title: PFI

description:
PFI
processed data files:
counts.txt
resTablePFI-v-C.txt

value: PFI


title: single doseH5/IVAX-1d28 (mouse ID 2.2)

status: Public on Jun 26 2021

type: genomic

city: Irvine

first: David

middle: Huw

last: Davies

state: CA

address: 812 Medical Plaza Drive, Med Surge II, Rm 376

department: Physiology & Biophysics

country: USA

institute: UC Irvine

description:
SAMPLE 19
Fig. 2b

hyb_protocol: Mouse plasma samples were diluted 1:100 in protein array blocking buffer (GVS, Sanford, ME, USA) supplemented with 10 mg/ml E. coli lysate  (GenScript, Piscataway, NJ, USA) and 10g/ml of amino acid peptide HHHHHHHHHHGGGG (Biomatik, Wilmington, DE) to block any anti-polyhistidine antibodies, and pre-incubated at room temperature (RT) for 30 min. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 min prior to replacement of the blocking buffer with pre-incubated sera. Arrays were incubated overnight at 4°C with gentle agitation. After washing 6 times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS) at RT, arrays were incubated in biotinylated-SP-conjugated goat anti-mouse IgG (Jackson Immunoresearch, West Grove, PA) diluted 1:200 in blocking buffer for 2h at RT. Arrays were then washed 6 times with T-TBS, followed by incubation with streptavidin-conjugated Qdot-800 (ThermoFisher) diluted 1:250 in blocking buffer for 1h at RT. Arrays were washed three times each with T-TBS followed by TBS, dipped in distilled water, and air-dried by centrifugation at 500 × g for 10 min.

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis, a floor of 10 was set for array signal intensities and the data transformed by Log2. Vaccine groups were compared using two-tailed Mann-Whitney test for unpaired data and the two-tailed Kruskal-Wallis test with Dunn’s multiple-comparisons using GraphPad Prism 6.7 (GraphPad, La Jolla, CA, USA). A P value of <0.05 was considered statistically significant. To determine antibody breadth, geometric means of Log2-transformed data for each antigen were determined for each vaccine group, and an antigen was scored seropositive if above a cutoff defined as the mean+2SD of the signals for an irrelevant protein on the array (NA) which was not used to immunize.

molecule: other

organism: Mus musculus

source_name: single doseH5/IVAX-1d28 (mouseID B1)

tag: vaccine regimen

value: single dose

tag: vaccine

tag: time point

tag: mouse id

tag: sample type

value: plasma


title: single doseH5/IVAX-1d10 (mouse ID 2.1)

description:
SAMPLE 13
Fig. 2b

source_name: single doseH5/IVAX-1d10 (mouseID B1)


title: single doseH1/IVAX-1d42 (mouse ID 1.4)

description:
SAMPLE 12
Fig. 2a

source_name: single doseH1/IVAX-1d42 (mouseID B1)


title: 23-Vero_E6-PC_plus_infection_lane2_20200605000

type: SRA

city: Iowa City

first: Wendy

last: Maury

state: Iowa

address: 51 Newton Rd, Bowen Science Building 3-615

department: Microbiology and Immunology

institute: University of Iowa

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were subject to alignment to suitable reference genomes: human GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells). Alignments to human and monkey genomes were performed using hisat2 v2.0.5, while to viral genome using bowtie2 v2.2.9. Aligned reads were counted using featureCounts from subread package v1.5.2. Counted reads were normalized in R, using DESeq2 v1.30.0 and subjected to statistical analysis. The statistical analysis included computation of median based fold changes, Student t-test p values and false discovery rate (multiple testing correction).
The only analysis we performed was alignment to the human genome and SARS-CoV-2 genome. In the VeroE6 samples nearly 80% of the reads aligned to the viral genome, making analysis of the human mRNA changes difficult.
Genome_build: GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells)
Supplementary_files_format_and_content: Processed data consists of % reads mapped to AGM/human genome and reads mapped to SARS-CoV-2 genomes. Summary gene counts are also provided for A549-ACE2 samples.

molecule: polyA RNA

organism:
Chlorocebus aethiops
Severe acute respiratory syndrome coronavirus 2

extract_protocol:
Rneasy miniprep kit. Cells lysed in buffer RLT+betamercaptoethanol and homogenized with QIAshredder columns. RNA isolated accoring to protocol after DNAse digestion step with QIAgen kit. RNA integrity analyzed by Agilent Bioanalyzer.
Library prepared by University of Iowa Genomics Core using TruSeq Stranded mRNA kit protocol. Oligo-dT purification of polyA RNA, reverse transcription to cDNA, fragment purification, end polishing, followed by barcode ligation.

treatment_protocol: Liposome and inhibitors were prepared in DMEM + 10% fetal calf serum + 1% penicillin streptomycin at 1 micromolar (bemcentinib) or 50 micrmolar (PS or PC liposomes). SARS-CoV-2 was diluted and added to cells at MOI = 0.01 (VeroE6) or 0.5 (A549-ACE2). RNA was extracted 18 hours after infection (VeroE6) or 24 hours after infection (A549-ACE2)

tag: cell line

tag: sars-cov-2 infected

value: TRUE

tag: treatment

value: 50 micromolar phosphatidylcholine liposomes


title: NaPhen

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

country: Spain

institute: CNIO

description:
NaPhen
processed data files:
counts.txt
resTableNaPhen-v-C.txt

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to fastq file format was performed with the bcl2fastq software from Illumina.
RNA-seq reads were aligned to the GRCh38/hg38 using STAR (2.5.3) with --quantMode GeneCounts option  (Dobin A et al. Bioinformatics 29:15, 2013).
Differential gene expression (DGE) analysis was subsequently performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: "Counts.txt" tab-delimited text file contains the read counts for the six samples as counted by STAR and normalised with function counts() from DESeq2.
Supplementary_files_format_and_content: DESeq2 results are presented in "resTable*-v-C.txt" tab-delimited text files, where (*) denotes each treatment name being compared with the control (C) sample.

molecule: total RNA

organism: Homo sapiens

source_name: Hybrid cell line, with properties of motor neurons

growth_protocol: NSC34 cells were grown on gelatin at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin/Streptomycin

extract_protocol:
RNA was purified by using absolutely RNA kit from Agilent.
1 µg of total RNA samples with RIN above 9 were converted to sequencing libraries with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) by following manufacturer instructions.

treatment_protocol: Cells were treated with 5 µM of PR20 during 24 hours, 10 µM PFI or 10 µM of NaPhen  for 48 hours, or in combination (24 hours of 10 µM PFI or 10 µM of NaPhen follow by 24 hours of 5 µM of PR20).

tag: cell type

value: NSC-34 is produced by fusion of motor neuron enriched, embryonic mouse spinal cord cells with mouse neuroblastoma

tag: genotype

value: WT

value: NaPhen


title: 22-Vero_E6-PC_plus_infection_lane2_20200605000


title: control

description:
Ctrl
processed data files:
counts.txt


title: 21-Vero_E6-PS_plus_infection_lane2_20200605000

value: 50 micromolar phosphatidylserine liposomes


title: single doseH1/IVAX-1d42 (mouse ID 1.3)

description:
SAMPLE 11
Fig. 2a


title: 20-Vero_E6-PS_plus_infection_lane2_20200605000


title: 19-Vero_E6-PS_plus_infection_lane2_20200605000


title: Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 2

city: Geneva

first: Léon

last: van Gurp

state: Geneva

address: Rue Michel Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description:
10x Genomics generated multiplexed single cell transcriptomics.
RNA transcriptome
Single cell RNA-seq

data_processing:
Cells were included if they contained at least 2000 UMIs, expressed at least 1000 genes and had a percentage of mitochondrial gene counts below 15%. Cells were removed if they were assigned as doublets by either DoubltFinder or Scrublet doublet detection tools. Cells originating from the gamma fraction and delta fraction were merged per donor.
Genome_build: GRCh38
Supplementary_files_format_and_content: Sparse MatrixMarket files (.mtx) with separate tab-separated values files (.tsv) containing gene- and barcode names.

source_name: donor 2

extract_protocol:
Islets were dissociated into single cells and labelled with cell-surface antibodies 2B4, 2D12 and CD9. For gamma cells, all CD9+ cells were complemented to 15000 cells with CD9- cells. For delta cells, 15000 CD9+ and FSC-H(low) cells were sorted.
Each population was processed as an independent experiment using the Chromium single cell gene expression protocol v3 (10x Genomics). A median of 55000 100bp paired-end reads per cell were sequenced using Illumina Hiseq4000. Data were mapped against the Homo sapiens transcriptome reference 38 (GRCh38) using 10x Genomics Cell Ranger v3.0.2.

treatment_protocol: Islets were cultured in ultra low attachment plates using standard culture conditions for 1-7 days.

value: pancreatic islets

tag: facs enrichment

value: delta cells

tag: diagnosis

value: non-diabetic

tag: donor


title: Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 3

source_name: donor 3

value: gamma- and epsilon cells


title: single doseH5/IVAX-1d10 (mouse ID 2.5)

description:
SAMPLE 17
Fig. 2b


title: single doseH1/IVAX-1d42 (mouse ID 1.2)

description:
SAMPLE 10
Fig. 2a


title: Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 3


title: Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 2


title: 24-Vero_E6-PC_plus_infection_n_lane2_20200605000


title: 12-Vero_E6-infection_plus_Bem_lane2_20200605000

value: 1 micromolar bemcentinib


title: 11-Vero_E6-infection_plus_Bem_lane2_20200605000


title: single doseH1/IVAX-1d28 (mouse ID 1.4)

description:
SAMPLE 8
Fig. 2a

source_name: single doseH1/IVAX-1d28 (mouseID B1)


title: single doseH1/IVAX-1d42 (mouse ID 1.1)

description:
SAMPLE 9
Fig. 2a


title: Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 1

source_name: donor 1


title: Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 1


title: 10-Vero_E6-infection_plus_Bem_lane2_20200605000


title: Bap1KO-EV-H2AK119Ub1-rep2

status: Public on Jun 27 2021

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

library_source: genomic

data_processing:
For ChIP-seq data, paired-end DNA reads were processed through fastp to trim adapters and to remove low quality nucleotides at read ends (Chen et al., 2018). Quality-filtered DNA reads were aligned to the mouse reference genome mm10, or mm10 and fly reference genome (dm6) for histone ChIP-Rx using Bowtie v1.2.2 retaining only uniquely aligned reads (-m 1) and using the parameters -I 10, -X 1000 (Langmead et al., 2009). Reads mapped to both mm10 and dm6 were discarded. Peaks were identified using MACS2 v2.1.1 in narrow mode with parameters –format BAMPE –keep-dup all -m 3 30 and p-value 1e-10 (Zhang et al., 2008). Peaks were annotated using the R package ChIPpeakAnno v3.15 using for each peak the 5 kbp region around the center of the peak  (Zhu et al., 2010).
For RNA-seq, reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing for multimapping. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Mapped reads were assigned to genes using featureCounts (Liao et al., 2014) with unstranded read counting on exons and using the gene name as attribute type in the annotation. Genes were annotated as in Gencode M21 (GRCm38) downloaded from https://www.genecodegenes.org/mouse/. Differentially expressed genes were identified using the R package DESeq2 v1.24 using default parameters (Love et al., 2014). The fold change of lowly expressed genes was corrected using the lfcShrink function of the apeglm R package with the type option set to apeglm v1.6 (Zhu et al., 2019). The adjusted p-value was corrected by the independent hypothesis weighting (IHW) method as implemented in the R package IHW v1.12 (Ignatiadis et al., 2016). Genes were considered differentially expressed when presenting an absolute log2 fold change equal or greater than 1.5 and an adjusted p-value lower than 0.05.
For HiC data, DNA reads were filtered for low-quality bases and adapters using fastp (Chen et al., 2018). Filtered DNA reads were processed through the HiCpro pipeline to obtain contact matrices reporting the chromatin interactions at the genome-wide level (Servant et al., 2015). Using default settings, DNA reads were aligned to the mouse reference genome mm10 using bowtie2 in end-to-end mode, uniquely aligned DNA reads were assigned to the DpnII genomic restriction fragments, valid interactions were identified and used to generate interaction matrices. The HiCpro matrices containing all of the valid pairs were converted in hic format using the hicpro2juicebox function (Robinson et al., 2018), and in cool format using the hic2cool function (https://github.com/4dn-dcic/hic2cool). Contact matrices in cool format where corrected using the ICE algorithm as implemented in the hicCorrectMatrix function (Wolff et al., 2020). Plots of the interactions occurring at single locus or whole-chromosome level were obtained by HiCplotter (Akdemir and Chin, 2015). Hi-C was performed in duplicate with key findings being overserved in each before pooling replicates to make the final high-depth analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed (MACS2), counts (counts.tsv), differential expression (DESeq2), validpairs (HiCPro).

molecule: genomic DNA

source_name: Mouse Embryonic Stem Cells

growth_protocol: mESCs (both E14 and TCF background) were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 μM and 1 μM, respectively. For ATRA stimulation of ESCs, cells were washed twice with PBS 24 hours after seeding and media was replaced with ESC media lacking LIF, GSK3β and MEK1/2 inhibitors, and instead supplemented with 1μM ATRA for 24 hours.

extract_protocol:
ChIP-seq: DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions. DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility and sequenced on an Illumina HiSeq 2000.
RNA-seq: RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)  with minor modifications. Briefly, poly-A containing mRNA molecules obtained from 1 μg of total RNA were copied into first-strand cDNA by reverse transcription and template-switching using oligo (dT) primers and an LNA-containing template-switching oligo (TSO). Resulting cDNA was pre-amplified with KAPA HotStart Taq enzyme (Kapa Biosystems) and then purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter). One nanogram of pre-amplified cDNA was tagmented with in-house produced Tn5 transposase and further amplified with KAPA HotStart Taq enzyme. After purification with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing. Each RNA-seq experiment was performed in triplicate.
Hi-C: In situ Hi-C was performed as described (Rao et al., 2014) with slight alterations to the protocol. 5x10^6 ESCs were crosslinked for 10 minutes in 1% formaldehyde before quenching in 125mM Glycine for 5 minutes. Cell pellets were washed twice in PBS before contact generation. Pellet was resuspended in 500uL Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP40 and protease inhibitors) and incubated with rotation for 30 minutes at 4°C. Cells were pelleted and washed in 500uL Hi-C lysis buffer. Pellet was resuspended in 100uL 0.5% SDS and incubated for 10 minutes at 62°C. 285uL of H20 and 50uL of 10% Triton X-100 was added to quench the SDS at 37°C for 15 minutes. 50uL of 10xNEB DpnII buffer and 750U of DpnII were added (NEB R0453M) then incubated at 37°C overnight with shaking. Digestion was heat inactivated the next day for 20 minutes at 62°C. Biotin fill in was performed by addition of 52uL fill-in mix (0.288mM dCTP/dTTP/dGTP, 50U DNA Polymerase I, Large Klenow fragment (NEB M0210) and 0.288mM biotin-dATP (Thermo 19524016)). Fill-in reaction was incubated at 37°C for 1 hour with shaking. Ligation was performed by adding 150uL 10x NEB T4 DNA ligase buffer, 125uL 10% Triton X-100, 3uL 50mg/mL BSA and 8000U of T4 DNA ligase and H20 up to 1.5mL. Ligation was performed overnight at 25°C with shaking. Nuclei were pelleted before resuspending in IP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3, 0.33% SDS, 1.66% Triton X-100) and sonicating to fragment size between 200-1000bp. 15uL of the sample was de-crosslinked overnight at 65°C with 85ul of decrosslinking buffer (0.1M NaHCO3, 1% SDS) before clean up using QiaQuick PCR clean up kit from Qiagen.
Library prep was performed as described (Mumbach et al., 2016). Streptavidin C-1 beads (Thermo 65001) were washed and resuspended in 2x biotin binding buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl). 10ng of DNA was used for biotin capture, streptavidin C-1 beads were added and incubated for 15 minutes at room temperature with shaking. Beads were washed twice at 55°C for 2 minutes in Tween wash buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween). Beads were washed once in 1xTD buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 20% DMF) before being tagmented with in-house produced Tn5 transposase in TD buffer for 55°C for 10 minutes. TN5 was quenched in 50mM EDTA for 30 minutes at 55°C before washing twice in 50mM EDTA, twice in Tween wash buffer and once in 10mM Tris. PCR amplification was carried out on beads using KAPA HotStart Taq enzyme. After purification of PCR product with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing.

treatment_protocol: To generate stable KO cell lines, 10ug pX458 2.0 plasmid pairs (Addgene) encoding Cas9 and sgRNAs (Table S3) were transfected using Lipofectamine 2000 (Invitrogen), according to manufacturer’s instruction. Sorting of GFP positive cells was carried out 48 hours after transfection and 1000 cells were seeded onto a 15-cm dish. Clones were isolated 10-14 days later and grown further before screening for knockout by Western blot. For rescue clone generation, mESCs were transfected with 10ug pCAG vectors encoding 2xFlag-HA-tagged BAP1 wild-type or BAP1 C91S using Lipofectamine 2000 (ThermoFisher Scientific), according to manufacturer’s instructions. 24 hours post-transfection puromycin selection (1µg/ml) was added for a further 24 hours. Cells were then split to clonal density (~1:40) onto a 15cm plate. Clones were isolated 10-14 days later and grown further before screening for rescue allele expression by Western blot.

value: Mouse embryonic stem cells

tag: chip antibody


title: single doseH1/IVAX-1d28 (mouse ID 1.2)

description:
SAMPLE 6
Fig. 2a


title: single doseH1/IVAX-1d28 (mouse ID 1.3)

description:
SAMPLE 7
Fig. 2a


title: single doseH1/IVAX-1d10 (mouse ID 1.4)

description:
SAMPLE 4
Fig. 2a

source_name: single doseH1/IVAX-1d10 (mouseID B1)


title: single doseH1/IVAX-1d28 (mouse ID 1.1)

description:
SAMPLE 5
Fig. 2a


title: single doseH1/IVAX-1d10 (mouse ID 1.3)

description:
SAMPLE 3
Fig. 2a


title: TGF-β2-treated primary mouse RPE cells replicate 3

type: RNA

city: Shanghai

first: Yuwei

last: Wang

address: 100 Haining Road

country: China

institute: Shanghai General Hospital

description:
TGF-B-3
Biological replicate 3 of 3. Primary mouse RPE cells, re-plated after confluence at a split of 1:3, harvested after several passages.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Scanned on an Agilent G2565AA scanner. After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
IP (Cy5-labelled) and Sup (Cy3-labelled) intensities were normalized by the RNA spike-in calibration controls. m6A methylation levels were calculated for the percentage of modified RNA of a transcript.
IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls. The normalized IP intensities represent the "m6A quantity" of the transcript comparable across samples.
Differentially m6A-methylated mRNAs, lncRNAs and other ncRNAs based on "m6A methylation level" and "m6A quantity" passing fold change and statistical significance cutoffs were identified and compiled.

source_name: primary mouse RPE cells treated with TGF-β2 (IP)

label_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs. "IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Primary RPE cells were kept in Dulbecco’s modified Eagle’s medium / Ham’s F-12 medium containing 10% fetal bovine serum, 1% non-essential amino acids, and 1% HEPES. The passage 0 cells were re-plated after confluence at a split of 1:1 for the control group. For the TGF-β2 group, cells were passaged at a 1:3 and treated with recombinant mouse TGF-β2 at a concentration of 10 ng/ml.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: strain

tag: age

value: 3 weeks

value: RPE cells

tag: antibody

source_name: primary mouse RPE cells treated with TGF-β2 (Sup)


title: 8-Vero_E6-infection_lane2_20200605000

value: Media


title: 9-Vero_E6-infection_lane2_20200605000


title: single doseH1/IVAX-1d10 (mouse ID 1.1)

description:
SAMPLE 1
Fig. 2a

tag: vaccine regimen

value: single dose


title: 7-Vero_E6-infection_lane2_20200605000


title: 22-Vero_E6-PC_plus_infection_lane1_20200605000


title: single doseH1/IVAX-1d10 (mouse ID 1.2)

description:
SAMPLE 2
Fig. 2a

tag: vaccine

value: plasma


title: 23-Vero_E6-PC_plus_infection_lane1_20200605000

value: TRUE


title: Primary mouse RPE cells replicate 1

description:
control-1
Biological replicate 1 of 3. Control primary mouse RPE cells, untreated, re-plated after confluence at a split of 1:1, harvested after one passage.

source_name: primary mouse RPE cells (IP)

value: PBS control

source_name: primary mouse RPE cells (Sup)


title: TGF-β2-treated primary mouse RPE cells replicate 1

description:
TGF-B-1
Biological replicate 1 of 3. Primary mouse RPE cells, re-plated after confluence at a split of 1:3, harvested after several passages.


title: 21-Vero_E6-PS_plus_infection_lane1_20200605000


title: Primary mouse RPE cells replicate 3

description:
control-3
Biological replicate 3 of 3. Control primary mouse RPE cells, untreated, re-plated after confluence at a split of 1:1, harvested after one passage.


title: Primary mouse RPE cells replicate 2

description:
control-2
Biological replicate 2 of 3. Control primary mouse RPE cells, untreated, re-plated after confluence at a split of 1:1, harvested after one passage.


title: rd10-3

city: Kunming

first: kangwei

last: Jiao

state: Yunnan

address: 176 Qingnian

department: Ophthalmology

institute: Yunnan University

data_processing:
The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.26.0). Pvalue <0.05 and |FoldChange|≥1.5 were set as the threshold for significantly differential expression.
For circRNA: From the raw FASTQ raw data, adapter sequences and low-quality paired-end sequences were removed, and sequences were aligned to the mouse genome using TopHat2 (v2.1.1). To identify circRNAs, the CIRCexplorer program (v2.2.3) was used with the fusion junctions obtained using TopHat2 to identify both the circularizing junction and the spliced sequence of circRNAs. All candidate circRNAs with junction reads greater than or equal to two were identified as true circRNAs.  The expression of identified circRNAs was determined as TPM (transcripts per million; circRNAs were normalized by TPM). We performed a TPM density distribution analysis to check the gene expression patterns of the identified circRNAs and perform a differential expression analysis of the circRNAs using the Limma R package (3.40.6). To screen out significantly differentially expressed circRNAs, P value < 0.05 and |fold change| ≥ 2 were set as the thresholds.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM/TPM values for each Sample

source_name: Retina Pde6brd10

extract_protocol:
Total retina RNA was extracted using TRIzol reagent (Invitrogen, South San Francisco, CA, USA) following the manufacturer’s instructions.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Postnatal day 23

tag: tag

value: peak of the photoreceptor cell death


title: rd2-2

source_name: Retina Prphrd2

value: Postnatal day 29

value: Peripherin (PRPH) / C57BL6/J


title: TGF-β2-treated primary mouse RPE cells replicate 2

description:
TGF-B-2
Biological replicate 2 of 3. Primary mouse RPE cells, re-plated after confluence at a split of 1:3, harvested after several passages.


title: 7-Vero_E6-infection_lane1_20200605000


title: 20-Vero_E6-PS_plus_infection_lane1_20200605000

value: 50 micromolar phosphatidylserine liposomes


title: 19-Vero_E6-PS_plus_infection_lane1_20200605000


title: rd2-1


title: rd10-2


title: rd10-1


title: 8-Vero_E6-infection_lane1_20200605000


title: Non-pregnant Day 21 Cow No. 4

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

hyb_protocol: Labeled RNA was hybridized to the microarray in hybridization buffer (miRNA Complete Labeling Reagent and Hyb Kit, Agilent Technologies) at 55°C for 20 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (SureScan) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters  (protocol miRNA_1100_Jul11 and Grid: 063969_D_F_20140126)  to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Non-pregnant Day 21 Cow No. 4_plasma miRNA

label_protocol: Fluorescence-labeled (Cy3) RNA  were prepared from 50 ng of  miRNA using  a miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Extraction of miRNA from plasma was performed using miRNeasy Serum/Plasma Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

tag: breed

value: Japanese-Black

tag: tissue

value: Plasma

tag: status

value: Non-pregnant Day 21


title: rd1-1

source_name: Retina Pde6brd1

value: Postnatal day 13


title: Non-pregnant Day 21 Cow No. 1

source_name: Non-pregnant Day 21 Cow No. 1_plasma miRNA


title: Pregnant Day 21 Cow No. 4

source_name: Pregnant Day 21 Cow No. 4_plasma miRNA

value: Pregnant Day 21


title: rd2-3


title: rd1-2


title: rd1-3


title: Non-pregnant Day 21 Cow No. 3

source_name: Non-pregnant Day 21 Cow No. 3_plasma miRNA


title: C3H-1

source_name: Retina WT

value: Wide type / PDE6B


title: H-A549-bem_only_lane2_20200605000

source_name: A549 (ACE2 overexpressing)

tag: cell line

value: A549 (ACE2 overexpressing)

tag: sars-cov-2 infected

value: FALSE

value: 1 micromolar bemcentinib


title: Pregnant Day 21 Cow No. 2

source_name: Pregnant Day 21 Cow No. 2_plasma miRNA


title: Pregnant Day 21 Cow No. 3

source_name: Pregnant Day 21 Cow No. 3_plasma miRNA


title: 9-Vero_E6-infection_lane1_20200605000

tag: treatment

value: Media


title: C3H-3


title: E-A549-bem_only_lane2_20200605000


title: D_A549-no_infection_lane2_20200605000


title: C-A549-no_infection_lane2_20200605000


title: Pregnant Day 21 Cow No. 1

source_name: Pregnant Day 21 Cow No. 1_plasma miRNA


title: SKNAS_tr_1

city: London

first: Zuzanna

last: Urban-Wojciuk

address: 15 Cotswold Rd

country: United Kingdom

institute: Institute of Cancer Research

description:
Biological replicate 3 of 3
6162_2_4

hyb_protocol: 600ng of labelled cRNA was hybridized to an Agilent SurePrint G3 Human GE v2 8x60K Microarray  AMADID 039494 , using Agilent’s Gene Expression Hybridization Kit (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 17 hours

scan_protocol: Microarrays were scanned on Agilent Microarray Scanner G2505C

data_processing: Images were quantified using Feature Extraction Software v10.7.3.1 and FE protocol  GE2_107_Sep09. Lowess normalized log 2 ratio (Test/Reference) in supplementary file.

source_name: SKNAS neuroblastoma cell line, treated

label_protocol: Agilent Low RNA Input Linear Amplification Kit PLUS to generate fluorescent cRNA (complimentary RNA) with a sample input of 200ng Total RNA. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP. Labelled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-8000.

growth_protocol: Cells were grown in DMEM with 10% FBS, without addition of antibiotics

extract_protocol: Total RNA was extracted using RNeasy Mini Kit, Qiagen, 1µg of RNA was sent to OGT (Oxford Gene Technology) who performed the experiments

treatment_protocol: Cells were treated with verlindamycin + ATRA on day 1 after seeding and then again on day 4; cells were harvested 7 days after seeding. Untreated cells were cultured with the addition of DMSO

value: SKNAS

value: verlindamycin + ATRA

source_name: Reference RNA

tag: source

value: Reference RNA


title: C3H-2

value: Postnatal day 23

value: peak of the photoreceptor cell death


title: G-A549-bem_only_lane2_20200605000


title: F-A549-bem_only_lane2_20200605000


title: BE2C_ctrl_2

description:
Biological replicate 3 of 3
6160_2_4

source_name: SK-N-BE(2)-C neuroblastoma cell line, untreated


title: 17-Vero_E6-PC_liposomes_50_uM_lane2_20200605000

organism: Chlorocebus aethiops

value: 50 micromolar phosphatidylcholine liposomes


title: B-A549-no_infection_lane2_20200605000


title: Female KO 1

first: zihan

last: zhang

address: No. 1665, Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were filtered using Cutadapt version 2.10. Sequenced reads with 3' adaptor-trimming and whose average quality score is lower than Q20 were removed.
Tophat Version 2.1.1 was used to align the filtered high quality sequence (Clean Data) to the reference genome Rnor_6.0. According to the comparison results, the expression of each gene is calculated.
The  difference expression analysis, enrichment analysis and cluster analysis were further performed. The reads on the alignment were spliced to restore the transcript sequence. In order to make the gene expression levels of different genes and different samples comparable, we use FPKM (Fragments Per Kilo bases per Million fragments) to normalize the expression level.
HTSeq version 0.12.4 was used to statistically compare the read count value of each gene as the original expression level of the gene. For pair-end sequencing, each fragments will have two reads, and FPKM only counts the number of fragments that can be compared to the same transcript by the two reads. In the participating transcriptome, we generally think that genes with FPKM>1 are expressed. RSeQC version 3.0.1 was used to analyze the expression saturation.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM expression values

organism: Rattus norvegicus

source_name: rat kidney cortex

extract_protocol:
Tissues were ground in liquid nitrogen. TRIzol reagent (Invitrogen, USA) was used to extract total RNA from tissues. Enrichment of mRNA with polyA structure in total RNA by Oligo(dT) magnetic beads.
The RNA was broken to a length of about 300bp by means of ion interruption. Synthesize cDNA with 6-base random primers and reverse transcriptase.The first strand of cDNA was synthesized using RNA as template, and the second strand of cDNA was synthesized using the first strand of cDNA as the template.

treatment_protocol: CRISPR/Cas9 editing system was used to get Slc7a9-deficient rats. Zygotes obtained from super-ovulated pregnant female Sprague Dawley rats (SLAC, Shanghai) were cultured in KSOM embryo culture medium (Millipore, USA) for 3–4 h at 37 °C, 5% CO2 before gene editing. Editing was performed by microinjection of TE solution containing 12.5 ng/μL of sgRNA-targeting exon 3 of the rat Slc7a9 gene, and 25 ng/μL of Cas9 mRNA into the embryos’ cytoplasm during the one-cell stage. After injection, those zygotes were immediately transferred into pseudopregnant female rats.

tag: genotype

value: Slc7a9 gene deficient

tag: gender

value: female


title: Female SD 3

value: wild type


title: Female SD 1


title: Female KO 3


title: Female KO 2


title: Female SD 2


title: BE2C_ctrl_1

description:
Biological replicate 2 of 3
5869_1_2


title: SKNAS_ctrl_1

description:
Biological replicate 3 of 3
6162_2_3

source_name: SKNAS neuroblastoma cell line, untreated


title: A-A549-no_infection_lane2_20200605000


title: H-A549-bem_only_lane1_20200605000


title: SKNAS_ctrl_3

description:
Biological replicate 2 of 3
5857_2_2


title: 16-Vero_E6-PC_liposomes_50_uM_lane2_20200605000


title: BE2C_tr_3

description:
Biological replicate 3 of 3
5857_1_3

source_name: SK-N-BE(2)-C neuroblastoma cell line, treated


title: 15-Vero_E6-PS_liposomes_50_uM_lane2_20200605000

value: 50 micromolar phosphatidylserine liposomes


title: 14-Vero_E6-PS_liposomes_50_uM_lane2_20200605000


title: G-A549-bem_only_lane1_20200605000


title: BE2C_tr_1

description:
Biological replicate 2 of 3
5856_2_1


title: F-A549-bem_only_lane1_20200605000


title: 13-Vero_E6-PS_liposomes_50_uM_lane2_20200605000


title: E-A549-bem_only_lane1_20200605000


title: SKNAS_tr_3

description:
Biological replicate 2 of 3
4570_2_3


title: 6-Vero_E6-no_inf_plus_Bem_lane2_20200605000


title: 5-Vero_E6-no_inf_plus_Bem_lane2_20200605000


title: 4-Vero_E6-no_inf_plus_Bem_lane2_20200605000


title: C-A549-no_infection_lane1_20200605000


title: B-A549-no_infection_lane1_20200605000


title: D_A549-no_infection_lane1_20200605000


title: 3-Vero_E6-no_infection_lane2_20200605000


title: 2-Vero_E6-no_infection_lane2_20200605000


title: 3+3h HS 2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the Nitab-v4.5 using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in Nitab-v4.5
Genome_build: Nicotiana tabacum version 4.5 (Nitab-v4.5) from Sol Genomic Network
Supplementary_files_format_and_content: Tab-delimited gene counts

organism: Nicotiana tabacum

source_name: pollen tubes

growth_protocol: 200 mg Nicotiana tabacum pollen were resuspended in 2 ml pollen tube medium (2.5 % w/v PEG 4000, 5 % w/v sucrose, 15 mM MES-KOH pH 5.9, 1 mM CaCl2,1 mM KCl, 0.8 mM MgSO4, 0.01 % v/v H3BO3, 30 µM CuSO4) and spread onto cellophane foil that was placed in a square petri dish on 50 ml of solid pollen tube medium (2 % Agarose w/v, 5 % sucrose w/v, 6 % PEG-4000 w/v, 15 mM MES-KOH pH 5.9, 1 mM CaCl2,1 mM KCl, 0.8 mM MgSO4, 0.01 % H3BO3 v/v, 30 µM CuSO4)

extract_protocol:
RNA extraction kit (SpectrumTM Plant Total RNA Kit, Sigma-Aldrich)
RNA-seq libraries were performed using the non stranded mRNA Kit from Illumina (Cat. N°RS-122-2001)

value: pollen tubes

tag: condition

value: 3 h RT + 3 h 37 °C


title: 3+3h HS 3


title: SKNAS_tr_2

description:
Biological replicate 1 of 3
4570_1_4


title: A-A549-no_infection_lane1_20200605000


title: 1-Vero_E6-no_infection_lane2_20200605000


title: 15-Vero_E6-PS_liposomes_50_uM_lane1_20200605000


title: 6h 3

value: 6 h RT


title: 25kPa_2

city: Beijing

first: Quanmei

last: Sun

address: No.11 ZhongGuanCun BeiYiTiao

institute: National Centre for Nanoscience and Technology

data_processing:
Illumina bcl2fastq2 software used for base calling.
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5)[1] and then low quality data were filtered using NGSQC (v2.3.3)[2].
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) [3]with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM or raw count values for every gene and every sample

growth_protocol: The SKOV-3 cells were seeded in Petri dishes (Matrigen, USA), coated with hydrogel substrates  of different stiffness (0.5kPa, 4kPa, 25kPa) for three days.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).
The triplicate samples of all assays were constructed an independent library, and do the following sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina).

tag: cell type

value: Epithelial ovarian cancer cells

tag: substrate stiffness


title: 3+3h HS 1


title: 25kPa_4


title: 5-Vero_E6-no_inf_plus_Bem_lane1_20200605000

value: FALSE


title: 4kPa_3


title: 6-Vero_E6-no_inf_plus_Bem_lane1_20200605000

value: 1 micromolar bemcentinib


title: 6h 2


title: BE2C_ctrl_3

description:
Biological replicate 1 of 3
5856_1_2


title: BE2C_tr_2

description:
Biological replicate 1 of 3
5855_1_4


title: 4kPa_2


title: SKNAS_ctrl_2

description:
Biological replicate 1 of 3
4570_1_1


title: 4-Vero_E6-no_inf_plus_Bem_lane1_20200605000


title: 4kPa_1


title: 25kPa_3


title: 3-Vero_E6-no_infection_lane1_20200605000

value: Media


title: 3h 3

value: 3 h RT


title: 2-Vero_E6-no_infection_lane1_20200605000


title: 1_2k_kPa_3


title: 3h 1


title: 1-Vero_E6-no_infection_lane1_20200605000


title: 3h 2


title: 1_2k_Pa_2


title: 1_2kPa_1


title: MNase_WT

status: Public on Jun 25 2021

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
Reads were mapped to the mouse genome (mm9) using Bowtie (Langmead et al. 2009) v1.0.0 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2. To generate the nucleosome position data track, we extracted read pairs which fragment sizes ranged between 100-200 bases. Then, we extracted the genomic coordinates of the midpoint (=nucleosome dyads) between the highest and lowest coordinates of the two read pairs.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using Deeptools bamCoverage v2.5.0 (Ramírez et al., 2016) with the following parameters "--MNase --binSize 1 --skipNonCoveredRegions --outFileFormat bigwig --normalizeTo1x 2150570000".

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin

extract_protocol:
Sub-confluent MEFs were lysed in hypotonic buffer (10 mM Tris-HCl at pH 7.65, 1.5 mM MgCl2, 10 mM KCl) and disrupted by Dounce homogenizer. The cytosolic fraction was separated from the nuclei by centrifugation at 4°C. Nuclei were re-suspended in sucrose buffer (20 mM Tris-HCl at pH 7.65, 15 mM KCl 60 mM NaCl, 0.15 mM spermine, 0.5 mM spermidine) adjusted with high-salt buffer (20 mM Tris-HCl at pH 7.65, 25 % glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 900 mM NaCl) to get a final NaCl concentration of 300 mM. The nuclear-soluble fraction was recovered by centrifugation at 4°C. The pellet containing chromatin fraction was incubated in sucrose buffer containing 1mM CaCl2, and MNase (2.5U/g of cells) 10 min at 37°C. Digestion was stopped with 4 mM EDTA and mononucleosomes were recovered by centrifugation at 4°C. Mononucleosomes were submitted to RNase and proteinase K digestion, and DNA was extracted by phenolchloroform.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as paired-end 100 bp reads following Illumina's instructions. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover v0.9.2 (https://sourceforge.net/projects/dimerremover/).

treatment_protocol: Mecp2fl/f MEFs were transfected with pCMV-CRE vector using FuGENE 6 Transfection Reagent (Promega) according to the manufacturer's instructions to generate KO cells (Mecp2-/-). Following selection, targeted clones were identified by RT-qPCR and further confirmed by Western-blot analysis.

tag: strain

tag: genotype/variation

value: Mouse embryonic fibroblasts (MEFs)

tag: age

value: MEFs were derived from E13.5 embryos


title: MNase_KO


title: RNA_KO_2

description: RNA.xlsx

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2. Reads were mapped to the mouse genome (mm9) using Tophat v2.0.14 and Bowtie v2-2.1.0. Quantification of gene expression was performed using HTSeq v0.6.1 and gene annotations from Ensembl release 67.
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in one single Excel file containing the following informations for each sample: gene name/ensemble_gene_id/raw read count/normalized read count/log2 fold change/p-value/p-value adjusted for multi-testing.

extract_protocol:
Total RNAs were purified from sub-confluent MEFs using standard methods.
Libraries of template molecules suitable for strand-specific high-throughput DNA sequencing were created using a TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (RS-122-2301; Illumina) as previously described (Ors et al. 2017).

value: Mouse embryonic fibroblasts

tag: cell fraction

value: Post-meiotic cell fraction


title: RNA_KO_1

description: RNA.xlsx


title: 6h 1


title: RNA_WT_1

description: RNA.xlsx

value: Meiotic cell fraction


title: RNA_WT_2

description: RNA.xlsx


title: EXP1.KO.1

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7
Genome_build: mm10, GENCODE release M14
Supplementary_files_format_and_content: CSV text file containing gene-level counts for all samples

source_name: E10.5 embryonic telencephalon

extract_protocol:
E10.5 embryonic telencephalon were quickly removed and stored in RNA later at 4C for a maximum of 1 week.  P35 cortex was quickly dissected in cold PBS and RNA immediately extracted.  RNA was extracted using Trizol and purified using mirVana miRNA Isolation Kit (Ambion/Life technologies )
RNA libraries were prepared for sequencing using Illiumina TruSeq Stranded mRNA library prep kit following standard Illumina protocols

value: dorsal embryonic telencephalon

tag: experiment

value: EMX

value: KO

tag: group

tag: replicate


title: EXP1.CONTROL.3

tag: tissue

value: CONTROL


title: EXP1.KO.3


title: EXP1.KO.4


title: EXP1.CONTROL.4


title: EXP1.KO.2


title: DIP_5hmC_KO

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover. Data were preprocessed with Cutadapt (http://journal.embnet.org/index.php/embnetjournal/article/view/200) v1.13 to remove the first 9 nucleotides and to remove sequences with a trailing polyT of at least 10 Ts. Cutdapt was used with the following parameters ‘-u 9 -a T{10} --discard-trimmed’. Reads were mapped to the mouse genome (mm9) using Bowtie v1.0.0 with default parameters except for “-p 3 –m 1 --strata --best --chunkmbs 128”.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Scores represent tag numbers per total uniquely mapped reads.

extract_protocol:
DNA immunoprecipitation assays were done as previously described (Papin et al. 2016).
20 ug DNA was used as input, then 2 uL 5mC monoclonal antibody (Active Motif, 39649), 2 µl monoclonal IgG control antibody (Abcam, ab81032), 4 uL 5hmC polyclonal antibody (Active Motif, 39791) or 4 µl IgG polyclonal antibody (Abcam) were used to immunoprecipitate DNA. DNA and antibodies were incubated at 4°C overnight in a final volume of 1 mL DIP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100). The bound material was recovered after incubation with 60 uL blocked protein G Dynabeads (beads washed three times with 1 mL DIP buffer and incubated for 4 hours minimum with BSA 1 mg/mL and yeast tRNA 0.5 mg/mL). The beads were washed three times with 1 mL DIP buffer, then treated overnight with RNase A at 65°C in the presence of 300 mM NaCl and then treated 4 hours with proteinase K at 55°C. Immunoprecipitated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. Two independent DNA immunoprecipitations were pooled for each condition before sequencing analysis. For each independent replicate, 5mC, 5hmC and IgG control DIP assays were performed using the same batches of genomic DNA.
Libraries were prepared using the SMART cDNA Library Construction Kit and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

tag: ip antibody


title: EXP1.CONTROL.2


title: DIP_5hmC_WT

value: 5hmC polyclonal antibody (Active Motif, 39791)


title: DIP_5mC_WT

value: 5mC monoclonal antibody (Active Motif, 39649)


title: DIP_IgG_poly_KO

value: IgG polyclonal antibody (Abcam)


title: DIP_IgG_mono_KO

value: monoclonal IgG control antibody (Abcam, ab81032)


title: DIP_IgG_poly_WT


title: ChIP_MeCP2_KO

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover v0.9.2. Reads were mapped to the mouse genome (mm9) using Bowtie v1.0.0 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Scores represent tag numbers per total uniquely mapped reads.

extract_protocol:
MeCP2 ChIP experiments were performed as previously described (Obri et al. 2014) in MEFs WT or KO for Mecp2. Briefly, 50 µg of sonicated chromatin isolated from sub-confluent MEFs WT or KO for Mecp2 were immunoprecipitated using 2 µg of antibody anti-MeCP2 (Proteintech®, 10861-1-AP). Six independent chromatin immunoprecipitations were pooled before sequencing analysis.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

tag: chip antibody

value: anti-MeCP2 (Proteintech, 10861-1-AP)


title: ChIP_rescue_R106W

extract_protocol:
Sub-confluent MEFs overexpressing FLAG-HA tagged MeCP2 were crosslinked with 0.4% formaldehyde for 10 min and quenched with 150 mM glycine for 10 min at room temperature. Cells were lysed in hypotonic buffer (10 mM Tris-HCl pH 7.65, 1.5 mM MgCl2, 10 mM KCl) and disrupted by dounce homogenizer. The cytosolic fraction was separated from the nuclei by centrifugation at 4°C. Nuclei were re-suspended in sucrose buffer (20 mM Tris-HCl at pH 7.65, 15 mM KCl 60 mM NaCl, 0.15 mM spermine, 0.5 mM spermidine) adjusted with high-salt buffer (20 mM Tris-HCl pH 7.65, 25 % glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 900 mM NaCl) to get a final NaCl concentration of 300 mM. The nuclear-soluble fraction was recovered by centrifugation at 4°C. The pellet containing chromatin fraction was incubated in sucrose buffer containing 1 mM CaCl2, and MNase (2.5 U/g of cells) 10 min at 37°C. Digestion was stopped with 4 mM EDTA and soluble chromatin was recovered by centrifugation at 4°C. Tagged MeCP2 was immunoprecipitated with anti-Flag M2-agarose (Sigma), eluted with Flag peptide (0.5 mg/mL), further affinity-purified with anti-HA antibody-conjugated agarose, and eluted with HA peptide (1 mg/mL). The HA and Flag peptides were first buffered with 50 mM Tris-Cl (pH 8.5), then diluted to 4 mg/mL in TGEN 150 buffer (20 mM Tris at pH 7.65, 150 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 10% glycerol, 0.01% NP40), and stored at -20°C until use. Between each step, beads were washed in TGEN 150 buffer. MeCP2-bound chromatin was submitted to RNase and proteinase K digestion, and DNA was extracted by phenolchloroform.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

treatment_protocol: For rescue experiments, MeCP2 WT, MeCP2 R133C or MeCP2 R106W mutant proteins fused to N-terminal Flag-and HA-epitope tags were stably expressed in Mecp2-/- MEFs by retroviral transduction.

value: MeCP2-/- + Flag-HA-MeCP2 R106W

value: anti-Flag M2-agarose (Sigma); anti-HA antibody-conjugated agarose


title: DIP_IgG_mono_WT


title: ChIP_MeCP2_WT


title: ChIP_input_KO


title: ChIP_input_WT


title: EXP1.CONTROL.1


title: ChIP_rescue_R133C

value: MeCP2-/- + Flag-HA-MeCP2 R133C


title: PPs2 (Bisulfite-Seq)

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

data_processing:
Raw data were trimmed by Trim galore v0.4.1 to produce clean data (clean reads).
The clean reads were processed by Bismark v0.15.0 for genome alignment (Rat6) and the PCR duplicates were removed.The information of cytosine (C), CpG C and methylated CpG C (5mC), as well as their distribution and frequency, can be extracted from the information of genome alignment.
The methylation level of 5mC  is calculated by C/C+T(frequency).
The reads with more than 10X read depth were then processed by R methylkit v0.9.5 to indicate the details of the read depth and methylation level of all 5mC.
The methylation level of 5mC between groups were compared and annotated by DSS Bioconductor package, and the 5mC with mean methylation level difference > 10% and p < 0.05 between groups was considered to be differentially methylated site (DMS).
Genome_build: Rat6
Supplementary_files_format_and_content: text files report methylation freq

source_name: Colonic epithelia

extract_protocol:
Colonic epithelia (>95%) were obtained by scraping at 4 0C . Genome DNA was extracted with gDNA Extraction Kit (Omega Bio-Tek Research，USA) and sheared to fragments of 150-200 bp (Covaris E-series instrument, Australia).
DNA libraries were prepared with Agilent SureSelectXT Methyl-seq Library Pre kit and then hybridized with hybridization reagents, blocking agents and the SureSelect capture library.

value: SD

value: colon

value: male

tag: treatment

value: PPs-treated rats

value: Colonic epithelia


title: PPs3 (Bisulfite-Seq)


title: PPs1 (Bisulfite-Seq)


title: CNP1 (Bisulfite-Seq)

value: CNP rats


title: CTL1 (Bisulfite-Seq)

value: control rats


title: ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, induced with aTc

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

data_processing:
Reads were aligned to Escherichia coli MG1655 (NC_000913.2) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
The change in gene expression was calculated by taking log2-RPKM ratio of each gene from the experimental condition to the control condition (GapR-3xFLAG induced / GapR-3xFLAG uninduced).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position. For RNA-seq, two files are provided, one for forward and reverse strand.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655

growth_protocol: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).

extract_protocol:
RNA was extracted as previously reported (Culviner and Laub, 2018).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).

treatment_protocol: As needed, cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr.

tag: growth stage

value: exponential phase

tag: media

value: LB + 25 ng/µL aTc


title: CTL3 (Bisulfite-Seq)

tag: gender


title: ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, induced with aTc, replicate 1

data_processing:
Reads were aligned to Escherichia coli MG1655 (NC_000913.2) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position.

growth_protocol: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and then fixed by the addition of 10 mM sodium phosphate [pH 7.6] and 1% formaldehyde (final concentrations). ChIP was then performed as previously reported (Guo et al, 2018).

extract_protocol:
ChIP was performed as previously reported (Guo et al, 2018). ChIP antibody is Mouse monoclonal anti-FLAG from Sigma (Cat #: F1804).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.

treatment_protocol: Cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr.


title: ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, induced with aTc and treated with rifampicin

growth_protocol: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3), 300 µg/mL rifampicin was added for 20 min, and then cells were fixed by the addition of 10 mM sodium phosphate [pH 7.6] and 1% formaldehyde (final concentrations). ChIP was then performed as previously reported (Guo et al, 2018).

treatment_protocol: Cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr then with 300 µg/mL rifampicin for 20 min.

value: LB + 25 ng/µL aTc + 300 µg/mL rifampicin


title: CNP2 (Bisulfite-Seq)


title: ML3285 (MG1655 pKVS45-GapR) in exponential phase, induced with aTc, replicate 2


title: CTL2 (Bisulfite-Seq)


title: ML3285 (MG1655 pKVS45-GapR) in exponential phase, induced with aTc, replicate 1


title: MM071 CFPAC1 polyA RNA-seq Inh 3day

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using HMM (Sanz et. al, 2016). For both, HTseq-count v0.6.0 was then used to count the total number of reads of each peak (sDRIP-seq) or genes (RNA-seq).
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). sDRIP-seq bed files were generated using HMM and converted into bigBed using bedToBigBed;

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
RNA-seq: Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.    sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
RNA-seq: Standard paired-end TruSeq protocol.    sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Cells were subjected to either DMSO or PRMT inhibitor for 1, 2, or 3 days.

value: Inh 3d


title: ChIP_rescue_WT

value: Mouse embryonic fibroblasts

value: MeCP2-/- + Flag-HA-MeCP2 WT

value: MEFs were derived from E13.5 embryos


title: MM072 CFPAC1 polyA RNA-seq Inh 3day


title: MM070 CFPAC1 polyA RNA-seq Inh 3day


title: MM067 CFPAC1 polyA RNA-seq DMSO 3day

value: DMSO 3d


title: MM068 CFPAC1 polyA RNA-seq DMSO 3day


title: MM069 CFPAC1 polyA RNA-seq DMSO 3day


title: MM062 CFPAC1 polyA RNA-seq DMSO 2day

value: DMSO 2d


title: MM066 CFPAC1 polyA RNA-seq Inh 2day

value: Inh 2d


title: ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, uninduced

growth_protocol: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01. Cells were grown for 2 hr (OD ~0.3) and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).

value: LB


title: MM064 CFPAC1 polyA RNA-seq Inh 2day


title: MM063 CFPAC1 polyA RNA-seq DMSO 2day


title: MM061 CFPAC1 polyA RNA-seq DMSO 2day


title: DIP_5mC_KO

value: 5mC monoclonal antibody (Active Motif, 39649)


title: CNP3 (Bisulfite-Seq)

value: SD

value: colon

value: male


title: MM065 CFPAC1 polyA RNA-seq Inh 2day


title: MM060 CFPAC1 polyA RNA-seq Inh 1day

value: Inh 1d


title: MM059 CFPAC1 polyA RNA-seq Inh 1day


title: MM058 CFPAC1 polyA RNA-seq Inh 1day


title: ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, induced with aTc, replicate 2


title: MM056 CFPAC1 polyA RNA-seq DMSO 1day

value: DMSO 1d


title: MM057 CFPAC1 polyA RNA-seq DMSO 1day


title: REH FASTKD1 sh2 replicate3

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

data_processing:
The sequenced reads were aligned from raw sequence fastq data using STAR v2.5.2b software on UCSC hg19 reference genome.
The aligned reads were normalized, and log transformed using the R bioconductor package DEseq2 (http://bioconductor.org/packages/3.12/bioc/html/DESeq2.html).
Genome_build: hg19

source_name: REH

growth_protocol: Human lymphoblastic leukemia cell line REH (Female, CVCL_1650) was obtained from National Collection of Authenticated Cell Cultures and was authenticated by STR analysis prior to use. REH and the derivative cells were maintained in RPMI-1640 (Gibco) supplemented with 10% FBS (Dominique DUTSCHER), 4mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Three independent RNA extractions from control and two knockdown cell lines (sh-1, sh-2) samples were sequenced.
For each sample, 1 µg RNA samples (RIN = 10) were used for libraries preparations with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Library prepared from FASTKD1 control and knockdown samples were sequenced on Hiseq 4000 (PE150) platform in Novagene company.

treatment_protocol: shRNAs were designed using GPP Web Portal(https://portals.broadinstitute.org) or referring to GeCKO v2 library (Sanjana et al., 2014) with the corresponding targeting sequences indicated in the Key Resource Table, and were cloned into pLVX-shRNA1 (Clontech, Cat#632177). All plasmids were confirmed by sanger sequencing.

tag: cell line

value: REH

tag: genotype

value: FASTKD1 sh2


title: REH FASTKD1 sh2 replicate2


title: REH FASTKD1 sh1 replicate3

value: FASTKD1 sh1


title: F2 5G rep3

city: Ube

first: Koichi

last: Fujisawa

state: Yamaguchi

address: Minamikogushi 1-1-1

institute: Yamaguchi University

data_processing:
Torrent_Suite v5.4.0 software used for data processing.
Genome_build: hg19

source_name: F2 5G replicate3

growth_protocol: HHSteC was purchased from ScienCell Research Laboratories, Inc. (catalog number 5300) and cells from passages 3-5 were used.  HHSteCs were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (GIBCO, NY, USA) supplemented with 10 % fetal bovine serum (FBS) (GIBCO) and penicillin/streptomycin (GIBCO) in a 12.5 cm2 culture flask (Falcon 353107) with an oxygen permeable cap. Cells were seeded at a density of 500-1000 cells/cm2.

extract_protocol:
Total RNA was isolated from the cell using RNeasy kit (Cat#74106, QIAGEN, Hilden, Germany) and purified according to the manufacturer's instructions. RNA samples were quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the quality was confirmed using the Experion System (Cat#7007106JA, Bio-Rad, Hercules, CA, USA).
The Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies) was used to construct a library. An Ion PI IC 200 Kit (Life Technologies) and an Ion PI Chip Kit v2 BC were used for sequencing, using an Ion Proton next-generation sequencer.

treatment_protocol: The cells were cultured in a 3D-clinostat (Zeromo CL5000, Kitagawa, Hiroshima, Japan) (F1 SMG) and kept in the same incubator as 1G control (F1 1G). The cells were cultured in Zeromo at 5G (F2 5G)and kept in the same inculbator as 1G control (F2 1G).

value: HHSteC

tag: gravity


title: REH FASTKD1sh1 replicate2


title: REH ctrl replicate3

value: Control


title: F2 5G rep1

source_name: F2 5G replicate1


title: F2 1G rep3

source_name: F2 1G replicate3


title: F2 5G rep2

source_name: F2 5G replicate2


title: REH ctrl replicate2


title: F2 1G rep1

source_name: F2 1G replicate1


title: F1 1G rep3

source_name: F1 1G replicate3


title: F2 1G rep2

source_name: F2 1G replicate2


title: F1 1G rep2

source_name: F1 1G replicate2


title: MM055 CFPAC1 polyA RNA-seq DMSO 1day

tag: cell type


title: REH FASTKD1 sh2 replicate1


title: F1 1G rep1

source_name: F1 1G replicate1


title: F1 SMG rep3

source_name: F1 SMG replicate3

value: SMG


title: REH FASTKD1 sh1 replicate1


title: A1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Unfractionated cells, replicate 1

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Mouse RMS cells were cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol: Total RNA was isolated using TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: No special treatments were administered. Cells were labeled with 7AAD to exclude dead cells and sorted twice using a MoFlo Astrios Flow Cytometer to distinguish YFPpos and YFPneg cell subsets (purity > 98%).

value: Rhabdomyosarcoma

tag: cell subset

value: Unfractionated cells


title: N1

source_name: YFPlow/P3Flow cells, replicate 1

value: YFPlow/P3Flow cells


title: A4

source_name: Unfractionated cells, replicate 4


title: A3

source_name: Unfractionated cells, replicate 3


title: P1

source_name: YFPhigh/P3Fhigh cells, replicate 1

value: YFPhigh/P3Fhigh cells


title: F1 SMG rep2

source_name: F1 SMG replicate2


title: P2

source_name: YFPhigh/P3Fhigh cells, replicate 2


title: P5

source_name: YFPhigh/P3Fhigh cells, replicate 5


title: A2

source_name: Unfractionated cells, replicate 2


title: N2

source_name: YFPlow/P3Flow cells, replicate 2


title: P4

source_name: YFPhigh/P3Fhigh cells, replicate 4


title: N3

source_name: YFPlow/P3Flow cells, replicate 3


title: F1 SMG rep1

source_name: F1 SMG replicate1


title: REH ctrl replicate1

source_name: REH


title: TB3

city: Toronto

first: Amro

last: Zayed

state: Ontario

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic 0.36
Sequenced were mapped to Bombus terricola genome [Kent et al. 2018 (https://doi.org/10.3389/fgene.2018.00316), (https://www.ncbi.nlm.nih.gov/bioproject/399520)] and counted using Spliced Transcripts Alignment to a Reference (STAR) software 2.7
Genome_build: We used the genome as assembled by Kent et al. 2018 (https://doi.org/10.3389/fgene.2018.00316), (https://www.ncbi.nlm.nih.gov/bioproject/399520)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene for each sample

organism: Bombus terricola

source_name: Abdomen

extract_protocol:
Frozen abdomens were lysated and RNA extracted using Qiagen RNease Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
mRNASeq stranded

tag: collection site

value: Terre Bleu Lavender Farm

tag: site type

value: Agricultural

value: Abdomen


title: SS1

value: Sulphur Springs Conservation Area


title: CL2

value: Conestogo Lake Conservation Area


title: GL2

value: Guelph Lake Conservation Area


title: SS2


title: Cp40_Late Rejector [H87T]

city: Durham

first: Jean

last: Kwun

state: NC

address: 207 Research Dr, Jones 362

department: Surgery

institute: Duke University

hyb_protocol: 300 ng total RNA was hybridized to gene-specific probes at 65˚C for 18 hours and then purified and deposited onto glass cartridges using the “high sensitivity” setting on the nCounter™ Prep Station (NanoString Technologies, Seattle, WA, USA).

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter™ Digital Analyzer with 555 fields of view setting.

data_processing: Normalization of RNA loading was performed using the geometric mean of 12 internal reference genes (housekeeping genes; ABCF1, G6PD, GUSB, NRDE2, OAZ1, POLR2A, PPIA, SDHA, STK11IP, TBC1D10B, TBP, and UBB).

organism: Macaca mulatta

source_name: Cp40_Late Rejector

extract_protocol: Formalin Fixed Paraffin Embedded (FFPE) samples were used for the extraction of total RNA from renal allograft. Samples were included in the final analysis if they passed a priori quality control criteria (260:280 ratio > 1.7).

tag: animal group

value: Animals responded to Cp40 treatment (Late Rejector)

tag: Sex

value: male

value: Renal, biopsy, FFPE


title: TB2


title: Cp40_Late Rejector [H77P Kd14]


title: B-ALL patient C105

growth_protocol: Bone marrow aspiration was conducted at diagnosis. Mononuclear cells were enriched from BM samples by density gradient centrifugation with LymphoPrep™ Solution (Axis Shield PoC, Cat#1114547) and were stored at -80°C as dry pellets for further experimental analysis.

extract_protocol:
32 samples from  25 B-ALL patients’ bone marrow samples were processed for RNA extractions and sequencing. For 7 patients two independent RNAseq experiments were performed (duplicates).
For each sample, 1 µg RNA samples (RIN = 10) were used for libraries preparations with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Library prepared from B-ALL patients’ samples were sequenced on Hiseq 4000 (PE150) platform in Novagene company.

value: Female

tag: age

tag: wbc at diagnosis (x109/l)

tag: ph chromosome

value: Neg.

tag: dct(hadhb-gapdh)

tag: h4k5 cr/h3

tag: h4k5 bu/h3

tag: h4k5 cr high low

value: high

tag: h4k5 bu high low


title: B-ALL patient CA80-2

tag: gender

value: low


title: B-ALL patient CA69-2


title: Cp40_Late Rejector [H72E]

tag: tissue


title: GL1


title: SS3


title: B-ALL patient C103


title: GL3


title: Cp40_Early Rejector [HADY]

source_name: Cp40_Early Rejector

value: Animals not responded to Cp40 treatment (Early Rejector)


title: B-ALL patient AC18

value: Male


title: TB1


title: VAL3

value: Val Therese

value: Non-Agricultural


title: VAL2


title: B-ALL patient AC17


title: Cp40_Early Rejector [H75W]


title: CL3


title: VAL1


title: DOW6

value: Dowling


title: B-ALL patient A99


title: CAP3

value: Capreol River


title: Cp40_Early Rejector [H49G]


title: 18LDKO_sham_2ndlane

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description:
7DPI_DKO_rawcounts.csv
7dpi_DeSeq2_result.csv

data_processing:
Illumina Pipeline  Casava 1.8.2
7dpi Raw fastq files were mapped using TopHat 2.1.1/HTSeq 0.10 (tophat -p 6 --min-intron-length 40 --max-intron-length 2000 --bowtie1 --no-novel-juncs --read-mismatches 2 -G /mnt/genomes/Mus_musculus/mm10/annotation/genes.gtf --transcriptome-index transcriptome_data --output-dir tophatFolder/ /mnt/genomes/Mus_musculus/mm10/bowtieIndex/genome /home/BIOTECH/sample.fastq.gz  )
1dpi Raw fastq files were mapped using Star-aligner 2.7.3a (STAR --runThreadN 12 --genomeDir mm10 --readFilesCommand zcat --readFilesIn RNAseq/inputFolder --outFileNamePrefix outputFolder --outSAMtype BAM SortedByCoordinate)
Data were analyzed using DEseq2
Genome_build: Genome_build: mm10

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water. Kdm6a/Kdm6b-floxed mice were mated to mP0TOTA-Cre (B6N.FVB-Tg(Mpz-cre)26Mes/J, obtained from Jackson Laboratory, RRID: IMSR_JAX:017927).

extract_protocol:
Total RNA was purified using Qiagen Rneasy Lipid Kit
Libraries were prepared using the Illumina TruSeq Stranded total RNA sample preparation kit V2

treatment_protocol: The sciatic nerves of adult mice at the age of 2 months were exposed and transected at the sciatic notch (Hung et al., 2015). As a control, the contralateral limb also rece a sham operation consisting of only a skin incision. The nerve tissues distal to the transection and contralateral (sham) nerves were isolated.

tag: treatment

value: Sham 1 dpi, contralateral nerve

tag: genotype

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: 18RDKO_cut_2ndlane

value: Injury 1 dpi, ipsilateral


title: BLE5

value: Blezard Valley

value: Agricultural

value: Abdomen


title: LEV4

value: Levack


title: BLE2


title: CAP1


title: B-ALL patient A90-2 replicate2

tag: replicate

value: Female


title: DOW2

tag: collection site


title: DOW1

tag: site type


title: B-ALL patient A90-2 replicate1

value: Neg.


title: 15RDKO_cut


title: LEV5


title: B-ALL patient A85-2 replicate2

value: high


title: 15LDKO_sham_2ndlane


title: CAP2


title: B-ALL patient A85-2 replicate1

value: low


title: 18RDKO_cut


title: B-ALL patient A98


title: B-ALL patient A81-2 replicate2


title: CL1

value: Conestogo Lake Conservation Area


title: P6

source_name: YFPhigh/P3Fhigh cells, replicate 6

tag: cell type

value: Rhabdomyosarcoma

tag: cell subset

value: YFPhigh/P3Fhigh cells


title: 18LDKO_sham

tag: age


title: CHE2

value: Chelmsford


title: B-ALL patient A81-2 replicate1

tag: wbc at diagnosis (x109/l)


title: 14RWT_cut

value: Kdm6a fl/y, Kdm6b fl/fl


title: LEV3

value: Non-Agricultural


title: 15RDKO_cut_2ndlane


title: Y567N Mut_d365_with147_d55

city: La Jolla

first: R. Luke

last: Wiseman

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

description: Y567N Mut_d365_with147_d55

data_processing:
Basescaling was performed by BGI
Single end, 50 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Counts Data were analyzed using DESeq
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX files contain counts data for each sample and DESeq differential expression analysis of Mutant vs. Heterozygous and Mutant +147 vs. Untreated Mutant

source_name: iPSC derived retinal organoid

growth_protocol: Retinal organoids were cultured from human iPSCs for listed number of days

extract_protocol:
Three independent experiments were performed for Y567N Mutant versus Heterozygous comparison. Single pooled samples used for Mut with or without 147 experiment. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard protocols at BGI

treatment_protocol: Subset of cultured organoids were treated with vehicle or AA 147 for 2 weeks

value: Mut

tag: agent

value: AA 147 for 2 weeks


title: Y567N Mut_d365_no147_d55

description: Y567N Mut_d365_no147_d55

value: Vehicle for 2 weeks


title: B-ALL patient A52-2 replicate2

tag: ph chromosome

tag: dct(hadhb-gapdh)


title: Y567N Mut_2_d290

description: Y567N Mut_2_d290


title: Y567N Mut_3_d290

description: Y567N Mut_3_d290


title: 14LWT_sham_2ndlane

value: Sham 1 dpi, contralateral nerve


title: B-ALL patient A52-2 replicate1

tag: h4k5 cr/h3

tag: h4k5 bu/h3


title: BLE3

value: Blezard Valley

value: Agricultural


title: 14LWT_sham


title: 15LDKO_sham

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: CHE3

value: Abdomen


title: CHE5


title: Y567N Het_3_d290

description: Y567N Het_3_d290

value: Het


title: B-ALL patient A50-2 replicate2

value: Female

value: Neg.

tag: h4k5 cr high low

value: high

tag: h4k5 bu high low


title: 12RDKO_cut_2ndlane

value: Injury 1 dpi, ipsilateral


title: B-ALL patient A50-2 replicate1

tag: gender

value: low


title: 14RWT_cut_2ndlane

tag: treatment


title: Y567N Het_1_d290

description: Y567N Het_1_d290

tag: genotype


title: Y567N Het_2_d290

description: Y567N Het_2_d290


title: B-ALL patient A44-2 replicate2

tag: replicate


title: B-ALL patient A44-2 replicate1


title: 12RDKO_cut


title: 12LDKO_sham_2ndlane


title: Y567N Mut_1_d290

description: Y567N Mut_1_d290


title: 10RWT_cut_2ndlane


title: 10RWT_cut


title: B-ALL patient A42-2 replicate1


title: 12LDKO_sham


title: 10LWT_sham_2ndlane


title: B-ALL patient A110


title: 10LWT_sham


title: B-ALL patient A112


title: B-ALL patient A109

value: Male

value: Pos.


title: 4RDKO_cut_2ndlane


title: Secretory cell - D5

city: Daejeon

first: HaeYon

last: Jeon

address: 291 Daehak-ro, Eoeun-dong, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
D5
PolyA RNA extracted from single cells
Single-cell RNA-seq (3', 10X Chromium, v2)

data_processing:
Single-cell RNA-seq data were processed using Cellranger (3.0.2), with "count" command in default option.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: h5 files containing single cell gene expression count, produced by Cellranger. These files can be used for further process with single-cell RNA-seq analysis tools (e.g. Seurat, SCE).

source_name: Scgb1a1-lineage cells

extract_protocol:
After 5 and 14 days of tamoxifen injection, lungs were extracted from euthanized mice. Cells were sorted with Aria II FACS sorter for CD31-CD45-EpCAM+tdtomato+ cells.
Single-cell RNA-sequencing libraries were constructed using 10X Chromium v.2 e'scRNA seq kit as manufacturer's instruction.

treatment_protocol: Mice were intraperitoneally injected with tamoxifen (250mg/kg) for Scgb1a1-specific cre induction to trace secretory cell knockout Lats1/2 genes.

tag: strain

value: Lats1/2fl/fl; Scgb1a1-creER;tdTomato

tag: tissue

value: lung

value: sorted CD31-CD45-EpCAM+tdTomato+ secretory cells

tag: time point

value: 5 days post tamoxifen


title: Secretory cell - D14

description:
D14
PolyA RNA extracted from single cells
Single-cell RNA-seq (3', 10X Chromium, v2)

tag: cell type

value: 14 days post tamoxifen


title: B-ALL patient A42-2 replicate2

tag: age


title: Gout patient peripheral blood mononuclear cells_rep2

city: Nanchong City

first: daifei

last: dai

state: Sichuan Province

address: No. 234, Fujiang Road, Shunqing District

institute: North Sichuan Medical College

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed and  fixed.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA purification was prepared using TRIzol reagent (Invitrogen, Gran Island, NY, USA) according to the manufacturer’s instructions followed by the application of PBMCs to RNeasy spin columns (Qiagen, Venlo, Limburg, Netherlands). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

treatment_protocol: Peripheral blood anticoagulated with ethelene diamine tetraccetic (EDTA) was obtained from all subjects. Human peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-Hypaque gradients.

tag: subject status

value: Patient with primary gout

tag: tissue/cell type

value: peripheral blood mononuclear cells

value: male


title: Gout patient peripheral blood mononuclear cells_rep5


title: Gout patient peripheral blood mononuclear cells_rep4


title: Gout patient peripheral blood mononuclear cells_rep1


title: Healthy control subject peripheral blood mononuclear cells_rep3

value: Healthy control had no evidence of disease


title: Gout patient peripheral blood mononuclear cells_rep3


title: PCM07: metastatic prostate cancer

city: Dublin 4

first: Antoinette

last: Perry

address: Belfield

country: Ireland

institute: University College Dublin

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to theIllumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadArrays were scanned and the raw signal intensities extracted from the *.IDAT files using the R package minfi.

data_processing:
RnBeads was used to normalize and filter the data
Beta values were calculated as (M/(M+U)), in which M and U refer to the mean methylated and unmethylated probe signal intensities, respectively

label: Cy3, Cy5

source_name: rapid autopsy, lymph node metastasis

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted and purified from prostate tissue samples using the QIAamp DNA micro kit (Qiagen)  according to standard instructions

value: metastatic prostate cancer

tag: age at surgery/autopsy (years)

tag: psa at diagnosis (ng/ml)

tag: grade of tumor area microdissected

value: Gleason 4+5


title: PCM11: metastatic prostate cancer

source_name: rapid autopsy, liver metastasis

value: Gleason 5+4


title: PBL-3: peripheral blood lymphocyte - intrachip technical replicate

description: This sample excluded from the final analysis

source_name: commerically available

value: peripheral blood lymphocyte


title: PBL-2: peripheral blood lymphocyte


title: PCM04: metastatic prostate cancer

value: Gleason 4+4


title: Secretory cell - Control

description:
Control
PolyA RNA extracted from single cells
Single-cell RNA-seq (3', 10X Chromium, v2)

value: Lats1/2fl/+; Scgb1a1-creER;tdTomato


title: B-ALL patient A104

value: Female

tag: wbc at diagnosis (x109/l)

tag: ph chromosome

tag: dct(hadhb-gapdh)

tag: h4k5 cr/h3

tag: h4k5 bu/h3

value: low

value: high


title: PCM05: metastatic prostate cancer

tag: gender


title: PBL-1: peripheral blood lymphocyte - interchip technical replicate


title: 4RDKO_cut

tag: treatment

value: Injury 1 dpi, ipsilateral

tag: genotype

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: 4LDKO_sham_2ndlane

value: Sham 1 dpi, contralateral nerve


title: Drug-tolerant cells and no-drug control cells

city: Nutley

first: Rocio

last: Garcia-Rubio

state: New Jersey

address: 111 Ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

description:
96 well plate
Wells A1-A12 logarithmic no-drug control; Wells B1-B12 stationary no-drug control; C1-E12 caspofungin tolerant cells; F1-H12 Micafungin tolerant cells

data_processing:
aligned to the reference using STAR and to genes using featureCounts
bam files produced by featureCounts were sorted and indexed with samtools
package umi_tools was used to assemble a count matrix
sctransform was used to normalize count data
Seurat was then used perform differential expression testing with Wilcoxon rank sum test between groups
Genome_build: GCF_000002545.3_ASM254v2
Supplementary_files_format_and_content: all_plates_umi_counts DECODED.csv, Dataset1.xlsx

organism: Nakaseomyces glabratus

source_name: Yeast cells

growth_protocol: YPD 37°C (C. glabrata)

extract_protocol:
zymolyase (5U per 10 µl of cells) for 30 minutes at 37°C
40U Maxima H- (ThermoFisher), 2X Maxima H- Buffer (ThermoFisher), 4U SuperaseIN (ThermoFisher), 15% polyethylene glycol, and 2uM Template Switching Oligo (IDT) in a total volume of 7.5 µl.

treatment_protocol: 0.06 µg/ml micafungin or 0.25 µg/ml caspofungin for 24 hours

tag: strain

value: mixed sample (non-demultiplexed) consisting of micafungin-tolerant cells, caspofungin-tolerant cells, logarithmic no-drug control, stationary no-drug control


title: PCM03: metastatic prostate cancer

tag: tissue


title: PCM01: metastatic prostate cancer

value: Gleason 5+5


title: Healthy control subject peripheral blood mononuclear cells_rep1

value: peripheral blood mononuclear cells


title: Healthy control subject peripheral blood mononuclear cells_rep2

value: male


title: B-ALL patient A103

value: Pos.

tag: h4k5 cr high low

tag: h4k5 bu high low


title: 4LDKO_sham

tag: age


title: B-ALL patient A107

value: Neg.


title: PCA10: primary prostate cancer epithelium

source_name: radical prostatectomy prostate FFPE

value: primary prostate cancer epithelium

value: Gleason 4+3, pT3b


title: 3RWT_cut_2ndlane

value: Kdm6a wt/y, Kdm6b fl/fl


title: B-ALL patient A102

value: Male


title: PCA08: primary prostate cancer epithelium

value: Gleason 4+4, pT3b


title: PCA06: primary prostate cancer epithelium


title: 3RWT_cut


title: PCA03: primary prostate cancer epithelium

value: Gleason 4+4, pT3a


title: B-ALL patient A101

value: low


title: PCA09: primary prostate cancer epithelium

value: Gleason 4+3, pT3a


title: PCA02: primary prostate cancer epithelium


title: B-ALL patient A100

value: high


title: PCI13: primary prostate cancer epithelium

value: Gleason 3+3, pT2c


title: PCA05: primary prostate cancer epithelium

value: Gleason 4+3, pT3


title: PCA01: primary prostate cancer epithelium

value: Gleason 5+3, pT3b


title: 3LWT_sham_2ndlane

value: Sham 1 dpi, contralateral nerve


title: PCI06-2: primary prostate cancer epithelium - FFPE interchip technical replicate


title: 3LWT_sham


title: 2RDKO_cut_2ndlane

value: Injury 1 dpi, ipsilateral

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: SVRS_2050 PANC1 polyA RNA-seq Inh 3day

data_processing:
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using HMM (Sanz et. al, 2016). For both, HTseq-count v0.6.0 was then used to count the total number of reads of each peak (sDRIP-seq) or genes (RNA-seq).
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). sDRIP-seq bed files were generated using HMM and converted into bigBed using bedToBigBed

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
RNA-seq: Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
RNA-seq: Standard paired-end TruSeq protocol.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

tag: disease state

value: PDAC

tag: cell line

value: Inh 3d


title: SVRS_2051 PANC1 polyA RNA-seq Inh 3day


title: PCI10: primary prostate cancer epithelium

value: primary prostate cancer epithelium

value: male

tag: age at surgery/autopsy (years)

tag: psa at diagnosis (ng/ml)


title: 2RDKO_cut


title: SVRS_2049 PANC1 polyA RNA-seq Inh 3day


title: PCI06-1: primary prostate cancer epithelium

tag: grade of tumor area microdissected


title: PCI04: primary prostate cancer epithelium


title: PCI05: primary prostate cancer epithelium


title: SVRS_2048 PANC1 polyA RNA-seq DMSO 3day

value: DMSO 3d


title: PCI02: primary prostate cancer epithelium


title: 2LDKO_sham_2ndlane


title: PCI01: primary prostate cancer epithelium


title: 2LDKO_sham


title: SVRS_2047 PANC1 polyA RNA-seq DMSO 3day


title: HGPIN07: High-grade prostatic intraepithelial neoplasia


title: HGPIN06: High-grade prostatic intraepithelial neoplasia


title: HGPIN05: High-grade prostatic intraepithelial neoplasia


title: SVRS_2045 PANC1 polyA RNA-seq Inh 2day

value: Inh 2d


title: SVRS_2046 PANC1 polyA RNA-seq DMSO 3day


title: PIA10: Proliferative inflammatory atrophy

value: Proliferative inflammatory atrophy


title: SVRS_2044 PANC1 polyA RNA-seq Inh 2day


title: HGPIN01: High-grade prostatic intraepithelial neoplasia


title: HGPIN02: High-grade prostatic intraepithelial neoplasia


title: PIA05: Proliferative inflammatory atrophy


title: PIA02: Proliferative inflammatory atrophy


title: PIA03: Proliferative inflammatory atrophy


title: PIA01: Proliferative inflammatory atrophy


title: PIA09: Proliferative inflammatory atrophy


title: SVRS_2041 PANC1 polyA RNA-seq DMSO 2day

value: DMSO 2d


title: SVRS_2042 PANC1 polyA RNA-seq DMSO 2day


title: B12: benign prostate epithelium

source_name: radical cystoprostatectomy prostate FFPE

value: benign prostate epithelium


title: SVRS_2043 PANC1 polyA RNA-seq Inh 2day


title: B11: benign prostate epithelium


title: SVRS_2040 PANC1 polyA RNA-seq DMSO 2day


title: B10: benign prostate epithelium

source_name: transurethral resection of the prostate FFPE


title: SVRS_2039 PANC1 polyA RNA-seq Inh 1day

value: Inh 1d


title: B08: benign prostate epithelium


title: SVRS_2038 PANC1 polyA RNA-seq Inh 1day


title: HGPIN08: High-grade prostatic intraepithelial neoplasia


title: B06: benign prostate epithelium


title: B05: benign prostate epithelium


title: SVRS_2037 PANC1 polyA RNA-seq Inh 1day


title: B03: benign prostate epithelium


title: B04: benign prostate epithelium


title: B01: benign prostate epithelium


title: B02: benign prostate epithelium


title: PIA07: Proliferative inflammatory atrophy


title: SVRS_2036 PANC1 polyA RNA-seq DMSO 1day

value: DMSO 1d


title: SVRS_2035 PANC1 polyA RNA-seq DMSO 1day


title: yth1-4

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 89
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis. primers.gff contains the primer sequences used in this analysis.

organism: Saccharomyces cerevisiae

source_name: Saccharoymces cerevisiae in YPAD media at 37ºC

growth_protocol: Yeast cells were grown at 25ºC until an OD600 of 0.6 then switched to 37ºC for 1 hour. 2 biological replicates were included.

extract_protocol:
Samples were harvested at 37ºC. Cells were spun down by centrifugation and stored at -80ºC until mPAT analysis.
Libraries were prepared according to the mPAT approach (Beilharz et al. 2017)


title: SVRS_2034 PANC1 polyA RNA-seq DMSO 1day


title: ysh1-13


title: yhh1-3


title: SVRS_2033 PATC53 polyA RNA-seq Inh 3day


title: ssu72-2


title: SVRS_2031 PATC53 polyA RNA-seq Inh 3day


title: SVRS_2030 PATC53 polyA RNA-seq DMSO 3day


title: rna15-1