title: ZT 12 KO IgA+ PC replicate 4

data_processing:
Raw non-normalised counts were imported into R and subsequently analysed using the DESeq2 package , using the default pipeline.
Genes with a total of fewer than ten counts across all samples were removed, and normalisation was calculated using the DESeq() function with default parameters for estimating size factors and dispersions. Differential expression was then calculated using the results() function with the default parameters. Genes with a significance value of less than 0.01 after correction for multiple comparisons using the Benjamini-Hochberg method were defined as “differentially expressed” and taken forward for further analysis. In some cases heatmaps were generated from normalised counts using the counts (normalised = TRUE) function followed by scaling and centring.
Hierarchical clustering of genes was then computed using the ComplexHeatmap package.. In other cases, clustering and normalised counts were then exported to excel and plotted in Graphpad Prism.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: DESeq Normalised Counts

value: Mb1Cre-/- x Arntlfl/fl


title: ZT 0 IgA+ PC replicate 5

status: Public on Sep 02 2022

type: SRA

city: Manchester

first: Matthew

last: Hepworth

address: AV Hill Building

country: United Kingdom

institute: University of Manchester

library_source: transcriptomic

data_processing:
FPKM values were generated
Heatmap outputs were generated in GraphPad Prism
Supplementary_files_format_and_content: Matrix table with raw gene counts or FPKM normalised values for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: IgA+ Plasma Cells (small intestinal)

extract_protocol:
Collagenase D and Dnase I isolation of single cell small intestinal lamina propria cells (see methods of above manuscript)
Sort-purfication of CD138+ IgA+ Plasma Cells via fluorscence activated cell sorting (FACS)
Samples lysed in Qiagen RLT buffer and processed as per manufacturer's instructions (RNA mini kit)
Normalised RNA was used to generate libraries using NEB Next Ultra RNA library Prep Kit (Illumina). Indices were included to multiplex samples and mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesised using random hexamer primers followed by second strand cDNA synthesis. Following end repair, A-tailing, adaptor ligation and size section libraries were further amplified and purified and insert size validated on an Agilent 2100, and quantified using quantitative PCR (qPCR). Libraries were then sequenced on an Illumina NovaSeq 6000 S4 flowcell with PE150 according to results from library quality control and expected data volume.

tag: genotype

value: Wild Type

tag: background strain

tag: zeitgeber time


title: SF1

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

country: USA

institute: University of Pittsburgh

library_source: genomic

data_processing:
We used Snakemake (Koster and Rahmann, 2012) to manage the bioinformatics workflow in a reproducible manner.
We used FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We used TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) to trim low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads. Reads shorter than 20bp after trimming are discarded. We aligned trimmed reads to hg19 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the ATAC specific parameters -X 2000 --no-mixed --no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked with Picard (Picard) (v2.20.2). Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard were removed, and alignments below a MAPQ threshold were removed (< 10). These filtering steps are performed with samtools (Li et al., 2009) (v1.2). Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) were removed with bedtools (Quinlan and Hall, 2010) (v2.28.0). Sample-wise peaks were called with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200. Peaks over all samples were then merged with bedops (Neph et al., 2012) (v2.4.36).
Finally, MultiQC (Ewels et al., 2016) (v1.7) generated a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. For ATAQ specific QC metrics we used ataqv (Ataqv) (v1.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Sample-wise narrowPeak files were generated with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200.

molecule: genomic DNA

organism: Homo sapiens

source_name: Dermal fibroblasts

growth_protocol: Two 4 mm punch biopsies from the distal forearm of healthy volunteers and SSc patients were obtained for cell isolation. After skin digestion, cells were grown to 75% confluency on collagen-coated plates before purification. ECs were purified through positive selection using the CD31 MicroBead Kit (Miltenyi Biotech) while negatively selected cells eluted were fibroblasts. A portion of the collected fibroblasts (passage 0) were lysed and underwent tagmentation. Purified ECs were grown on collagen-coated plates maintained in EBM-2 media supplemented with EGM-2 MV Microvascular Endothelial SingleQuots Kit from Lonza. These cells underwent several rounds of purification during expansion and cells with passages between 2 and 6 were used for ATAC-seq library preparation.

extract_protocol:
To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
We followed the steps decribed in "Nature Methods volume 10, pages1213–1218(2013)". For both fibroblasts and ECs (from 6 patients and 6 controls), 50,000 cells were used for the Tn5 transposition reaction, and DNA libraries were prepared.

tag: tissue

value: Skin

tag: cell type

value: Fibroblasts

tag: subject

value: diffuse cutaneous systemic sclerosis patient


title: Col-0, 6h IDL, rep1

city: Umea

first: Clement

last: Boussardon

address: Umeå Plant Science Centre Department of Plant Physiology Umeå University

department: Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

description: Novogene Technology Co., Ltd (HiSeq platforms, paired-end 150 bp sequencing strategy)

data_processing:
The quality of the raw sequence data was assessed using FastQC, v0.11.4. Residual ribosomal RNA (rRNA) contamination was assessed and filtered using SortMeRNA using the rRNA sequences provided with SortMeRNA.
Data were then filtered to remove adapters and trimmed for quality using Trimmomatic. After both filtering steps, FastQC was run again to ensure that no technical artefacts were introduced. Read counts were obtained using kallisto (v0.43.0) with the parameters quant -b 100 --pseudobam -t 1 --rf-stranded and using the TAIR10 cDNA sequences as a reference (retrieved from the TAIR resource).
The kallisto abundance values were imported into R using the Bioconductor58 (v3.3) tximport package. For the data quality assessment and visualization, the read counts were normalized using a variance stabilizing transformation as implemented in DESeq2.
Statistical analysis of gene and transcript differential expression (DE) between conditions was performed in R using the Bioconductor DESeq2 package (v1.14.1), with the following model: ~Line*Hours to account for both the genotype (WT or rpn12a-236) and harvesting time (d0, h6, d1, d3, d6).
FDR adjusted p-values were used to assess significance; a common threshold of 1% was used.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include z-score for each replicate/genotype/time point

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: WT and rpn12a-236 plants were grown under short-day photoperiod, and samples of leaf blades were collected at 8 am, for the 0 day, 1 day, 3 days, 6 days time points for IDL/light control treatments and at 2 pm, for the 6 hours time point for IDL/light control treatments.

extract_protocol:
For all conditions, three biological replicates were used, each of them being a pool of two leaves from independent plants. RNA was extracted from approximately 40 mg of frozen material using an EZNA plant RNA kit following provider recommendations (Omega Bio-tek, R6834-01).
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

value: Leaf

tag: ecotype

tag: time

value: 6 hours

value: Wild type

tag: treatment

value: Individually darkened leaf


title: Col-0, control, rep3

value: 0 day

value: Light control


title: ZT 12 KO IgA+ PC replicate 2


title: ZT 12 KO IgA+ PC replicate 1


title: Col-0, control, rep2


title: NF4

value: Healthy


title: NF5


title: ZT 0 KO IgA+ PC replicate 4


title: ZT 12 KO IgA+ PC replicate 5


title: Group 1_H1_Ap2A_RNAs1

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: 12793_10099_147162_HGHM3BGXK_H1_Ap2A_RNAs1_CTTGTAAT

data_processing:
Demultiplexing, bcl2fastq
Trimming, Group #1 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0, Groups #2-4 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Group #1 Alignment 'hisat2  --phred33 --rna-strandness RF --dta --no-unal' , Group #2 -4 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000'
Groups #2-4 Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group #2 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73, Group #3, callpeak -f BAMPE -g 2913022398 -q 0.05 --call-summits Group #4, callpeak -f BAMPE -g 1218492533  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73
RNA-Seq Quantification Group #1 featureCounts -t exon -s 2 -g gene_id
Assembly: Group #1,2,3 UCSC hg38 Group #4 ENSEMBL galGal6
Supplementary files format and content: .narrowPeak, MACS2 peaks
Supplementary files format and content: .txt, FeatureCounts quantification file
Supplementary files format and content: .bam, alignment files

molecule: polyA RNA

source_name: Human H1 ESC TFAP2A Overexpressing 1

extract_protocol:
Groups #1-3 H1 cells were transfected with virus expressing either GFP or TFAP2A. After one week, transfected cells were isolated via FACS and then processed for various sequencing libraries. Group #4 Chicken embryos were electroporated with a TFAP2AE1-GFP reporter and subjected to FACS sorting. 10,000 GFP negative cells were collected and spun down before ATAC-Seq library construction
Group #1  30k sorted cells were used per sample. RNA was extracted using RNA-Aqueous Micro kit, normalized, and used for NEB Next Ultra II Directional RNA-Sequencing Kit, Group #2 30k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep, Group #3 CUT&RUN libraries with samples of 300k cells each were input normalized and contructed as in Rothstein & Simoes-Costa, Genome Research 2020, Group #4 10k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep.
Group #1 RNA-Seq, Group #2 ATAC-Seq, Group #3 CUT&RUN, Group #4 ATAC-Seq

tag: tissue/cell type

value: Human H1-derived cells

value: TFAP2A Overexpression

tag: group


title: Group 2_H1_GFP_ATAC2

description: 12793_10099_147157_HGHM3BGXK_H1_GFP_ATAC2_CGTACTAG

source_name: Human H1 ESC GFP Overexpressing 2

value: GFP Overexpression


title: Group 1_H1_Ap2A_RNAs2

description: 12793_10099_147163_HGHM3BGXK_H1_Ap2A_RNAs2_AGTCAACA

source_name: Human H1 ESC TFAP2A Overexpressing 2


title: rpn12a-236, 6d IDL, rep3

value: 6 day

value: EMS mutant Q236 => Stop


title: Group 1_H1_GFP_RNAs1

description: 12793_10099_147160_HGHM3BGXK_H1_GFP_RNAs1_TAGCTTAT

source_name: Human H1 ESC GFP Overexpressing 1


title: Group 1_H1_GFP_RNAs2

description: 12793_10099_147161_HGHM3BGXK_H1_GFP_RNAs2_GGCTACAT


title: rpn12a-236, 6d IDL, rep2


title: NF2


title: Col-0, control, rep1


title: ZT 12 KO IgA+ PC replicate 3

value: Mb1Cre-/- x Arntlfl/fl


title: NF3


title: ZT 0 KO IgA+ PC replicate 1

value: Mb1Cre+/- x Arntlfl/fl


title: ZT 0 KO IgA+ PC replicate 2


title: NF1

value: Skin


title: iNCC_Sox2_D3_2_hg38

data_processing:
Library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Alignment, bowtie2, Group #1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --x ~/genome/bowtie2-hg38/hg38 -I 10 -X 1000  Group #2 --x ~/genome/bowtie2-GRCg6a/GRCg6a
Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group#1 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits, Group #2 -g 1218492533
Genome_build: Group #1, UCSC hg38
Genome_build: Group #2, ENSEMBL galGal6 (GRCg6a)
Supplementary_files_format_and_content: .narrowPeak, MACS2 peaks
Supplementary_files_format_and_content: .bed, peak file
Supplementary_files_format_and_content: .bam, alignment files

source_name: iNCC induction Day 3

extract_protocol:
Group #1 - Cultures were dissociated using Accutase and counted to normalize cell input. Group #2, cranial neural fold dissections in HH9 stage chicken embryos.
Libraries were cell input normalized and contructed as in Rothstein & Simoes-Costa, Genome Research 2020

tag: condition

value: D3 CHIR induced iNCC

value: iNCC induction Day 3

tag: antibody

value: Sox2, R&D Systems (AF 2018) 1:50


title: iNCC_Sox2_D3_1_hg38


title: iNCC_Sox2_D5_1_hg38

source_name: iNCC induction Day 5

value: D5 CHIR induced iNCC

value: iNCC induction Day 5


title: ZT 12 WT IgA+ PC replicate 6


title: SEC6

source_name: Dermal microvascular endothelial cells

value: Endothelial cells

value: diffuse cutaneous systemic sclerosis patient


title: rpn12a-236, 3d IDL, rep3

value: Leaf

value: 3 day

value: Individually darkened leaf


title: rpn12a-236, 3d IDL, rep2


title: SEC5


title: ZT 0 KO IgA+ PC replicate 3


title: ZT 12 WT IgA+ PC replicate 5


title: rpn12a-236, 3d IDL, rep1


title: iNCC_Myo_Sox2_D14_2_hg38

source_name: iNCC Myofibril Differentiation Day 14

value: D14 Myofibril differentiation protocol

value: iNCC Myofibril Differentiation Day 14


title: rpn12a-236, 6d IDL, rep1

value: 6 day


title: ZT 12 WT IgA+ PC replicate 4


title: rpn12a-236, 1d IDL, rep3

value: 1 day

value: EMS mutant Q236 => Stop


title: SEC3


title: SEC4


title: SEC1


title: ATAC_Myo_D14_1

data_processing:
Demultiplexing, bcl2fastq
Trimming, CutAdapt v2.10, -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25 -j 0
Alignment, bowtie2, (Groups #1,#2 bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --threads 16 -x ~/genome/bowtie2-GRCg6a/GRCg6a -X 2000), (Group #3,  -x~/genome/hg38/hg38_bt2/GRCh38)
Mark Duplicates, picard MarkDuplicates
Filter Duplicates, samtools v1.9, samtools view -@ 16 -F 1804 -f 2
Call peaks, MACS2, (Groups #1,#2 macs2 callpeak -t "$FILE"  -n "$FILE" -f BAMPE -g 1218492533 -q 0.05 --call-summits  --nomodel --shift 37 --ext 73 -B --SPMR)(Group #3 -g 2913022398)
Combine datasets/R analysis, DiffBind
Genome_build: for Gallus gallus, ENSEMBL galGal6 (GRCg6a)
Genome_build: for Homo sapiens, UCSC hg38
narrowPeak, peak file from MACS2
.RDS, R data file, specifically the S3 Object of class DBA from DiffBind. Contains peak by sample count matrix.
.txt, tab-delim text file, peak by sample matrix for each experiment.

extract_protocol:
Group #1 - Cranial dissection and dissociation using Accumax, Group #2 - Half-head cranial dissection and dissociation using Accumax, Group #3 - culture dissociation using Accutase and counting to normalize cell input.
Cells were processed using the OMNI-ATAC-Seq protocol. Frozen cells were quickly thawed at 37℃ and ATAC-RSB buffer was added to a total volume of 1.5mL. Samples were centrifuged at 500rcf for 5 minutes at 4℃ and the supernatant was removed. Next, cells were resuspended in 100µl of ATAC-RSB-LYSIS and kept on ice for 3-5 minutes, depending on input cell type. To stop lysis, 1mL of ATAC-RSB-WASH was added to each sample and they were again centrifuged for 5 minutes at 500rcf. The supernatant was removed, and cells were resuspended in 50µl of OMNI-ATAC Mix (~100nM concentration of Illumina TDE1 enzyme). Cells were then tagmented on a mixing (500rpm) thermoblock at 37℃ for one hour. Tagmented DNA was recovered using a Qiagen MinElute Kit (#28204), with 21µl of elution buffer warmed to 55℃. Library amplification PCR was performed with the NEBNext Ultra II Q5 2X Master Mix (NEB #M0544S) using Nextera primers for 13-15 cycles.

treatment_protocol: D14, Myofibril differentiation protocol, dissociated via Accutase and normalized cell # input

value: Myofibril


title: SEC2

value: Skin


title: ATAC_Myo_D14_2


title: rpn12a-236, 1d IDL, rep1


title: rpn12a-236, 1d IDL, rep2


title: ATAC_NC_D5_2

treatment_protocol: D5, CHIR induced iNCC, dissociation using Accutase and input cell # normalized for OMNI-ATAC-Seq

value: iNCC


title: iNCC_Myo_Sox2_D14_1_hg38


title: ZT 12 WT IgA+ PC replicate 3

value: Mb1Cre-/- x Arntlfl/fl


title: ZT 12 WT IgA+ PC replicate 1


title: rpn12a-236, 6h IDL, rep3

value: 6 hours


title: ATAC_NC_D5_1


title: ZT 0 WT IgA+ PC replicate 6


title: ZT 12 WT IgA+ PC replicate 2


title: NEC6

value: Healthy


title: NEC5


title: ZT 0 WT IgA+ PC replicate 5


title: ATAC_NC_D3_2

treatment_protocol: D3, CHIR induced iNCC, dissociation using Accutase and input cell # normalized for OMNI-ATAC-Seq

value: iNCC induction Day 3


title: NEC4

value: Endothelial cells


title: NEC3


title: ATAC_NC_D3_1


title: ZT 0 WT IgA+ PC replicate 4


title: ZT 0 WT IgA+ PC replicate 3


title: ZT 0 WT IgA+ PC replicate 2


title: NEC2


title: ZT 0 WT IgA+ PC replicate 1


title: ATAC_ES_D0_2

source_name: hESC without treatment

treatment_protocol: D0, no treatment hESCs, dissociation using Accutase and input cell # normalized for OMNI-ATAC-Seq

value: ESCs

value: hESC without treatment


title: rpn12a-236, control, rep2

value: Leaf

value: 0 day

value: Light control


title: rpn12a-236, 6h IDL, rep2

value: Individually darkened leaf


title: rpn12a-236, control, rep1


title: ATAC_ES_D0_1


title: AphPulsed-MLH1KO-clone3-WGS

status: Public on Sep 01 2022

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

data_processing:
PacBio circular consensus sequencing (CCS) reads were aligned by SMRT analysis (v10.1.0) pbmm2 (https://github.com/PacificBiosciences/pbmm2) to hg19 reference genome with parameters --preset CCS.
Mutations and indels in pacBio data were called by DeepVariant (v1.1.0) 72 and structure variations were identified by pbsv (https://github.com/PacificBiosciences/pbsv) command of SMRT analysis.

Assembly: hg19
Library strategy: WGS

source_name: Human retinal pigment epithelial-1

growth_protocol: RPE-hTERT TP53KO cells were grown in medium supplemented with 10% fetal bovine serum (FBS), penicillin 100 μg ml−1 (Sigma Aldrich), streptomycin 100 μg ml−1 (Sigma Aldrich), and L-glutamine 292 μg ml−1 (Gibco).

extract_protocol:
Approximately 20 million cells were harvested by centrifuging at 500 g for 5 min at 4 degree. High molecular weight DNA was prepared using Nanobind Big DNA CBB kit (Circulomics) according to manufacturer’s instructions. In brief, cells were washed with PBS and resuspended in 20 ul PBS followed by 20 μl proteinase K and 20 μl CLE3 buffer. The tube was pulse vortexed 10 times and incubated in thermomixture at 55 degree for 10 minutes at 900 rpm, followed by RNAse A treatment for 3 minutes at room temperature (RT). To lyse the cells, 200 μl of BL3 buffer were added, pulse vortexed 10 times, and incubated at 55 dgree at 900 rpm for 10 minutes. Nanodisk was added to the cell lysate followed by 300 μl of isopropanol, mixed 5x by inversion, followed by further mixing at 9 rpm using tube rotator at RT for 10 minutes. Tubes were placed on magnetic tube rack in a way that Nanobind bead remained captured near the top to avoid touching DNA with pipette tip. Supernatant were discarded and beads were washed 4 times each with buffer CW1 and CW2. High molecular weight DNA was eluted by 100 μl of Qiagen EB buffer. Purity of the DNA was analyzed using TapeStation.
DNA samples were sheared 10-13 kb fragments for library preparation. WGS libraries of the samples were sequenced on PacBio SMRT cell using Sequel II with standard PacBio protocol. Samples yielded 1.78 M to 2.35 M ccs reads, with mean read length 9.44 kb and mean quality QV38.0.

treatment_protocol: The MLH1-/- parental clone was treated with a low dose of APH for 24 hours and allowed cells to recover for 2 to 3 days. APH pulses were then applied 20 additional times, after which individual clones were isolated.

value: Human retinal pigment epithelial-1

value: 20 cycles Aph pulsed

value: MLH1KO p53KO


title: NonAphPulsed-MLH1KO-WGS

institute: Center for Excellence in Molecular Cell Science

value: NT


title: AphPulsed-MLH1KO-clone2-WGS


title: Apeltes_f8_dorsal_spine_3_L/L_rep3

city: Stanford

first: David

middle: M

last: Kingsley

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

data_processing:
Trimming: all raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 2.4) and FastQC (ver. 0.11.9) with adapter overlap stringency of 1 and Phred quality score cutoff of 20.
Mapping: STAR 2-pass mapping (ver. 2.7.4)
Read counts: FeatureCounts in the Subread package (v.2.0.1) was used to count the reads in each gene
Genome_build: 4apeltes_draft.1.0un.fa
Supplementary_files_format_and_content: gene count table

organism: Apeltes quadracus

source_name: dorsal spine 3

extract_protocol:
tissues were dissected from fish and flash frozen in liquid nitrogen and stored at -80 degrees.  The tissues were homogenized in a MP FastPrep with Matrix A for embryos and Matrix M for all other tissues.  RNA was extracted with Takara NucleoSpin RNA XS kit with an on-column DNase step.
20-200 ng of RNA was used to make sequencing libraries with Illumina Stranded mRNA Prep kit according to manufacturer's instructions. PCR cycle number was determined by qPCR
RNA-seq; All RNA-Seq libraries were sequenced on a Illumina NovaSeq 6000 by Novogene

tag: Stage

value: finfold stage (stage 31)

tag: parental populations

value: Louisbourg

tag: hoxdb genotype

value: L/L


title: Apeltes_f3_dorsal_spine_last_L/L_rep2

source_name: last dorsal spine


title: Apeltes_f8_dorsal_fin_L/L_rep3

source_name: dorsal fin


title: AphPulsed-MLH1KO-clone1-WGS


title: Apeltes_f8_pterygiophore_L/L_rep3

source_name: pterygiophore


title: Apeltes_f8_dorsal_spine_last_L/L_rep3


title: Apeltes_f8_dorsal_spine_1_L/L_rep3

source_name: dorsal spine 1


title: Apeltes_f3_anal_fin_L/L_rep2

source_name: anal fin


title: NEC1

value: Skin


title: rpn12a-236, 6h IDL, rep1

source_name: Leaf

value: 6 hours

value: EMS mutant Q236 => Stop


title: Apeltes_f3_dorsal_spine_1_L/L_rep2


title: rpn12a-236, control, rep3


title: Apeltes_f3_pterygiophore_L/L_rep2


title: Apeltes_f1_anal_fin_L/L_rep1


title: Apeltes_f3_dorsal_spine_2_L/L_rep2

source_name: dorsal spine 2


title: Apeltes_f8_anal_fin_L/L_rep3


title: Apeltes_f3_dorsal_spine_3_L/L_rep2


title: Apeltes_f1_dorsal_spine_2_L/L_rep1


title: Apeltes_f1_pterygiophore_L/L_rep1


title: Apeltes_f1_dorsal_spine_1_L/L_rep1


title: Apeltes_f1_dorsal_spine_last_L/L_rep1


title: Apeltes_f1_dorsal_spine_3_L/L_rep1


title: Apeltes_f1_dorsal_fin_L/L_rep1


title: Apeltes_f8_dorsal_spine_2_L/L_rep3


title: Apeltes_f39_dorsal_spine_last_L/LHR_rep4

data_processing:
Sequencing: All RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 by Novogene.
Trimming: All raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 2.4) and FastQC (ver. 0.11.9) with adapter overlap stringency of 1 and Phred quality score cutoff of 20.
Mapping: STAR 2-pass mapping (ver. 2.7.4).
Data cleanup: The best practices as outlined by gatk for RNA-seq short variant discovery were followed using picard (ver. 2.23.4) to mark and sort duplicates, samtools (ver.1.10) to index, splitNCigarReads (ver. gatk4/4.1.4.1), and Base Recalibration (ver. gatk4/4.1.4.1). This produced the analysis ready .bam files for read counts.
Variant Discovery: HaplotypeCaller (ver. gatk4/4.1.4.1) was used to identify variants in the dataset, and bcftools (ver 1.11) was used to identify only the biallelic SNPs for further downstream analysis. This produced a .vcf file that was used to generate the read counts.
Read Counts: ASEReadCounter (ver. gatk4/4.1.4.1) was used to generate a table of allele counts at variants found in the populations (.vcf).
Genome_build: 4apeltes_draft.1.0un.fa
Supplementary_files_format_and_content: *.tab: Tables of allele counts at SNPs present in the two populations.

growth_protocol: Fry were generated by in vitro fertilization and raised in 10% seawater at 16 degrees C in a petri dish until they were 11-13mm in standard length.

extract_protocol:
Tissues were dissected from fish and flash frozen in liquid nitrogen and stored at -80 degrees. The tissues were homogenized in a MP FastPrep with Matrix M. RNA was extracted with Takara NucleoSpin RNA XS kit with an on-column DNase step.
20-100 ng of RNA was used to make sequencing libraries with Illumina Stranded mRNA Prep kit according to manufacturer's instructions. PCR cycle number was determined by qPCR.

value: L/LHR

value: last dorsal spine


title: Apeltes_f39_pterygiophore_L/LHR_rep4

value: pterygiophore


title: Apeltes_f38_anal_fin_L/LHR_rep3

value: anal fin


title: Apeltes_f38_pterygiophore_L/LHR_rep3


title: Apeltes_f38_dorsal_fin_L/LHR_rep3

value: dorsal fin


title: Apeltes_f39_dorsal_spine_3_L/LHR_rep4

value: dorsal spine 3


title: Apeltes_f39_dorsal_spine_1_L/LHR_rep4

value: dorsal spine 1


title: Apeltes_f38_dorsal_spine_last_L/LHR_rep3


title: Apeltes_f39_anal_fin_L/LHR_rep4


title: Apeltes_f38_dorsal_spine_1_L/LHR_rep3


title: Apeltes_f21_dorsal_fin_L/LHR_rep2


title: Apeltes_f21_pterygiophore_L/LHR_rep2


title: Apeltes_f21_dorsal_spine_3_L/LHR_rep2


title: Apeltes_f21_dorsal_spine_1_L/LHR_rep2


title: Apeltes_f21_dorsal_spine_last_L/LHR_rep2


title: Apeltes_f21_anal_fin_L/LHR_rep2


title: Apeltes_f21_dorsal_spine_2_L/LHR_rep2

value: dorsal spine 2


title: Apeltes_f6_anal_fin_L/LHR_rep1


title: Apeltes_f3_dorsal_fin_L/L_rep2


title: Apeltes_f6_dorsal_spine_3_L/LHR_rep1


title: Apeltes_f6_dorsal_fin_L/LHR_rep1


title: Apeltes_f6_dorsal_spine_last_L/LHR_rep1


title: Apeltes_f6_pterygiophore_L/LHR_rep1


title: Apeltes_f6_dorsal_spine_4_L/LHR_rep1

source_name: dorsal spine 4

value: dorsal spine 4


title: Apeltes_f6_dorsal_spine_1_L/LHR_rep1


title: Apeltes_f38_dorsal_spine_3_L/LHR_rep3


title: Apeltes_f39_dorsal_fin_L/LHR_rep4


title: Apeltes_f38_dorsal_spine_2_L/LHR_rep3


title: Apeltes_f36_dorsal_spine_last_H/L_rep4

value: H/L


title: Apeltes_f36_dorsal_spine_4_H/L_rep4


title: Apeltes_f36_dorsal_fin_H/L_rep4


title: Apeltes_f36_dorsal_spine_3_H/L_rep4


title: Apeltes_f36_dorsal_spine_2_H/L_rep4


title: Apeltes_f36_pterygiophore_H/L_rep4


title: Apeltes_f39_dorsal_spine_2_L/LHR_rep4


title: Apeltes_f34_dorsal_fin_H/L_rep3


title: Apeltes_f34_dorsal_spine_last_H/L_rep3


title: Apeltes_f34_pterygiophore_H/L_rep3


title: Apeltes_f6_dorsal_spine_2_L/LHR_rep1


title: Apeltes_f34_dorsal_spine_2_H/L_rep3


title: Apeltes_f34_dorsal_spine_4_H/L_rep3


title: Apeltes_f34_dorsal_spine_3_H/L_rep3


title: Apeltes_f34_dorsal_spine_1_H/L_rep3


title: Apeltes_f31_pterygiophore_H/L_rep2


title: Apeltes_f31_dorsal_spine_last_H/L_rep2


title: Apeltes_f31_dorsal_spine_2_H/L_rep2


title: Apeltes_f31_dorsal_spine_4_H/L_rep2


title: Apeltes_f31_dorsal_spine_3_H/L_rep2


title: Apeltes_f31_dorsal_spine_1_H/L_rep2


title: Apeltes_f24_dorsal_fin_H/L_rep1


title: Apeltes_f36_anal_fin_H/L_rep4


title: Apeltes_f36_dorsal_spine_1_H/L_rep4


title: Apeltes_f24_dorsal_spine_last_H/L_rep1


title: Apeltes_f34_anal_fin_H/L_rep3


title: Apeltes_f24_dorsal_spine_2_H/L_rep1


title: Apeltes_f24_dorsal_spine_4_H/L_rep1


title: Apeltes_f24_pterygiophore_H/L_rep1


title: Apeltes_f24_anal_fin_H/L_rep1


title: Apeltes_f29_dorsal_fin_H/LHR_rep3

value: H/LHR


title: Apeltes_f24_dorsal_spine_3_H/L_rep1

value: finfold stage (stage 31)


title: Apeltes_f24_dorsal_spine_1_H/L_rep1

value: Louisbourg


title: Apeltes_f29_anal_fin_H/LHR_rep3


title: Apeltes_f29_dorsal_spine_last_H/LHR_rep3


title: Apeltes_f31_anal_fin_H/L_rep2


title: Apeltes_f29_pterygiophore_H/LHR_rep3


title: Apeltes_f29_dorsal_spine_4_H/LHR_rep3


title: Apeltes_f31_dorsal_fin_H/L_rep2


title: Apeltes_f5_anal_fin_H/LHR_rep2


title: Apeltes_f29_dorsal_spine_1_H/LHR_rep3


title: Apeltes_f29_dorsal_spine_2_H/LHR_rep3


title: Apeltes_f5_pterygiophore_H/LHR_rep2


title: Apeltes_f5_dorsal_spine_last_H/LHR_rep2


title: Apeltes_f5_dorsal_fin_H/LHR_rep2


title: Apeltes_f5_dorsal_spine_4_H/LHR_rep2


title: Apeltes_f4_anal_fin_H/LHR_rep1


title: Apeltes_f5_dorsal_spine_3_H/LHR_rep2


title: Apeltes_f4_pterygiophore_H/LHR_rep1


title: Apeltes_f4_dorsal_fin_H/LHR_rep1


title: Apeltes_f4_dorsal_spine_last_H/LHR_rep1


title: Apeltes_f4_dorsal_spine_4_H/LHR_rep1


title: Apeltes_f4_dorsal_spine_3_H/LHR_rep1


title: LITC x High-spine Embryo236 Rep12

data_processing:
Sequencing: All RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 by Novogene.
Trimming: All raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 2.4) and FastQC (ver. 0.11.9) with adapter overlap stringency of 1 and Phred quality score cutoff of 20.
Mapping: STAR 2-pass mapping (ver. 2.7.4).
Data cleanup: The best practices as outlined by gatk for RNA-seq short variant discovery were followed using picard (ver. 2.23.4) to mark and sort duplicates, samtools (ver.1.10) to index, splitNCigarReads (ver. gatk4/4.1.4.1), and Base Recalibration (ver. gatk4/4.1.4.1). This produced the analysis ready .bam files for read counts.
Variant Discovery: HaplotypeCaller (ver. gatk4/4.1.4.1) was used to identify variants in the dataset, and bcftools (ver 1.11) was used to identify only the biallelic SNPs for further downstream analysis. This produced a .vcf file that was used to generate the read counts.
Read Counts: ASEReadCounter (ver. gatk4/4.1.4.1) was used to generate a table of allele counts at variants found in the populations (.vcf).
Genome_build: gasAcu1-4 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.547d7wm6t)
Supplementary_files_format_and_content: *.tab: Tables of allele counts at SNPs present in the two populations.

organism: Gasterosteus aculeatus

source_name: whole embryo

growth_protocol: Embryos were generated by in vitro fertilization and raised in 10% seawater at 16 degrees C in a petri dish until 72 hours post fertilization.

extract_protocol:
Embryos were flash frozen in liquid nitrogen at 72 hours post fertilization and stored at -80 degrees. The tissues were homogenized in a MP FastPrep with Matrix A. RNA was extracted with Qiagen All-prep DNA/RNA kit.
200 ng of total RNA was used to make sequencing libraries with Illumina Stranded mRNA Prep kit according to manufacturer's instructions. 12 PCR cycle were done to generate the libraries.

value: 72 hours post fertilization; stage 19/20

value: LITC x High-spine

value: Whole embryo


title: LITC x High-spine Embryo229 Rep10


title: LITC x High-spine Embryo230 Rep11


title: Apeltes_f4_dorsal_spine_2_H/LHR_rep1


title: Apeltes_f4_dorsal_spine_1_H/LHR_rep1


title: LITC x High-spine Embryo228 Rep9


title: LITC x High-spine Embryo223 Rep7


title: Apeltes_f29_dorsal_spine_3_H/LHR_rep3


title: LITC x High-spine Embryo215 Rep4


title: LITC x High-spine Embryo219 Rep5


title: Gasterosteus_f55_dorsal_fin_3sp_rep12


title: LITC x High-spine Embryo2_9 Rep2


title: Gasterosteus_f55_anal_fin_3sp_rep12


title: LITC x High-spine Embryo2_4 Rep1


title: Gasterosteus_f55_dorsal_spine_last_3sp_rep12

source_name: dorsal spine last

value: dorsal spine last


title: Apeltes_f5_dorsal_spine_1_H/LHR_rep2


title: Gasterosteus_f53_anal_fin_3sp_rep11


title: Gasterosteus_f55_dorsal_spine_1_3sp_rep12


title: Apeltes_f5_dorsal_spine_2_H/LHR_rep2


title: Gasterosteus_f55_dorsal_spine_2_3sp_rep12


title: LITC x High-spine Embryo213 Rep3


title: Gasterosteus_f53_pterygiophore_3sp_rep11


title: Gasterosteus_f51_anal_fin_3sp_rep10


title: Gasterosteus_f53_dorsal_spine_last_3sp_rep11


title: Gasterosteus_f53_dorsal_spine_1_3sp_rep11


title: Gasterosteus_f55_pterygiophore_3sp_rep12


title: LITC x High-spine Embryo225 Rep8


title: Gasterosteus_f51_dorsal_spine_last_3sp_rep10


title: Gasterosteus_f51_dorsal_fin_3sp_rep10


title: LITC x High-spine Embryo220 Rep6


title: Gasterosteus_f53_dorsal_fin_3sp_rep11


title: Gasterosteus_f53_dorsal_spine_2_3sp_rep11


title: Gasterosteus_f51_dorsal_spine_2_3sp_rep10


title: Gasterosteus_f45_dorsal_fin_3sp_rep9


title: Gasterosteus_f51_dorsal_spine_1_3sp_rep10


title: Gasterosteus_f45_anal_fin_3sp_rep9


title: Gasterosteus_f45_dorsal_spine_last_3sp_rep9


title: Gasterosteus_f45_pterygiophore_3sp_rep9


title: Gasterosteus_f51_pterygiophore_3sp_rep10


title: Gasterosteus_f45_dorsal_spine_1_3sp_rep9


title: Gasterosteus_f38_anal_fin_3sp_rep8


title: Gasterosteus_f45_dorsal_spine_2_3sp_rep9


title: Gasterosteus_f38_dorsal_spine_1_3sp_rep8


title: Gasterosteus_f38_dorsal_fin_3sp_rep8


title: Gasterosteus_f38_dorsal_spine_last_3sp_rep8


title: Gasterosteus_f34_dorsal_spine_last_3sp_rep7


title: Gasterosteus_f38_dorsal_spine_2_3sp_rep8


title: Gasterosteus_f34_dorsal_fin_3sp_rep7


title: Gasterosteus_f34_dorsal_spine_1_3sp_rep7


title: Gasterosteus_f34_pterygiophore_3sp_rep7


title: Gasterosteus_f34_dorsal_spine_2_3sp_rep7


title: Gasterosteus_f30_dorsal_spine_last_3sp_rep6


title: Gasterosteus_f30_dorsal_fin_3sp_rep6


title: Gasterosteus_f30_pterygiophore_3sp_rep6


title: Gasterosteus_f30_dorsal_spine_2_3sp_rep6


title: Gasterosteus_f30_anal_fin_3sp_rep6


title: Gasterosteus_f30_dorsal_spine_1_3sp_rep6


title: Gasterosteus_f28_anal_fin_3sp_rep5


title: Gasterosteus_f28_dorsal_fin_3sp_rep5


title: Gasterosteus_f28_pterygiophore_3sp_rep5


title: Gasterosteus_f28_dorsal_spine_last_3sp_rep5


title: Gasterosteus_f28_dorsal_spine_2_3sp_rep5


title: Gasterosteus_f38_pterygiophore_3sp_rep8


title: Gasterosteus_f22_dorsal_spine_last_3sp_rep4


title: Gasterosteus_f22_anal_fin_3sp_rep4


title: Gasterosteus_f22_dorsal_fin_3sp_rep4


title: Gasterosteus_f34_anal_fin_3sp_rep7


title: Gasterosteus_f22_pterygiophore_3sp_rep4


title: Gasterosteus_f22_dorsal_spine_1_3sp_rep4


title: Gasterosteus_f21_dorsal_spine_last_3sp_rep3


title: Gasterosteus_f21_dorsal_fin_3sp_rep3


title: Gasterosteus_f21_anal_fin_3sp_rep3


title: Gasterosteus_f21_pterygiophore_3sp_rep3


title: Gasterosteus_f22_dorsal_spine_2_3sp_rep4


title: Gasterosteus_f21_dorsal_spine_2_3sp_rep3


title: Gasterosteus_f14_anal_fin_3sp_rep2


title: Gasterosteus_f21_dorsal_spine_1_3sp_rep3


title: Gasterosteus_f14_dorsal_spine_last_3sp_rep2


title: Gasterosteus_f14_pterygiophore_3sp_rep2


title: Gasterosteus_f14_dorsal_spine_2_3sp_rep2


title: Gasterosteus_f14_dorsal_spine_1_3sp_rep2


title: Gasterosteus_f7_dorsal_spine_last_3sp_rep1


title: Gasterosteus_f7_anal_fin_3sp_rep1


title: Gasterosteus_f14_dorsal_fin_3sp_rep2


title: Gasterosteus_f7_dorsal_spine_2_3sp_rep1


title: Gasterosteus_f7_pterygiophore_3sp_rep1


title: Gasterosteus_f7_dorsal_spine_1_3sp_rep1


title: Gasterosteus_f28_dorsal_spine_1_3sp_rep5


title: Gasterosteus_f7_dorsal_fin_3sp_rep1


title: Gasterosteus_f54_dorsal_fin_4sp_rep6


title: Gasterosteus_f54_dorsal_spine_last_4sp_rep6


title: Gasterosteus_f54_dorsal_spine_3_4sp_rep6


title: Gasterosteus_f54_pterygiophore_4sp_rep6


title: Gasterosteus_f54_dorsal_spine_2_4sp_rep6


title: Gasterosteus_f54_dorsal_spine_1_4sp_rep6


title: Gasterosteus_f54_anal_fin_4sp_rep6


title: Gasterosteus_f36_anal_fin_4sp_rep5


title: Gasterosteus_f36_dorsal_spine_3_4sp_rep5


title: Gasterosteus_f36_dorsal_spine_2_4sp_rep5


title: Gasterosteus_f36_pterygiophore_4sp_rep5


title: Gasterosteus_f36_dorsal_fin_4sp_rep5


title: Gasterosteus_f36_dorsal_spine_last_4sp_rep5


title: Gasterosteus_f35_anal_fin_4sp_rep4


title: Gasterosteus_f35_dorsal_fin_4sp_rep4


title: Gasterosteus_f35_pterygiophore_4sp_rep4


title: Gasterosteus_f35_dorsal_spine_last_4sp_rep4


title: Gasterosteus_f32_anal_fin_4sp_rep3


title: Gasterosteus_f36_dorsal_spine_1_4sp_rep5


title: Gasterosteus_f35_dorsal_spine_3_4sp_rep4


title: Gasterosteus_f32_dorsal_fin_4sp_rep3


title: Gasterosteus_f35_dorsal_spine_2_4sp_rep4


title: Gasterosteus_f32_pterygiophore_4sp_rep3


title: Gasterosteus_f32_dorsal_spine_last_4sp_rep3


title: Gasterosteus_f35_dorsal_spine_1_4sp_rep4


title: Gasterosteus_f32_dorsal_spine_2_4sp_rep3


title: Gasterosteus_f32_dorsal_spine_3_4sp_rep3


title: Gasterosteus_f15_anal_fin_4sp_rep2


title: Gasterosteus_f32_dorsal_spine_1_4sp_rep3


title: Gasterosteus_f15_dorsal_spine_3_4sp_rep2


title: Gasterosteus_f15_dorsal_spine_2_4sp_rep2


title: Gasterosteus_f15_dorsal_spine_1_4sp_rep2


title: Gasterosteus_f15_dorsal_spine_last_4sp_rep2


title: Gasterosteus_f11_anal_fin_4sp_rep1


title: Gasterosteus_f11_dorsal_spine_last_4sp_rep1


title: Gasterosteus_f11_dorsal_spine_3_4sp_rep1


title: Gasterosteus_f11_dorsal_spine_1_4sp_rep1


title: Gasterosteus_f11_dorsal_spine_2_4sp_rep1


title: Gasterosteus_f11_dorsal_fin_4sp_rep1


title: Gasterosteus_f15_pterygiophore_4sp_rep2


title: Gasterosteus_f15_dorsal_fin_4sp_rep2


title: PCa_35

type: RNA

city: Brno

first: Jaroslav

last: Juracek

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

description:
Test
miRNAs from prostate cancer tissue

data_processing:
The data normalization was performed using GenEx software.
Data were recalculated using interplate calibration (IPC, UniSp3) and normalized on geometric mean of reference genes expression level (hsa‑miR‑26a‑5p, hsa-miR‑26b‑5p, and hsa-miR‑30e‑5p).
Target gene signals normalized to reference miRNAs; 2^-deltaCt, where deltaCt = (Ct_Target − gMean of Ct_hsa‑miR‑26a‑5p, hsa-miR‑26b‑5p, and hsa-miR‑30e‑5p).

label: SYBR Green

source_name: prostatic tissue, FFPE

extract_protocol: Total RNA was extracted with mirVana miRNA Isolation Kit (Ambion Inc, Austin, TX, USA)

tag: age

tag: isup grade

tag: ct

tag: cgs

tag: iPSa

tag: pt

tag: pgs


title: PCa_36

description:
Test
miRNAs from prostate cancer tissue


title: PCa_38

description:
Test
miRNAs from prostate cancer tissue


title: PCa_37

description:
Test
miRNAs from prostate cancer tissue


title: PCa_39

description:
Test
miRNAs from prostate cancer tissue


title: PCa_30

description:
Test
miRNAs from prostate cancer tissue


title: PCa_29

description:
Test
miRNAs from prostate cancer tissue


title: PCa_33

description:
Test
miRNAs from prostate cancer tissue


title: PCa_31

description:
Test
miRNAs from prostate cancer tissue


title: PCa_32

description:
Test
miRNAs from prostate cancer tissue


title: PCa_34

description:
Test
miRNAs from prostate cancer tissue


title: PCa_28

description:
Test
miRNAs from prostate cancer tissue


title: PCa_40

description:
Test
miRNAs from prostate cancer tissue


title: Gasterosteus_f11_pterygiophore_4sp_rep1

tag: tissue


title: PCa_24

description:
Test
miRNAs from prostate cancer tissue


title: PCa_27

description:
Test
miRNAs from prostate cancer tissue


title: PCa_26

description:
Test
miRNAs from prostate cancer tissue


title: PCa_23

description:
Test
miRNAs from prostate cancer tissue


title: PCa_25

description:
Test
miRNAs from prostate cancer tissue


title: PCa_22

description:
Test
miRNAs from prostate cancer tissue


title: PCa_20

description:
Test
miRNAs from prostate cancer tissue


title: PCa_18

description:
Test
miRNAs from prostate cancer tissue


title: PCa_19

description:
Test
miRNAs from prostate cancer tissue


title: PCa_17

description:
Test
miRNAs from prostate cancer tissue


title: PCa_16

description:
Test
miRNAs from prostate cancer tissue


title: PCa_15

description:
Test
miRNAs from prostate cancer tissue


title: PCa_10

description:
Test
miRNAs from prostate cancer tissue


title: PCa_06

description:
Test
miRNAs from prostate cancer tissue


title: PCa_09

description:
Test
miRNAs from prostate cancer tissue


title: PCa_11

description:
Test
miRNAs from prostate cancer tissue


title: PCa_13

description:
Test
miRNAs from prostate cancer tissue


title: PCa_12

description:
Test
miRNAs from prostate cancer tissue


title: Late CTL rep1

city: Bethesda

first: Taehoon

last: Shin

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina HiSeq 3000 per cycle basecall files were demultiplexed and converted to FASTQ files with adaptor masking using bcl2fastq
High-quality reads were mapped to the ENSEMBL Mmul_8.0.1 whole genome reference FASTA and annotated with the ENSEMBL Mmul_8.0.1 release 95 GTF
Tools from bioconductor in a standard workflow were used to produce BAM files and count matrices for primary analysis
Secondary analysis was carried out with a custom pipeline written in R
Genome_build: ENSEMBL Mmul_8.0.1
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

organism: Macaca mulatta

source_name: Peripheral blood

growth_protocol: Rhesus macaque peripheral blood mononuclear cells (PBMNCs) were isolated via centrifugation over Lymphocyte Separation Medium (LSM) and treatment with ACK lysing buffer. Cells were stained with CD14-PE, CD16-BV605 and CD163-BV421 antibodies and CD14+CD16-CD163+ macrophage population was purified usgin a FACSARIA-II flow sorter (BD).

extract_protocol:
RNA was extracted using RNAzol reagent.
cDNA was synthesized using the SMART-Seq V4 Ultra Low Input RNA Kit and libraries were generated using the Nextera XT DNA Library Preparation Kit.

treatment_protocol: Sorted macrophages were plated at a density of 250,000 cells/well in a 24-well plate and incubated for 8 hours in the presence (activated: ACT) or absence (control: CTL) of 100 ng/ml lipopolysaccharide (LPS) and 20 ng/ml interferon-gamma (IFN-r).

tag: cell type

value: Macrophages

value: Peripheral blood

tag: timing

value: 19 months post-transplantation

value: control


title: Early ACT rep 3

value: 4.5 months post-transplantation

tag: treatment

value: activated (LPS)


title: PCa_05

description:
Test
miRNAs from prostate cancer tissue


title: PCa_04

description:
Test
miRNAs from prostate cancer tissue


title: PCa_02

description:
Test
miRNAs from prostate cancer tissue


title: Late CTL rep3


title: PCa_08

description:
Test
miRNAs from prostate cancer tissue


title: PCa_01

description:
Test
miRNAs from prostate cancer tissue


title: Early ACT rep 2


title: PCa_21

description:
Test
miRNAs from prostate cancer tissue


title: Late ACT rep2


title: Late CTL rep2


title: Early ACT rep 1


title: Early CTL rep3


title: Late ACT rep1


title: Early CTL rep2


title: Early CTL rep1


title: PCa_14

description:
Test
miRNAs from prostate cancer tissue


title: S1_END_seq_KM12_G2arrest_replicate2

data_processing:
END-seq reads were aligned to hg19 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Assembly: hg19

growth_protocol: iPS cell culture was performed as previously described. Tissue culture-treated dishes were coated with human embryonic cell (hES cell)-qualified matrigel (Corning, ref 354277). Matrigel was removed and iPS cells were plated in Essential 8 Medium (E8; Thermo Fisher Scientific, cat. no. A1517001) and 10 μM ROCK inhibitor (RI; Y-27632; Selleckchem, cat. no. S1049). iPS cells were maintained in an incubator at 37 °C with 5% CO2 and fed every 1–2 days as needed. Cells were split using either accutase (Life Technologies, cat. no. A1110501) for enzymatic dissociation into single cells or EDTA (0.5 mM; Life Technologies, cat. no. 15575020) for routine passaging. Medium was supplemented with 10 μM RI to promote survival during passaging. As necessary, iPS cells were frozen in 90% ES cell-qualified fetal bovine serum (FBS) (Sigma Aldrich, cat. no. ES-009-B) and 10% DMSO (Mediatech, cat. no. 25-950-CQC), and then thawed rapidly at 37 °C, followed by removal of FBS/DMSO and plating in E8 + RI medium. Colon cancer cancer (KM12, SW837, SW48, SW620 and RKO). KM12, SW837, and SW48 cells were grown in RPMI1640 media (Gibco), SW620 was grown in Leibovitz’s L-15 (Gibco) media. RKO was grown in Dulbecco's Modified Eagle Medium (DMEM – Gibco). FRDA patient (GM15850) and an unaffected sibling (GM15851) lymphoblasts were grown in RPMI1640 media (Gibco) supplemented with 15% FBS, penicillin 100 μg ml−1 and streptomycin 100 μg ml−1. Cell lines were tested for mycoplama contamination. Cells were maintained at 37°C and 5% CO2.

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: shWRN induction was perfomed using doxycycline 2mg/mL for 48 hours. For G2 arrest, cells were treated with CDK1 inhibitor (RO3306) for 24 hours. For induction of replication stress, cells were treated with aphidicolin 600 nM for 24 hours. G1 arrest was performed using CDK4/6 inhibitor (palbociclib) for 24 hours. Disruption of triplex formation was performed by treatting cells with the polyamide PA1 1 mM for 48 hours. iPSC differentiation into neurons was performed through the treatment with doxycycline (CONCENTRATION)

value: CDK1 inhibitor (RO3306) for 24 hours

tag: endseq type

tag: genotype

value: WT


title: Late ACT rep3


title: S1_END_seq_KM12_DMSO_replicate2

value: DMSO 0,1% for 24 hours


title: S1_END_seq_KM12_APH600nM_replicate2

value: Aphidicolin 600 nM for 24 hours


title: PCa_03

description:
Test
miRNAs from prostate cancer tissue


title: S1-END-seq_HACAT

data_processing:
END-seq reads were aligned to hg19 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser

Assembly: hg19
Library strategy: END-seq

source_name: HACAT

value: HACAT

value: NT


title: S1_END_seq_KM12_Paired_with_P1-END-seq


title: S1-END-seq_NHEK

source_name: Primary normal human epithelial keratinocytes (NHEK)


title: S1-END-seq_PrimaryFibroblasts

source_name: Primary human skin fibroblast

value: Primary human skin fibroblast


title: S1-END-seq_GM15850_G1arrest

source_name: v-ABL immortalyzed human lymphocytes - GM15850

value: CDK4/6 inhibitor (palbociclib) for 24 hours

value: Friedrich's ataxia patient cells


title: S1-END-seq_GM15850_DMSO

value: v-ABL immortalyzed human lymphocytes - GM15850

value: DMSO 0,1% 24 for hours


title: S1-END-seq_MCF10A_DMSO


title: S1_END_seq_iPSC_i3N_day2_replicate2

data_processing:
END-seq reads were aligned to hg19 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser

Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: ENDseq

source_name: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 2 days

tag: cell line


title: S1-END-seq_MCF10A_G1arrest


title: S1_END_seq_iPSC_i3N_day5

source_name: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 5 days


title: S1_END_seq_iPSC_replicate1

source_name: Human induced pluripotent stem cell (hiPSC)


title: S1_END_seq_iPSC_i3N_day2_replicate1

value: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 2 days


title: S1-END-seq_SW48_G1arrest


title: END_seq_KM12_replicate1

value: END-seq

value: Doxycycline inducible shWRN


title: END_seq_KM12_replicate2


title: S1-END-seq_SW48_DMSO


title: END_Seq_KM12_shWRN_NT


title: S1_END_seq_iPSC_i3N_day1_replicate2

source_name: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 1 days


title: S1_END_seq_iPSC_i3N_day1_replicate1

value: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 1 days


title: END_Seq_KM12_shWRN_Dox48h

value: Doxycycline 2mg/mL for 48 hours


title: S1_END_seq_iPSC_i3N_day3_replicate1

source_name: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 3 days


title: P1_END_seq_GM15851

source_name: v-ABL immortalyzed human lymphocytes - GM15851


title: S1_END_seq_GM15850_PA1_replicate1

value: PA1 1 microM for 48 hours


title: S1_END_seq_GM15850_DMSO_replicate2


title: S1_END_seq_GM15851_PairedwithP1_END_Seq

value: v-ABL immortalyzed human lymphocytes - GM15851


title: S1_END_seq_GM15850_PA1_replicate2


title: S1_END_seq_GM15850_DMSO_replicate1


title: S1_END_seq_iPSC_replicate2

value: Human induced pluripotent stem cell (hiPSC)


title: S1_END_seq_iPSC_i3N_day3_replicate2

value: Human induced pluripotent stem cell (hiPSC), neuronal differentiation via i3N for 3 days


title: S1_END_seq_KM12_G1arrest


title: S1_END_seq_GM15851_DMSO

value: DMSO 0,1% for 48 hours

value: WT


title: S1_END_seq_KM12_G2arrest

value: CDK1 inhibitor (RO3306) for 24 hours


title: S1_END_seq_KM12_DMSO

value: DMSO 0,1% for 24 hours


title: S1_END_seq_KM12_APH600nM

value: Aphidicolin 600 nM for 24 hours


title: S1_END_seq_KM12_shWRN_Dox48h


title: S1_END_seq_SW837_replicate2

value: NT


title: S1_END_seq_KM12_replicate2


title: S1_END_seq_KM12_replicate3


title: S1_END_seq_SW48_replicate2


title: S1_END_seq_RKO_replicate2

source_name: RKO

value: RKO


title: S1_END_seq_SW620_replicate2


title: S1_END_seq_SW837_replicate1


title: S1_END_seq_RKO_replicate1


title: S1_END_seq_GM15851_PA1


title: S1_END_seq_SW48_replicate1


title: S1_END_seq_KM12_replicate1


title: S1_END_seq_KM12_shWRN_NT


title: c42b_Veh

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
Assembly: hg38
Supplementary files format and content: fastq

growth_protocol: C4-2B cells were maintained in media, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Cells were treated overnight with 1 µM (R)-9b (dz67)

value: Human breast cancer

value: cell line

value: Vehicle treated


title: c42b_9b

value: (R)-9b treated


title: glioblastoma tissue 33t

city: Jinan

first: Gang

state: Shandong

address: 107 Wenhua Xi Road

department: Neurosurgery

institute: Qilu Hospital of Shandong University

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-2.0.4 and  paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then  FPKM was calculated.It normalizes for both  sequencing depth and genome size.
(For samples with biological replicates, edgeR_3.24.3 (lncRNA)) Differential expression analysis of two conditions/groups  (at least two biological replicates per condition/group) was performed using the edgeR.The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for  controlling the false discovery rate . Genes with an adjusted P-value <0.05 were  assigned as differentially expressed ones.
Assembly: Ensembl 91
Supplementary files format and content: csv files include readcount values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: glioblastoma tissue

extract_protocol:
Total RNA was extracted from glioblastoma tissue using TRIzol reagent (Life Technologies, Carlsbad, CA, USA).
A total of 1 µg total RNA per sample was used as input material for the lncRNA  library preparation. Strand-specific libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Flash-frozen in liquid nitrogen after surgical resection

value: glioblastoma tissue


title: glioblastoma tissue 34t


title: glioblastoma tissue 44t


title: S1_END_seq_SW620_replicate1


title: G2/M_control_rep2

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: WT drosophila S2 cells

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: Arrays were processed in Bioconductor, using RMA background correction, quantile normalization and RMA summarization.

label: biotin

organism: Drosophila melanogaster

source_name: WT drosophila S2 cells

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: RNA was isolated using magnetic beads from 25000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 15 cycles.

tag: genotype/variation

tag: cell cycle status


title: G1_SLIMPKD_rep2

description: SLIMP knockdown drosophila S2 cells

source_name: SLIMP knockdown drosophila S2 cells

value: SLIMP knockdown


title: glioblastoma tissue 32t


title: glioblastoma tissue 26t


title: G2/M_control_rep1

description: WT drosophila S2 cells


title: G1_SLIMPKD_rep3

description: SLIMP knockdown drosophila S2 cells


title: G2/M_SLIMPKD_rep3

description: SLIMP knockdown drosophila S2 cells


title: G1_control_rep2

description: WT drosophila S2 cells


title: glioblastoma tissue 43t


title: HCC15-CTNNB1

city: Maebashi

first: Noriaki

last: Sunaga

state: Gunma

address: 3-39-15 Showa-machi

department: Department of Respiratory Medicine

country: Japan

institute: Gunma University Graduate School of Medicine

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250

source_name: HCC15 treated with CTNNB1 siRNA

label_protocol: biotin

growth_protocol: RPMI 1640 medium with 5% fetal bovine serum was used for culturing cell lines.

extract_protocol: Qiagen RNeasy kit including DNase1 treatment

treatment_protocol: HCC15 cells were transfected with an siRNA targeting CTNNB1 and were collected at 48 h post-transfection, followed by tRNA extraction from the cells.

tag: histology

value: Lung cancer cell line

tag: subtype

value: Squamous

value: CTNNB1 siRNA


title: G2/M_control_rep3

description: WT drosophila S2 cells


title: G1_control_rep1

description: WT drosophila S2 cells


title: HCC15-Tax

source_name: HCC15 treated with control siRNA

value: control siRNA


title: HRGECs-NETs4

city: Chongiqng

first: Fengfan

last: Zheng

address: No.1 Youyi Street, Yuzhong District, Chongqing, China

institute: Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Clean reads were aligned to the mus musculus ensembl 92 using HISAT2(Langmead,  B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set  as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow  algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
Genome_build: human_genes_Ensembl_98
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

source_name: renal glomerular endothelial cells

growth_protocol: human renal glomerular endothelial cells were cultured in Endothelial Cell Medium  (ECM, ScienCell, Cat. #1001).

extract_protocol:
Total RNA from cells was extracted using Trizol reagent.
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 rRNAdepleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Five replicates were NETs or vehicle treated for 12 hours.

value: NETs


title: G1_control_rep3

description: WT drosophila S2 cells

value: WT


title: G2/M_SLIMPKD_rep2

description: SLIMP knockdown drosophila S2 cells


title: glioblastoma tissue 15t


title: P1_END_seq_KM12


title: glioblastoma tissue 24t


title: HRGECs-NETs2

value: human renal glomerular endothelial cells


title: HRGECs-NETs1


title: glioblastoma tissue 12t


title: glioblastoma tissue 10t


title: glioblastoma tissue 11t


title: HRGECs-NETs3


title: glioblastoma tissue 1t


title: HRGECs-vehicle control5

value: vehicle


title: DHF4b

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

institute: University of Oxford

data_processing:
Quality control analysis with the fastQC package (www.bioinformatics.babraham.ac.uk/projects/fastqc)
Reads were aligned using STAR against the hg38 human genome assembly
Nonuniquely mapped reads and reads that were identified as PCR duplicates using SAMtools were discarded.
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package with default parameters.
Expression counts were transformed using variance stabilizing transformation (vst) using the DESeq2 R package (v1.34.0.
Differential expression analyses were performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include variance stabilizing transformation values for each Sample ...

source_name: blood cells

extract_protocol:
ILC2 were sorted directly into lysis buffer (0.2% Triton X-100 solution) containing RNase inhibitor
Lysed samples were processed to form cDNA libraries using Nextera XT and SmartSeq2 protocols. RNA-Sequencing was performed in triplicate on an Illumina Hi-Seq 4000 generating 75bp reads

treatment_protocol: ILC2 were isolated from PBMCs of healthy individuals and patients with DF and DHF

tag: disease state

value: dengue hemorrhagic fever

value: blood

tag: cell lineage

value: Lineage -, CD3 -, CD45+, CRTH2 +, IL-7Ra+


title: HRGECs-vehicle control4


title: HRGECs-vehicle control2


title: HRGECs-vehicle control3


title: HRGECs-NETs5


title: DHF3


title: DHF4


title: DHF3c


title: DHF3b


title: DHF4c


title: DHF2b


title: DHF2


title: XXT

city: Durham

first: Xiling

last: Shen

state: NC

address: 101 Science Dr., CIEMAS

department: Biomedical Engineering

institute: Duke University

data_processing:
Drop-seq datasets were analyzed using the Broad Institute Drop-seq pipeline software (https://github.com/broadinstitute/Drop-seq).
10x Genomics datasets were analyzed using the CellRanger pipeline software (version 3.1.0) to demultiplex BCL files, generate fastqs, and generate feature counts.
Gene expression matrices for the drop-seq datasets were produced using the first 4,000 cellular barcodes with the largest number of reads associated with each index.
All default parameter values for both the Drop-seq pipeline and CellRanger v3.1.0 pipeline software were used to generate processed data files.
Genome_build: hg19
Supplementary_files_format_and_content: "tab-separated expression matrix" is the output from the Broad Drop-seq proccessing pipeline and is a gene x cell barcode matrix of integer counts. "hdf5 feature barcode matrix" is the output from the 10x Genomics CellRanger proccessing pipeline and is a binary encoding of a gene x cell barcode matrix of integer counts.

source_name: lung

growth_protocol: Micro organospheres were grown in tumor culture medium supplemented with required growth factors in basal medium.

extract_protocol:
We extracted cells from droplets by dissociating 3D matrix using TypLE and incubation.
For drop seq technology, we followed Dolomite Drop-seq scRNA library protocol. For 10X scRNA librariy preparation, we followed 10X Next GEM 3' scRNA seq library kit (V3.1) protocol.

treatment_protocol: We treated micro organospheres with either ESK1* drug or negative control drug, or no drug for 24 hours before the cells were dissociated for singlec cell RNA-seq assays.

tag: subject id

value: XX

tag: tissue/cell type

value: tumor

value: untreated

value: lung

value: cancer


title: XXD

value: droplet organoid


title: 532T


title: DHF2c


title: DHF1b


title: 516T

source_name: kidney

value: kidney


title: HRGECs-vehicle control1


title: DHF1c


title: DF3b

value: dengue fever


title: 500T


title: 500D


title: 506D

source_name: ovarian

value: ovarian


title: DF3


title: DF2c


title: 516D


title: inactive_ALKBH5_dox_plus_input1

city: Guangzhou

first: Guoshi

last: Chai

address: No. 135, Xingang Xi Road

department: School Of Life Sciences

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Library strategy: m6A-RIP-Seq
m6A-seq reads were aligned to the hg9 genome assembly using hisat2 with default parameters
Multiple-alignment reads were filtered using Samtools to retain reads with map quality (MapQ) scores above 30 and with properly oriented read mates
macs2 was used to call m6A peaks
exomePeak was used to call differential m6A peaks
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2; differential peak files were generated using exomePeak.

source_name: Human embryonic stem cells

growth_protocol: NKX2-5eGFP/w hESCs were maintained in E8 medium (STEMCELL Technologies) on Matrigel-coated (BD Biosciences) plates with daily medium changes. At about 60%–70% confluency, NKX2-5eGFP/w hESCs were washed with phosphate-buffered saline (PBS, Hyclone) once and incubated in 0.5 mM EDTA (Thermo Fisher Scientific) for 3–5 minutes at room temperature. EDTA was removed from the plate and the cells were gently washed off via E8 medium containing Rho-associated protein kinase (Rock) inhibitor Y-27632 (5 μΜ, Selleck) (Watanabe et al., 2007) and passaged onto Matrigel-coated plates at 1:6 to 1:8 dilutions. Rock inhibitor was removed on the next day after passage. Both cells were incubated at 37 °C with 5% CO2.

extract_protocol:
Cells were washed with PBS and lysed with TRIzol (Thermo Fisher Scientific). Then trichloromethane (Guangzhou Chemical Reagent Factory) was used to extract the total RNA from the TRIzol lysate. Isopropanol (Sangon Biotech) was used to precipitates RNA from the mixture. mRNA was separated from the total RNA by using the Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
The m6A immunoprecipitation method was the same as above. Input samples and IP samples were applied for NGS library construction by using the NEBNext® Ultra II Directional RNA Library Prep (NEB) according to the manufacturer’s guide. The adaptor ligated DNAs amplified by PCR for 15 cycles were sequenced on the HiSeqX sequencing platform.

value: Human embryonic stem cells

tag: passages

tag: strain

tag: ip antibody


title: DF4

tag: tissue


title: DF1c


title: DF4b


title: inactive_ALKBH5_dox_minus_ip1

tag: cell type

value: rabbit monoclonal anti-m6A antibody (NEB, E1610S)


title: active_ALKBH5_dox_plus_ip1


title: DF2b


title: DF1


title: DF2


title: 532D

tag: treatment


title: inactive_ALKBH5_dox_minus_input1


title: active_ALKBH5_dox_plus_input1


title: DF1b


title: DHF1


title: 506T


title: active_ALKBH5_dox_minus_ip2


title: HC4b

value: healthy


title: inactive_ALKBH5_dox_plus_ip1


title: active_ALKBH5_dox_minus_ip1


title: active_ALKBH5_dox_plus_ip2


title: active_ALKBH5_dox_minus_input1


title: HC4


title: HC3c


title: HC3


title: ETOH_7DPF_2

city: Boston

first: Olivia

last: Weeks

state: MA

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

description:
OW5_FAE_7dpf_2
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 1% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.

data_processing:
Reads were aligned to the GRCz10 reference assembly with the STAR aligner and differential gene expression was performed with DESeq2 software. Heatmap visualization and hierarchical clustering was performed using the R package pheatmap with the default parameters.
Genome_build: GRCz10
Supplementary_files_format_and_content: raw_counts.sort.primary_7dpf.csv: Comma-separated text file containing gene names, raw read counts, and normalized read counts.

organism: Danio rerio

source_name: whole zebrafish larvae

growth_protocol: Larval zebrafish were housed on the nursery in 0.8L tanks with mesh baffles at a density of 32 fish per tank beginning at 5 dpf. At 5 dpf, fish received a paramecia starter culture and were kept overnight without flow. At 6 dpf, flow was initiated, and larvae were administered a specified diet. Normal larval diet included hatched artemia two times per day at a density of ~8.8mg dry weight/fish. All larvae were maintained on their diet until the point of collection.

extract_protocol:
RNA was extracted in TRIzol (Life Technologies) from whole pooled (30 individuals/sample) larvae and purified using the Qiagen RNeasy Mini Kit. RNA quality was verified on the Agilent Bioanalyzer and DNA contamination was removed with the TURBO DNA-free (Invitrogen) kit.
Single-end NextSeq Series High-Output RNA sequencing was performed on poly-A selected coding mRNAs at the Dana Farber Center for Cancer Computational Biology.

treatment_protocol: Zebrafish larvae were exposed to 0% or 1.0% EtOH dissolved in fish water from 12 hpf – 5 dpf. Fish were removed from EtOH at 5 dpf, and kept in 28C system water with paramecia starter culture (food) from 5 - 7 dpf.

value: AB

value: WT

tag: developmental stage

value: 7 dpf

value: homogenized whole animals

value: EtOH


title: ETOH_7DPF_3

description:
OW6_FAE_7dpf_3
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 1% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.

tag: genotype


title: HC2b

value: blood

value: Lineage -, CD3 -, CD45+, CRTH2 +, IL-7Ra+


title: active_ALKBH5_dox_plus_input2


title: ETOH_7DPF_1

description:
OW4_FAE_7dpf_1
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 1% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.


title: HC2c


title: HC4c


title: CT_7DPF_3

description:
OW3_CT_7dpf_3
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 0% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.

value: Control


title: CT_7DPF_2

description:
OW2_CT_7dpf_2
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 0% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.


title: HC2


title: HC1


title: HC1b


title: active_ALKBH5_dox_minus_input2


title: HeLa cells, LrGA20 treatment, 12hour, biol rep3

city: College Station

first: Jonathan

middle: Thomas

last: Sczepanski

state: Texas

address: 580 Ross Street

department: Chemistr y

institute: Texas A&M University

data_processing:
Raw data was trimmed by Trim Galore (version 0.6.6), aligned using STAR (version 2.7.7a), and counts were generating using FeatureCounts (Subread version 2.0.2)
Assembly: human reference genome (hg38)
Supplementary files format and content: counts

source_name: HeLa

extract_protocol:
total RNA was extracted by TriaZol reagent, and purified by PureLink RNA mini kit
Library was perpared using NEBNext® Ultra™ II RNA Library Prep Kit

tag: cell line

value: HeLa

value: epithelial cell


title: HeLa cells, lipofectamine only, 12hour, biol rep3

value: lipofectamine


title: HeLa cells, LrGGAA8 treatment, 12hour, biol rep3


title: HC3b


title: C_CK3

city: Qingdao

first: Mei

last: Wang

address: Binhai road 72

institute: Shandong University

description: Triticum aestivum L.

data_processing:
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, and paired-end clean reads were aligned to the reference genome using Hisat2v2.0.5.
featureCounts v1.5.0-p3 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.
Supplementary_files_format_and_content: FPKMs, counts

organism: Triticum aestivum

source_name: wild type, upper part of the seedlings

extract_protocol:
wheat seedlings without roots were frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: age

value: two months after germination

value: untreated

value: upper part of the seedlings


title: HeLa cells, LrGA20 treatment, 12hour, biol rep2


title: HeLa cells, untreated, 12hour, biol rep3


title: HeLa cells, LrGCGC treatment, 12hour, biol rep2

value: LrGCGC


title: C_CK1

description: Triticum aestivum L.


title: HC1c

value: healthy


title: CT_7DPF_1

description:
OW1_CT_7dpf_1
Whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Fish were treated with 0% EtOH from 12 hpf - 5 dpf and placed into system water (28C) containing paramecium starter culture from 5 - 7 dpf.

value: AB


title: HeLa cells, LrGGAA8 treatment, 12hour, biol rep2

value: WT


title: C22_3

description: Triticum aestivum L.

source_name: TaSIP1∆C overexpression line C22, upper part of the seedlings

value: TaSIP1{delta}C overexpression line C22


title: HeLa cells, lipofectamine only, 12hour, biol rep2


title: HeLa cells, LrGCGC treatment, 12hour, biol rep3


title: HeLa cells, untreated, 12hour, biol rep2


title: C22_1

description: Triticum aestivum L.


title: C22_2

description: Triticum aestivum L.


title: HeLa cells, LrGA20 treatment, 12hour, biol rep1


title: C20_3

description: Triticum aestivum L.

source_name: TaSIP1∆C overexpression line C20, upper part of the seedlings

value: TaSIP1{delta}C overexpression line C20


title: Recombinant human thrombomodulin treated mouse 3 30 hours after LPS administration_heart

city: Gifu

first: Hideshi

last: Okada

address: 1-1 Yanagido

department: Emergency and Disaster Medicine

institute: Gifu University Graduate School of Medicine

description:
obtained from C57BL6 male heart
10 weeks old

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse treated by recombinant human thrombomodulin after LPS administration

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ten week-old male C57BL6 mice were obtained from Chubu Kagaku Shizai Co. Ltd. (Nagoya, Japan).

extract_protocol: Total RNA was extracted using a RNeasy kit (Qiagen, TX, USA) according to the manufacturer’s protocol. cDNAs were synthesized using a SuperScript III First-Strand Synthesis Kit (Life Technologies, Inc., MD, USA).

treatment_protocol: Following 16-h starvation, mice were intraperitoneally injected with LPS (20 mg/kg; MilliporeSigma, Burlington, MA), and in some assays, with saline or recombinant human thrombomodulin (rhTM; Asahi Kasei Pharma Corporation, Tokyo, Japan) at 3 and 24 h post-LPS injection.

value: heart

tag: Sex

value: Male

value: 10 weeks old


title: HeLa cells, LrGCGC treatment, 12hour, biol rep1


title: Recombinant human thrombomodulin treated mouse 1 30 hours after LPS administration_heart


title: C20_2

description: Triticum aestivum L.


title: Recombinant human thrombomodulin treated mouse 2 30 hours after LPS administration_heart


title: C20_1

description: Triticum aestivum L.


title: HeLa cells, LrGGAA8 treatment, 12hour, biol rep1


title: Saline treated mouse 2 30 hours after LPS injected_heart

source_name: mouse treated by saline after LPS administration


title: Saline treated mouse 3 30 hours after LPS injected_heart


title: Saline treated mouse 1 30 hours after LPS injected_heart


title: HeLa cells, lipofectamine only, 12hour, biol rep1


title: C40_3

description: Triticum aestivum L.

source_name: TaSIP1∆C overexpression line 40C, upper part of the seedlings

value: TaSIP1{delta}C overexpression line 40C


title: C_CK2

description: Triticum aestivum L.


title: C40_2

description: Triticum aestivum L.


title: C40_1

description: Triticum aestivum L.


title: HeLa cells, untreated, 12hour, biol rep1

value: HeLa


title: hiPSC-L1 OT 3

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

institute: Michigan State University

data_processing:
FastQC for basic quality control
HISAT2 for alignment
featureCounts for read counts
edgeR for normalization and differential expression analysis
Assembly: hg38
Supplementary files format and content: Excel sheet with normalized counts and differential expression analysis

source_name: Epicardial cells

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and concentration was determined using a Qubit Fluorometer (Thermo Fisher Scientific); RNA quality was tested using the Agilent 2100 Bioanalyzer, and samples were sequenced using an Illumina HiSeq 4000
Libraries were prepared using the Illumina TruSeq Stranded mRNA-Seq Library Preparation Kit with IDT for Illumina Unique Dual Index adapters following manufacturer's recommendations.
Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were then pooled in equimolar proportions for multiplexed sequencing and the pool quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit. This pool was loaded onto one (1) lane of an Illumina HiSeq 4000 flow cell and sequencing was performed in a 1x50bp single read format using HiSeq 4000 SBS reagents. Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.

value: hiPSC-derived epicardial cells

value: 100 nM OXT


title: hiPSC-L1 OT 1


title: hiPSC-L1 OT 2


title: Ddr2 slie/slie uninjured [Day_7_DDR2_sli_uninjured_S2]

city: Dallas

first: Alec

last: Bancroft

address: 6000 Harry Hines Blvd

department: Surgery

institute: University of Texas Southwestern Medical Center

library_source: transcriptomic single cell

data_processing:
Cell Ranger Single Cell Software Suite was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) by the UT Southwestern McDermott Sequencing Core.
Assembly: mm10
Supplementary files format and content: filtered matrix files and raw, unfiltered fastq

source_name: hindlimb tissue

extract_protocol:
Tenotomy injury site, which includes the Achilles’ tendon, from the tendon-muscular junction at the gastrocnemius muscle to the calcaneal enthesis, and surrounding tissue posterior to the tibia, was dissected one week following injury. Tissue was finely minced then digested for 20 minutes in 750 ul/ml type 1 collagenase and 7 U/ml dispase II mixture (Gibco) with Roswell Park Memorial Institute (RPMI) medium at 37oC with agitation at 160 rpm. Digestions were quenched with 2% FBS and filtered through 40 micron strainers. The resulting cell suspension was washed in 2% FBS in PBS. Cells were counted and resuspended at 1000-12000 cells/ul. Viability was determined using Countess II (Thermo Fisher Scientific). Samples with greater than 85% viability were submitted for sequencing.
50K reads per cell. 3 Prime gene expression. 150 cycle high output (500 M). Read 1 Run Configuration: 28bp. Read 2 Run Configuration: 98bp. i7: 10bp. i5: 10bp.

treatment_protocol: Ddr2 slie/slie mice (n=2) and littermate controls (n=2) were placed under isoflurane anesthesia and provided subcutaneous buprenorphine analgesic prior to 30% total body surface area dorsal burn and concurrent left Achilles’ tenotomy by fine dissection. Following surgery, mice were placed in a cage on a heating pad and observed during recovery.

value: hindlimb tissue

value: DDR2 slie/slie

value: uninjured hindlimb


title: Ddr2 slie/slie injured [Day_7_DDR2_sli_injured_S1]

value: Burn/tenotomy injury


title: Littermate control uninjured [Day_7_WT_uninjured_S4]

value: littermate control


title: hiPSC-L1 CTRL 3

value: Untreated


title: hiPSC-L1 CTRL 1


title: RA-HA_K27L_24_rep1-RNA

city: Jerusalem

first: Lea

last: Cohen

address: Edmond J. Safra Campus

country: Israel

institute: HUJI

data_processing:
RNA FASTQ files were aligned to the mm9 genome using STAR  (version 2.7.1)
Assembly: mm9
Supplementary files format and content: raw counts

source_name: RA-treated embriyonic stem cells

growth_protocol: Cells were cultured on gelatin-coated tissue culture plates in ESC media without Lif, with RA

extract_protocol:
Cells were flash frozen in liquid nitrogen, RNA was prepared using RNeasy (Qiagen) according to the manufacturer's instructions.
Library preparation was done using QuantSeq 3′-mRNA-Seq Library Prep Kit (Lexogen) or KAPA mRNA-seq kit (Roche). Libraries were subjected to single-end sequencing using Illumina NextSeq500.

treatment_protocol: 1uM Dox for 4, 8, 24 or 72 (renewed every 24 ) hours pre- extraction of DNA/RNA

value: ES-derived neural progenitor cells

value: Dox for 24 hours


title: hiPSC-L1 CTRL 2


title: Littermate control injured [Day_7_WT_injured_S3]


title: NC-5 [CircRNA]

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

data_processing:
Use Ribo-Zero rRNA Removal Kits (Illumina, USA) to remove rRNAs from total RNA. Use TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) to preprocess RNA to construct a sequencing library. A BioAnalyzer 2100 instrument (Agilent Technologies, USA) was used for library quality control and quantification. According to the Illumina sequencing instructions, the 10 pM library was denatured into single-stranded DNA molecules, captured on an Illumina flowcell, amplified into clusters in situ, and performed 150 cycles in the paired-end mode (PE mode) on the Illumina HiSeq sequencer Sequencing.
Use Q30 for quality control, use cutadapt[1] software (v1.9.3) to remove connectors, remove low-quality reads, and obtain high-quality reads.
Use hisat2 software (v2.0.4) to compare high-quality reads to the human reference genome (UCSC HG19). Then, under the guidance of the gtf gene annotation file, use the cuffdiff software (v2.2.1, part of the cufflinks software suite) to obtain the FPKM (Fragments per kilobase of exon per million fragments mapped) value of the transcript level circRNA as the expression profile of the circRNA, And calculate the fold change and p-value between two/group samples to screen for differential expression of circRNA and mRNA.
Supplementary_files_format_and_content: tpm

source_name: peripheral blood mononuclear cells

extract_protocol:
Human PBMCs were isolated by density-gradient
centrifugation over Ficoll-Hypaque solution (Tianjin Haoyang Biological Technology Co., Tianjin, China) according to the manufacturer’s instructions and stored at -80 °C   until use for circRNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: Adult female

value: Blood


title: NC-3 [CircRNA]


title: RA-HA_K27M_24_rep1-RNA


title: NC-4 [CircRNA]


title: RA-HA_WT_24_rep1-RNA


title: GD-5 [CircRNA]


title: CD8T_6hr_D2HG_3

city: boston

first: Giulia

last: Notarangelo

state: Massachusetts

address: 45 shattuck street

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Spleen

growth_protocol: Murine naïve CD8+ T cells were cultured in RPMI-1640 supplemented with 10% FBS, 10 mM HEPES, 0.05 mM BME, and 1% P/S, and were activated with 4 μg/mL of plate-bound aCD3/CD28 antibodies.

extract_protocol:
Cells were washed with PBS once, and resusponded in TLC buffer freshly supplemented with 1% BME in the proprotion of 5 μL per 100 cells. Lysates were incubated at room temperature for 5 minutes and then stored at -80C .
Total RNA was captured and purified on RNAClean XP beads. Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5'AAGCAGTGGTATCAACGCAGAGTACT30VN-3') and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit.

treatment_protocol: 20 mM D-2HG or L-2HG was added at the time of stimulation

value: Spleen

value: CD8 T cell

value: WT

value: 20 mM D-2HG


title: DF3c

source_name: blood cells

value: dengue fever

value: blood

value: Lineage -, CD3 -, CD45+, CRTH2 +, IL-7Ra+


title: GD-4 [CircRNA]


title: NC-2 [CircRNA]


title: NC-1 [CircRNA]


title: CD8T_6hr_L2HG_1

value: 20 mM L-2HG


title: CD8T_6hr_L2HG_3


title: GD-3 [CircRNA]


title: CD8T_6hr_L2HG_2


title: CD8T_6hr_D2HG_2


title: GD-2 [CircRNA]


title: CD8T_6hr_D2HG_1


title: CD8T_6hr_Ctrl_2


title: CD8T_6hr_Ctrl_1


title: GD-1 [CircRNA]


title: CD8T_6hr_Ctrl_3


title: TPC1input

city: Aurora

first: Joaquin

last: Espinosa

state: CO

department: Pharmacology, Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.11.0) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using Bowtie2 (v2.2.9, --sensitive –-end-to-end)  with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
BigWig files for visualization of p53 occupancy were generated with deepTools [8] (version 2.2.2, settings --binSize=1 –extendReads FRAGMENT_LENGTH --minMappingQuality 10 –normalizeUsingRPKM). Read density was displayed at 1 bp resolution as reads per million of mapped reads per 1 kb (RPM/kb).
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: BigWig - coverage visualization

growth_protocol: TPC1 and K1 cells were cultivated in RPMI (TPC1) or DMEM (K1) media (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Peak Serum) and 1% antibiotic-antimycotic mixture (Gibco). Cells were plated a day before the treatment and maintained in a humidified atmosphere with 5% of CO2 at 37°C.

extract_protocol:
Sub-confluent cultures of TPC1 and K1 cells were treated for 24 hours with indicated compounds. After the treatment period, cultivation media was replaced with crosslinking solution (1% formaldehyde in PBS) and plates were incubated for 15 minutes at room temperature. Next, formaldehyde was quenched with glycine (0.125 mM final) for 5 minutes and cells were washed twice with ice-cold PBS. Crosslinked cells were lysed in RIPA buffer (150 mM NaCl, 50 mM Tris pH 8.5 mM EDTA, 1% IGEPAL 630 (NP-40 substituent), 0.5% sodium deoxycholate, 0.1% SDS and protease/phosphatase inhibitors) and sonicated to generate 200-300 bp fragments of DNA (Qsonica Q800R, 70% amplitude, 30 sec on/30 sec off cycle, 20 cycles for TPC1 lysates and 25 cycles for K1 lysates). Next, samples were centrifugated at 20 000 g for 20 min at °C, protein concentration in collected supernatants was measured using a BCA Protein Assay Kit and all samples were diluted to final protein concentration of 1 mg/ml. Lysates were pre-cleared with 15 l of Dynabeads M-280 (sheep anti-mouse IgG, Thermo Fisher Scientific) and immunoprecipitated overnight with 5 l/sample of anti-p53 antibody (DO-1, EMD Millipore) and 30 l of Dynabeads at 4C. In total, 4 (TPC1) or 5 (K1) lysate aliquots per sample were used in immunoprecipitation reactions. Next day beads were washed (5 minutes each washing step) twice with RIPA, four times with IP wash buffer (500 mM LiCl, 100 mM Tris pH 8.5, 1% IGEPAL, 1% sodium deoxycholate), again twice with RIPA and twice briefly with TE (10 mM Tris pH 8, 1 mM EDTA). Washed beads were resuspended in 100 l of TE and 200 l of elution buffer (70 mM Tris pH 8, 1 mM EDTA and 1.5% SDS) and incubated at 65C for 10 minutes. After adding NaCl to final concentration of 200 mM, eluted immunocomplexes were incubated at 65C for 5 hours to reverse formaldehyde crosslinks. Remaining protein was digested by proteinase K (20 g/sample, 45C for 30 minutes). DNA was recovered by one phenol/chloroform and one chloroform extraction followed by ethanol precipitation and resuspension in 50 l of TE. Input DNA was extracted from reverse cross-linked lysates using the same extraction protocol as for sample DNA.
NEBNext Ultra II DNA sequencing library preparation kit

treatment_protocol: Cells were treated treated with vehicle (0.2% DMSO), 10 microM Nutlin-3a, 25 microM GSK2830371, and drug combinations for 24 hours.

value: papillary thyroid carcinoma


title: K1584R-FV5_Input_Rep1

city: Philadelphia

first: Anna

last: Bieluszewska

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
Alignment (CUT&RUN): Bowtie2
Alignment (ChIP-Seq): Bowtie2
Alignment (RNA-Seq): STAR
CUT&RUN bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and a spike-in normalization factor determined by alignment of reads to the Drosophila genome.
ChIP-Seq bigwig files were made from .bam files using "deepTools bamCoverage --ignoreDuplicates --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization.
RNA expected counts were generated with RSEM.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C.

extract_protocol:
CUT&RUN was performed on cells as previously described (Skene and Henikoff, eLife 2017).
ChIP was performed on cells as previously described (Trizzino et al., Cell Rep 2018).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

value: ATRX Flag-V5-Tag Knock-in-K1584R


title: K1584R-FV5_ATRX_Rep2

tag: antibody

value: ATRX


title: K1584R-FV5_Input_Rep2


title: Sample_p53_ChiPseq_K1 - GSK - rep2

tag: chip antibody


title: Sample_p53_ChiPseq_K1 - NutlinGSK - rep2


title: K1584R-FV5_ATRX_Rep1


title: PHD-FV5_Input_Rep2

value: ATRX Flag-V5-Tag Knock-in-PHDmut


title: Sample_p53_ChiPseq_K1 - Nutlin - rep2

value: Nutlin


title: Sample_p53_ChiPseq_K1 - DMSO - rep2

value: DMSO


title: PHD-FV5_ATRX_Rep1


title: WT_ATRX_Rep2

value: Wildtype


title: Sample_p53_ChiPseq_TPC1 - GSK - rep2


title: Sample_p53_ChiPseq_TPC1 - NutlinGSK - rep2


title: Sample_p53_ChiPseq_TPC1 - Nutlin - rep2


title: Sample_p53_ChiPseq_K1 - DMSO - rep1


title: PHD-FV5_Input_Rep1


title: Sample_p53_ChiPseq_TPC1 - NutlinGSK - rep1


title: Sample_p53_ChiPseq_K1 - GSK - rep1


title: PHD-FV5_ATRX_Rep2


title: Sample_p53_ChiPseq_K1 - Nutlin - rep1


title: Sample_p53_ChiPseq_TPC1 - Nutlin - rep1


title: Sample_p53_ChiPseq_TPC1 - DMSO - rep1


title: WT_Input_Rep2