title: PPIL1 KO- JTE-013+ S1P lyase inhibitor

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Raw data from illumina was transformed to Sequenced Reads by CASAVA base recognition (Base  Calling)
Raw data was filtered by Novogene Corporation Inc. according to the following steps; 1) reads containing adaptors were removed, and 2)reads containing bases that could not be determined were also removed.
STAR software was used to align reads to reference genome
FPKM was used to estimate gene expression levels. This method considers both sequencing depth and gene length on counting of fragments. (Mortazavi et al. 2008, https://doi.org/10.1038/nmeth.1226)
The readcount from Gene Expression Analysis was used to determine the differential expression analysis
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Processed_data_AJ.txt  (file that include FPKM values, gene names, gene id, gene_chr, gene_start, gene_end, gene_strand, gene_biotype, and gene descriptions for each Sample_

source_name: B16 cell line

growth_protocol: Cells were maintained in RPMI growth media, supplemented with 10% FBS, 1%Penicillin streptomyocin(100x), and plasmocin prophylactic.

extract_protocol:
Total RNA was extracted from B16 cell lines using QIAzol Lysis Reagent(Qiagen, Cat No./ID: 79306) and processed as per manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols from Novogene Corporation Inc.(Sacramento, CA 95826)

treatment_protocol: B16 cell line were treated with JTE-013 overnight, and S1P lyase inhibitor treatment for ~5-8hrs

tag: disease state

value: Melanoma

value: PPIL1 KO

value: JTE-013+ S1P lyase inhibitor


title: PPIL1 KO

status: Public on Mar 23 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: genotype

tag: treatment

value: control


title: Scramble-JTE-013+ S1P lyase inhibitor


title: SH1000 neg control rep 2

city: Brno

first: Adela

last: Finstrlova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Masaryk University

data_processing:
Raw reads quality control with FastQC
Quality trimming and filtering performed using Trimmomatic toolkit (v 0.36) with the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 SLIDINGWINDOW:4:15 LEADING:22 TRAILING:22 MINLEN:20 AVGQUAL:22
Alignment to the reference genome and read counting using using STAR v 2.5.2b with the following parameters: outFilterMultimapScoreRange 0, outFilterMatchNmin 30, outFilterMatchNminOverLread, 0.95, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.02, outFilterMismatchNoverReadLmax 1, alignIntronMin 20, alignIntronMax 1
Normalization of counts within the triplicates and DGE analysis was performed with DESeq2 package
Genome_build: Staphylococcus aureus SH1000 de novo sequenced genome (Bioproject Accession: PRJNA769253), Staphylococcus aureus Newman (Genbank Accession: NC_009641.1), Staphylococcus virus K (GenBank Accession: NC_005880.2 )
Supplementary_files_format_and_content: csv file with raw counts generated using aligner STAR for each sample
Supplementary_files_format_and_content: csv file with normalized counts generated using DESeq2 for each sample
Supplementary_files_format_and_content: csv file with DESeq2 results for each sampling time

organism: Staphylococcus aureus

source_name: Staphylococcus aureus SH1000 growing exponentionally in MPB

growth_protocol: MPB exponential growth

extract_protocol:
The total RNA was extracted using organic extraction with TRIzol. Genomic DNA was removed using a Turbo DNA-free kit. The rrRNA depletion was performed using a RiboMinus Bacteria 2.0 Transcriptome Isolation Kit according to the manufacturer’s instructions.
Sequencing libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, following the standard protocol.

tag: strain

tag: infection

value: before infection

tag: time


title: SH1000 neg control rep 1


title: SH1000 neg control rep 3


type: RNA

city: Xi'an

first: Xuan

last: Li

address: 145, Changlexi Road

country: China

institute: School of Stomatology, Fourth Military Medical University

description: lncRNA expression data from PDLSC incubated in medium with the presence of cementoblastic inducer EMD (EMD), 7 days, replicate 2

hyb_protocol: The cRNAs were hybridized onto the Arraystar Human LncRNA Array (ArrayStar, Rockville, MD, USA), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software package. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

organism: Homo sapiens

label_protocol: The samples were amplified and transcribed to fluorescent cRNAs using ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: cells were incubated in α-MEM (Gibco BRL, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS; Hangzhou Sijiqing Biological Engineering Materials, Zhejiang, China), 100 U/mL penicillin (Invitrogen, Carlsbad, CA, USA) and 100 mg/mL streptomycin (Invitrogen)

extract_protocol: Total RNA was extracted using the TRIzol Reagent (Invitrogen)

treatment_protocol: PDLSCs were incubated in normal α-MEM medium (Nor), medium with the presence of inflammatory cytokines TNF-α plus IL-1β (Infla), medium with the presence of cementoblastic inducer EMD (EMD), or medium with the presence of both inflammatory cytokines and EMD (Infla-EMD)

tag: age

value: 18 to 30 year


description: lncRNA expression data from PDLSC incubated in medium with the presence of both inflammatory cytokines and EMD (Infla-EMD), 7 days, replicate 3


title: 14SD08743

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a), with the annotation of known genes from gencode v33.
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode v33
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw counts from salmon for each sample

extract_protocol:
RNA was extracted from FFPE sections with the RNeasy FFPE Kit (Qiagen)
RNA libraries were prepared with the TruSeq RNA exome kit (Illumina).

tag: tissue

value: Cutaneous tumor

tag: cell type

value: melanoma


title: ExponentialPhase_2

status: Public on Mar 22 2022

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.39
Trimmed reads were then mapped to the reference genome (E. coli MG1655, NC_000913.3) using STAR v.2.5.2b aligner
featureCounts from Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts. Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10, were removed.
Gene hit counts were used for subsequent differential expression analysis, using DESeq2 R package (v.1.24.0) to compare gene expression between samples and calculate p-values and log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest).
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing normalized raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing results from differential expression analysis

growth_protocol: Growth rates were measured by spectrophotometry (BioTek Synergy HTX Multi-Mode Microplate Reader). From a glycerol stock (-80 °C), cells were streaked on LB agar plates (2%) and incubated at 37 °C, overnight. Next, a single colony was picked, inoculated in LB medium with antibiotics and incubated at 30°C overnight with shaking. Overnight cultures were diluted into fresh medium to an optical density of 600 nm (O.D.600) of 0.01 and incubated for growth by shaking at 250 rpm at 37°C. We used Luria-Bertani (LB) medium with 10 g peptone, 10 g NaCl, and 5 g yeast extract in 1000 ml distilled water and the antibiotics kanamycin and chloramphenicol from Sigma Aldrich, U.S.A. Cells were grown until reaching either the exponential or stationary growth phases.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.

treatment_protocol: Cells from 3 independent biological replicates of MG1655 in exponential and stationary growth phase conditions were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.

tag: phase

value: exponential


title: ExponentialPhase_1

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


title: SH1000 2 min rep 3

source_name: Staphylococcus aureus SH1000 growing exponentionally in MPB infected with phage K

value: Staphylococcus virus K

value: 2 min


title: GCA_2_37

city: Bei Jing

first: chen

last: yulu

address: changbai road 155

institute: Chinese Center for Disease Control and Prevention

description: △fyuAGCAdel

data_processing:
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Yersinia pestis biovar Microtus str. 91001 (enterobacteria) whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Yersinia pestis biovar Microtus str. 91001 (enterobacteria).
Supplementary files format and content: gene_count.txt: Tab-delimited text file includes read count values for each Sample.
Supplementary files format and content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Yersinia pestis

source_name: bacteria

growth_protocol: Y. pestis WT strain 201 and the fyuA mutants were grown at 26 ℃ or 37 ℃ in TMH to OD620 nm=1.0, and each sample had three biological replicates.

extract_protocol:
Total RNA was extracted using the PureLink™ RNA Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cultured in TMH at 37C

value: <delta>fyuAGCAdel


title: GCA_3_37

description: △fyuAGCAdel


title: GCA_1_37

description: △fyuAGCAdel


description: lncRNA expression data from PDLSC incubated in medium with the presence of cementoblastic inducer EMD (EMD), 7 days, replicate 3


title: fyuA_1_37

description: △fyuA

value: <delta>fyuA


description: lncRNA expression data from PDLSC incubated in medium with the presence of cementoblastic inducer EMD (EMD), 7 days, replicate 1


title: 14SD08679


description: lncRNA expression data from PDLSC incubated in medium with the presence of both inflammatory cytokines and EMD (Infla-EMD), 7 days, replicate 2


description: lncRNA expression data from PDLSC incubated in medium with the presence of both inflammatory cytokines and EMD (Infla-EMD), 7 days, replicate 1


title: Scramble


title: TR_201_3_37

value: wildtype


title: 16SD07590


title: StationaryPhase_3

value: stationary


title: StationaryPhase_2


title: TR_201_2_37


title: StationaryPhase_1


title: TR_201_1_37


title: ExponentialPhase_3


title: GCA_2_26

description: △fyuAGCAdel

value: cultured in TMH at 26C


title: fyuA_1_26

description: △fyuA


title: fyuA_2_37

description: △fyuA


title: TW_201_2_26


title: GCA_3_26

description: △fyuAGCAdel


title: fyuA_3_26

description: △fyuA


title: sample3_ccs

city: Cardiff

first: Vincent

last: Dion

address: Hadyn Ellis Building

department: Dementia Research Institute

country: United Kingdom

institute: Cardiff University

library_source: genomic

data_processing:
FASTQ files converted to FASTA
Repeat Size measured using Repeat Detector
Supplementary files format and content: FASTA files
Supplementary files format and content: Text files containing histograms of repeat size
Library strategy: long read sequencing

molecule: genomic DNA

source_name: HEK293-derived GFP(CAG)15

growth_protocol: The GFP(CAG)x cell lines were cultured in Gibco™ Dulbecco’s modified Eagle’s medium (DMEM) with GlutaMAX™, 10% foetal bovine serum (FBS), 100 U ml−1 of penicillin/streptomycin, 15 μg ml−1 blasticidine and 150 μg ml−1 hygromycin. The HD LBCs or their DNA used for SMRT sequencing were obtained from the Coriell BioRepository (Table S1 from Taylor et al - https://doi.org/10.1101/2022.03.08.483398). The LBCs were grown in Gibco™ RPMI with GlutaMAX™ supplemented with 15% Gibco™ FBS (Thermo Fisher), and 1% penicillin-streptomycin. Both the LBCs and the GFP(CAG)x cells were grown at 37 °C with 5% CO2 and tested negative for mycoplasma by Eurofins’ ‘Mycoplasmacheck’ service.      GFP(CAG)91 is identical to the previously characterised GFP(CAG)101 but contained a contraction in the cultures used here. Similarly, GFP(CAG)51 had a one CAG expansion compared to when it was first derived and GFP(CAG)308 had a repeat tract above 270 that we could not fully sequence with Sanger sequencing at the time. GFP(CAG)15, GFP(CAG)51, and GFP(CAG)308 are derived from GFP(CAG)101.

extract_protocol:
The HD LBCs and GFP(CAG)x datasets were generated by first isolating DNA using the Macherey-Nagel Nucleospin™ Tissue Mini kit. PCR products were generated from samples using barcoded primers as listed in Table S1 and Thermo™ Phusion II High Fidelity polymerase. To obtain sufficient quantities of PCR product to proceed with library preparation, multiple identical PCRs were pooled and purified using Macherey-Nagel™ Gel and PCR Clean-up kit columns. The library was generated using the SMRTbell Template Prep Kit (1.0-SPv3) according to manufacturer’s instructions. Samples to be sequenced on the same flowcell were combined in equimolar pools. We loaded between 10 and 12 pM. SMRT sequencing was done using a Sequel at Cardiff University School of Medicine. CCSs were generated from the resulting sequences and processed using SMRT Link.
SMRTbell Template Prep Kit (1.0-SPv3)

tag: cell samples


title: sample4_ccs

source_name: HEK293-derived GFP(CAG)51


title: sample5_ccs

source_name: HEK293-derived GFP(CAG)91


title: fyuA_2_26

description: △fyuA


title: sample1_sub21_unfilteredCCS

source_name: Lymphoblastoid cell line

value: HD


title: sample1_sub18_unfilteredCCS


title: TW_201_3_26


title: sample1_sub12_unfilteredCCS


title: sample1_sub10_unfilteredCCS


title: sample1_sub11_unfilteredCCS


title: sample1_sub8_unfilteredCCS


title: TW_201_1_26


title: sample6_ccs

source_name: HEK293-derived GFP(CAG)308


title: sample1_sub5_unfilteredCCS


title: sample1_sub20_unfilteredCCS


title: sample1_sub22_unfilteredCCS


title: sample1_sub16_unfilteredCCS


title: sample1_sub15_unfilteredCCS


title: fyuA_3_37

description: △fyuA


title: sample1_sub2_unfilteredCCS


title: sample1_sub13_unfilteredCCS


title: sample1_sub9_unfilteredCCS


title: Tg(hsp70l:sflt4) .rep1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: ventrciles extracted at 24 hpci

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.38 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses.
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package.
Only reads mapping at least partially inside exons were admitted and aggregated per gene, while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses.
Differentially expressed genes were identified using DESeq2 version 1.18.1
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

source_name: ventricles at 24 hpci

extract_protocol:
Ventricles of WT and Tg(hsp70l:sflt4) were cryoinjured, followed by heat shock treatment at 39 degrees.  A pool of 3 ventricles per replicate were extracted for RNAseq at 24 hpci.
500 ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

value: AB

value: ventrcile

value: adult


title: sample1_sub1_unfilteredCCS


title: WT .rep1

description: ventrciles extracted at 24 hpci


title: sample1_sub7_unfilteredCCS


title: sample1_sub6_unfilteredCCS


title: sample1_sub4_unfilteredCCS


title: sample1_sub17_unfilteredCCS


title: GCA_1_26

description: △fyuAGCAdel


title: sample1_sub3_unfilteredCCS


title: sample1_sub14_unfilteredCCS


title: NC_EBL_rep5

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2  by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized by DEseq2
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: text files include normalized reads counts calculated by DESeq2 for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: embryo

tag: developmental stage

value: early blastocyst

value: 7.0 day after fertilization

value: embryos were injected with BE3 mRNA at zygote stage


title: Tg(hsp70l:sflt4) .rep2

description: ventrciles extracted at 24 hpci


title: SOX2KO_EBL_rep5

value: embryos were injected with BE3 mRNA and SOX2 sgRNAs mixture at zygote stage


title: SOX2KO_EBL_rep3


title: SOX2KO_EBL_rep2


title: sample1_sub19_unfilteredCCS


title: NC_EBL_rep4


title: NC_EBL_rep3


title: WP_mitf_rep1

city: Yokohama

first: Tadayoshi

last: Murakawa

state: Kanagawa

address: Midori Nagatsuta 4259 S2-201

department: Department of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

data_processing:
The base callsbinary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were quantified using salmon (v1.5.2) with parameters  -l A -p 8 --validateMappings.
Assembly: BDGP6.32
Supplementary files format and content: Comma-delimited text files include RLE normalized values for each Sample using DESeq2

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: Laid eggs were reared at 21°C on standard cornmeal/yeast/agar media for 21 h. Then they were reared at 25°C until they grew to 3IL or to white prepupa.

extract_protocol:
Fat bodies were collected from staged five larvae or pupae. The isolated fat bodies were lysed in the TRIzol (Thermo Fisher) and frozen at −80°C. The lysates were quickly thawed and homogenized through a 27-gauge needle for 10 strokes. The total RNA was collected following the manufacturer’s instructions. The samples were then further purified using ReliaPrep tissue RNA Miniprep System (Promega). cDNA libraries were constructed from the total RNAs using TruSeq stranded mRNA library platform (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fat body

value: white pupa

value: UAS-Mitf/+; Lsp2-GAL4/+


title: WP_mitf_rep2


title: WP_LacZ_rep1


title: WP_mitf_rep3


title: e3IL_LacZ_rep2

value: third instar larvae

value: UAS-LacZ/+; Lsp2-GAL4/+


title: N2_DNAseq_youngadult_rep2

city: New York

first: Sevinc

last: Ercan

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

data_processing:
Library strategy: DNA-seq
DNA-seq: aligned to genome version WS220 (ce10) using Bowtie2 (version 2.3.2) with default settings (Langmead and Salzberg 2012). All replicate and read number information is provided in Supplemental File 1. Samtools version 1.6 (Li 2011) was used to merge replicates before running bamCompare tool from Deeptools version 3.3.1 (Ramirez et al. 2016), using the following options:  --binSize 500, --scaleFactorsMethod None,  --normalizeUsing CPM, --operation log2, --minMappingQuality 30,  --outFileFormat bedgraph, --ignoreDuplicates. Copy number analysis was performed with Root-cern version 6.08.06 and CNVnator version 0.3.3 (Abyzov et al. 2011) comparing data from mutant strains to reference genome version WS220 (ce10) using bin_size = 1000. Output files listing deletions and duplications are provided in Supplemental File 2. Overlap of CNVs with genes were determined by Galaxy (https://usegalaxy.org/) tools “Operate on Genomic Intervals” (Afgan et al. 2018).
Assembly: WS220
Supplementary files format and content: DNA-seq: bedgraphs from bamCoverage of aligned reads.   RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.

extract_protocol:
DNA-seq: Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp.
cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

value: young adult


title: NC_EBL_rep1


title: NC_EBL_rep2


title: e3IL_LacZ_rep1


title: Sample 8: Arid1a FL/FL; UbcCreERT2 -  PPx

city: Dallas

first: Hao

last: Zhu

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Cetern

data_processing:
Adaptors and low quality sequences (Phred<20) were removed by trimming raw sequencing reads using galore package
The sequence reads were aligned to the GRCm38/mm10 with HiSAT2 (Kim et al. 2015).
After duplicate removal by SAMtools (Li et al. 2009), read counts were generated for the annotated genes based on GENCODE V20, using featureCounts (Harrow et al. 2012; Liao et al. 2014)
Differential gene expression analysis was performed on edgeR, using FDR < 0.05 as cutoff (McCarthy et al. 2012; Robinson et al. 2010).
Heatmaps to visualize the data were generated by using GENE-E (Robinson et al. 2010).
Assembly: mm10

source_name: Arid1a FL/FL; UbcCreERT2 -  PPx

extract_protocol:
RNA was isolated using TRIzol reagent
RNA-seq libraries were prepared using Ovation RNA-Seq Systems 1-16 (Nugen).
Indexed libraries were multiplexed in a single flow cell and underwent 75 base pair single-end sequencing on an Illumina NextSeq500 using the High Output kit v2 (75 cycles) at the Children’s Research Institute Sequencing Facility.

treatment_protocol: Islets were isolated from 2 Arid1aFl/Fl and 5 Ubc-CreER; Arid1aFl/Fl mice for no-PPx and 2 Arid1aFl/Fl and 2 Ubiquitin-CreER; Arid1aFl/Fl mice 6 days post-PPx, all males. Deletion was induced in 45-60 day old mice by administration of 10 mg tamoxifen per day for two consecutive days by oral gavage. Two weeks after tamoxifen, PPx was performed and post-PPx islets were isolated 6 days after the surgery.

value: pancreatic islets

value: 3 months

value: Arid1a KO

tag: Sex

value: male


title: Sample 7: Arid1a FL/FL; UbcCreERT2 -  PPx


title: WP_LacZ_rep3


title: N2_DNAseq_youngadult_rep3


title: SOX2KO_EBL_rep6


title: WT .rep2

description: ventrciles extracted at 24 hpci

value: AB


title: Sample 15: Arid1a FL/FL; UbcCreERT2 - no PPx

source_name: Arid1a FL/FL; UbcCreERT2 - no PPx


title: Sample 13: Arid1a FL/FL; UbcCreERT2 - no PPx


title: Sample 14: Arid1a FL/FL; UbcCreERT2 - no PPx


title: Sample 6: Arid1a FL/FL -  PPx

source_name: Arid1a FL/FL -  PPx

value: control


title: Sample 5: Arid1a FL/FL -  PPx


title: Sample 11: Arid1a FL/FL - no PPx

source_name: Arid1a FL/FL - no PPx


title: Sample 9: Arid1a FL/FL - no PPx


title: SOX2KO_EBL_rep1


title: Sample 14: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)

data_processing:
Sequences were trimmed by Cutadapt to remove the Nextera transposase adaptor (Martin 2011).
The trimmed sequences were aligned with BWA to mouse mm10. Peaks were called using MACS14 with default parameters (Zhang et al. 2008).
Differentially bound peaks were called using DiffBind (Stark and Brown 2011; Ross-Innes et al. 2012).
Peaks were annotated by CHIPseeker (Yu et al. 2015).
Peak heatmaps and average profile of peaks were visualized using CHIPseeker.
Assembly: mm10

source_name: pancreatic islets

extract_protocol:
40,000 isolated islet cells in single cell suspension were used to prepare crude nuclei, which were immediately used for the transposition reaction following a published protocol (Buenrostro et al. 2015).
Transposition reaction using Nextera Tn5 transposase (Nextera Tn5 Transposase, Illumina #FC-121-1030) was incubated at 37 °C for 30 min with gentle shaking. DNA was eluted using Qiagen MinElute PCR Purification kit and transposed DNA fragments were amplified using Nextera PCR Primer 1 and Primer 2 (containing barcode). Thermal cycle settings were as follows: 1 cycle of 72°C for 5 min, 98°C for 30 sec, 5 cycles of 98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min. 5-6 additional cycles were used as determined for each sample with a qPCR reaction to avoid artifacts due to over-amplification. Amplified library was purified using Qiagen MinElute PCR Purification kit. Amplified libraries were size selected using Ampure XP beads and quality was analyzed using Bioanalyzer High Sensitivity DNA kit. Indexed libraries were multiplexed in a single flow cell and underwent 75 base pair single-end sequencing on an Illumina NextSeq500 using the High Output kit v2 (75 cycles)
75 base pair single-end sequencing on an Illumina NextSeq500 using the High Output kit v2 (75 cycles)

treatment_protocol: Islets were freshly isolated from 4 control and 3 Arid1a βKO mice pre-PPx and 4 control and 4 Arid1a βKO mice 6 days post-PPx, all males. Mice were given 1 g/L dox in the drinking water for two weeks. PPx was performed one week after dox withdrawal. Animals were sacrificed and islets were isolated 6 days after the PPx.

value: Arid1a {beta}KO


title: Sample 12: Arid1a FL/FL; UbcCreERT2 - no PPx


title: Sample 10: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: Sample 17: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: Sample 12: Post-PPx: Arid1aFl/Fl; MIP-rtTA control


title: Sample 16: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: Sample 3: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control


title: scr-day4-PBRM1-rep2

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were check for sequencing quality with FastQC (v0.11.2). After that, reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.2.9) with soft-clipping allowed. SAMtools (v0.1.19) was used to filter out non-primary alignments, alignments with mapping quality score less than 10, PCA duplicates, alignments on non-chromosome contigs and on ENCODE blacklist regions.
Peaks were detected for each sample against the corresponding input control using SICER (v1.1) with default parameters. Bedtools (v2.27.1) was used to generate bedgraph files for visualization on genome browser, in which each sample was normalized to 10 million reads per library and corresponding input subtracted.
Genome_build: mm9
Supplementary_files_format_and_content: peaks called for each IP library over corresponding input control.

source_name: CCE-Nanog-GFP mESCs

extract_protocol:
ChIP-seq was done as previously reported (Lin-Shiao et al., 2018) . Briefly, 1X107 mESCs were fixed in 1% formaldehyde in PBS for 10 minutes, the fixation was quenched with 125mm glycine for 5 minutes.  Chromatin was sonicated with a S220 Focused-ultrasonicator (Covaris) for 15 min and immunoprecipitated with H2AK9ac (Abcam). Antibodies were conjugated to protein G Dynabeads (Thermo). Eluted samples were reverse cross-linked overnight at 65°C, and DNA as purified after treatment with RNAse (Thermo) and Proteinase K (Thermo).
Purified DNA was quantified using Qubit dsDNA kit (Thermo) and 50ng was used to prepare sequencing libraries. Input samples were also included and prepared using the same protocol. NEBNext Ultra DNA library kit from Illumina (New England Biolabs) was used to prepare the libraries and the quality was assessed by Agilent BioAnalyzer 2100 (Agilent). Quantification was done using KAPA library quantification kits (KAPA Biosystems) or NEBNext library Quant kit (New England Biolabs).

value: WT

value: CCE-Nanog-GFP mESCs

tag: chip antibody


title: Sample 6: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control


title: scr-day4-PBRM1-rep1


title: YTHDC2_iCLIP_rep1 [RR1034; iCLIP]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: iCLIP

data_processing:
For gene expression profiling the reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (Ensembl release 102) either using salmon v1.3.0 (salmon quant with options -l A  --validateMappings --gcBias)(Patro et al., 2017) or kallisto (quant v0.46.2 with options --plaintext)(Bray et al., 2016). The DESeq function of DESeq2_1.25.10 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression between wild-type and knock-in/mutant samples and the adjusted p-values. Log2 fold change of 1.5 and adjusted p-value 0.05 was used as a threshold for statistical significance. The individual mouse tissues were analyzed separately.
The whole single-cell RNAseq (scRNA-seq) analysis strategy was based on a previously published approach (Luecken and Theis, 2019). Demultiplexed raw sequencing data were processed by cellranger pipeline (v3.0.2) developed by 10x Genomics. Reads were aligned to the custom mm10 reference by cellranger count. Cell count matrix, gene and barcode tables were taken as final output for further processing. Scanpy scRNA-seq toolkit (v1.4.5) was mainly used to integrate, normalize, and process the data. Once integrated, scRNA-seq dataset was filtered based on the following criteria: 1) transcript counts per cell (cells containing less than 1500 or more than 40000 transcripts were discarded) using filter_cells function; 2) genes expressed per cell (cells with less than 2000 genes expressed were discarded) using filter_cells function; 3) mitochondrial gene fraction (cells with more that 20% of mt genes per total number of genes expressed were discarded); 4) gene occurrence (genes which were found in less than 20 cells were discarded) with filter_genes function. Ythdc2+/+ sample was removed from the analysis because of very low sequencing quality, only Ythdc2+/- and Ythdc2-/- samples were processed. Finally, 4528 cells were retained for further analysis. Scran bioconductor package was used for the normalization with default parameters on count matrices before constructing single-cell maps. To reduce the dimentionality of the data and construct single-cell maps UMAP algorithm was applied to the normalized count matrices based on 3000 highly variable genes identified. Batch correction was done by MNN algorithm with mnnpy package. Leiden clustering algorithm (leiden function of the scanpy package) was used to identify cell populations. MAST algorithm  was used to perform differential gene expression analysis (diffxpy.api python package). Pseudotime variable for the developmental trajectory analyses was inferred with the Slingshot software (v1.4.0).
Reads were QC-checked with FastQC (v0.11.5) and adapters were removed with Flexbar (v3.5.0, SeqAn v2.4.0). Trimmed reads were aligned to the mouse genome reference (GRCm38) by STAR (v2.7.9a) with the following iCLIP-specific parameters: --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1. BAM files were further deduplicated with umi_tools dedup (v1.1.1). The 2 replicas were merged together with samtools merge (v1.7). PureCLIP was used to identify binding sites from the merged library.
Genome_build: Ensembl release 102
Supplementary_files_format_and_content: ScRNA-seq files contain either gene expression matrix per cell, or cell-related parameters (mitochondrial gene fraction per cell, cell type annotated, etc.), or gene-related parameters (highly variable gene label, total gene expression counts in cells, etc.). YTH mutant RNA-seq supplementary file contains tables with DESeq2-specific differential gene expression parameters (baseMean, log2 fold change, adjusted p-value, etc.), as well as DESeq2-normalized gene counts per replica per condition both for 2N and for 4N cells. Ythdc2 cat-dead mutant RNA-seq supplementary file contains DESeq2-specific differential gene expression parameters table (baseMean, log2 fold change, adjusted p-value, etc.), as well as DESeq2-normalized gene counts matrix per replica per condition. ICLIP supplementary file contains a summary table with the total number of filtered binding sites (0<log2(BS coverage)<4.5) per 5’UTR, CDS, and 3’UTR of the YTHDC2 binding target, a table of the ubiquitination pathway genes, as well as a BED file of all the PureCLIP-defined and annotated binding sites.

source_name: Testes

growth_protocol: Mutant mice were generated at the Transgenic Mouse Facility, University of Geneva. The mice were bred in the Animal Facility of Sciences III, University of Geneva. The generation of Ythdc2 knockout mouse line is described previously (Wojtas et al., 2017). The exon 7 encodes for parts of the N-terminal RecA domain of the RNA helicase module in YTHDC2, and specifically the ATPase motif DEVH. YTH domain is encoded in exon 27-29. We targeted the endogenous Ythdc2 locus in mouse embryos of the hybrid background B6D2F1 (50% C57BL/6 and 50% DBA/2) with specific guide RNAs and homology repair templates to create Ythdc2 mutant lines inactivating the RNA helicase domain and the m6A-binding capacity of the YTH domain.

extract_protocol:
iCLIP extract: Testes from five P15 mice from Ythdc2-3xFLAG; 2xHA-Meioc double homozygous knock-in line (Figure 2C) were used for one experiment. The five pairs of P15 testes were digested with collagenase IV (1mg/ml in DMEM, 2ml/pair testis) at 33°C with gentle intermittent mixing in a Thermomixer (Eppendorf). After 15 minutes, digested testes were removed from thermomixer and gently mixed with a 1ml pipette for several times to get a single-cell suspension. The testes suspension was spun at 300xg for 5 minutes at 4°C. The medium was removed and the cells were collected in 10 ml cold DMEM. Cells were transferred into a 10 cm2 Petri dish (cell culture grade) and UV cross-linked with 200mj/cm2 (254 nm wavelength UV lamps) for 3 times on ice. After UV cross-linking, cells were collected in 15 ml falcon tubes and spun at 500xg for five minutes in at 4°C. The cell pellet was washed twice with ice-cold 1X PBS and snap-frozen in liquid nitrogen and stored at -80°C until use. The remaining procedure for iCLIP was performed as described by (Huppertz et al., 2014). RNase I digestion was done at 1:200 dilution for 3 minutes at 37°C with 1100 rpm mixing in a Thermomixer (Eppendorf). Anti-FLAG M2 Magnetic Beads (Sigma; Cat. No. M8823) (100µl/reaction) were used for immunoprecipitation.
iCLIP library: The PCR amplification was performed with Platinum™ II Hot-Start PCR Master Mix (ThermoFisherScientific; Cat. No. 14000012) for 30 cycles. The PCR product was precipitated with sodium acetate and ethanol, separated on 3% MetaPhor agarose (Lonza; Cat. No. 50180) in 1xTAE buffer. The DNA band corresponding to 100-200 bp was cut from the gel and purified using MiniElute kit (Qiagen; Cat. No. 28004). Purified iCLIP libraries were sequenced on NextSeq 500 illumina sequencer for 75 cycles single end.

value: Testes

tag: experiment

value: iCLIP


title: YTHDC2_iCLIP_rep2 [RR1035; iCLIP]

description: iCLIP


title: WP_LacZ_rep2

value: Fat body


title: Sample 16: Arid1a FL/FL; UbcCreERT2 - no PPx


title: scr-day4-ARID2-rep2


title: Sample 18: Post-PPx: Arid1aFl/Fl; MIP-rtTA control


title: scr-day4-ARID2-rep1


title: Sample 13: Post-PPx: Arid1aFl/Fl; MIP-rtTA control


title: Sample 4: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: scr-day2-Input-rep2


title: scr-day2-PBRM1-rep2


title: Sample 5: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: Sample 7: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO)


title: e3IL_LacZ_rep3


title: Sample 8: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control


title: Sample 2: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control


title: scr-day2-ARID2-rep2


title: scr-day4-Input-rep2


title: scr-day2-ARID2-rep1


title: scr-day4-Input-rep1


title: scr-day0-Input-rep2


title: scr-day2-PBRM1-rep1


title: scr-day2-Input-rep1


title: Sample 11: Post-PPx: Arid1aFl/Fl; MIP-rtTA control


title: scr-day0-ARID2-rep2


title: scr-day0-PBRM1-rep2


title: scr-day0-PBRM1-rep1


title: scr-day0-ARID2-rep1


title: KD-day4-PBRM1-rep2

value: CTSL KD


title: KD-day2-PBRM1-rep1


title: KD-day4-PBRM1-rep1


title: KD-day4-Input-rep1


title: KD-day2-Input-rep2


title: KD-day4-ARID2-rep2


title: KD-day4-ARID2-rep1


title: KD-day2-PBRM1-rep2


title: KD-day0-Input-rep2


title: KD-day0-PBRM1-rep2


title: KD-day0-PBRM1-rep1


title: KD-day0-Input-rep1


title: KD-day0-ARID2-rep2


title: KD-day2-ARID2-rep2


title: KD-day2-Input-rep1


title: KD-day2-ARID2-rep1


title: ALS_WholeTissue_SOD_Input_rep6

first: Eric

middle: F

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sequence and transcript coordinates for mouse mm10 UCSC genome and gene models were retrieved from the Bioconductor Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0) Bioconductor libraries respectively.
RNA-seq reads are aligned to the genome using Rsubread's subjunc method (version 1.30.6)
BigWigs normalised to reads per million were exported using the rtracklayer package (version 1.40.6).
Counts in genes were generated using featureCounts within the Rsubread package(version 1.30.6) with default settings and the TxDb.Mmusculus.UCSC.mm10.knownGenegene models.
Differential expression was calculated by DESeq2 v1.26.0 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: CSV format; Data output from DESeq2 on all genes for each sample in the analysis including: gene symbol, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, isSig, normalized counts for each sample.

source_name: Whole tissue input RNA from M1 cortex of Gprin3-bacTRAP:SOD1*G93A mouse

extract_protocol:
Motor cortex (or whole cortex for samples 15-21) was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol. Total RNA from "input" samples was purified from the pre-IP tissue homogentates using the Agilent Nanoprep kit.
15 ng total RNA from TRAP IP or input was amplified using the NuGEN Ovation RNA-Seq System V2 and libraries were prepared from 10 ug amplified cDNA using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocols.

treatment_protocol: EGFP-L10a transgene was expressed in lower layer 5b pyramidal cells in cortex of Gprin3-bacTRAP mice and upper layer 5b pyramidal cells in Colgalt2-bacTRAP mice. For ALS experiments, both bacTRAP lines were crossed to SOD1*G93A mice. TRAP was performed in adult (8-17 week old) animals.

tag: brain region

value: M1 Cortex

value: Lower L5b pyramidal cells

value: SOD+

tag: rna

value: Whole tissue input


title: ALS_WholeTissue_SOD_Input_rep2


title: ALS_WholeTissue_SOD_Input_rep3


title: ALS_WholeTissue_SOD_Input_rep5


title: ALS_WholeTissue_SOD_Input_rep1


title: ALS_WholeTissue_WT_Input_rep5

source_name: Whole tissue input RNA from M1 cortex of wildype littermate of Gprin3-bacTRAP:SOD1*G93A mice

value: SOD-


title: ALS_WholeTissue_WT_Input_rep4


title: ALS_WholeTissue_WT_Input_rep3


title: ALS_WholeTissue_WT_Input_rep2


title: scr-day0-Input-rep1


title: ALS_Gprin3_SOD_TRAP_IP_rep3

source_name: TRAP IP RNA from M1 cortex of Gprin3-bacTRAP::SOD1*G93A mouse

value: TRAP IP


title: ALS_Gprin3_SOD_TRAP_IP_rep2


title: human vascular smooth muscle cell - cholesterol2

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

data_processing:
Fastq reads were mapped to genome by using hisat2
Genes reads were calculated by using htseq-count
Genome_build: Rnor_6.0, hg38
Supplementary_files_format_and_content: Counts files were generated using htseq-count; Scores represent reads number assigned to each gene

source_name: human vascular smooth muscle cell

growth_protocol: VSMCs were cultured with DMEM supplemented with 10% PBS and 1% penicillin and streptomycin.

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Invitrogen 15596018) following manufacture’s instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: VSMCs were cultured with water soluble cholesterol (Chol:MβCD) or NOTCH inhibitor DAPT or both for 48 hours.

value: primary aortic vascular smooth muscle cell

tag: agent

value: cholesterol


title: KD-day4-Input-rep2

tag: genotype


title: ALS_Gprin3_SOD_TRAP_IP_rep1


title: human vascular smooth muscle cell - DMSO2

value: DSMO


title: human vascular smooth muscle cell - DMSO1


title: ALS_Gprin3_WT_TRAP_IP_rep2

source_name: TRAP IP RNA from M1 cortex of wildtype littermate of Gprin3-bacTRAP::SOD1*G93A mice


title: human vascular smooth muscle cell - cholesterol1


title: ALS_Gprin3_WT_TRAP_IP_rep1


title: zfish, embryo, 72hpf, controlc

city: San Diego

first: Goran

last: Bozinovic

state: CA

address: 3030 Bunker Hill St

institute: Boz Life Science Research and Teaching Institute

description: Sample 19

data_processing:
Basecalls performed using Illumina NextSeq2000
The high throughput RNAseq data was initially processed with in-house custom scripts using BBTools to obtain demultiplexed reads for each sample based on the inline barcodes. The 5’-end 10-base barcodes and 3’-end 12-base UMI information from read1 fastq were first incorporated into read2 fastq as part of sequence ID using UMI-tools.
Raw RNA-Seq data quality was assessed using FastQCR (version 3.3), and UMIs were extracted using UMI-tools (version 1.1.2). To remove adapters and optimize for differential expression detection, Trimmomatic (version 0.40) was used to remove the first 16 bases of each read, trim reads according to a sliding-window of length 4 and minimum Phred score 20, and remove resulting reads shorter than 20 bases. SortmeRNA (version 2.1) was used to filter out contaminating rRNA.
The remaining reads were aligned to zebrafish genome assembly version 10 (GRCz10), due to lack of alignment-ready data for GRCz11. Reads were aligned using Spliced Transcripts Alignments to a Reference (STAR; version 2.7.3a). PCR deduplication was performed using extracted UMIs via UMI-tools (version 1.1.2)
Read counts per gene were quantified using HTSeq (version 0.13.5) with default settings
Transcript variants were compiled into single gene expressions. Gene expression for each library was normalized using trimmed mean of M values (TMM).
Count per million (CPM) filtering was performed from 0 to 5 CPM in increments of 0.25, and pairwise differential gene expression analysis was performed using the noiseqbio function of NOISeq (version 2.14.1) at each CPM threshold
Detected differentially expressed genes were plotted by CPM to select an optimal threshold for CPM filtering. Analysis proceeded with only genes of an average CPM above 2.75
Assembly: grcz10
Supplementary files format and content: fish_outlierrm_tmm.csv, lists for Samples 1 - 20 (column names), normalized and filter counts for gene (row names)

source_name: whole embryo

growth_protocol: Adult breeding populations of Danio rerio were maintained in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. AB strain adult zebrafish were obtained from Carolina Biological (Danio rerios, Burlington, NC, US) and acclimated to lab conditions for six months; embryos laid by the F1 generation were used for assays. Zebrafish were housed in a recirculating system in 1.3 or 3.3-liter polycarbonate tanks at a density of 10 fish/L and maintained at 28.5±1°C on a 14h light:10h dark cycle. Adults were fed twice daily with Tetramin® Tropical Flake Food (Tetra, Blacksburg, VA, US) in the morning (9 - 10AM) and freshly hatched brine shrimp (Brine Shrimp Direct, Ogden, UT, US) in the late afternoon (5 - 6PM) on weekdays and once daily with brine shrimp on weekends. Breeding tanks containing one female and two males were prepared one day before embryo collection. Following the onset of the light cycle, adult zebrafish were bred for one hour and embryos were collected in Pyrex glass dishes covered with mesh; embryos were staged per Kimmel et al. 49 under a stereo microscope (AmScope Compact Multi-Lens Stereo Microscope, model #SE306R-A) at 30X magnification. Debris and abnormally developing embryos exhibiting severe asymmetry in cleavage, detached cytoplasm, or broken chorions were removed from the batch before exposure. Developing embryos were kept in embryo water consisting of deionized water reconstituted with Instant Ocean® (Instant Ocean Spectrum Brands, Blacksburg, VA, US) to 60 μg/L, adjusted to pH 6.6 - 7.6 and 28.5°C until exposure.

extract_protocol:
Total RNA was isolated from pooled samples of 8-10 embryos (four pools for each exposure) using the TRIzol reagent protocol with modifications (Invitrogen, Carlsbad, CA). Briefly, TRIzol was added to frozen embryos, before allowing embryos to thaw. Samples were homogenized in a Bead Mill 4 (Fisher Scientific, PA) using sterile 2 mm glass beads. RNA was resuspended in 50 µL RNase-free water. Quantity and quality of samples were determined using a NanoDrop 2000 (A260/280 and A260/230 > 1.8). Between 500 – 750 ng of total RNA per sample were sent to the Scripps Research Institute Next Generation Sequencing Core (TSRI, San Diego, CA) for shallow RNA-sequencing.
cDNA library preparation and shallow RNA-Seq was performed at TSRI. Sample quality was assessed using a 2100 Bioanalyzer 2100 (Agilent Technologies) (RIN>8.5). Library preparation for RNA-Seq was performed using the HTP RNA-Seq Library Prep Kit (iGenomX Inc, San Francisco, CA). Briefly, barcoded oligo dT primers were added to 50 ng RNA per sample, and reverse transcribed. Sample cDNA products were combined, cleaned, and run through PCR with 0.5 µM barcoded PCR primers (p5 and p7 sequences, Illumina, San Diego, CA).  Purified PCR products were sequenced using a NextSeq2000 sequencer (Paired-end mode; read1: 26 bases, read2: 94bp) at TSRI. Greater than 1.5 million paired-end reads were generated for each sample.

treatment_protocol: Undecafluoro-2-methyl-3-oxahexanoic acid (HFPO-DA, GenX (CASRN: 13252-13-6; Catalog No. 2121-3-13, SynQuest)) was purchased from SynQuest (Alachua, FL, USA, 97% purity). Exposure solutions were prepared one day before exposures by adding GenX to embryo water and stored at 4°C in a glass bottle. Since pH is known to affect embryo mortality 75, assays using pH neutralized GenX (titrated using NaOH and HCl, pH 6.6 – 7.6) were performed. Embryos were exposed to 0.5, 1, 2, 10, 1000, 4000, 6000, 8000, 10000, 12000, 16000, and 20000 mg/L titrated GenX concentrations from the sphere developmental stage (3 – 4 hpf) 49 until 72 hpf. Embryos were housed individually with 2 mL exposure solution in wells of 24-well plates. Negative controls were embryos grown in embryo water, while positive control embryos were exposed to 4 mg/L 3, 4-dichloroaniline. Fifty percent of the exposure solution in each well was refreshed daily. pH and dissolved oxygen (DO) for each plate were monitored and noted daily. Plates were discarded if more than 20% of embryos in plate controls died, or more than 20% of embryos in the negative control died. In the positive control, at least 30% mortality was necessary to maintain test validity 76.

value: AB

value: protruding mouth

tag: treatment

value: untreated

value: whole embryo

tag: number of embryos


title: Baseline_Colgalt2_M1_TRAP_IP_rep2

description:
Baseline_Colgalt2_M1_TRAP_IPvInput.csv
Baseline_Gprin3_vs_Colgalt2_TRAP_IP.csv

source_name: TRAP IP RNA from M1 cortex of Colgalt2-bacTRAP mice

tag: strain

value: Colgalt2-bacTRAP DU9

value: Upper L5b pyramidal cells

value: Wildtype


title: zfish, embryo, 72hpf, controld

description:
Sample 20
Sample 20 was an outlier (it appeared to be a large technical variation during seq protocol), so the sample was removed from the dataset.


title: zfish, embryo, 72hpf, controlb

description: Sample 18


title: KD-day0-ARID2-rep1

value: CTSL KD

value: CCE-Nanog-GFP mESCs


title: zfish, embryo, 72hpf, controla

description: Sample 17


title: zfish, embryo, 72hpf, 2d

description: Sample 16

value: 2 mg/L GenX


title: Baseline_Gprin3_M1_Input_rep2

source_name: Whole tissue input RNA from M1 cortex of Gprin3-bacTRAP mice

value: Gprin3-bacTRAP ES152

value: M1 Cortex

value: Mixed


title: Baseline_Gprin3_M1_TRAP_IP_rep2

description:
Baseline_Gprin3_M1_TRAP_IPvInput.csv
Baseline_Gprin3_vs_Colgalt2_TRAP_IP.csv

source_name: TRAP IP RNA from M1 cortex of Gprin3-bacTRAP mice

value: Lower L5b pyramidal cells

value: TRAP IP


title: Baseline_Gprin3_M1_Input_rep1

value: Whole tissue input


title: ALS_WholeTissue_SOD_Input_rep4

value: SOD+


title: zfish, embryo, 72hpf, 2b

description: Sample 14

value: AB


title: IL-13-treated STAT6

city: Cincinnati

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

description:
single read
EPC2 IL-13 STAT6 peaks.txt

data_processing:
RNA-Seq paired-end  and ChIP single-read analysis pipelines are uploaded at https://github.com/datirium/workflows . For RNAseq, adapter sequences were trimmed from unaligned reads using TrimGalore.
Alignment of trimmed raw sequencing data to Homo sapiens (GRCh37/hg19) reference genome is done by STAR allowing maximum 5 mismatches and reporting only uniquelly mapped reads.
Mapped reads are then being sorted and indexed by Samtools sort and index utilities. Sorted reads are used for RPKM calculation and generating genome coverage bigWig file
For Chip-seq, following trimming with TrimGalore data was aligned to Homo sapiens (GRCh37/hg19) reference genome by Bowtie reporting only uniquelly mapped reads with maximum 3 mismatches.
Peak calling was performed by MACS2, only peaks with FDR cutoff of 0.05 are reported and genome coverage and generated bigWig file. For each of the called peaks the nearest genes are assigned within +20kb distance from TSS for upstream regions and +-1kb from TSS for promoter regions.
Genome_build: HG19
Supplementary_files_format_and_content: text files

source_name: EPC2 esophageal epithelial cells

growth_protocol: EPC2 cells were seeded at high confluency (1 mln cells per 1 well of the 6-weel plate) in standard KSFM medium 1 day prior to the experiment.

extract_protocol:
For RNA isolation, cells were collected in Tripure and RNA was expracted by Quick-RNA MicroPrep Kit (Zymo Research). For ChIP, cells were fixed in 0.8% PFA and sonicated by Covaris sonicator. ChIP was performed in IP-Star Compact automation system (Diagenode)
Illumina standard protocol

treatment_protocol: IL-13 was at 100 ng/ml, Vitamin D was at 100 nM

tag: cell line


title: Baseline_Gprin3_M1_TRAP_IP_rep1


title: Untreated STAT6

description:
single read
EPC2 UT STAT6 peaks.txt


title: ALS_WholeTissue_WT_Input_rep1

value: SOD-


title: zfish, embryo, 72hpf, 2c

description: Sample 15

value: protruding mouth


title: zfish, embryo, 72hpf, 2a

description: Sample 13

value: whole embryo


title: VitD-treated VDR

description:
single read
EPC2 Vit D VDR peaks.txt


title: Cas9+sgRNA [WIXL125]

city: Boston

first: Richard

last: Novak

state: MASSACHUSETTS

address: 3 Blackfan Cir

department: Wyss Institute

institute: Harvard University

description: Experiment 1: CRISPR edited model of Rett syndrome

hyb_protocol: RNA samples were processed using a Nugen Ovation PICO WTA System V2 kit. The resulting cDNAs were purified using a Qiagen MinElute PCR Purification Kit following the modifications outlined in the Nugen protocol. The cDNAs were fragmented and labeled using a Nugen Encore Biotin Module. Hybridization solutions were prepared by combining the fragmented, biotin-labeled cDNAs with hybridization cocktail (Affymetrix Hybridization, Wash, and Stain Kit). The mixtures were incubated in a thermal cycler at 99 °C for 2 min followed by 45 °C for 5 min. then loaded on Xenopus laevis Genome 2.0 arrays and incubated for 16-20 hours at 45 ºC and 60 rpm in an Affymetrix Hybridization Oven 645.

scan_protocol: Following hybridization, arrays were washed and stained on Affymetrix Fluidics Station 450s using the Affymetrix FS450_0001 protocol with the stains and buffers supplied in the Affymetrix Hybridization, Wash, and Stain Kit.  The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were extracted from CEL files and Robust Multi-array Average (RMA) normalized in Matlab (Mathworks; Natick, MA) and output with linear scaling.

label: biotin

organism: Xenopus laevis

source_name: Xenopus, MeCP2 knockdown

label_protocol: Microarray measurements were performed using the GeneChip Xenopus laevis Genome 2.0 Array (Affymetrix; Santa Clara, CA) at the Advanced Biomedical Laboratories (Cinnaminson, NJ).

growth_protocol: Xenopus embryos and tadpoles were housed at 18C with a 12/12 h light/dark cycle in 0.1X Marc’s Modified Ringer’s (MMR) medium. Tadpoles were fed 3x/week with sera Micron Nature fry food.

extract_protocol: Tadpoles were sacrificed at stage 50 of development and lysed using a QIAGEN TissueLyser II bead mill (30 Hz, 2 x 30 sec) in a 2 mL tube with a 2.4 mm steel beads (Omni) and 1 mL phosphate buffered saline buffer at 4oC. 250 mL of lysate was used for RNA extraction using a QIAGEN RNeasy mini kit. RNA samples were DNAse treated.

treatment_protocol: Cas9 target sites were selected using CHOPCHOP on the X. laevis J-strain 9.2 version, which facilitated the selection of guide RNA with no predicted off-targets. We used the default settings to generate a list of target sequences. We selected 4 targets from this list for each of the L and S forms. This selection was based primarily on the ranking provided by CHOPCHOP and as a function of their location on MeCP2 to target exons coding for the methyl-CpG-binding domain (MBD, exons 2 and 3) and Transcriptional repression domain (TRD, exon 3). The sgRNA were resuspended to 100 μM in 0.1X Tris EDTA (pH 8.0). Then, an equimolar sgRNA mix was made using 2 μl of each sgRNA, for a total of 16 ul.  The Cas9 RNP complex was formed by mixing 75 pmol of the sgRNA mix with 75 pmol of Cas9 in annealing buffer (5 mM HEPES, 50 mM KCl, pH 7.5), for a total volume of 100 μL, then incubated at 37C for 10 minutes. The RNP was kept frozen at -20C until the day of the injection. To generate MeCP2 knockdown models of Rett syndrome, Xenopus embryos were fertilized and maintained at 14C until the 4-cell stage. Each cell was injected with ~2 nL RNP per injection resulting in a final amount of 1.5 fmol of RNP per injection per cell.

value: Tadpoles

tag: mecp2 status

value: indel


title: zfish, embryo, 72hpf, 1d

description: Sample 12

value: 1 mg/L GenX

tag: tissue


title: VitD H3K27Ac

description:
single read
EPC2 Vit D K27ac peaks.txt


title: Cas9+sgRNA [WIXL126]


title: zfish, embryo, 72hpf, 1c

description: Sample 11


title: Untreated VDR

description:
single read
EPC2 UT VDR peaks.txt


title: Cas9+sgRNA [WIXL124]


title: Baseline_Colgalt2_M1_Input_rep1

source_name: Whole tissue input RNA from M1 cortex of Colgalt2-bacTRAP mice

value: Colgalt2-bacTRAP DU9

tag: cell type

value: Wildtype


title: Baseline_Colgalt2_M1_Input_rep2


title: Baseline_Colgalt2_M1_TRAP_IP_rep1

value: Upper L5b pyramidal cells


title: sgRNA [WIXL123]

source_name: Xenopus, sgRNA control

value: sgRNA

value: wild type


title: sgRNA [WIXL122]


title: zfish, embryo, 72hpf, 1b

description: Sample 10


title: IL-13+VitD H3K4me3

description:
single read
EPC2 13+Vit D K4me3.txt


title: Untreated H3K27Ac

description:
single read
EPC2 UT K27ac peaks.txt


title: zfish, embryo, 72hpf, 1a

description: Sample 9


title: VitD H3K4me3

description:
single read
EPC2 Vit D K4me3 peaks.txt


title: zfish, embryo, 72hpf, 10d

description: Sample 8

value: 10 mg/L GenX


title: Baseline_Gprin3_M1_Input_rep3

value: Gprin3-bacTRAP ES152

value: M1 Cortex

value: Mixed


title: IL-13 H3K4me3

description:
single read
EPC2 IL-13 K4me3 peaks.txt


title: sgRNA [WIXL121]


title: Untreated H3K4me3

description:
single read
EPC2 UT K4me3 peaks.txt


title: Cas9 [WIXL120]

source_name: Xenopus, Cas9 control


title: IL-13+VitD H3K9Ac

description:
single read
EPC2 13+Vit D K9ac.txt


title: VitD H3K9Ac

description:
single read
EPC2 Vit D K9ac peaks.txt


title: IL-13 H3K9Ac

description:
single read
EPC2 IL-13 K9Ac peaks.txt


title: zfish, embryo, 72hpf, 10b

description: Sample 6


title: Cas9 [WIXL119]


title: IL-13+VitD H3K27Ac

description:
single read
EPC2 13+Vit D K27ac.txt


title: zfish, embryo, 72hpf, 10c

description: Sample 7


title: Untreated H3K9Ac

description:
single read
EPC2 UT K9Ac peaks.txt


title: IL-13+VitD_1

description:
pair-end
EPC2 UT vs IL-13+Vit D.txt


title: IL-13+VitD_3

description: pair-end


title: IL-13 H3K27Ac

description:
single read
EPC2 IL-13 K27ac peaks.txt


title: IL-13+VitD_2

description:
pair-end
EPC2 IL-13 vs IL-13+Vit D.txt


title: Cas9 [WIXL118]


title: zfish, embryo, 72hpf, 10a

description: Sample 5


title: zfish, embryo, 72hpf, 05d

description: Sample 4

value: 0.5 mg/L GenX


title: VitD_3

description: pair-end


title: VitD_2

description: pair-end


title: Uninjected [WIXL116]

source_name: Xenopus, control

value: Uninjected


title: IL-13_3

description: pair-end


title: zfish, embryo, 72hpf, 05c

description: Sample 3

value: AB


title: Uninjected [WIXL117]


title: VitD_1

description:
pair-end
EPC2 UT vs VitD.txt


title: OP37_RNAseq_embryo_rep3

data_processing:
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
DNA-seq: aligned to genome version WS220 (ce10) using Bowtie2 (version 2.3.2) with default settings (Langmead and Salzberg 2012). All replicate and read number information is provided in Supplemental File 1. Samtools version 1.6 (Li 2011) was used to merge replicates before running bamCompare tool from Deeptools version 3.3.1 (Ramirez et al. 2016), using the following options:  --binSize 500, --scaleFactorsMethod None,  --normalizeUsing CPM, --operation log2, --minMappingQuality 30,  --outFileFormat bedgraph, --ignoreDuplicates. Copy number analysis was performed with Root-cern version 6.08.06 and CNVnator version 0.3.3 (Abyzov et al. 2011) comparing data from mutant strains to reference genome version WS220 (ce10) using bin_size = 1000. Output files listing deletions and duplications are provided in Supplemental File 2. Overlap of CNVs with genes were determined by Galaxy (https://usegalaxy.org/) tools “Operate on Genomic Intervals” (Afgan et al. 2018).
Assembly: WS220
Supplementary files format and content: DNA-seq: bedgraphs from bamCoverage of aligned reads.   RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2

source_name: whole worms

extract_protocol:
RNA-seq: Total RNA was purified following Trizol manufacturer’s instructions after freeze-cracking samples five times. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific) from 10 µg of total RNA. cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.   DNA-seq: Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp.
cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

value: embryos


title: IL-13_1

description:
pair-end
EPC2 UT vs IL-13.txt


title: IL-13_2

description: pair-end


title: zfish, embryo, 72hpf, 05b

description: Sample 2

value: protruding mouth

value: whole embryo


title: Untreated_3

description: pair-end


title: Untreated_2

description: pair-end


title: zfish, embryo, 72hpf, 05a

description: Sample 1


title: Untreated_1

description: pair-end


title: OP37_RNAseq_embryo_rep1


title: OP37_RNAseq_embryo_rep2


title: Uninjected [WIXL115]

value: Tadpoles


title: Uninjected [WIXL114]


title: UC357

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post deplexing, .fastq files were 3' clipped to remove adaptor sequence using the FASTQ/A Clipper tool (http://hannonlab.cshl.edu).
Post adaptor clipping, .fastq files were import into the CLCbio Genomics Workbench (www.clcbio.com) for quality inspection, quality trimming, filtering, and mapping. Per quality trimming, 15bp from the 5' end of each read for each sample was globally removed along with 1bp from the 3' end. Bases with a call accuracy < 95% were also removed. Per filtering, read pairs having more than two ambiguities in at least one read were discarded along with pairs < 15bp in length. Per mapping, the RNA-Seq tool was used under default parameters to align reads in pairs to the human genome (hg19).
Post mapping, the number of aligned reads falling in known annotated genes and transcripts were enumerated then converted into number of Reads Per Kilo base of transcript Million mapped reads (RPKM). RPKM values were then import into R (http://www.r-project.org/), pedestalled by 2 (RPKM+2), log (base 2) transformed (Log2(RPKM+2), then filtered to remove genes not having a transformed value >1 for at least one sample.
Post filtering, transformed values for remaining genes and transcripts were quantile normalized (Quantile(Log2(RPKM+2))). After, the coefficient of variation (CV) and mean expression for each gene and transcript was calculated by sample class then modeled via locally weighted scatter plot smoothing (CV ~ mean). Resulting model fits were then inspected and used to define system noise as the mean expression value across sample classes at which the linear relationship between CV (i.e., noise) and mean expression (i.e., signal) is grossly lost (expression value = 4). Genes and transcripts not having at least one normalized value (Quantile(Log2(RPKM+2))) greater than this value were discarded as noise-biased. While, normalized values for remaining genes and transcripts were floored to equal this value if less. It is this floored expressed data that was used to identify differential expressed genes and transcripts across samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing the RPKM expression values for each gene and transcript by sample in matrix format.

source_name: Muscle biopsy

extract_protocol:
Snap frozen muscle biopsies were sectioned with a Thermo Scientific Microm HM 560 cryostat (Thermo Scientific, Wilmington, DE). Fifteen 10 μm cryosections were collected in Trizol (Life Technologies, Carlsbad, CA). The RNA was isolated using standard Trizol protocol, and further purified using miRNeasy Mini Kit (Qiagen, Valencia, CA). After isolation, the RNA concentration was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE). The RNA samples were analyzed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) to obtain RNA integrity numbers (RIN) as measure of quality. Only samples having a RIN quality ≥ 6 were subject to RNA-Seq Analysis.
Libraries were prepared from isolated RNA according to Illumina protocols (Illumina, Inc, San Diego, CA) and sequenced by Beckman Coulter Genomics (Danvers, Massachusetts). Briefly, mRNA libraries were constructed from 150 ng of total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2. The resulting cDNA was fragmented using a Covaris E210. Library amplification was performed using 12-15 cycles to minimize the risk of over-amplification. Unique barcode adapters were applied to each library. Equal volumes of individual libraries were pooled and run on a MiSeq. The libraries were then repooled based on the MiSeq demultiplexing results and sequenced on a HiSeq 2000 with version 3 flow cells and sequencing reagents. On average, 69 million 100-base read pairs were generated for each individual library. Data was processed using RTA 1.13.48 and deplexed via CASAVA 1.8.2.

tag: sample group

tag: read length

tag: end-type

value: Paired

tag: strand-type

value: Unstranded

tag: total reads


title: Refed 60 min trl-1(cas1078) rep2 RNA-Seq

city: Beijing

first: Dou

last: Wu

address: Haidian street

institute: Tsinghua university

description: mRNA

data_processing:
Remove reads mapped to ribosome RNA using bowtie
Tophat (v2.1.1) was used to align all reads from individual samples to C. elegans genome, parameters are the following: splice-mismatches 0; max-multihits 20; segment-mismatches 2; segment length 25; -no-novel-juncs.
HTseq-count (v0.9.1) with default setting was used to calculate exon or CDS abundance (--type) using bam files generated by Tophat with gene annotation.
Counts normalization and differential expession analysis by DESeq2.
For the Ribo-Seq data, the length range of the RPF reads, the P-site location and the non-canonical ORFs were analyzed by RiboCode.
Genome_build: ce11
Supplementary_files_format_and_content: Tab-delimited text files include raw counts values for all sample;
Supplementary_files_format_and_content: Tab-delimited text files include normalized counts (CPM) for all sample;
Supplementary_files_format_and_content: CPM normalized bigwig converted from bam file by bamCoverage with the following setting: --binSize 5 --normalizeUsing CPM

source_name: larvae

extract_protocol:
worms were flash-frozen and stored in liquid nitrogen. RNA was harvested using Trizol reagent.
Libraries were performed as Ingolia et al. 2012 published protocol described.

value: starved for 6 days and refed with food for 60 min


title: UC77


title: UC129


title: UC98


title: Refed 60 min trl-1(cas1078) rep1 RNA-Seq

description: mRNA


title: UC43


title: UC50


title: Refed 30 min trl-1(cas1078) rep2 RNA-Seq

description: mRNA

value: starved for 6 days and refed with food for 30 min


title: UC50

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina GenomeStudio Gene Expression Module was used to generate summarized expression measurements per probe.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Snap frozen muscle biopsies were sectioned with a Thermo Scientific Microm HM 560 cryostat (Thermo Scientific, Wilmington, DE). Fifteen 10 μm cryosections were collected in Trizol (Life Technologies, Carlsbad, CA). The RNA was isolated using standard Trizol protocol, and further purified using miRNeasy Mini Kit (Qiagen, Valencia, CA). After isolation, the RNA concentration was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE). The RNA samples were analyzed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) to obtain RNA integrity numbers (RIN) as measure of quality. Only samples having a RIN quality ≥ 6 were subject to Microarray Analysis.


title: UC100


title: Refed 10 min trl-1(cas1078) rep2 RNA-Seq

description: mRNA

value: starved for 6 days and refed with food for 10 min


title: UC98


title: UC338


title: UC384


title: Refed 30 min trl-1(cas1078) rep1 RNA-Seq

description: mRNA


title: UC95


title: UC99


title: UC56


title: UC129


title: Starved trl-1(cas1078) rep2 RNA-Seq

description: mRNA

value: starved for 6 days


title: Starved trl-1(cas1078) rep1 RNA-Seq

description: mRNA


title: UC175


title: UC54


title: Refed 10 min trl-1(cas1078) rep1 RNA-Seq

description: mRNA


title: UC222


title: UC30


title: UC66


title: UC95


title: UC13


title: UC264


title: UC397-1


title: UC384


title: Refed 60 min trl-1(cas1078) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment

data_processing:
Library strategy: Ribo-seq
Remove reads mapped to ribosome RNA using bowtie
Tophat (v2.1.1) was used to align all reads from individual samples to C. elegans genome, parameters are the following: splice-mismatches 0; max-multihits 20; segment-mismatches 2; segment length 25; -no-novel-juncs.
HTseq-count (v0.9.1) with default setting was used to calculate exon or CDS abundance (--type) using bam files generated by Tophat with gene annotation.
Counts normalization and differential expession analysis by DESeq2.
For the Ribo-Seq data, the length range of the RPF reads, the P-site location and the non-canonical ORFs were analyzed by RiboCode.
Genome_build: ce11
Supplementary_files_format_and_content: Tab-delimited text files include raw counts values for all sample;
Supplementary_files_format_and_content: Tab-delimited text files include normalized counts (CPM) for all sample;
Supplementary_files_format_and_content: CPM normalized bigwig converted from bam file by bamCoverage with the following setting: --binSize 5 --normalizeUsing CPM

extract_protocol:
Worms were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion
Libraries were performed as Ingolia et al. 2012 published protocol described.


title: Non-starved trl-1(cas1078) rep2 RNA-Seq

description: mRNA

value: non-starved


title: UC21


title: UC99


title: UC220


title: Non-starved trl-1(cas1078) rep1 RNA-Seq

description: mRNA


title: UC357


title: Refed 60 min trl-1(cas1078) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-45

description: Control

value: Control


title: M13-43

description: Control


title: M13-35

description: Control


title: Refed 30 min trl-1(cas1078) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: UC13


title: M13-49

description: Control


title: Refed 30 min trl-1(cas1078) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: UC179


title: UC54


title: UC100


title: M13-40

description: Control


title: M13-47

description: Control


title: UC51


title: M13-33

description: Control


title: Refed 10 min trl-1(cas1078) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: Refed 10 min trl-1(cas1078) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-30

description: Control


title: Starved trl-1(cas1078) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-7

description: Control


title: M13-25

description: Control


title: UC30


title: M13-23

description: Control


title: M13-18

description: Control


title: UC220


title: UC21


title: vc100_RNAseq_embryo_rep3

tag: developmental stage


title: Non-starved trl-1(cas1078) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-16

description: Control


title: UC158-1


title: UC222


title: sp117_RNAseq_youngadult_rep3

value: young adult


title: M13-1

description: Control


title: Starved trl-1(cas1078) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: UC179


title: Non-starved trl-1(cas1078) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: vc100_RNAseq_embryo_rep1


title: sp117_RNAseq_youngadult_rep1


title: vc100_RNAseq_embryo_rep2


title: sp117_RNAseq_L2_rep3


title: UC264


title: UC103


title: ty1916_RNAseq_embryo_rep1


title: ty1916_RNAseq_embryo_rep3


title: ty1916_RNAseq_embryo_rep2


title: Refed 60 min trl-1(cas1077) rep2 RNA-Seq

description: mRNA


title: UC397-1


title: Refed 60 min trl-1(cas1077) rep1 RNA-Seq

description: mRNA


title: Refed 10 min trl-1(cas1077) rep2 RNA-Seq

description: mRNA


title: sp117_RNAseq_youngadult_rep2


title: Refed 30 min trl-1(cas1077) rep1 RNA-Seq

description: mRNA


title: sp117_RNAseq_L2_rep4


title: Refed 30 min trl-1(cas1077) rep2 RNA-Seq

description: mRNA


title: sp117_RNAseq_L2_rep2


title: sp117_RNAseq_embryo_rep2


title: Refed 10 min trl-1(cas1077) rep1 RNA-Seq

description: mRNA


title: sp117_RNAseq_embryo_rep1


title: bc4289_RNAseq_L2_rep2


title: bc4289_RNAseq_youngadults_rep3


title: UC106-1


title: Starved trl-1(cas1077) rep2 RNA-Seq

description: mRNA


title: bc4289_RNAseq_youngadults_rep1


title: M13-11

description: Control


title: bc4289_RNAseq_L2_rep1


title: vc100_DNAseq_youngadults_rep1

data_processing:
Library strategy: DNA-seq
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
DNA-seq: aligned to genome version WS220 (ce10) using Bowtie2 (version 2.3.2) with default settings (Langmead and Salzberg 2012). All replicate and read number information is provided in Supplemental File 1. Samtools version 1.6 (Li 2011) was used to merge replicates before running bamCompare tool from Deeptools version 3.3.1 (Ramirez et al. 2016), using the following options:  --binSize 500, --scaleFactorsMethod None,  --normalizeUsing CPM, --operation log2, --minMappingQuality 30,  --outFileFormat bedgraph, --ignoreDuplicates. Copy number analysis was performed with Root-cern version 6.08.06 and CNVnator version 0.3.3 (Abyzov et al. 2011) comparing data from mutant strains to reference genome version WS220 (ce10) using bin_size = 1000. Output files listing deletions and duplications are provided in Supplemental File 2. Overlap of CNVs with genes were determined by Galaxy (https://usegalaxy.org/) tools “Operate on Genomic Intervals” (Afgan et al. 2018).
Assembly: WS220
Supplementary files format and content: DNA-seq: bedgraphs from bamCoverage of aligned reads.   RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2


title: ty1916_DNAseq_youngadults_rep3


title: bc4289_RNAseq_youngadults_rep2


title: Non-starved trl-1(cas1077) rep2 RNA-Seq

description: mRNA


title: ty1909_DNAseq_youngadults_rep3


title: Non-starved trl-1(cas1077) rep1 RNA-Seq

description: mRNA


title: Starved trl-1(cas1077) rep1 RNA-Seq

description: mRNA


title: sp117_RNAseq_L2_rep1


title: ty1916_DNAseq_youngadults_rep2


title: Refed 60 min trl-1(cas1077) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: Refed 60 min trl-1(cas1077) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-43

description: Control


title: M13-25

description: Control


title: M13-45

description: Control


title: sp219_DNAseq_youngadults_rep1


title: M13-40

description: Control


title: ty1916_DNAseq_youngadults_rep1


title: M13-33

description: Control


title: ty1909_DNAseq_youngadults_rep2


title: ty1909_DNAseq_youngadults_rep1


title: sp117_DNAseq_youngadults_rep4


title: M13-18

description: Control


title: sp219_DNAseq_youngadults_rep3


title: Refed 10 min trl-1(cas1077) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: sp219_DNAseq_youngadults_rep2


title: M13-1

description: Control


title: M13-7

description: Control


title: E33942_2

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

data_processing:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA).
PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
Assembly: dm6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: male adult fly

extract_protocol:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA). PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gal80ts; Tub>lncRNA-CR33942

value: adult

value: 12 hours after E. coli infection

tag: Sex

value: male


title: M13-30

description: Control


title: M13-16

description: Control


title: E33942_1


title: sp117_DNAseq_youngadults_rep2


title: Refed 30 min trl-1(cas1077) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: ESCC EC0781B

type: genomic

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description:
ESCC EC0781B
Hybridized to SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: ESCC EC0781B

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Germline DNA from whole blood was extracted and purified using the standard phenol/chloroform method. DNA was extracted from tumor by using the Allprep kit (Qiagen). DNA quality and quantity were determined using NanoDrop 2000 (Thermo Scientific).

tag: disease state

value: Esophageal squamous cell carcinoma (ESCC)

value: Blood

tag: individual id


title: sp1981_DNAseq_youngadults_rep1


title: E25C_3

value: Gal80ts; Tub-Gal4/P{CaryP}attP40


title: Refed 30 min trl-1(cas1077) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment

tag: genotype


title: M13-49

description: Control


title: ESCC E1902B

description:
ESCC E1902B
Hybridized to SNP6.0

source_name: ESCC E1902B


title: sp117_DNAseq_youngadults_rep3


title: E33942_3

tag: treatment


title: Non-starved trl-1(cas1077) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: ESCC E1901B

description:
ESCC E1901B
Hybridized to SNP6.0

source_name: ESCC E1901B


title: Starved trl-1(cas1077) rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: Refed 10 min trl-1(cas1077) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-35

description: Control


title: sp117_DNAseq_youngadults_rep1


title: Non-starved trl-1(cas1077) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: ESCC E1892B

description:
ESCC E1892B
Hybridized to SNP6.0

source_name: ESCC E1892B


title: ESCC EC0782B

description:
ESCC EC0782B
Hybridized to SNP6.0

source_name: ESCC EC0782B


title: Refed 60 min WT rep2 RNA-Seq

description: mRNA

value: wide-type


title: Starved trl-1(cas1077) rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: M13-23

description: Control


title: Refed 60 min WT rep1 RNA-Seq

description: mRNA


title: ESCC E1633B

description:
ESCC E1633B
Hybridized to SNP6.0

source_name: ESCC E1633B


title: BC_Pt6

city: Singapore

first: XI

last: REN

state: Choose State

address: National University of Singapore, 14 Medical Drive, MD6, #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

description: strand-specific RNA-Seq

data_processing:
Clean raw reads were mapped to the reference human genome (hg19) by using STAR (2.7.9a) with default parameters.
Expression at the transcriptal level (TPM) was quantified by Salmon (v0.14.1) from RNA-seq reads.
Genome_build: hg19
Supplementary_files_format_and_content: Name — This is the name of the target transcript provided in the input transcript database (FASTA file).
Supplementary_files_format_and_content: Length — This is the length of the target transcript in nucleotides.
Supplementary_files_format_and_content: EffectiveLength — This is the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled).
Supplementary_files_format_and_content: TPM — This is salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
Supplementary_files_format_and_content: NumReads — This is salmon’s estimate of the number of reads mapping to each transcript that was quantified. It is an “estimate” insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

source_name: breast cancer patient tissue

extract_protocol:
Tumor genomic DNA and RNA were extracted from frozen tumor tissues using an AllPrep DNA/RNA Mini Kit (Qiagen). Peripheral blood mononuclear cells (PBMC) were isolated from the freshly withdrawn blood samples, and subsequently, the germline DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) kit.
The RNA seq library from tumor RNA was prepared using Illumina TruSeq Stranded mRNA Library Prep Kit as per the manufacturer's instruction.

value: Breast cancer tumor

tag: subtype

value: Triple negative breast cancer (TNBC)


title: BC_Pt7

description: strand-specific RNA-Seq


title: BC_Pt5

description: strand-specific RNA-Seq


title: ESCC E1628B

description:
ESCC E1628B
Hybridized to SNP6.0

source_name: ESCC E1628B


title: ESCC E1875B

description:
ESCC E1875B
Hybridized to SNP6.0

source_name: ESCC E1875B


title: E25C_1

tag: strain


title: Refed 30 min WT rep1 RNA-Seq

description: mRNA


title: bc4289_DNAseq_youngadults_rep1


title: BC_Pt4

description: strand-specific RNA-Seq


title: ESCC E1627B

description:
ESCC E1627B
Hybridized to SNP6.0

source_name: ESCC E1627B


title: Refed 30 min WT rep2 RNA-Seq

description: mRNA


title: E25C_2


title: ESCC E1577B

description:
ESCC E1577B
Hybridized to SNP6.0

source_name: ESCC E1577B


title: Refed 10 min WT rep2 RNA-Seq

description: mRNA


title: BC_Pt2

description: strand-specific RNA-Seq

value: Estrogen receptor (ER) positive


title: ESCC E1270B

description:
ESCC E1270B
Hybridized to SNP6.0

source_name: ESCC E1270B


title: BC_Pt1

description: strand-specific RNA-Seq


title: Refed 10 min WT rep1 RNA-Seq

description: mRNA


title: Starved WT rep2 RNA-Seq

description: mRNA


title: ESCC E1187B

description:
ESCC E1187B
Hybridized to SNP6.0

source_name: ESCC E1187B


title: Starved WT rep1 RNA-Seq

description: mRNA


title: Non-starved WT rep1 RNA-Seq

description: mRNA


title: CD14_TGF(-)_D0_rep1

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
Sequenced reads were mapped to reference human genome (hg38 assembly) using Bowtie2  with default parameters.
MACS2 to identify peaks of ATAC-seq enrichment over background.
Genome_build: hg38

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll  and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in MEMa (Invitrogen) supplemented with 10% heat-inactivated defined FBS, penicillin/streptomycin, L-glutamine, and 20 ng/mL human macrophage colony-stimulating factor (M-CSF) with or without TGFb(10 ng/mL).

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (Omni-ATAC-seq) protocol developed by (Corces et al., 2017); single end protocol.

treatment_protocol: CD14+ cells cultured in M-CSF (20ng/ml)  with or without TGFb (10 ng/ml) for 3 days and then stimulated with TNFa (40 ng/ml) for 24hrs.

value: CD14+ monocyte

value: peripheral blood

value: untreatment


title: Refed 60 min WT rep2 Ribo-Seq

description: Ribosome protected mRNA fragment

value: starved for 6 days and refed with food for 60 min


title: CD14_TGF(+)_TNFD1_rep1


title: ESCC E0892B

description:
ESCC E0892B
Hybridized to SNP6.0

source_name: ESCC E0892B


title: CD14_TGF(+)_TNFD6_rep3

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads.  RNA-seq reads were aligned to the human genome (hg38) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

treatment_protocol: CD14+ cells cultured in M-CSF (20ng/ml)  with or without TGFb (10 ng/ml) for 3 days and then stimulated with TNFa (40 ng/ml) for various time points(day0, day1, day6)


title: CD14_TGF(-)_TNFD1_rep1


title: BC_Pt3

description: strand-specific RNA-Seq


title: Refed 60 min WT rep1 Ribo-Seq

description: Ribosome protected mRNA fragment

source_name: larvae


title: CD14_TGF(+)_D0_rep1

value: TGF-priming


title: Refed 30 min WT rep2 Ribo-Seq

description: Ribosome protected mRNA fragment

value: starved for 6 days and refed with food for 30 min


title: Non-starved WT rep2 RNA-Seq

description: mRNA

value: non-starved


title: ESCC E0891B

description:
ESCC E0891B
Hybridized to SNP6.0

source_name: ESCC E0891B


title: ESCC E0948B-repeat

description:
ESCC E0948B-repeat
Hybridized to SNP6.0

source_name: ESCC E0948B


title: Refed 30 min WT rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: Refed 10 min WT rep2 Ribo-Seq

description: Ribosome protected mRNA fragment

value: starved for 6 days and refed with food for 10 min


title: ESCC E1241B

description:
ESCC E1241B
Hybridized to SNP6.0

source_name: ESCC E1241B


title: CD14_TGF(-)_TNFD6_rep3


title: ESCC E0842B

description:
ESCC E0842B
Hybridized to SNP6.0

source_name: ESCC E0842B


title: ESCC EC0782T

description:
ESCC EC0782T
Hybridized to SNP6.0

source_name: ESCC EC0782T

value: Tumor


title: ESCC E0379B

description:
ESCC E0379B
Hybridized to SNP6.0

source_name: ESCC E0379B


title: CD14_TGF(-)_TNFD1_rep3


title: ESCC EC0781T

description:
ESCC EC0781T
Hybridized to SNP6.0

source_name: ESCC EC0781T


title: ESCC E1902T

description:
ESCC E1902T
Hybridized to SNP6.0

source_name: ESCC E1902T


title: CD14_TGF(+)_TNFD6_rep2


title: Starved WT rep1 Ribo-Seq

description: Ribosome protected mRNA fragment

value: starved for 6 days


title: Refed 10 min WT rep1 Ribo-Seq

description: Ribosome protected mRNA fragment


title: Non-starved WT rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: CD14_TGF(-)_D0_rep3


title: CD14_TGF(+)_TNFD1_rep2


title: Starved WT rep2 Ribo-Seq

description: Ribosome protected mRNA fragment


title: ESCC E1892T

description:
ESCC E1892T
Hybridized to SNP6.0

source_name: ESCC E1892T

value: Esophageal squamous cell carcinoma (ESCC)


title: ESCC E1901T

description:
ESCC E1901T
Hybridized to SNP6.0

source_name: ESCC E1901T


title: CD14_TGF(+)_D0_rep2


title: ESCC E1633T

description:
ESCC E1633T
Hybridized to SNP6.0

source_name: ESCC E1633T


title: ESCC E0863B-repeat2

description:
ESCC E0863B-repeat2
Hybridized to SNP6.0

source_name: ESCC E0863B

value: Blood


title: CD14_TGF(+)_TNFD1_rep3


title: ESCC E0848B

description:
ESCC E0848B
Hybridized to SNP6.0

source_name: ESCC E0848B


title: GCA-F-59

city: Groningen

first: Rosanne

last: Reitsema

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description:
filtered_counts_barcodes.tsv.gz
filtered_counts_data.mtx.gz
filtered_counts_genes.tsv.gz
metadata_percell.csv

data_processing:
BCL files resulting from sequencing were transformed to FASTQ files with 10x Genomics Cell Ranger mkfastq.
FASTQ files were mapped with Cell Ranger count. During sequencing, 28 bp read 1 were used for identification of the Illumina library barcode, cell barcode and UMI. Read 2 was used to map to the reference transcriptome GRCh38. Filtering of empty barcodes was done in Cell Ranger.
The data from all samples were loaded in R (R version 3.6.2) and processed using the Seurat package (version 3.2.0)3. Cells with at least 2000 UMI’s per cell and less than 20% mitochondrial gene content were retained for analysis. The data of all 10X libraries was merged and processed together. The merged dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. The patient-effect was corrected using the integration function of Seurat. The most variable genes in the dataset were identified and the top 2000 was used for dimensionality reduction and clustering. Principal component analysis was performed on the 2000 variable genes to identify the dimensionality in the dataset and the first 10 principal components were selected for downstream analysis. Cells were clustered using graph-based clustering as implemented in Seurat. The original Louvain algorithm was utilized for modularity optimization. The top differentially expressed genes per cluster were used to identify cell types. The B cell population was selected and clustered separately to identify cell types. To evaluate the differences between samples and clusters, differential expression analysis was performed using the Wilcoxon rank sum test.
Assembly: Human: Hg38
Supplementary files format and content: filtered_counts_data.mtx.gz; final dataset containing the expression counts for all genes across filtered cells
Supplementary files format and content: filtered_counts_barcodes.tsv.gz; cell-associated barcodes corresponding to the column indices of filtered_counts_data.mtx
Supplementary files format and content: filtered_counts_genes.tsv.gz; feature names corresponding to the row indices of filtered_counts_data.mtx
Supplementary files format and content: metadata_percell.csv; file containing metadata per single cell
Supplementary files format and content: matrix.mtx.gz; barcodes.tsv.gz, features.tsv.gz; cell ranger output for each 10X library

source_name: PBMCs

growth_protocol: Human PBMCs were isolated from whole heparin blood by density gradient centrifugation using Lymphoprep. PBMCs were cultured at 1 x 107/mL in RPMI 1640 containing 10% heat-inactivated fetal calf serum and 10% DMSO. Samples were stored in liquid nitrogen prior to use.

extract_protocol:
Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO.
Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3’ V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol.

treatment_protocol: Not applicable to this study.

value: Giant cell arteritis

tag: gender

value: F

tag: age


title: CD14_TGF(-)_TNFD6_rep2

source_name: Primary human monocyte-derived macrophages

tag: tissue


title: ESCC E1875T

description:
ESCC E1875T
Hybridized to SNP6.0

source_name: ESCC E1875T


title: Non-starved WT rep1 Ribo-Seq

description: Ribosome protected mRNA fragment

source_name: larvae

value: wide-type


title: CD14_TGF(-)_TNFD1_rep2

tag: cell type


title: GCA-F-61


title: ESCC E1628T

description:
ESCC E1628T
Hybridized to SNP6.0

source_name: ESCC E1628T


title: GCA-F-72


title: CD14_TGF(-)_D0_rep2


title: CD14_TGF(+)_D0_rep3


title: HC-F-67

value: Healthy controls


title: CD14_TGF(+)_TNFD6_rep1


title: ESCC E1627T

description:
ESCC E1627T
Hybridized to SNP6.0

source_name: ESCC E1627T


title: ESCC E1577T

description:
ESCC E1577T
Hybridized to SNP6.0

source_name: ESCC E1577T