setG_counts_table.xlsx


title: LPS246 FBP2-3


title: wt_gonads_2_mRNA_setA

description:
Wild Type Dissected Gonads, Rep 2
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx


title: Merged UMI-4C ATF3 cytokine-treated


title: 122.1-48h

description:
epithelial culture
sample name:
RHP5610


title: henn-1_gonads_3_sRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 3
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. miRNA annotations were based on miRBase release 20. WAGO class 22G-RNA annotation was based on (Phillips et al 2012). CSR-1 class 22G-RNA annotation was based on (Claycomb et al 2009). piRNA annotation was based on WormBase release WS230. Differential expression analysis was done using DESeq2 v. 1.18.1.
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230


title: wt_gonads_1_mRNA_setA

description:
Wild Type Dissected Gonads, Rep 1
rRNAs Depleted mRNAs
Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
mRNA_setA_DESeq2_counts_table.xlsx


title: henn-1_gonads_2_sRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 2
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx


title: Merged UMI-4C TNFSF10 control

value: Control


title: 122.1-0h

description:
epithelial culture
sample name:
RHP5606


title: Merged UMI-4C rs78037977 control


title: 122.1-24h

description:
epithelial culture
sample name:
RHP5609


title: Merged UMI-4C DEXI cytokine-treated

value: DEXI


title: Merged UMI-4C SOCS1 control


title: wt_gonads_3_sRNA_setA

description:
Wild Type Dissected Gonads, Rep 3
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx


title: wt_gonads_2_sRNA_setA

description:
Wild Type Dissected Gonads, Rep 2
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx


title: 17.1-48h

description:
epithelial culture
sample name:
RHP5598


title: 122.1-8h

description:
epithelial culture
sample name:
RHP5607


title: henn-1_gonads_1_sRNA_setA

description:
henn-1(pk2295) Mutant Dissected Gonads, Rep 1
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx

value: henn-1(pk2295) III


title: wt_gonads_1_sRNA_setA

description:
Wild Type Dissected Gonads, Rep 1
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setA_DESeq2_counts_table.xlsx


title: rde-1_1_Ox_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 1
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: Merged UMI-4C RSAD2 control


title: rde-1_3_Ox_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 3
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: 17.1-24h

description:
epithelial culture
sample name:
RHP5597


title: rde-1_2_Ox_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 2
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: 17.1-8h

description:
epithelial culture
sample name:
RHP5595


title: wt_2_Ox_sRNA_setF

description:
Wild Type L4s, Rep 2
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: Merged UMI-4C LAMP3 control


title: wt_3_Ox_sRNA_setF

description:
Wild Type L4s, Rep 3
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: 17.1-0h

description:
epithelial culture
sample name:
RHP5594


title: rde-1_3_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 3
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: rde-1_2_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 2
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: rde-1_1_sRNA_setF

description:
rde-1(ne219) Mutant L4s, Rep 1
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_rde-1_DESeq2_counts_table.xlsx


title: 62.4-48h

description:
epithelial culture
sample name:
RHP5589


title: Merged UMI-4C IFIT1 control


title: wt_3_sRNA_setF

description:
Wild Type L4s, Rep 3
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: Merged UMI-4C IFIH1 control


title: wt_2_sRNA_setF

description:
Wild Type L4s, Rep 2
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: wt_1_sRNA_setF

description:
Wild Type L4s, Rep 1
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: 62.4-24h

description:
epithelial culture
sample name:
RHP5588


title: Merged UMI-4C GBP1 control


title: 62.4-8h

description:
epithelial culture
sample name:
RHP5587


title: Direct bisulfite

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Library strategy: SMRF-seq
Pacbio reads were pre-processed into CCS reads using Pacbio SMRT Link v6.0 (default parameters).
Raw Pacbio CCS reads were mapped using bismark v0.20.0 with the following parameters: -q --score-min L,0,-0.3 --rdg 5,3 --rfg 5,3 --ignore-quals
SMRF-seq peaks were called using a sliding window algorithm with the following parameters: minimum cytosine conversion threshold of 55% and peak length of 100bp.
DRIPc-seq reads were trimmed with fastq-mcf v2.4.4 and mapped with bowtie2 v2.2.6 (sDRIP-seq) with defaulte parameters.
Genome_build: hg19
Supplementary_files_format_and_content: GFF files were generated using sliding window algorithm; Each row represents the coordinates of an R-loop peak in a specific read (read names are specified in column 9). DRIPc-seq bedGraph files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; Scores (Column 4) indicate tag per million (x30).

source_name: NTERA-2 cell line

extract_protocol:
Pelleted cells were lysed with Proteinase K and 20% SDS. Nucleic acids were extracted using phenol:chloroform:isoamyl alcohol and phase separated using phase lock tubes. Samples were then digested using restriction enzyme cocktails then treated with sodium bisulfite in a non-denaturing way.
SMRTbell libraries were constructed using Pacific Bioscience's amplicon template preparation protocol.

value: Direct bisulfite treatment


title: Merged UMI-4C DOCK9 control


title: DRIP enriched and no RNaseH

value: +S9.6 -RNaseH


title: 62.4-0h

description:
epithelial culture
sample name:
RHP5586


title: DRIP independent


title: Merged UMI-4C DEXI control


title: 121.2-48h

description:
epithelial culture
sample name:
RHP5581


title: DRIP enriched


title: wt_1_Ox_sRNA_setF

description:
Wild Type L4s, Rep 1
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setF_wt_DESeq2_counts_table.xlsx


title: 121.2-24h

description:
epithelial culture
sample name:
RHP5580


title: All samples combined

value: All samples combined


title: Merged UMI-4C CMPK2 control


title: Merged UMI-4C CXCL11 control


title: 121.2-8h

description:
epithelial culture
sample name:
RHP5579


title: Merged UMI-4C CIITA control


title: 121.2-0h

description:
epithelial culture
sample name:
RHP5578


title: Merged UMI-4C ATF3 control


title: Merged UMI-4C IRF1 control


title: 96.1-48h

description:
epithelial culture
sample name:
RHP5577


title: Persister polysome m6A-IP

city: Villejuif

first: Shensi

last: SHEN

address: 114 Rue Edouard Vaillant

country: France

institute: Gustave Roussy Institute

description: messenger RNA

data_processing:
Illumina Casava1.4 software used for basecalling.
m6A-seq reads were aligned to the hg38 genome assembly using EasyAlign
Quanlity control was performed and visualized with multiQC
Genome_build: hg38
Supplementary_files_format_and_content: Aligned Bam file were generated for m6A peak distribution analysis

source_name: A375 melanoma

growth_protocol: A375 melanoma cells were cultured according to the ATCC protocol

extract_protocol:
Trizol extraction of total RNA and polysomal associated RNA was performed according to the manufacturer's instructions. The total RNA was then sent to LC Science, Texas for the m6A-seq
RNA libraries were prepared for sequencing using standard Illumina protocols
m6A antibody immunoprecipitation followed by high-throughput RNA sequencing

treatment_protocol: One day after spliting A375 cells were treated for 3 days with DMSO or Vemurafenib and combimetinib

value: melanoma


title: Persister polysome input

description: messenger RNA


title: Persister ctrl input rep2

description: messenger RNA


title: Parental polysome input

description: messenger RNA


title: Persister ctrl m6A-IP rep2

description: messenger RNA


title: Persister ctrl input rep1

description: messenger RNA


title: Persister ctrl m6A-IP rep1

description: messenger RNA


title: Parental polysome m6A-IP

description: messenger RNA


title: Parental ctrl m6A-IP rep2

description: messenger RNA


title: 96.1-24h

description:
epithelial culture
sample name:
RHP5576


title: Parental ctrl m6A-IP rep1

description: messenger RNA


title: Human islet cytokine-treated rep HI40 [ChIP-Seq]

description: IFN-γ + IL-1β 48h

data_processing:
Reads were aligned using Bowtie2 (version 2.3.4.1) with default parameters.
Reads mapping to ENCODE blacklist regions or to non-autosomal chromosomes were discarded. Duplicates were removed using Picard Mark Duplicates  (version 2.5.0)
Peaks were called with MACS2 (version 2.1) callpeak using the following parameters “--broad --broad-cutoff 0.1 –nomodel”.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files generated from BAM files. First, BAM files were RPKM-scaled and converted to bedgraph using bedtools (version 2.26) genomeCoverageBed.  Finally, bedGraph files were converted to BigWig using bedGraphToBigWig UCSC tool.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using standard Illumina protocols

value: IFN-gamma + IL-1beta  48h

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: Parental ctrl input rep1

description: messenger RNA


title: Human islet cytokine-treated rep HI37 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: Human islet cytokine-treated rep HI19 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: Parental ctrl input rep2

description: messenger RNA


title: 96.1-0h

description:
epithelial culture
sample name:
RHP5574


title: 96.1-8h

description:
epithelial culture
sample name:
RHP5575


title: pFC53 control plasmid

description: plasmid DNA

organism: Escherichia coli

source_name: bacterial cells

value: -S9.6 -RNaseH


title: 61.1-48h

description:
epithelial culture
sample name:
RHP5573


title: Human islet cytokine-treated rep HI22 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: pLjUBI:GFPcontrol_forLBD_rep3

city: Cologne

first: Tak

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description:
lbdox_rpkm.txt
18028-0014

data_processing:
The quality of the fastq files were validated with fastqc
Sequence reads were trimmed for adapter and repetitive sequences with Cutadept
The resulting reads from the raw fastq data were quality controlled and and mapped to the M. truncatula reference genome version 4.0  using R package STAR
The FPKM (Fragments per kilobase per million mapped reads) and RPKM (Reads per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread
Genome_build: Mt4.0v1

organism: Medicago truncatula

source_name: regenerated root structure

growth_protocol: Seeds were scarified, surface sterilized with 10% (v/v) bleach solution, stratified for 3 days at 4 °C and germinated on water agar plates. Plants were grown in sterile conditions in controlled environment rooms at 22 °C (80% humidity, 16 h light/8 h dark, 300 μmol m2 s-1 light intensity) on filter paper-lined agar media in sealed plates

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, Germantown, USA), the RNase free DNase kit (Qiagen, Germantown, USA) was used to remove genomic DNA.
RNA-Seq libraries were prepared with the Illumina TruSeq® Stranded mRNA HT kit

tag: tissue

value: regenerated root structure

value: wild type ecotype jemalong cultivar Jester transformed with pLjUBI:GFP

tag: treatments

value: no treatment


title: pLjUBI:GFPcontrol_forLBD_rep4

description:
lbdox_rpkm.txt
18028-0015


title: pLjUBI:GFPcontrol_forLBD_rep2

description:
lbdox_rpkm.txt
18028-0013


title: pLjUBI:GFPcontrol_forLBD_rep1

description:
lbdox_rpkm.txt
18028-0012


title: Human islet control rep HI40 [ChIP-Seq]

description: Control


title: pLjUBI:LBD11_rep3

description:
lbdox_rpkm.txt
18028-0007

value: wild type ecotype jemalong cultivar Jester transformed with pLjUBI:LBD11


title: pLjUBI:LBD11_rep2

description:
lbdox_rpkm.txt
18028-0006


title: pLjUBI:LBD16_rep3

description:
lbdox_rpkm.txt
18028-0003

value: wild type ecotype jemalong cultivar Jester transformed with pLjUBI:LBD16


title: Human islet control rep HI19 [ChIP-Seq]

description: Control


title: pLjUBI:LBD16_rep2

description:
lbdox_rpkm.txt
18028-0002


title: pLjUBI:LBD16_rep4

description:
lbdox_rpkm.txt
18028-0004


title: Human islet control rep HI22 [ChIP-Seq]

description: Control


title: 33-3 48h

description:
epithelial culture
sample name:
RHP3959

value: In vitro differentiated nasal epithelial cells


title: pLjUBI:LBD16_rep1

description:
lbdox_rpkm.txt
18028-0001


title: Human islet control rep HI37 [ChIP-Seq]

description: Control


title: pLjUBI:LBD11_rep1

description:
lbdox_rpkm.txt
18028-0005


title: EndoC-βH1 cytokine-treated  rep 4 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: 33-3 8h

description:
epithelial culture
sample name:
RHP3957


title: latroot_72h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0054

source_name: 2-3mm segment of root

tag: time

value: 72h of lateral root initiation

value: 2-3mm segment of root

value: wild type ecotype jemalong cultivar Jester

value: turned 135° for 12 hours


title: EndoC-βH1 cytokine-treated  rep 3 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: latroot_72h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0056


title: 33-3 0h

description:
epithelial culture
sample name:
RHP3956


title: EndoC-βH1 cytokine-treated  rep 2 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: latroot_72h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0053


title: latroot_72h_control_rep4

description:
latroot_rpkm.txt
NG-135_0052


title: latroot_72h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0055


title: S02-1 48h

description:
epithelial culture
sample name:
RHP3955


title: EndoC-βH1 cytokine-treated  rep 1 [ChIP-Seq]

description: IFN-γ + IL-1β 48h


title: latroot_72h_control_rep3

description:
latroot_rpkm.txt
NG-135_0051


title: 61.1-24h

description:
epithelial culture
sample name:
RHP5572


title: S02-1 8h

description:
epithelial culture
sample name:
RHP3953


title: 61.1-8h

description:
epithelial culture
sample name:
RHP5571


title: latroot_72h_control_rep2

description:
latroot_rpkm.txt
NG-135_0050


title: 61.1-0h

description:
epithelial culture
sample name:
RHP5570


title: latroot_72h_control_rep1

description:
latroot_rpkm.txt
NG-135_0049


title: latroot_60h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0048

value: 60h of lateral root initiation


title: EndoC-βH1 control rep 4 [ChIP-Seq]

description: Control

value: Control


title: EndoC-βH1 control rep 3 [ChIP-Seq]

description: Control


title: latroot_60h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0046


title: S19-1 48h

description:
epithelial culture
sample name:
RHP3947


title: S02-1 0h

description:
epithelial culture
sample name:
RHP3952


title: EndoC-βH1 control rep 2 [ChIP-Seq]

description: Control


title: latroot_60h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0047


title: latroot_60h_control_rep3

description:
latroot_rpkm.txt
NG-135_0043


title: EndoC-βH1 control rep 1 [ChIP-Seq]

description: Control


title: S19-1 8h

description:
epithelial culture
sample name:
RHP3945


title: latroot_60h_control_rep4

description:
latroot_rpkm.txt
NG-135_0044


title: latroot_60h_control_rep2

description:
latroot_rpkm.txt
NG-135_0042


title: latroot_60h_control_rep1

description:
latroot_rpkm.txt
NG-135_0041


title: latroot_48h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0040

value: 48h of lateral root initiation


title: Human islet cytokine-treated rep HI44

data_processing:
Reads were trimmed to match 49 bp with fastx_trimmer.
Reads were aligned using Bowtie2 (version 2.3.4.1) with default parameters.
Reads mapping to ENCODE blacklist regions or to non-autosomal chromosomes were discarded. Duplicates were removed using Picard Mark Duplicates  (version 2.5.0)
Peaks were called with MACS2 (version 2.1) callpeak using the following parameters “-q 0.05 --nomodel --shift -100 --extsize 200”.
Genome_build: GSE123404
Supplementary_files_format_and_content: BigWig files generated from BAM files. First, BAM files were RPKM-scaled and converted to bedgraph using bedtools (version 2.26) genomeCoverageBed.  Finally, bedGraph files were converted to BigWig using bedGraphToBigWig UCSC tool.

extract_protocol:
Nuclei from 50,000 cells were isolated and then lysed to extract DNA.
ATAC-seq libraries were prepared using standard Illumina protocols

value: IFN-gamma + IL-1-beta 48h


title: latroot_48h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0039


title: DRIPc-seq RNaseA treated

value: +RNase A


title: Human islet cytokine-treated rep HI42


title: Human islet control rep HI44


title: latroot_48h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0037


title: latroot_48h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0038


title: latroot_48h_control_rep4

description:
latroot_rpkm.txt
NG-135_0036


title: Human islet control rep HI42


title: latroot_48h_control_rep2

description:
latroot_rpkm.txt
NG-135_0034


title: HCT116_S15_BrdU

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

data_processing:
Library strategy: Repli-Seq
The fastq reads for G1 WGS control and BrdU pull down libraries for S1-S16 are aligned to hg38 for 3 human cell lines and mm10 for 2 mouse cell lines. The resulting sam files are dduplicated. The log2 ratio between RPM of BrdU pull-down and that of G1 WGS was calculated for each S phase fraction, which was subsequently used to construct a matrix consisting of 16 rows where each row represented an S phase fraction ranging from S1 to S16 and each column represented a 50kb genomic bin. The matrix is subsequently Gaussian smoothed with a lambda of 1 and scaled such that the column sum for each bin amounts to 100.
Genome_build: hg38,mm10
Supplementary_files_format_and_content: The final data matrix consists of 3 rows indicating genomic bins and 16 rows where each row represents a S phase fraction from S1 to S16 and the values represent percentage of replication for the corresponding bin during the corresponding S phase fraction.

source_name: human colon cancer cells

growth_protocol: H1 and H9 cells were cultured in mTeSR1 (StemCell Technologies #85850) on hESC-qualified Matrigel (Corning #354277) -coated dishes according to WiCell instruction. For the maintenance and expansion, cells were detached using ReLeSR (StemCell Technologies #95872). When the cell reached approximately 70% confluent, cells were pulse-labeled with 400uM BrdU for 30 minutes. To obtain single-cell suspension easily, the BrdU-labeled WA01 and WA09 cells were harvested using Gentle Cell Dissociating Reagent (StemCell Technologies #07174). HCT116 cells were cultured in McCoy’s 5A  medium supplemented with 10% FBS according to ATCC’s instruction.  F121-9 mouse mouse embryonic stem cell was cultured in 2i media on gelatin-coated dish as described in (PMID:29735606). F121-9 differentiation to NPC was performed using RHB-A (TakaraBio #Y40001) as described in (PMID:29735606) for 10 days. F121-9 ESC and NPC were pulse-labeled with 400uM BrdU for 30 minutes and harvested using ESGRO Complete Accutase (Millipore Sigma #SF006). NPC differentiation was confirmed by 1) cell morphology, 2) qPCR for marker genes; Oct4 (ESC marker), Sox1 (NPC marker), Ptn (NPC marker), Nestin (NPC marker).

extract_protocol: DNA from G1 fraction was made into whole-genome sequencing library to normalize any bias during library preparation, sequencing and sequence read mapping. DNA from S1-S16 fractions were made into repli-seq library basically as described in (PMID: 29599440) but from 80K sorted cells instead of 20K sorted cells.

treatment_protocol: When the cell reached approximately 70% confluent, asynchronously growing cells were pulse-labeled with 400uM BrdU for 30 minutes, harvested and ethanol fixed, then retroactively synchronized by FACS sorting according to the DNA content.

tag: developmental stage

value: colon cancer cells


title: HCT116_S16_BrdU


title: latroot_48h_control_rep3

description:
latroot_rpkm.txt
NG-135_0035


title: latroot_60h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0045


title: latroot_48h_control_rep1

description:
latroot_rpkm.txt
NG-135_0033


title: EndoC-βH1 cytokine-treated rep 5

tag: treatment


title: S19-1 0h

description:
epithelial culture
sample name:
RHP3944


title: HCT116_S13_BrdU


title: latroot_36h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0032

value: 36h of lateral root initiation

tag: genotype


title: EndoC-βH1 cytokine-treated rep 4


title: EndoC-βH1 control rep 5


title: HCT116_S12_BrdU


title: latroot_36h_control_rep4

description:
latroot_rpkm.txt
NG-135_0028


title: latroot_36h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0031


title: latroot_36h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0029


title: latroot_36h_control_rep2

description:
latroot_rpkm.txt
NG-135_0026


title: latroot_36h_control_rep1

description:
latroot_rpkm.txt
NG-135_0025


title: HCT116_S11_BrdU


title: HCT116_S10_BrdU


title: EndoC-βH1 control rep 4


title: latroot_24h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0023

value: 24h of lateral root initiation


title: latroot_24h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0024


title: HCT116_S9_BrdU


title: latroot_24h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0022


title: latroot_24h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0021


title: HCT116_S14_BrdU


title: DRIP enriched and RNaseH treated

value: +S9.6 +RNaseH


title: latroot_24h_control_rep4

description:
latroot_rpkm.txt
NG-135_0020

value: no treatment


title: Human islet cytokine-treated rep HI19

data_processing:
Reads were trimmed to match 49 bp with fastx_trimmer.
Reads were aligned using Bowtie2 (version 2.3.4.1) with default parameters.
Reads mapping to ENCODE blacklist regions or to non-autosomal chromosomes were discarded. Duplicates were removed using Picard Mark Duplicates  (version 2.5.0)
Peaks were called with MACS2 (version 2.1) callpeak using the following parameters “-q 0.05 --nomodel --shift -100 --extsize 200”.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files generated from BAM files. First, BAM files were RPKM-scaled and converted to bedgraph using bedtools (version 2.26) genomeCoverageBed.  Finally, bedGraph files were converted to BigWig using bedGraphToBigWig UCSC tool.

value: IFN-γ + IL-1[beta] 48h

value: Human pancreatic islets


title: HCT116_S8_BrdU


title: Human islet cytokine-treated rep HI24


title: Human islet control rep HI24


title: latroot_24h_control_rep3

description:
latroot_rpkm.txt
NG-135_0019


title: latroot_24h_control_rep2

description:
latroot_rpkm.txt
NG-135_0018


title: HCT116_S6_BrdU


title: latroot_36h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0030


title: latroot_36h_control_rep3

description:
latroot_rpkm.txt
NG-135_0027


title: latroot_12h_turned_rep4

description:
latroot_rpkm.txt
NG-135_0016

value: 12h of lateral root initiation


title: Human islet control rep HI19


title: latroot_12h_turned_rep3

description:
latroot_rpkm.txt
NG-135_0015


title: HCT116_S5_BrdU


title: latroot_12h_turned_rep2

description:
latroot_rpkm.txt
NG-135_0014


title: HCT116_S4_BrdU


title: latroot_12h_control_rep4

description:
latroot_rpkm.txt
NG-135_0012


title: HCT116_S3_BrdU


title: latroot_12h_control_rep3

description:
latroot_rpkm.txt
NG-135_0011


title: EndoC-βH1 cytokine-treated  rep 2


title: latroot_12h_control_rep2

description:
latroot_rpkm.txt
NG-135_0010


title: HCT116_S2_BrdU


title: HCT116_S7_BrdU


title: latroot_12h_control_rep1

description:
latroot_rpkm.txt
NG-135_0009


title: HCT116_S1_BrdU


title: EndoC-βH1 cytokine-treated  rep 1


title: R108_24hrs_mock_rep3

description:
R108_lbd_fpkm.txt
18144-0079

value: wild type ecotype R108

value: mock


title: R108_24hrs_mock_rep4

description:
R108_lbd_fpkm.txt
18144-0080

value: 2-3mm segment of root


title: EndoC-βH1 control rep 3


title: Human islet control rep HI22


title: HCT116_G1_WGS


title: latroot_24h_control_rep1

description:
latroot_rpkm.txt
NG-135_0017

value: wild type ecotype jemalong cultivar Jester


title: EndoC-βH1 control rep 2


title: R108_24hrs_mock_rep2

description:
R108_lbd_fpkm.txt
18144-0078


title: R108_24hrs_mock_rep1

description:
R108_lbd_fpkm.txt
18144-0077


title: R108_24hrs_S.meliloti_rep4

description:
R108_lbd_fpkm.txt
18144-0076

value: Sinorhizobium meliloti strain 2011


title: H9_S16_BrdU

source_name: human embryonic stem cells

value: embryonic stem cells


title: Human islet cytokine-treated rep HI22


title: R108_24hrs_S.meliloti_rep3

description:
R108_lbd_fpkm.txt
18144-0075


title: EndoC-βH1 control rep 1

value: Control


title: latroot_12h_turned_rep1

description:
latroot_rpkm.txt
NG-135_0013

value: turned 135° for 12 hours


title: R108_24hrs_S.meliloti_rep1

description:
R108_lbd_fpkm.txt
18144-0073


title: H9_S14_BrdU


title: MESO-MDA4

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

data_processing:
Raw sequences obtained from the Illumina platform in FASTQ format were analyzed using publicly available tools.
Quality reads were analyzed using FastQC. Due to the high quality of reads there was no need to trim of filter them.
The sequences were mapped to the GRCh38.p2 human reference genome sequence using a series of programs, including Bowtie2 for short-read mapping, and TopHat for defining exon–intron junctions.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: The expression level of each transcript was expressed as the fragments per transcript kilobase per million fragments mapped (FPKM) value, which was calculated based on the number of mapped reads using Cufflinks.

extract_protocol:
Samples were lysed in TRI Reagent (Ambion) to obtain total RNA. The RNA integrity was checked using the Agilent Bioanalyzer 2100® (Agilent Technologies, Santa Clara, CA, USA). Samples were depleted of rRNA, then RNA was sheared into smaller fragments with Covaris S220 (Covaris, Woburn, MA, USA).
The cDNA library was prepared using the Beckman SPRIworks system (Beckman Coulter Inc., Fullerton, CA, USA). Library fragments hybridize to complementary oligonucleotides, and clusters of clones are generated in the Illumina cBOT instrument (Illumina).

value: Ascitic fluid-isolated mesothelial cells from ovarian cancer


title: lbd11-16_24h_mock_rep2

description:
R108_lbd_fpkm.txt
18144-0065


title: MESO-MDA3

source_name: Ascitic fluid-isolated mesothelial cells


title: lbd11-16_24h_mock_rep1

description:
R108_lbd_fpkm.txt
18144-0064


title: H9_S13_BrdU


title: lbd11-16_24h_S.meliloti_rep4

description:
R108_lbd_fpkm.txt
18144-0063


title: MESO-MDA2


title: lbd11-16_24h_S.meliloti_rep3

description:
R108_lbd_fpkm.txt
18144-0062


title: MESO-MDA1


title: lbd16_24h_mock_rep3

description:
R108_lbd_fpkm.txt
18144-0052


title: H9_S11_BrdU


title: lbd16_24h_mock_rep4

description:
R108_lbd_fpkm.txt
18144-0053


title: H9_S12_BrdU


title: MESO-N3

source_name: Human peritoneal mesothelial cells

value: control human peritoneal mesothelial cells


title: lbd11-16_24h_S.meliloti_rep1

description:
R108_lbd_fpkm.txt
18144-0060


title: H9_S10_BrdU


title: lbd16_24h_mock_rep2

description:
R108_lbd_fpkm.txt
18144-0051


title: lbd16_24h_mock_rep1

description:
R108_lbd_fpkm.txt
18144-0050


title: R108_24hrs_S.meliloti_rep2

description:
R108_lbd_fpkm.txt
18144-0074


title: H9_S9_BrdU


title: lbd16_24h_S.meliloti_rep4

description:
R108_lbd_fpkm.txt
18144-0049


title: EndoC-βH1 cytokine-treated  rep 3


title: H9_S15_BrdU


title: MESO-N2


title: MESO-N1


title: lbd16_24h_S.meliloti_rep3

description:
R108_lbd_fpkm.txt
18144-0048


title: lbd11-16_24h_mock_rep3

description:
R108_lbd_fpkm.txt
18144-0066


title: H9_S8_BrdU


title: H9_S7_BrdU


title: lbd16_24h_S.meliloti_rep1

description:
R108_lbd_fpkm.txt
18144-0046


title: lbd16_24h_S.meliloti_rep2

description:
R108_lbd_fpkm.txt
18144-0047


title: cre1_24h_S.meliloti_rep3

description:
cre1_rpkm.txt
16090-0052

value: cre1 mutant ecotype jemalong cultivar Jester


title: lbd11-16_24h_S.meliloti_rep2

description:
R108_lbd_fpkm.txt
18144-0061


title: cre1_24h_S.meliloti_rep2

description:
cre1_rpkm.txt
16090-0051


title: H9_S6_BrdU


title: cre1_24h_mock_rep1

description:
cre1_rpkm.txt
16090-0047


title: cre1_24h_S.meliloti_rep1

description:
cre1_rpkm.txt
16090-0050


title: cre1_12h_S.meliloti_rep3

description:
cre1_rpkm.txt
16090-0046


title: cre1_12h_S.meliloti_rep1

description:
cre1_rpkm.txt
16090-0044


title: H9_S5_BrdU


title: cre1_12h_mock_rep3

description:
cre1_rpkm.txt
16090-0043


title: H9_S2_BrdU


title: cre1_12h_S.meliloti_rep2

description:
cre1_rpkm.txt
16090-0045


title: H9_S1_BrdU


title: HDF

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate methylation levels, the MBD Seq reads were mapped to the genome of Homo sapiens(hg19) using Bowtie 1.1.1.
PCR duplicates were removed with Picard Mark Duplicates (version 1.118).
Raw data (the reads for mapped in genome) were normalized by RMS (Relative Methylayion Score) each ROI region using MEDIPS package (version 1.16.0).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited table includes RMS values for each Sample and ROI

source_name: dermal fibroblast cells

extract_protocol:
1ug of gDNA was sheared to 200~400bp using the Covaris LE220 sonicator (Covaris Inc. Woburn, MA). The fragmented products were immunoprecipitated using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) following the manufacture’s recommended protocol. Briefly, Methylated DNA was isolated from fragmented whole genomic DNA by binding to the methyl-CpG binding domain of human MBD2 protein, which is coupled to paramagnetic Dynabeads® M-280 Streptavidin via a biotin linker. The methylated fragments were eluted as a single enriched population with a 2000 mM NaCl elution buffer.
DNA libraries were prepared for sequencing using MethylMiner Methylated DNA Enrichment Kit (Invitrogen).

value: skin

value: dermal fibroblast cells


title: cre1_12h_mock_rep2

description:
cre1_rpkm.txt
16090-0042


title: nin_24h_S.meliloti_rep2

description:
nin_rpkm.txt
16090-0039

value: nin mutant ecotype jemalong cultivar Jester


title: cre1_12h_mock_rep1

description:
cre1_rpkm.txt
16090-0041


title: H9_G1_WGS


title: cre1_24h_mock_rep3

description:
cre1_rpkm.txt
16090-0049


title: H9_S4_BrdU


title: cre1_24h_mock_rep2

description:
cre1_rpkm.txt
16090-0048


title: H9_S3_BrdU


title: nin_24h_mock_rep3

description:
nin_rpkm.txt
16090-0037


title: H1_S16_BrdU


title: nin_24h_mock_rep2

description:
nin_rpkm.txt
16090-0036


title: H1_S15_BrdU


title: nin_24h_mock_rep1

description:
nin_rpkm.txt
16090-0035


title: nin_12h_S.meliloti_rep3

description:
nin_rpkm.txt
16090-0034


title: nin_12h_S.meliloti_rep2

description:
nin_rpkm.txt
16090-0033


title: H1_S14_BrdU


title: nin_12h_S.meliloti_rep1

description:
nin_rpkm.txt
16090-0032


title: nin_24h_S.meliloti_rep3

description:
nin_rpkm.txt
16090-0040


title: nin_24h_S.meliloti_rep1

description:
nin_rpkm.txt
16090-0038


title: nin_12h_mock_rep3

description:
nin_rpkm.txt
16090-0031


title: H1_S13_BrdU


title: nin_12h_mock_rep2

description:
nin_rpkm.txt
16090-0030


title: nin_12h_mock_rep1

description:
nin_rpkm.txt
16090-0029


title: AML with normal karyotype (NK) AML91_nk

type: RNA

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: AML with normal karyotype (NK)

hyb_protocol: Fifteen ug mRNA was hybridized to the ABI Human Genome Survey Microarray v1

scan_protocol: DIG-labeled targets hybridize to the probes on the arrays and anti-digoxigenin-alkaline phosphatase is added to bind digoxigenin in cDNA targets. The ABI 1700 Expression Array System (ABI, U.S) was used to scan the arrays for chemiluminescence

data_processing: Signal intensity, S/N ratio (signal to noise ratio), and flags values were extracted for each array. The S/N ratio value of 3.0 and flags value of 5000 were used to exclude false positives and/or missing data. For those probes that passed the filtering criterion, the signal values were log2 transformed and normalized across arrays with quantile normalization method after control probes were removed.

label: digoxigenin (DIG)

source_name: peripheral blood

label_protocol: Labeling was done with the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit  (P/N 4340472) using 2 ug high quality total RNA

growth_protocol: Patients’ samples (peripheral blood or bone marrow) were stored in the tissue bank of the St Bartholomew’s Hospital after informed written consent was obtained.

extract_protocol: Total RNA of AML patient samples was extracted from a total of 10 - 20 x 106 thawed cells using Trizol (Gibco-BRL) purification method. RNA quality  was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).

value: Normal Karyotype (NK)

value: peripheral blood

tag: disease state

value: Acute Myeloid Leukaemia


title: AML with inv(16) AML92_inv16

description: AML with inv(16)


title: H1_S12_BrdU


title: AML with t(15;17) AML96_1517

description: AML with t(15;17)


title: AML with normal karyotype (NK) AML97_nk

description: AML with normal karyotype (NK)


title: AML with 11q23 AML98_11q23

description: AML with 11q23


title: H1_S11_BrdU


title: WT_168h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
16061-0016


title: AML with normal karyotype (NK) AML95_nk

description: AML with normal karyotype (NK)


title: AML with t(15;17) AML94_1517

description: AML with t(15;17)


title: AML with t(15;17) AML93_1517

description: AML with t(15;17)


title: WT_168h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
16061-0015


title: WT_168h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
16061-0014


title: AML with normal karyotype (NK) AML90_nk

description: AML with normal karyotype (NK)


title: WT_168h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
16061-0013


title: H1_S10_BrdU


title: AML with 11q23 AML88_11q23

description: AML with 11q23


title: AML with normal karyotype (NK) AML89_nk

description: AML with normal karyotype (NK)


title: AML with other karyotype AML87_other

description: AML with other karyotype

value: Other


title: H1_S9_BrdU


title: AML with normal karyotype (NK) AML83_nk

description: AML with normal karyotype (NK)


title: WT_168h_mock_rep1

description:
wt_mock_rpkm.txt
16061-0009

value: mock


title: WT_168h_mock_rep4

description:
wt_mock_rpkm.txt
16061-0012

value: 2-3mm segment of root


title: WT_168h_mock_rep2

description:
wt_mock_rpkm.txt
16061-0010

value: wild type ecotype jemalong cultivar Jester


title: AML with inv(16) AML86_inv16

description: AML with inv(16)


title: WT_168h_mock_rep3

description:
wt_mock_rpkm.txt
16061-0011


title: H1_S8_BrdU


title: WT_120h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
16061-0008

value: Sinorhizobium meliloti strain 2011


title: H1_S7_BrdU

value: embryonic stem cells


title: WT_120h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
16061-0006


title: AML with other karyotype AML81_other

description: AML with other karyotype


title: WT_120h_mock_rep4

description:
wt_mock_rpkm.txt
16061-0004


title: H1_S6_BrdU


title: H1_S5_BrdU


title: WT_120h_mock_rep3

description:
wt_mock_rpkm.txt
16061-0003


title: WT_96h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0095


title: WT_120h_mock_rep1

description:
wt_mock_rpkm.txt
16061-0001


title: WT_96h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0096


title: H1_S4_BrdU


title: AML with t(15;17) AML80_1517

description: AML with t(15;17)


title: WT_96h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0094


title: WT_120h_mock_rep2

description:
wt_mock_rpkm.txt
16061-0002


title: H1_S2_BrdU


title: AML with other karyotype AML75_other

description: AML with other karyotype


title: WT_96h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0092


title: AML with inv(16) AML78_inv16

description: AML with inv(16)


title: WT_96h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0093


title: H1_S3_BrdU


title: WT_96h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0091


title: WT_96h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0090


title: WT_120h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
16061-0005


title: H1_S1_BrdU


title: H1_G1_WGS


title: WT_96h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0089


title: WT_72h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0088


title: WT_120h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
16061-0007


title: WT_72h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0086


title: AML with inv(16) AML76_inv16

description: AML with inv(16)


title: WT_72h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0085


title: AML with other karyotype AML79_other

description: AML with other karyotype


title: AML with inv(16) AML74_inv16

description: AML with inv(16)


title: RIP-input-Bcell

city: Ann Arbor

first: Zhengwei

last: Zhu

address: 210 Washtenaw Ave

institute: University of Michigan

data_processing:
Illumina high-seq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
PAR-clip reads were aligned to the human genome hg19 using PARalyzer. DRIP-seq reads were analyzed using MACS2.0 program. RNA-IP reads were analyzed using Antanaviciute's M6A program.
normalized reads and clusters were combined in a csv file
Genome_build: hg19
Supplementary_files_format_and_content: Output from PARalyzer, MACS2.0, M6A viewer. Files are in excel format.

source_name: Human cultured B-cells

growth_protocol: Immortalized B cells (Coriell) were cultured to a density of 5X10^5 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin.

extract_protocol:
Beads-bound immunoprecipitates were then washed six times using cold Wash Buffer with RNase inhibitor, and incubated with protease K in presence of 1% SDS at 55°C for 30 minutes.  RNA and DNA were then extracted from supernatants using phenol:chloroform:isoamyl alcohol and precipitated using ethanol.  Precipitated RNA was digested by DNase I (DNA-free kit, Ambion).  cDNA was synthesized using random hexamer primer by Taqman Reverse Transcription Reagent kit (Applied Biosystems).
RNA from anti-SRSF1 immunoprecipitate and input RNA were prepared into RNA-seq libraries using Illumina TruSeq Stranded Total RNA Library Prep kit (Illumina, #20020596).

treatment_protocol: 2X10^7 cultured human B-cells or primary skin fibroblasts were harvested and lysed in 100 µl of Lysis Buffer with protease and RNase inhibitors.  5 µg of anti-SRSF1 antibody (ABCAM, #ab38107) ornegative control IgG (Millipore) were conjugated to Magnetic Protein A/G beads.  100 µl of cell lysate was added into 900 µl Immunoprecipitation Buffer with RNase inhibitor and incubated with 50 µl beads-antibody complex at 4°C overnight.

tag: cells

value: Human cultured B-cells

tag: passages

tag: ip-antibody

value: input


title: DRIP-input-C-cell

extract_protocol:
DNA was eluted from protein G beads using elution buffer (0.1M NaHCO3, 1% SDS).  DNA was precipitated in 0.3M NaAc, pH 5.5 and 100% EtOH.
DRIP-seq libraries were prepared from DRIP DNA and corresponding input DNA using Ovation Ultralow System (NuGen).

treatment_protocol: 5X10^6 cultured B-cells were lysed in 400 μL cell lysis buffer (50 mM PIPES, pH 8.0, 100 mM KCl, 0.5% NP-40) and nuclei were collected by centrifugation.  Nuclei pellet was resuspended in 200 μL nuclear lysis buffer (25 mM Tris-HCl, pH 8.0, 1% SDS, 5 mM EDTA).  Genomic DNA containing R-loops was then extracted by phenol:chloroform and precipitated by ethanol.  Purified material was resuspended in 200 μL IP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.01% SDS, 1% Triton X-100, 167 mM NaCl) and sonicated at 4°C in Bioruptor (Diagenode) at Hi setting (30sec on/30sec off) for 5 minutes, three times to fragments with average size of 500 bp.  3 μg of S9.6 monoclonal antibody (a gift from Dr. Stephen H. Leppla at NIH) or non-specific mouse IgG (Santa Cruz) was used for each immunoprecipitation.


title: AML with other karyotype AML71_other

description: AML with other karyotype


title: Pictilisib_IFNg_rep2.rpm

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie-1.1.1 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are normalized to reads per million (rpm) using R/Bioconductor
Supplementary_files_format_and_content: tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.

source_name: SqCC/Y1 cells

growth_protocol: SqCC/Y1 cells were grown in Dulbecco’s Modified Eagle Medium with 4.5 g/L D-glucose and L-Glutamine with 10% fetal bovine serum at 5% CO2

extract_protocol: 50,000 cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin, 0.1% Tween-20) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: SqCC/Y1 cells were treated with either DMSO, 100 ng/ul IFNg, and/or 0.5 uM Pictilisib (GDC-0941) for 48 hours

tag: agent

value: 0.5 micromolar Pictilisib and 100 ng/ul IFNg


title: AML with normal karyotype (NK) AML77_nk

description: AML with normal karyotype (NK)


title: Pictilisib_IFNg_rep3.rpm


title: WT_72h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0084


title: Pictilisib_IFNg_rep1.rpm


title: AML with other karyotype AML72_other

description: AML with other karyotype


title: WT_72h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0083


title: AML with normal karyotype (NK) AML73_nk

description: AML with normal karyotype (NK)


title: 1D n/Entr


title: NSC

source_name: neural stem cells

value: brain

value: neural stem cells


title: WT_72h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0087


title: glp-4_pos-1_PolyP_Ox_sRNA_setD

description:
glp-4(bn2) Mutant Gravid Adults (no germline) Undergoing pos-1 RNAi
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from pos-1 were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel.
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

source_name: Whole worms, gravid adults (48h, 25 C)

extract_protocol:
Small RNAs (~16-28-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase or Tobacco Alkaline Phosphatase to facilitate capture of 22G-RNAs and/or oxidized with sodium periodate to distinguish methylated small RNAs (as indicated in the molecule section), followed by ligation of preadenylated 3’ adapters and non-adenylated 5’ adapters. Adapter-ligated small RNAs were size selected at each ligation step from 12-15% polyacrylamide gels. Adapter-bound small RNAs were reverse transcribed and then amplified using PCR. PCR products (~134-146 bp) were size selected from 10% polyacrylamide gels
Added to SAMPLES section.
Added to SAMPLES section.

value: glp-4(bn2) I


title: WT_72h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0082


title: WT_72h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0081


title: Pictilisib_rep2.rpm

value: 0.5 micromolar Pictilisib


title: glp-4_pos-1_Ox_sRNA_setD

description:
glp-4(bn2) Mutant Gravid Adults (no germline) Undergoing pos-1 RNAi
Sodium periodate small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: Pictilisib_rep1.rpm


title: WT_48h_mock_rep6

description:
wt_mock_rpkm.txt
NG-112_0080


title: glp-4_pos-1_PolyP_sRNA_setD

description:
glp-4(bn2) Mutant Gravid Adults (no germline) Undergoing pos-1 RNAi
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: AML with other karyotype AML66_other

description: AML with other karyotype


title: AML with other karyotype AML65_other

description: AML with other karyotype


title: AML with normal karyotype (NK) AML70_nk

description: AML with normal karyotype (NK)


title: WT_48h_mock_rep5

description:
wt_mock_rpkm.txt
NG-112_0079


title: WT_48h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0078


title: AML with normal karyotype (NK) AML64_nk

description: AML with normal karyotype (NK)


title: DMSO_IFNg_rep3.rpm

value: 100 ng/ul IFNg


title: AML with normal karyotype (NK) AML68_nk

description: AML with normal karyotype (NK)

value: Normal Karyotype (NK)


title: DMSO_IFNg_rep1.rpm


title: DMSO_IFNg_rep2.rpm


title: AML with normal karyotype (NK) AML63_nk

description: AML with normal karyotype (NK)

value: peripheral blood


title: wt_pos-1_PolyP_Ox_sRNA_setD

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Sodium periodate and polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: WT_48h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0077


title: WT_48h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0076


title: wt_pos-1_Ox_sRNA_setD

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Sodium periodate small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: DMSO_rep2.rpm

value: DMSO


title: wt_pos-1_PolyP_sRNA_setD

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: AML with inv(16) AML59_inv16

description: AML with inv(16)

value: Acute Myeloid Leukaemia


title: Pictilisib_rep3.rpm


title: AML with normal karyotype (NK) AML60_nk

description: AML with normal karyotype (NK)


title: glp-4_pos-1_untreated_sRNA_setD

description:
glp-4(bn2) Mutant Gravid Adults (no germline) Undergoing pos-1 RNAi
Untreated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: AML with normal karyotype (NK) AML61_nk

description: AML with normal karyotype (NK)


title: WT_48h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0075

value: mock


title: AML with other karyotype AML58_other

description: AML with other karyotype

value: Other


title: henn-1_68h_sRNA_setB

description:
henn-1(pk2295) Mutant Gravid Adults
Polyphosphatase treated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setB_counts_table.xlsx

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v. 2.3.
Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3.
Reads from specific features were counted using CASHX v. 2.3. Data analysis was done using custom scripts in Python, Perl, and R, and with Excel. WAGO class 22G-RNA annotation was based on (Phillips et al 2012).
Normalized abundance table in Excel format
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230

source_name: Whole worms, gravid adults (68h, 20 C)

value: henn-1(pk2295) III


title: DMSO_rep1.rpm


title: DMSO_rep3.rpm


title: WT_48h_S.meliloti_rep6

description:
wt_inoc_rpkm.txt
NG-112_0074

value: 2-3mm segment of root

value: wild type ecotype jemalong cultivar Jester

value: Sinorhizobium meliloti strain 2011


title: WT_48h_S.meliloti_rep5

description:
wt_inoc_rpkm.txt
NG-112_0073


title: WT_PlusZn_repeat2

city: Columbus

first: Stevin

last: Wilson

state: Ohio

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Splice sites generated using HISAT2 and 'Schizosaccharomyces_pombe.ASM294v2.39.gtf' from Ensembl
Sequenced reads mapped to the S.pombe genome with parameter --dta-cufflinks
Using Samtools, converted SAM files to BAM files, and sorted them based on coordinates
FPKM values for each sample was generated using Cufflinks
Cuffdiff was used to compare gene expression across samples
Genome_build: Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: wild-type and loz1 deletion strains were grown in zinc-limited EMM supplemented with 100 mM Zn to an OD600 of ~6.0

extract_protocol:
Total RNA was isolated using the RiboPureTM RNA Purification Kit for yeast (ThermoFisher Scientific) according to the manufacturer's instructions
Library preparation and next generation sequencing performed by Beckman Coulter Genomics. RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: zn supplementation

value: yes


title: WT_PlusZn_repeat1


title: WT_48h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0072


title: Loz1-deletion_PlusZn_repeat2

value: loz1 delta


title: AML with normal karyotype (NK) AML62_nk

description: AML with normal karyotype (NK)


title: WT_48h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0071


title: WT_48h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0070


title: wt_pos-1_untreated_sRNA_setD

description:
Wild Type Gravid Adults Undergoing pos-1 RNAi
Untreated small RNAs
Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
sRNA_setD_counts_table.xlsx


title: AML with normal karyotype (NK) AML57_nk

description: AML with normal karyotype (NK)


title: WT_48h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0069


title: 29.2 WDLPS - resection

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description:
well differentiated liposarcoma
WDLPS - resection

data_processing: The expression of a specific miRNA in a sample was normalized to the median CT of all detectable miRNAs in that sample (ΔCT = CT miR-X – median CT all miRNAs in a sample). The normalized expression (ΔCT) was subsequently used to calculate the relative expression values (2^-ΔCT) for each specific miRNA. The normalized miRNA expression data were median centered to acquire relative expression values that were eventually used for clustering analyses. In the matrix templates blue cells designate flagged wells whereas green cells indicate wells with undetermined values which were arbitrarily set at Ct39.99.

label: FAM

source_name: formalin-fixed paraffin embedded tumor material

label_protocol: MicroRNA expression was determined using TaqMan® Low Density Array (TLDA) cards (A card v2.0, B card v3.0, Applied Biosystems/Thermo Fisher Scientific). Megaplex™ RT Primers (Human Pool, pool A v2.1, pool B v3.0, Applied Biosystems/Thermo Fisher Scientific) were used for cDNA synthesis, followed by a standard pre-amplification protocol using Megaplex™ PreAmp Primers (Human Pool, pool A v2.1, pool B v3.0, Applied Biosystems/Thermo Fisher Scientific). The TLDA cards were analysed using a 7900HT Real-Time PCR system (Applied Biosystems). The paired samples were processed in three batches for logistical and technical reasons, with each primary and its matching recurrent tumour being placed within the same batch.

extract_protocol: Total RNA was isolated using the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion/Life Technologies) according to manufacturer's instructions.

treatment_protocol: Patients with available tumour samples of a primary and matching first recurrent WDLPS who were treated with surgery only were included. The formalin-fixed and paraffin-embedded (FFPE) tissue blocks were obtained through PALGA, the Dutch nationwide pathology registry, and the pathology department of the Maria Skłodowska-Curie Institute-Oncology Center together with anonymized clinicopathological information. The archival tumour samples were examined by an expert pathologist to confirm the initial histopathological diagnosis and to determine the percentage of tumour cells. Only sections containing approximately 100% tumour cells were used for isolation.

value: recurrent tumor


title: 28.2 WDLPS - resection


title: 30.2 WDLPS - resection


title: 27.2 WDLPS - resection


title: WT_36h_mock_rep4

last: Lee

description:
wt_mock_rpkm.txt
NG-112_0068


title: 26.2 WDLPS - resection


title: AML with t(8;21) AML56_821

description: AML with t(8;21)


title: 25.2 WDLPS - resection


title: Loz1-deletion_PlusZn_repeat1


title: WT_36h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0067


title: WT_36h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0066


title: 24.2 WDLPS - resection


title: AML with other karyotype AML55_other

description: AML with other karyotype


title: WT_36h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0065


title: 23.2 WDLPS - resection


title: AML with other karyotype AML54_other

description: AML with other karyotype


title: WT_36h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0064


title: 22.2 WDLPS - resection


title: AML with normal karyotype (NK) AML52_nk

description: AML with normal karyotype (NK)


title: WT_36h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0063


title: AML with other karyotype AML53_other

description: AML with other karyotype


title: 20.2 WDLPS - resection


title: 21.2 WDLPS - resection


title: AML with other karyotype AML50_other

description: AML with other karyotype


title: WT_36h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0062


title: AML with other karyotype AML48_other

description: AML with other karyotype


title: 840_ CPT tube Replicate 3

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: Biological replicate 3 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.

hyb_protocol: cRNA was hybridized to SurePrint G3 Human GE v2 8x60K microarrays (Agilent Technologies) following manufacturer's instructions

scan_protocol: Slides were scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and R script v3.3 software was used to conduct the preliminary data filtration and statistical analysis.

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Low Input Quick Amp Two-Color Kit (Agilent Technologies).The labelled cRNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol:
Blood was collected and preserved in PAXgene™ RNA tubes, RNAgard® Blood Tubes and CPT tubes from eight healthy volunteers. In parallel, PBMCs were isolated from the CPT tubes following the manufacturer’s instructions.
Total RNA was extracted using PAXgene™ RNA blood miRNA kit (Qiagen, Hilden, Germany) from blood preserved in PAXgene™ RNA tubes and RNAgard® Blood Tubes following manufacturer's instructions. RNA from PBMC in Trizol (from CPT tubes) was extracted following manufacturer's instructions

tag: reference

source_name: Whole blood

tag: test


title: WT_36h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0061


title: AML with normal karyotype (NK) AML51_nk

description: AML with normal karyotype (NK)


title: 840_ RNAgard tube Replicate 2

description: Biological replicate 2 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.

value: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues


title: 840_ CPT tube Replicate 2

description: Biological replicate 2 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: 19.2 WDLPS - resection


title: 840_ PAXgene RNA tube Replicate 2

description: Biological replicate 2 of 2. RNA extracted from whole blood preserved in PAXgene RNA blood tubes.


title: 17.2 WDLPS - resection


title: 16.2 WDLPS - resection


title: AML with normal karyotype (NK) AML49_nk

description: AML with normal karyotype (NK)


title: AML with normal karyotype (NK) AML47_nk

description: AML with normal karyotype (NK)