title: GAL1_SMC2_K38I_smc2_td_yH2A_rep2

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: scc1_7_ top2_4_H2A_rep2

status: Public on Mar 03 2020

type: SRA

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description:
processed data file:
N180209_top2-4-scc1-73-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

library_source: genomic

data_processing:
FASTQ files were generated by Illumina basespace   (https://basespace.illumina.com/home/index).
The resulting sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were  not trimmed.  Command for MySeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 25 --trim5 1 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]     Command for NextSeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 0 --trim5 0 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):    samtools sort [name of the .sam file generated with bowtie2] -o [name for the resulting .bam file] -O bam -T [name for resulting .bam file wo .bam]
BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks. Example command:     macs2 callpeak -t [sorted BAM file from yh2a data]-c  [sorted BAM file from h2a data]-f BAMPE -g 12100000 -n [name for output file] -B -q 0.01 --SPMR
The data then was sorted into 50 bp bins and used for meta data analysis using custom made R programs.
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: wig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: top2-td cell cultures for alpha factor release experiments were prepared as described previously -S. A. Schalbetter, S. Mansoubi, A. L. Chambers, J. A. Downs, J. Baxter, Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proceedings of the National Academy of Sciences. 112, E4565–70 (2015).

extract_protocol:
Pellets from 50 ml culture were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)). Cells were lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Lysate was spun out and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to a final volume of 1 ml. Samples were sonicated using the Focused-Ultrasonicator (Covaris, M220) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min). The sample was centrifuged for 20 min at 13,000 rpm at 4°C. Supernatant was then diluted to 1:10 (5 ml total).  50 μl protein A Dynabeads (Invitrogen, 10002D) and 50 μl protein G Dynabeads (Invitrogen, 10004D), were washed 3 times in IP buffer followed by adding to the sample and incubating for 2 h at 4°C. Supernatant was split, with 2X 2 ml being taken to 15 ml Falcon tubes, and 1 ml being kept at -20°C as an input sample. To the two 2 ml samples antibody was added, either H2A 1:500 (active motif) or 1.6 μg/ml H2AP (Abcam), and these were placed on a rotating wheel at 4°C for 15 – 20 h. For experiments where RPA1 ChIP was performed on the same sample, 75 ml starting cultures were used meaning supernatant could be split into 3X 2ml and 1 ml for input, with RPA1 antibody (1:10000, Agrisera) added to one 2 ml aliquot. For experiments where RPA1 ChIP was exclusively performed, 25 ml starting cultures were used to make a split of 1X 2ml for antibody addition and 1ml for input.
A preparation of Dynabeads (Invitrogen), Protein A (30 μl) and Protein G (30 μl), was washed 3 times in IP buffer. This was added to each sample and incubated at 4°C for 4 h. Supernatant was removed and beads were washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Elution was carried out in 400 μl elution buffer, for 30 min at room temperature. At the same time 50 μl from the input sample was added to 150 μl of elution buffer. 20 μl of 5 M NaCl and 10 μl of 10 mg/ml proteinase K (Invitrogen) was then added to the input, and 40 μl and 20 μl to the IP samples respectively. These were incubated at 65°C overnight. Then 10 μl of DNase-free RNase (Roche) was added to the input and 20 μl to the IP samples, and they were left at 37°C for 30 min. All DNA was purified with a Qiagen PCR purification kit and eluted in 50 μl for H2A or H2AP or 40 μl for RPA1. DNA amount was measured using the Qubit 2.0 Fluorometer (Life technologies) as per the manufacturer’s instructions.            For H2A or H2AP samples, libraries were prepared using the NEBnext Ultra II library kit (NEB) as per the manufacturer’s instructions. PCR enrichment required 13 cycles. PCR purification was carried out using AMPure XP beads. For RPA1 library preparation 34 ul from the RPA1 samples and 1 ng DNA in 34 ul water from the input were used. 5 µl 10 x NEB2.1 buffer and 5 µl of  random  primers  (8N,  3  mg/ml  stock)  were  added  and  the  samples  were  boiled  at  95°C  for  5  minutes  and  immediately placed  to  ice  for  5  minutes. 5 µl 10 x dNTP with dUTP instead of  dTTP (2  mM each)  and 1 µl T4  polymerase  (NEB)  were  added  and  the  mixture  was  incubated  at 37°C  in  a  thermal  cycler  for  20  min,  and  5  µl  0.5  M  EDTA (pH  8)  was  immediately  added  to  stop  the  reaction.  The resulting dsDNA was used to create libraries using the Ultra II library kit (NEB) as  per  the  manufacturer’s  instructions.

treatment_protocol: Cultures were fixed at 25°C  in  YP  + 1%  formaldehyde  (Sigma)  for  45  min. 125 mM glycine was then added for 5 min. Cells were washed with PBS before being pelleted and frozen in liquid nitrogen.

tag: strain

tag: genotype

value: Mat a ade2-1 leu2-3 his4-539/his3-11 ura3-52/ura3-1 can1-100     top2-4   scc1-73    trp1<delta>::hphNT1

tag: chip antibody


title: 786-O-sh-IMPDH1 2

city: wuhan

first: Hailong

last: Ruan

state: hubei

address: 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, China

country: China

institute: wuhan union hospital

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads. Clean reads for each sample were retained for subsequent analyses
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count
Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution
Genome_build: GR38 p7
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: cell

extract_protocol:
Cell lysates were used to extract RNA using Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: ccRCC-derived renal cancer cells

tag: passages

tag: shRNA

value: against IMPDH1


title: 786-O-sh-IMPDH1 3


title: 786-O-sh-IMPDH1 1


title: Mm4_ret_ChIP_input

city: Seattle

first: Timothy

middle: J

last: Cherry

state: WA

department: Developmental Biology and Regenerative Medicine

country: USA

institute: Seattle Children's Research Institute

data_processing: QUANTIFICATION AND STATISTICAL ANALYSIS: Sequence read data processing (ATAC_Seq, ChIP_Seq): Read processing and alignment: Demultiplexed FASTQ files were trimmed with Trimmomatic (version 0.33) using the parameter SLIDINGWINDOW:5:30 (Bolger et al., 2014). Trimmed reads were indexed and aligned to the human or mouse genomes (Human GRCh38/hg38 assembly December 2013; Mouse GRCm38/mm10 assembly, December 2011) using the Burrows_Wheeler Aligner (bwa) tool (Li and Durbin, 2010) with the parameters: bwa aln  _q 0  _t 4  _n 2  _k 2  _l 32  _e _1  _o 0 and bwa samse  _n 5. Tag directories of reads were created using HOMER (version 4.6) makeTagDirectory (Heinz et al., 2010). Peak calling: High confidence peaks across concordant biological replicates were identified via ENCODE’s Irreproducible Discovery Rate (IDR) pipeline using a 1% IDR threshold (Landt et al., 2012). For each set of replicates, bam files of reads were pooled and 2 pseudoreplicate files were generated by samtools view with the parameters _h _b _s 1.5 and _h _b _2.5. Peaks in biological replicate, pooled replicate, and pseudoreplicate samples were called over pooled input samples using MACS2 (version 2.1.1) (Zhang et al., 2008) with the parameters –nomodel _g <hs or mm> _p 1e_1 –extsize 200, where hs or mm refers to human or mouse genomes. An optimal final set of IDR_filtered peaks was obtained from the peak caller and used as the final high_confidence peak set for further analyses and the centers of these peaks were used as summits for analyses with HOMER. Sequence read data processing (Total RNA Nuc_Seq): Read processing and alignment: Reads were trimmed to 70bp and aligned to the human genome (Human GRCh38/hg38 assembly December 2013) using the Burrows_Wheeler Aligner (bwa) tool. Two sets of target sequences were provided and incorporated into the bwa index in addition to the usual 23 chromosomal targets: (1) the human mitochondrial genome (GenBank accession NC_012920.1); and (2) a set of ~10 million short (≤138bp) exon_exon splice_junction sequences (see below). For RNA_seq data, a third set of 92 short (< 2.1kb) spike_in oligos representing a wide range of reference concentrations (ERCC RNA Spike_In Mix, Life Technologies; Mix 2) was also incorporated into the index. Typically ~90% of all reads were mappable, allowing up to 2 mismatches, and of these ~70_85% were mapped uniquely. Multiple reads whose 5ʹ ends were assigned to the same locus were not flattened to a single count. The splice_junction target sequences were based on the NCBI RefSeq database for GRCh38. For each annotated transcript, we noted all subsets of two or more exons, not necessarily adjacent, that could be spliced together to produce a sequence at least as long as the read length. Each of these sequences were then trimmed to the maximum number of bases such that a read mapping to the sequence would necessarily cross these ordered exons’ splice junction(s). This procedure produced a library of all unique sets of exons whose intragenic splice junctions could possibly be covered by a read of the given length, based on the RefSeq annotation of exonic loci. Aligned reads thus had the opportunity to align either to genomic (chromosomal) sequences or to exon_junction_crossing sequences found only in mature mRNA. Expression level quantification: An in_house software tool, MAPtoFeatures (Gray et al., 2014), was used to quantify expression levels for individual genes as follows. A database of genic features (CDSs and UTRs) was constructed from ~103,000 genomic transcripts annotated in RefSeq for GRCh38. Merged genes were constructed by unioning all exons in all transcripts assigned to each distinct gene; the resulting segments defined the gene’s exonic coordinates used here (with the gaps between them defining introns). Genes with zero CDS exons were labeled ‘‘noncoding’’. These 24,644 genes were supplemented with 37 mitochondrial genes and 1,752 additional noncoding genes specified by the loci of all ribosomal RNA genes obtained from RepeatMasker (where the options Variations and Repeats, rmsk.repFamily=‘‘rRNA’’ yielded 414 LSU_rRNA_Hsa; 74 SSU_rRNA_Hsa; ,1264 5S). The purpose of this step was to allow the filtering out of reads stemming from transcription of repeats and rRNA genes, which tend to get populated to inconsistent degrees from sample to sample depending on the variable quality of rRNA depletion. Reads that aligned uniquely were then queried for their intersection with the exonic ranges of any of the above 26,433 genes, including exon_exon splice junctions. The total number of read bases that overlapped an exonic range was divided by the range’s length to give an average exonic read density (i.e., coverage). All reads were assigned to genes or to intergenic regions. However, only those reads not assigned to noncoding genes counted towards the total normalization count N, which ultimately afforded a more stable comparison of expression levels between samples than simply using the total number of reads. All read densities were normalized to a reference total of 10 million reads and a reference read length of 35 bp through multiplication by the factor (107/N)*(35 bp/70 bp). (Division of these normalized densities by 0.35 yields expression levels in alternative units of reads per kilobase of transcript per million mapped reads, RPKM.) For downstream analyses, genes with a normalized exon density value of 0 in any replicate at any timepoint were discarded to remove lowly expressed genes. Sequence read data processing (Single_nucleus RNA_Seq): inDrops sequencing_data processing: Transcripts were processed according to a previously published pipeline (Hrvatin et al., 2018; Klein et al., 2015). Briefly, this pipeline was used to build a custom transcriptome from the Ensembl GRCh38 genome and annotation with Bowtie 1.1.1 (Langmead et al., 2009), after filtering the annotation gtf file (gencode.v17. annotation.gtf filtered for feature_type=‘gene’, gene_type=‘protein_coding’ and gene_status=‘KNOWN’). Read quality control and mapping against this transcriptome were then performed. Finally, unique molecular identifiers were used to reference sequence reads back to individual captured molecules, thus yielding values denoted UMIFM counts. All steps of the pipeline were run with default parameters unless explicitly specified. Quality control for cell inclusion: Our initial dataset contained ~30,000 cells with more than 1,000 reads assigned to each cell. All mitochondrially encoded genes were removed from the dataset. Cells with fewer than 400 or more than 15,000 unique_molecular_identifier counts were next excluded, thus yielding 4,763 high quality cells isolated from three donors. Dimensionality reduction and clustering: All 4,763 cells were combined into a single dataset. The Seurat R package (Macosko et al., 2015; Satija et al., 2015) was used to cluster cells. The data were log normalized and scaled to 10,000 transcripts per cell. Variable genes were identified with the MeanVarPlot() function, which calculates the average expression and dispersion for each gene, then bins genes and calculates a z score for dispersion within each bin. The following parameters were used to set the minimum and maximum average expression and the minimum dispersion: x.low.cutoff=0.0125, x.high.cutoff=3, y.cutoff=0.5. Next, PCA was carried out, and the top 20 principal components were retained. The clustering resolution was set to 0.6. This method resulted in 14 initial clusters across 4,763 cells. Quantifying bioreplicate correlations: To validate the reproducibility of our epigenomic and transcriptomic assays, we compared the correlation of bioreplicates performed on distinct samples for ATAC_Seq/DNase_Seq, H3K27ac ChIP_Seq and total RNA Nuc_Seq experiments. For each assay, we found a high degree of correlation between samples of the same tissue type (Figure S1A). As expected, retinal and macular samples

organism: Mus musculus

source_name: p11 mouse retina

extract_protocol:
METHOD DETAILS: DNA accessibility: ATAC_Seq: Flash_frozen tissue was thawed by addition of 700ul of lysis buffer (10 mM Tris_HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP_40), homogenized by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, and transferred back to original 1.5mL LoBind tube (Eppendorf). Dounce was washed with an additional 700ul ice cold lysis buffer and buffer was transferred to tube with sample for a final volume of 1.4mL. Sample was then centrifuged in a microcentrifuge at 4C for 10min at 500 rcf. The pellet was re_eluted in 1.4mL ice cold lysis buffer, transferred to a pre_chilled dounce, homogenized again 12x with tight pestle, and transferred back to 1.5mL LoBind tube. Nuclei were counted on a hemocytometer and the volume of lysis buffer/nuclei suspension needed for 20,000 nuclei was aliquoted into a separate 1.5mL LoBind tube. Samples were centrifuged along with tube containing remaining nuclei (for nuclear localized RNA) at 4C for 5min at 500g (RCF). The supernatant was removed from samples and remaining nuclei. Subsequent ATAC libraries were generated with 20,000 nuclei per sample using the Nextera DNA library prep kit (FC_121_1030; Illumina, San Diego, CA USA) according to the protocol described in (Buenrostro et al., 2013; Buenrostro et al., 2015). DNase I_Seq: Sequence files from the ENCODE Consortium (Consortium, 2012) for human retinal pigment epithelium (ENCBS420ENC, ENCBS893GDP), embryonic human retina (ENCSR820ICX, ENCSR474GZQ, ENCSR621ENC), and 8 week mouse retina (ENCSR000CNW) described in (Wilken et al., 2015) were analyzed in parallel with ATAC_Seq data. Chromatin immunoprecipitation: Crosslinking: Flash frozen human or mouse tissue was homogenized in crosslinking buffer (10 mM HEPES_NaOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) containing 1% formaldehyde (added immediately before crosslinking) by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, transferred back to original 1.5mL LoBind tube (Eppendorf), and incubated while rotating gently at room temperature for 10 min. Crosslinks were quenched by addition of glycine to a final concentration of 0.125 M and incubated while rotating gently at room temperature for 5 min. Cells were pelleted by centrifugation 5 min at 1,350 g at 4C. Cell pellets were resuspended once with cold PBS and re_spun for 5 min at 1,350 g at 4C. Nuclei prep: Crosslinked cell pellets were resuspended in cold 5mL L1 buffer (50 mM HEPES_NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X_100, 0.5% NP_40, 10% glycerol, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) by pipetting and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 5mL L2 by pipetting (10mM Tris_HCl pH 8.0, 200mM NaCl, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 1.5 mL LB3 (10mM Tris_HCl pH 8.0, 100mM NaCl, 1mMEDTA, 0.5mMEGTA, 0.1% sodium deoxycholate, 0.5% N_lauroylsarcosine, protease inhibitors; 10mM sodium butyrate added for H3K27ac ChIPs) by pipetting and transferred to polystyrene tubes (Thermo Fisher 352099) for sonication. Sonication: Nuclei pellets were sonicated (Bioruptor Plus, Diagenode) in polystyrene tubes on high power with 36 cycles of 30 sec ‘‘on’’, 45 sec ‘‘off’’. After sonication, Triton X_100 was added to 1% final concentration and sonicated chromatin was centrifuged at 16,000 g for 5 min at 4C. The supernatant was used for preclearing and ChIP. All subsequent steps were performed using DNA LoBind tubes (Eppendorf). Preclearing and antibody_bead coupling: Protein A Dynabeads (Life Technologies) were washed twice with blocking buffer (0.1% BSA in LB3 + 1% Triton X_100) and aliquoted for preclearing and antibody_bead coupling. Antibodies were coupled to beads in 1.8 mL of blocking buffer by vertical rotation at 4C for 4 hr. In parallel, each sample of sonicated chromatin was incubated with an equivalent volume of washed bead slurry for preclearing. Each ChIP was performed in 1.8 mL LB3 + 1% Triton X_100 and rotated vertically at 4C for 16 hr. For input samples, 1% of sample was saved for de_crosslinking and DNA purification. Washes and elution: For each wash, beads were rotated vertically in wash buffer at 4C for 5 min. Beads were washed twice with low salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 500 mM NaCl), twice with lithium chloride wash buffer (0.25 M LiCl, 1% NP_40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris_HCl pH 8.0), and once with TE (50 mM Tris, 10 mM EDTA). Beads were then incubated at 65C in 200 mL of TE + 1% SDS per sample for 30 min with vortexing every 10 min. Eluted protein_DNA complexes were separated from the beads and incubated at 65C for 16 hr to reverse crosslinks. Purification of immunoprecipitated DNA: Elutions were incubated with 10mg RNase A for 1 hr at 37C, followed by 140 mg proteinase K for 2_3 hr at 55C with shaking. DNA was extracted with 1 volume of 25:24:1 phenol_chloroform_isoamyl alcohol and purified with a Qiagen PCR purification kit. ChIP DNA concentrations were determined by Qubit dsDNA HS Assay Kit (Thermo Fisher). Gene expression: Total RNA Nuc_seq: To determine RNA expression in adult human retina, macula and RPE nuclei, RNA was extracted from excess nuclei (~80M) from the ATAC nuclear preparation protocol using Trizol (ThermoFisher; 15596026). Prior to RNA extraction, an equal amount of ERCC spike_in control RNA (Mix 2) was added to each sample, following the manufacturer’s specifications. RNA was extracted using the Qiagen RNeasy Mini Kit with on_column DNase I digestion (Qiagen 79254). Single Nucleus RNA_seq: Generation of single_nucleus suspensions were prepared by isolating nuclei from flash frozen human retina as described above and purified using an iodixanol gradient (Optiprep; Sigma_Aldrich, St. Louis, MO, USA) with RNase_inhibitor. After gradient centrifugation, the nuclei were washed in dissociation solution (Hrvatin et al., 2018; Klein et al., 2015) containing 0.04% BSA and were resuspended in dissociation solution containing 0.04% BSA and 15% Optiprep for single_nucleus RNA sequencing using a modified inDrops protocol (Klein et al., 2015).
Library preparation and sequencing: ATAC_seq: ATAC_Seq libraries were prepared as described above and sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads. ChIP_seq: 2_40 ng of each ChIP sample was used to prepare libraries with the NuGEN Ovation Ultralow Library System v2 kit per manufacturer’s protocol. Libraries were sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads.Total RNA Nuc_seq: RNA_seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (E7420L, NEB) and either NEB rRNA depletion kit (E6310, NEB) or Qiagen GeneRead rRNA Depletion Nano kit (180211, Qiagen). Spike_in RNA (Fisher 4456740) were used for sample_to_sample normalization. Samples were then sequenced on the Illumina NextSeq 500 platform with 2x 150 bp paired_end reads. Single_nucleus RNA_seq: Single_nucleus RNA sequencing (inDrops): One or two libraries of approximately 3,000 cells were collected from each donor retina. inDrops was performed as previously described (Klein et al., 2015; Zilionis et al., 2017), generating indexed libraries that were then pooled and sequenced on the NextSeq 500 (Illumina) platform.

tag: donor apparent sex

value: Male

tag: donor age

value: postnatal day 11

value: C57Bl/6J; Jackson Laboratories

tag: donor apparent race

tag: postmortem interval

tag: chip_seq antibody


title: P5 Control(Vangl1/2) rep3

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

description: Sox9Cre-Vangl2 at P5.txt

data_processing:
Remove adaptor, align the reading to genome and create table counts
Generate DEG table with DeSeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: lung left lobe

extract_protocol:
The left lung lobe from control and mutant mice were homogenized in 1 ml TRIzol(Life Technologies) and 200 μl chloroform was then added. After centrifugation, the upper aqueous layer was removed and mixed with an equal volume of 70% ethanol. RNA was extracted with the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quality was evaluated using the Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: mouse lung

tag: developmental stage

value: postnatal day 5

value: WT


title: P5 Sox9Cre; Vangl2f/f rep1

description: Sox9Cre-Vangl2 at P5.txt

value: Sox9Cre/+; Ror2f/f


title: scc1_7_ top2_4_yH2A_rep2


title: Skin biopsy, PT1093lesional skinDay0

type: RNA

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: One Gustave L. Levy Place, Box 1077

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

description: PF-06700841 30 MG QD (P)

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: preprocessed using GCRMA packages in R/Bioconductor. Adjustement for batch was done using sva::ComBat function.

label: biotin

source_name: lesional skinDay0PF.30

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: subjid

value: lesional skin

tag: time

tag: treatment

tag: Sex

value: Female

tag: age

tag: race

value: WHITE

tag: ethnicity

value: NOT HISPANIC/LATINO


title: 786-O-sh-vector 3

tag: cell type

tag: strain

value: scrambled control


title: P5 Control(Vangl1/2) rep2

description: Sox9Cre-Vangl2 at P5.txt

tag: genotype


title: Mm4_ret_ChIP_RORB

tag: donor apparent sex

value: Diagenode Cat# C15410001


title: 786-O-sh-vector 2

tag: passages

tag: shRNA


title: scc1_7_ top2_4_yH2A_rep1

description:
processed data file:
N180118_scc1-73-top2-4_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

tag: chip antibody

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: 786-O-sh-vector 1


title: P5 Control(Vangl1/2) rep1

description: Sox9Cre-Vangl2 at P5.txt


title: uninfected control mouse 3

city: bern

first: Ghalia

last: Boubaker

state: Bern

address: Länggassstrasse, 122

department: INSTITUT OF PARASITOLOGY

country: Switzerland

institute: UNIVERSITY OF BERN

data_processing:
de-multiplexing and trimming of the TriLink adapter residuals (Illumina bcl2fastq v2 analysis software.
Quality of reads was checked with the software FastQC (v. 0.11.5)
Clean reads of samples derived from the same experimental group (AE-1pm or ctr-1pm) were pooled together and then dereplicated using the software usearch (v. 8.1.1681). This resulted in a list of unique sequences that were annotated and recorded based on their frequency of occurrence.
Mapping of cleaned reads using the RNA mapping software STAR (v. 2.5.1b).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 1-month non-infected mice

growth_protocol: Ten 8-week-old female C57BL/6 mice

extract_protocol:
The obtained liver tissues were minced quickly, mixed at a ratio of 1:10 with QIAzol lysis reagent and homogenized by bead beating. Total RNA was extracted according to the manufacturer’s instruction of the QIAzol lysis reagent with the exception that chloroform was replaced by 1-bromo-3-chloropropane for the phase separation step. To remove genomic DNA contamination in RNA samples, an enzymatic digestion step using DNase I was carried out. Finally, total RNA was re-suspended in RNase-free water. RNA quantity and RNA quality number (RQN ≥ 8) was determined by the Fragment Analyzer CE12.
Five libraries were generated from five mice (three mice from E. multilocularis-infected group and two mice from the uninfected control group). The total RNA was checked on an Agilent 2100 Bioanalyzer instrument for degradation. Subsequently, the CleanTag Ligation Kit (was used to prepare small RNA stranded libraries from total RNA (1µg RNA per library). Libraries were analyzed a second time on the Bioanalyzer to check for the expected miRNAs fragment peak at 141 bp and subsequently a Sage Science Pippin Prep instrument was used to select the expected fragment size range. In a last step before the deep sequencing, the quality and concentration of each final library (the eluted 141 bp band) were submitted to PicoGreen analysis.

treatment_protocol: The animals were divided into two groups: The control group remained uninfected, and the other group was orally infected with E. multilocularis eggs.

value: female

value: uninfected

tag: infection stage

value: 1 month

value: liver

tag: molecule subtype

value: small RNA


title: Skin biopsy, PT1091non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

source_name: non-lesional skinDay0PF.30

tag: tissue

value: non-lesional skin

value: Male

value: HISPANIC/LATINO


title: Mm4_ret_ChIP_H3K27ac

tag: donor age

value: postnatal day 11

value: C57Bl/6J; Jackson Laboratories

tag: donor apparent race

tag: postmortem interval

tag: chip_seq antibody


title: scc1_73_H2A_rep2

description:
processed data file:
N180209_scc1-73-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a  ade2-1 his3-11 leu2-3   ura3-1 can1-100   scc1-73    trp1<delta>::hphNT1


title: P2 Sox9Cre; Ror2f/f rep2

description: Sox9Cre-Ror2 at P2.txt

value: mouse lung

tag: developmental stage

value: postnatal day 2

value: Sox9Cre/+; Vangl2f/f


title: P2 Sox9Cre; Ror2f/f rep3

description: Sox9Cre-Ror2 at P2.txt


title: Mm4_ret_ChIP_H3K4me2


title: scc1_73_yH2A_rep2


title: Mm1_ret_ATAC_100k


title: scc1_73_H2A_rep1

description:
processed data file:
N180118_scc1-73_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: scc1_7_ top2_4_H2A_rep1

value: Mat a ade2-1 leu2-3 his4-539/his3-11 ura3-52/ura3-1 can1-100     top2-4   scc1-73    trp1<delta>::hphNT1


title: P2 Sox9Cre; Ror2f/f rep1

description: Sox9Cre-Ror2 at P2.txt


title: Mm1_ret_ATAC_20k


title: scc1_73_yH2A_rep1


title: Control10_DKH_RNA, biological

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

department: Neurology

country: South Korea

institute: Pusan National University Yangsan Hospital

description: Gene expression data from Control

hyb_protocol: Approximately 5.5 μg of the labeled cDNAs were hybridized onto the Affymetrix GeneChip Array at 45℃ for 16 hours.

scan_protocol: After washing, the arrays were stained on a GeneChip Fluidics Station 450 and scanned on the GeneChip Scanner 3000.

data_processing:
Raw data were analyzed using Affymetrix GeneChip Command Console Software (AGCC). The raw data were summarized and normalized with Robust Multi-array Average (RMA) module implemented in Affymetrix Power Tools.
The differentially expressed genes (DEGs) between AUV and normal control samples were screened by fold-change (fc) filtering combined with student’s t-test. False discovery rate (FDR) was controlled by adjusted p-value using Benjamini-Hochberg algorithm. Genes were considered differentially expressed at |fold changes| > 1.5 and p-value < 0.05.

source_name: peripheral whole blood

label_protocol: Purified RNA sample was transcribed to double-strand cDNA using the GeneChip Whole Transcript (WT) Amplication kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: The samples were incubated for a minimum of 2 hours at room temperature (15-25℃) to achieve complete lysis of blood cells. And then, the samples were centrifuged for 10 minutes at 5000 x g using a swing-out rotor. The supernatant was decanted, and 4 mL of RNase-free water was added to the pellet. The samples were vortexed until the pellet was visibly dissolved, and centrifuged for 10 minutes at 5000 x g. After the entire supernatant was removed, the remaining pellet was resuspended in 350 μL of buffer BR1 and transferred to microcentrifuge tube, followed by automated RNA purification using QIAcube. The purity and quantity of RNA were measured using a NanoDrop ND-1000 (Thermo Fisher Scientiﬁc, Wilmington, DE, USA). The quality of RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an RNA Integrity Number.

treatment_protocol: Peripheral whole blood (2.5 ml) was collected from the patients and ten healthy normal controls. The samples immediately placed into PAXgene Blood RNA Tubes (QIAGEN), and were stored under refrigerated conditions (2-8℃) before RNA extraction.

value: Whole blood

tag: disease

value: Control


title: P2 Control(Ror2) rep1

description: Sox9Cre-Ror2 at P2.txt

value: WT


title: scc1_73_top2_td_yH2A_rep2

description:
processed data file:
N170317_171-scc1-73_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker   scc1-73    pRS316

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: Mm1_ret_ATAC_50k


title: P2 Sox9Cre; Vangl2f/f rep3

description: Sox9Cre-Vangl2 at P2.txt


title: Control9_KUJ_RNA, biological

description: Gene expression data from Control


title: Control7_GIS_RNA, biological

description: Gene expression data from Control


title: P2 Sox9Cre; Vangl2f/f rep2

description: Sox9Cre-Vangl2 at P2.txt


title: Control8_KSS_RNA, biological

description: Gene expression data from Control


title: top2_4 H2A rep2

description:
processed data file:
N180209_top2-4-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a his4-539 ura3-52 top2-4


title: Hu33_ret_ChIP_CREB

source_name: Adult human retina

value: caucasian

value: Millipore Cat# 06_863, RRID:AB_310268


title: scc1_73_top2_td_H2A_rep1

description:
processed data file:
N170222_SCC1_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: P2 Control(Ror2) rep3

description: Sox9Cre-Ror2 at P2.txt


title: scc1_73_top2_td_H2A_rep2


title: Hu29_ret_ChIP_CREB

value: Female

value: other


title: P2 Sox9Cre; Vangl2f/f rep1

description: Sox9Cre-Vangl2 at P2.txt


title: P2 Control(Ror2) rep2

description: Sox9Cre-Ror2 at P2.txt


title: top2_4 yH2A rep2


title: scc1_73_top2_td_yH2A_rep1


title: eco1_1_H2A_rep2

description:
processed data file:
N180214_eco1-830-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3  eco1-1 (G211H)


title: Control6_LCW_RNA, biological

description: Gene expression data from Control


title: FSG16 [bulk RNA-seq]

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: Raw reads extracted using HTSeq from the  single end fastq files generated from glomerular fraction of disease biopsy tissue of FSGS patient

data_processing:
Further data analyses were performed on the CellRanger output data files using Seurat 3 R package. As a quality control step, cells with less than 500 genes per cell were filtered out. The percentage of mitochondrial gene read content has emerged as a quality measure for the cell viability in single-cell studies. High percentage of mitochondrial reads indicates that the cells are less viable, as much of their cytoplasmic mRNAs were lost due to the breakage of plasma membrane during dissociation process. For the tumor-nephrectomy data generated by 10Xgenomics version2, a threshold of < 20% mitochondrial reads per cell was used, whereas, a cutoff of < 50% mitochondrial reads per cell was applied for the data from 10X genomics version 3. It has been observed by us and other groups that for certain tissues, including kidney, 10X genomics version 3 chemistry results in higher percentage of mitochondrial reads irrespective of the viability status of the cells. This issue was circumvented by deeper sequencing of the samples to obtain more genes per cell. After the quality control step, the data from the three sample types (tumor-nephrectomy, surveillance biopsy and pre-perfusion biopsy) were merged and further analyzed. In order to exclude cells that were doublets or multiplets from the analysis, we used a cutoff of > 500 and < 5000 genes per cell.
Genome_build: Grch38
Supplementary_files_format_and_content: read counts

source_name: disease biopsy

extract_protocol:
For tissue dissociation, samples were quickly thawed in a 37˚C waterbath for one minute, transferred to a small dish containing 1 ml DMEM/F12 medium (with L-Glutamine, HEPES, and high glucose) supplemented with 10% heat inactivated FBS, and incubated for 10 minutes at room temperature. Tissue/biopsy samples were cut into 1 mm3 small pieces to increase the surface area before they were transferred to a 1.5 ml tube containing 500 µl DMEM/F12 digestion media containing 125 ng Liberase TL (Sigma) enzyme (conc.: 0.25 mg/mL). Samples were incubated on an orbital shaker (500 rpm) for 12 minutes at 37˚C with a mild trituration step using a wide bore 1000P tip applied after 6 minutes. Digestion was stopped by adding 500 µl DMEM/F12 medium containing 10% FBS and incubated at room temperature for 1 minute. The cell suspension was then filtered through a 30 µl strainer (Milteny Biotech) into a 15 ml conical tube. Remaining solid tissue was passed through the nylon mesh using the rubber end of a 5 ml syringe pestle and the filter was washed with 10 ml DMEM/F12/10%FBS medium. Cells were pelleted by centrifugation for 10 minutes at 200 x g and 4˚C. The supernatant was immediately, completely removed by vacuum suction using a glass Pasteur pipet. The cell pellet was then gently re-suspended in 55 µl DMEM/F12/10%FBS medium and cell viability was analyzed with a Countess II FL automated cell counter exploiting the Trypan Blue dye exclusion method.
Single cell samples were immediately transferred to the University of Michigan Sequencing Core facility (in up to 46 µl DMEM/F12/10%FBS) per sample were added to each channel of a chip on the droplet based high-throughput 10XGenomics™ Chromium™ platform allowing cell lysis, individual cell barcoding, and reverse RNA transcription. We used the 10X Single Cell 3' GEX – version 2 chemistry for all tumor-nephrectomy samples and the enhanced 10X Single Cell 3' GEX – version3 for the more recently processed transplant surveillance biopsies and pre-perfusion biopsies. Single cell library preparation based on 10X Genomics technology  included emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter and Illumina sample index addition. Libraries have been pooled and sequenced on an Illumina HiSeq4000 platform as asymmetric paired end runs (26x115 bases) with a median of 100 million raw sequencing reads per sample. The output from the sequencer was first processed by CellRanger, the proprietary 10X Chromium single cell gene expression analysis software
Bulk glomerular RNAseq expression data were obtained for 74 participants with biopsy proven FSGS enrolled in the NEPTUNE study. Briefly, mRNA samples were prepared using the Illumina TruSeq mRNA Sample Prep v2 kit (Illumina, San Diego, CA, USA). Multiplex amplification was used to prepare cDNA with a paired‐end read length of 100 bases using an Illumina HiSeq2000 (Illumina Inc., San Diego, CA, USA). RNA‐sequencing was performed by the University of Michigan DNA Sequencing Core (http://seqcore.brcf.med.umich.edu/). Quality of the sequencing data was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read counts were extracted from the fastq files using HTSeq (version 0.11). The objectives and study design of NEPTUNE can be found in the clinicaltrials.gov database under NCT1209000 (42).

tag: subject status

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease

value: adult kidney


title: Control5_JMH_RNA, biological

description: Gene expression data from Control


title: Control4_JYJ_RNA, biological

description: Gene expression data from Control


title: top2_4 H2A rep1

description:
processed data file:
N180118_top2-4_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: Hu26_mac_ChIP_input

source_name: Adult human macula

value: Male


title: Control2_YJS_RNA, biological

description: Gene expression data from Control


title: RBE cell infected with GFP adenovirus

city: Shanghai

first: Tian-Yi

last: Jiang

address: 366 Qianju Road

institute: National Center for Liver Cancer, the Second Military Medical University

description:
RBE CON
Gene expression data from RBE-GFP

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: not provided; requested

source_name: cell infected with GFP adenovirus

label_protocol: standard Affymetrix protocol

extract_protocol: not provided; requested

tag: cell line

value: RBE

tag: cell type

value: cholangiocarcinoma cell line

tag: treatment

value: infected with GFP adenovirus


title: Control3_PKJ_RNA, biological

description: Gene expression data from Control

value: Whole blood


title: RBE cell infected with PTEN adenovirus

description:
RBE PTEN
Gene expression data from RBE-PTEN

source_name: cell infected with PTEN adenovirus

value: infected with PTEN adenovirus


title: top2_4 yH2A rep1

tag: strain

tag: genotype

value: Mat a his4-539 ura3-52 top2-


title: HCCC-9810 cell infected with GFP adenovirus

description:
9810 CON
Gene expression data from 9810-GFP


title: P2 Control(Vangl1/2) rep2

description: Sox9Cre-Vangl2 at P2.txt

value: mouse lung

value: postnatal day 2

value: WT


title: HCCC-9810 cell infected with PTEN adenovirus

description:
9810 PTEN
Gene expression data from 9810-PTEN


title: Control1_OG_RNA, biological

description: Gene expression data from Control

value: Control


title: P2 Control(Vangl1/2) rep1

description: Sox9Cre-Vangl2 at P2.txt


title: P2 Control(Vangl1/2) rep3

description: Sox9Cre-Vangl2 at P2.txt


title: w303 wildtype H2A rep2

description:
processed data file:
N180209_w303-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100


title: w303 wildtype yH2A rep2

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: Hu25_ret_ChIP_CTCF

tag: donor apparent sex

value: Female

value: caucasian

value: Santa Cruz Biotechnology cat# sc_15914; RRID:AB_2086899


title: Hu22_ret_ChIP_RORB

value: unknown

value: Diagenode Cat# C15410001


title: Hu25_ret_ChIP_MEF2D

value: Greenberg Lab cat#2373; Andzelm, Cherry et al., 2015


title: w303 wildtype yH2A rep1

description:
processed data file:
N180118_w303_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

tag: chip antibody


title: Hu22_ret_ChIP_CTCF


title: Hu21_ret_ChIP_CRX

value: Santa Cruz Biotechnology cat# sc_30150 (H_120) X; Lot# A2113; RRID:AB_2276566


title: Hu21_ret_ChIP_MEF2D


title: AUV7_CCS_RNA, biological

description: Gene expression data from AUV

value: acute unilateral vestibulopathy (AUV)


title: FT Tumor Organoid 4 M1 plus Wnt medium

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Epithelial progenitor isolation from fallopian tube samples and organoid culture was done as previously described (Nat Commun. 2015 Dec 8;6:8989. doi: 10.1038/ncomms9989.) Ovarian cancer progenitors were isolated and cultured according to the following protocol:  Ovarian cancer tissue was received from the Department of Gynecology, Charité University Hospital, Campus Virchow Clinic. Cancer samples, surgically removed from patients with a diagnosis of high-grade serous ovarian cancer, were retrieved by clinicians from tumors of specified sites within the abdominal cavity. The tumor material was transported and processed within few hours after surgery and each sample was divided into 3 pieces for cell preparation, tissue fixation and RNA/DNA isolation. For isolation of HGSOC progenitors, the tissue pieces were washed with DPBS, minced with a scalpel into very small pieces and incubated in a 1:1 mixture of Collagenase I and II (Sigma) for at least 60 min at 37°C on a shaker. Afterwards, the enzyme-tissue mixture was vigorously vortexed to separate the cells. Next, the cell suspension was washed with ADF medium and centrifuged (5min, 300 x g, 4°C). After initial isolation from the tumor tissue, ovarian cancer cells (OCCs), were seeded in MatrigelTM at a concentration of approx. 30.000 cells/ 50µL. Because cancer cells did not form organoids or were difficult to expand in the beginning different media compositions were tested to support in vitro growth. Basically, the final ovarian cancer medium contained the following supplements and growth factors: ADF supplemented with 12 mM HEPES, 1% GlutaMAXTM, 2% B27, 1% N2, human EGF, 1 mM nicotinamide, 9 µM ROCK inhibitor (Y-27632) and 0.5 µM TGF-β RI Kinase Inhibitor IV (SB431542). In some cases organoids were growing in the presence of conditioned Rspo1 medium, Noggin or BMP2. Upon proper organoid maturation and growth under specified conditions the cells were split at an expansion rate of 1:3 every 1-2 weeks. To expand the organoids they were released from MatrigelTM using ice-cold ADF, centrifuged and resuspended in pre-warmed TrypLETM. Enzymatic digestion was carried out for 7 min at 37°C. Afterwards, the organoid suspension was vortexed, mixed with cold ADF and centrifuged (300xg, 5min). Next, the supernatant was removed, the cell pellet resuspended in MatrigelTM  and seeded into a pre-warmed cell culture plates. After ~20min the MatrigelTM was overlaid with the respective ovarian cancer medium. The medium was changed twice per week and the organoids kept all the time in a humidified incubator with 37°C and 5% CO2.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Tissue samples were immediately snap frozen upon arrival of patient material and RNA islaoted later from the frozen samples. Organoids derived from either ovarian cancer samples or Fallopian tubes were grown in Matrigel and RNA isolated from mature stable growing cultures treated with or without Wnt3a/Rspo1 supplemented medium.

tag: donor

tag: sourcetype

value: Organoid

tag: condition

value: Tumor

tag: medium


title: Hu21_mac_ChIP_H3K27ac

tag: donor age

tag: donor apparent race


title: AUV9_LYA_RNA, biological

description: Gene expression data from AUV

tag: tissue

value: Whole blood


title: w303 wildtype H2A rep1


title: AUV10_SJS_RNA, biological

description: Gene expression data from AUV


title: AUV8_HYS_RNA, biological

description: Gene expression data from AUV


title: FT Tumor Organoid 4 M1 medium


title: FT Tumor Organoid 7 M1 plus Wnt medium


title: AUV5_KJR_RNA, biological

description: Gene expression data from AUV


title: AUV4_PJS_RNA, biological

description: Gene expression data from AUV


title: AUV6_MMS_RNA, biological

description: Gene expression data from AUV


title: Hu20_ret_ChIP_CRX

tag: postmortem interval

tag: chip_seq antibody

value: Santa Cruz Biotechnology cat# sc_377207 (B_11) X  Lot# I1212


title: FT Tumor Organoid 7 M1 medium


title: top2-td H2A rep1

description:
processed data file:
N170317_13-top2td_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3  top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)  pRS316


title: top2-td H2A rep2

description:
processed data file:
N170222_top2dt_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub -DHFRL80P-ts - Myc -linker )


title: top2-td yH2A rep1


title: Hu18_ret_ChIP_H3K4me2

value: Male


title: top2-td yH2A rep2


title: degron background wt H2A rep2

description:
processed data file:
e46_wt_BYAK171-noco_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3


title: degron background wt yH2A rep2

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: MRR-2

first: Hongyu

last: Han

address: No.518, Ziyue Road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description: drug-resistant type

data_processing:
Raw fastq sequencing data were produced by Illumina HiSeq 2000
Raw reads were subjected to quality control and filtered into clean reads by removing dirty raw reads, including the sequence of adapters, sequences with a high content of unknown bases and low-quality reads.
Clean reads were mapped to the E. tenella Houghton strain genome scaffold version 8.1 (available on www.toxodb.org) using BWA and to E. tenella Houghton strain gene reference using Bowtie (version 2.1.0) (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Gene expression levels were calculated using the fragments per kilobase of exon model per million mapped reads (FPKM) method, which eliminated the influence of different gene lengths and sequencing discrepancies
Genome_build: E. tenella Houghton strain genome scaffold version 8.1 (available on www.toxodb.org)
Supplementary_files_format_and_content: tab-delimited files include transcript ID,  gene ID corresponding to this transcript, length of transcript, support reads number to this transcript after model regulation,FPKM value of this transcript for each sample

organism: Eimeria tenella

source_name: Sporulated oocysts

extract_protocol:
Three strains sporulated oocysts of Eimeria tenella were collected and purified, then they were homogenized by vortexing with an equal volume of glass beads(710–1180 μm, Sigma, MO, USA) until oocyst and sporocyst walls were completely broken, Total RNA was extracted using TRIzol® Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: maduramicin-resistant strain

tag: developmental stage

value: Sporulated oocysts


title: Hu15_ret_ChIP_CREB

value: Female

value: caucasian

value: Millipore Cat# 06_863, RRID:AB_310268


title: AUV3_PSK_RNA, biological

description: Gene expression data from AUV

tag: disease


title: Hu17_ret_ChIP_H3K4me2


title: FT Normal Organoid 231

value: Normal

value: StandardFT


title: MRR-1

description: drug-resistant type


title: Hu14_ret_ChIP_NRL

value: Abcam cat# AB137193


title: degron background wt H2A rep1

description:
processed data file:
N170317_12-wt-pl_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3  pRS316


title: AUV2_KHK_RNA, biological

description: Gene expression data from AUV

value: acute unilateral vestibulopathy (AUV)


title: DZR-3

description: drug-resistant type

value: diclazuril-resistant strain


title: FT Tumor Tissue 1

value: Tissue

value: Tumor


title: AUV1_SYK_RNA, biological

description: Gene expression data from AUV

value: Whole blood


title: DZR-2

description: drug-resistant type


title: Hu14_ret_ChIP_H3K4me2

value: Male


title: FT Tumor Tissue 2


title: Hu13_ret_ChIP_NRL


title: MRR-3

description: drug-resistant type


title: FT Normal Organoid 223

value: Organoid


title: FT Normal Organoid 217


title: FT Normal Tissue 223


title: FT Normal Tissue 231


title: Hu13_ret_ChIP_MEF2D

value: Greenberg Lab cat#2373; Andzelm, Cherry et al., 2015


title: LD-8

city: Wenzhou city

first: Huirong

last: Li

state: Zhejiang province

address: NO.268, Xueyuan road, Lucheng district

department: School of Ophthalmology and Optometry and Eye Hospital

institute: Wenzhou medical university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2-month-old albino mice were first dark-adapted for 12h and then exposed to normal light (200 lux) or high-intensity light (15,000 lux) in non-reflective cages for 1 day

value: BALB/c

tag: age

value: 2-month old

tag: treatment

value: exposed to high-intensity light (LD)

value: Retina


title: LD-7

tag: strain


title: FT Normal Tissue 217


title: FT Tumor Organoid 2


title: FT Tumor Organoid 1


title: DZR-1

description: drug-resistant type

value: Sporulated oocysts


title: degron background wt yH2A rep1

tag: genotype

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: DS-3

description: drug-sensitive type

value: drug-sensitive strain


title: LD-6


title: LD-1


title: Hu12_RPE_ChIP_input

source_name: Adult human retinal pigment epithelium and choroid

tag: donor apparent sex

value: Female

value: caucasian


title: LD-4


title: DS-1

description: drug-sensitive type


title: NL-8

value: exposed to normal light (NL)


title: DS-2

description: drug-sensitive type


title: Hu11_ret_ChIP_OTX2_R1

value: R and D Systems Cat# AF1979, RRID:AB_2157172


title: FT Normal Organoid 2

source_name: FT OC2-O

tag: donor

value: Normal

value: StandardFT


title: summ2_mpk4_flg22_rep3

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases
trimmed reads were aligned to the TAIR10 genome using TOPHAT 2-2.1.1
Fragments Per Kilobase of sequence per Million mapped reads (FPKM) were calculated using Cufflinks V2.1.1
Alternative splicing between two samples were identified using rMATS V3.5
Genome_build: TAIR10
Supplementary_files_format_and_content: RNASeq_fpkm.xlsx, excel, fpkm values

organism: Arabidopsis thaliana

source_name: summ2 mpk4  flg22 treatment, rep3

growth_protocol: Seeds were surface sterilized and stratified on MS plates (1/2 MS, 0.5% sucrose, 1% agar, and 0.05% MES, pH 5.7) for 3 days at 4°C. Then, plants were grown in a growth chamber at 23°C with a 16-h photoperiod.

extract_protocol:
RNA was extracted using NucleoSpin RNA Plant kit (Macherey Nagel).
mRNA sequencing libraries were constructed in KAUST Bioscience Core Lab using TruSeq Stranded mRNA LT Sample Prep Kit and manufacturer’s instructions (Illumina).
Sequencing was performed on each library to generate 151-bp paired-end reads for transcriptome sequencing on Illumina Genome Analyzer platform (HiSeq 4000).

treatment_protocol: Fourteen-day-old seedlings were treated with 1 uM flg22 or H2O for 0.5 h, and three biological repeat samples were proceeded to total RNA extraction.

value: 14 days

value: seedlings

value: summ2 mpk4


title: Hu12_RPE_ChIP_H3K27ac


title: NL-7


title: Hu10_ret_ChIP_OTX2

value: Male

value: Abcam cat# ab21990, RRID:AB_776930


title: NL-5

value: BALB/c

value: 2-month old


title: summ2_mpk4_flg22_rep2

source_name: summ2 mpk4  flg22 treatment, rep2


title: Hu9_ret_ChIP_NRL

value: Abcam cat# AB137193


title: summ2_mpk4_flg22_rep1

source_name: summ2 mpk4  flg22 treatment, rep1


title: NL-4

value: Retina


title: Hu9_mac_ChIP_H3K27ac


title: summ2_flg22_rep3

source_name: summ2  flg22 treatment, rep3


title: NL-1


title: FT Tumor Organoid 6

tag: sourcetype

value: Organoid

value: Tumor


title: Hu10_ret_ChIP_OTX2_2


title: summ2_flg22_rep2

source_name: summ2  flg22 treatment, rep2


title: WGBS-KspCreDKO-3W-Cdh16Pos

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For WGBS data, after trimming adapter and low-quality reads by Trim Galore Bismark was used for alignment to mouse genome (mm10), deduplication and quantification of methylation level for each CpG site.
For RRBS data, after trimming adapter and low-quality reads by Trim Galore v0.5.0 with option '--rrbs, Bismark v0.19.1 was used for align reads to mouse genome (mm10).
For RNA-seq data, sequencing reads were aligned to mouse genome using STAR v2.2.1 and gene expression was quantified by RSEM v1.3.1. Comprehensive gene annotation (gencode.vM18.annotation.gtf) was obtained from GENCODE database.
Genome_build: mm10
Supplementary_files_format_and_content: For WGBS and RRBS, Bismark coverage file. For RNA-seq, tab-delimited text files include TPM values for each Sample.

source_name: Cdh16+ cells from kidney

extract_protocol:
Genomic DNA from isolated Cdh16 positive cell was isolated using MagAttract HMW DNA Kit (Qiagen) according to manufacturer’s instruction. The concentration of DNA was measured using Quant-iT PicoGreen dsDNA Assay kit (Life Technologies) by following manufacturer’s instruction.
WGBS libraries were constructed from the purified genomic DNAs using the Illumina TruSeq DNA Methylation Library Preparation kit.

value: kidney

value: post natal day 21

value: KspCre Dnmt3ab f/f


title: WGBS-Control-3W-Cdh16Pos

value: Dnmt3ab f/f


title: FT Tumor Tissue 6

value: Tissue

tag: condition


title: FT Tumor Organoid 4

tag: medium


title: FT Tumor Tissue 4


title: FT Tumor Tissue 5


title: K25

city: Galveston

first: Anna

last: Nia

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

data_processing:
STAR alignment program, version 2.5.3a, with the recommended ENCODE options (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013;29(1):15-21 doi: 10.1093/bioinformatics/bts635published Online First: Epub Date]|.) -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: comma-seperated text file which includes raw transcript expression counts (with corresponding ENSEMBL ID) for each sample

source_name: Left liver lobes

extract_protocol:
Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA)
rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500.

tag: treatment type

value: 56Fe Irradiated

tag: time

value: 12 months

tag: biological replicate


title: Hu8_ret_ChIP_NRL

value: Female

tag: donor age

tag: donor apparent race

value: caucasian

tag: postmortem interval


title: K24


title: col0_flg22_rep2

source_name: wild type flg22 treatment, rep2

value: 14 days

tag: tissue

value: seedlings

value: wild type


title: Hu8_ret_ATAC

tag: chip_seq antibody


title: FT Tumor Organoid 8


title: FT Tumor Tissue 8


title: FT Tumor Organoid 5


title: Hu8_retina_1_snRNA

description:
single nucleus polyA RNA
Hu8_retina_1_snRNA
Hu1_Hu4_Hu8_single_nuclei_rawcount_matrix.txt

molecule: polyA RNA


title: col0_flg22_rep1

source_name: wild type flg22 treatment, rep1

tag: age


title: Hu8_ret_nuclei_RNA

description:
total nuclear RNA
Hu8_ret_nuclei_RNA

source_name: Adult human retina


title: K23


title: Hu7_ret_nuclei_RNA

description:
total nuclear RNA
Hu7_ret_nuclei_RNA

value: black


title: Hu7_ret_ChIP_OTX2

value: Abcam cat# ab21990, RRID:AB_776930


title: FT Tumor Organoid 9


title: summ2_mpk4_mock_rep2

source_name: summ2 mpk4  H2O treatment, rep2

value: summ2 mpk4

tag: treatment


title: col0_flg22_rep3

source_name: wild type flg22 treatment, rep3


title: summ2_mpk4_mock_rep3

source_name: summ2 mpk4  H2O treatment, rep3


title: Hu7_ret_ATAC


title: K17

value: 9 months

tag: strain


title: K18


title: summ2_mpk4_mock_rep1

source_name: summ2 mpk4  H2O treatment, rep1

tag: genotype


title: FT Tumor Tissue 9

value: Tumor


title: Hu6_ret_nuclei_RNA

description:
total nuclear RNA
Hu6_ret_nuclei_RNA

tag: donor apparent sex

value: Male


title: K16


title: summ2_flg22_rep1

source_name: summ2  flg22 treatment, rep1


title: FT Tumor Organoid 7

tag: donor

value: Organoid


title: FT Tumor Tissue 7

tag: sourcetype


title: summ2_mock_rep3

source_name: summ2  H2O treatment, rep3


title: K14

value: 4 months


title: SgriRibo_S2

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

institute: KAIST

description:
treated RNA
Sgri_Ribo_ETLS_readcount.txt

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
Raw reads were mapped to PhiX control sequence (NCBI Genbank accession number : NC_001422) to eliminate the PhiX control reads with the following parameters; Mismatch cost : 2, Insertion cost : 3, Deletion cost : 3, Length fraction : 0.9, Similarity fraction 0.9, non-specific matches were randomly mapped.
The adaptor sequence was trimmed before being aligned to the genome.
The reads were aligned to the S. griseus or S. venezuelae genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
Genome_build: NC_010572 for S. griseus, NZ_CP013129 for S. venezuelae
Supplementary_files_format_and_content: Sgri_Ribo_ETLS_readcount.txt, and Sven_Ribo_ETLS_readcount.txt : tab-delimited txt files that raw mapped read count within each gene and normalized expression of each gene in each sample.

organism: Streptomyces griseus

source_name: Mycelium cells from liquid culture

growth_protocol: The cells were inoculated from its 20% glycerol stock of spores to 50 ml of R5- liquid complex medium with 8 g of glass beads (3 ± 0.3 mm diameter) in 250 ml of a baffled flask, and grown at 30 °C, 250 rpm

extract_protocol:
Thiostrepton (Sigma) was added to cultures to a final concentration of 20 μM to stall the translating ribosomes, and the cultures were incubated for 5 min at 30 °C, and subsequently harvested for the construction of ribosome profiling libraries. Lysate for all samples were prepared by resuspended at polysome buffer and grinding in liquid nitrogen
The mycelium treated by thiostrepton was collected by centrifugation at 4 °C for 10 min at 3,000 g, and the cell pellet was washed with 2 ml polysome buffer composed of 20 mM Tris-HCl (pH 7.5), 140 mM NaCl, and 5 mM MgCl2 with 20 μM thiostrepton. The washed pellet was resuspended in 1 ml lysis buffer composed of 950 μl of polysome buffer and 50 μl of 20% triton X-100 with 20 μM thiostrepton. The resuspended cells were dripped into a mortar filled with liquid nitrogen and then ground with pestle. The cell debris was removed by centrifugation at 4 °C for 5 min at 3,000 g. The supernatant was further clarified and collected by centrifugation at 4 °C for 10 min at 16,000 g. To digest RNA, MNase was treated to the samples. Then, the samples were loaded onto illustra MicroSpin S-400 HR Columns. The ribosome-protected RNA fragments (RPF) between 26 and 34 bp were separated by electrophoresis for 65 min at 200 V using 15% polyacrylamide TBE-urea gel (Invitrogen), and eluted in 400 μl of RNA gel extraction buffer.
Ribosome profiling

value: Streptomyces griseus NBRC13350

tag: sampling time

value: Stationary phase (S)

tag: sequencing

value: Ribosome profiling

tag: cell sample

value: thiostrepton


title: SgriRibo_S1


title: SgriRibo_L2

value: Late-exponential phase (L)


title: Hu6_ret_ChIP_CTCF

value: caucasian

value: Santa Cruz Biotechnology cat# sc_15914; RRID:AB_2086899


title: Hu6_ret_ATAC


title: K13

tag: treatment type

value: 56Fe Irradiated

tag: time


title: summ2_mock_rep2

source_name: summ2  H2O treatment, rep2

value: 14 days

value: seedlings


title: SgriRibo_L1


title: K12

tag: biological replicate


title: summ2_mock_rep1

source_name: summ2  H2O treatment, rep1


title: Hu5_ret_ATAC

tag: donor age

tag: donor apparent race

value: unknown


title: K8

value: 2 months


title: SgriRibo_T2

value: Transition phase (T)


title: col0_mock_rep3

source_name: wild type H2O treatment, rep3

tag: tissue

value: wild type


title: col0_mock_rep2

source_name: wild type H2O treatment, rep2


title: K7


title: SgriRibo_E2

value: Early-exponential phase (E)


title: Hu26_mac_ChIP_H3K27ac

source_name: Adult human macula

value: Male

tag: postmortem interval

tag: chip_seq antibody


title: K6


title: SgriRibo_T1

tag: treatment


title: Hu6_ret_ChIP_CRX

value: Santa Cruz Biotechnology cat# sc_377207 (B_11) X  Lot# I1212


title: SgriRibo_E1

tag: strain

value: Streptomyces griseus NBRC13350


title: Hu4_ret_ATAC

value: Female


title: JD18 [miRNA-seq]

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
The raw sequences were quality assessed using fastqc
Primer sequences were removed using cutadapt v1.9 and parameters -b CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA -b TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -O 15 -m 17 -n 5 -q 20
Trimmed sequences were “collapsed” to generate a non-redundant set of sequences in a fasta format suitable for mirdeep2 analysis
Alignments to the reference miRNA transcript set from mirBase v21 were performed using the mirdeep2.pl software, with parameters -o 20 -l 17 -r 100 -c
Raw "tag counts" per sample were scale normalised to the sample with the lowest number of alignments, and counts converted to log2; "abundance normalised" data were not further quantile normalised for linear model fitting purposes.
Pairwise comparisons of the two sample groups (e.g. cases relative to controls) were performed on the normalised tag counts using linear modeling (Bioconductor limma package).
Genome_build: GRCz10; mirBase v21
Supplementary_files_format_and_content: fasta formatted non-redundant sequences.  The frequency of each read is given in the read name eg. x8601610 means that there were 8601610 reads with that sequence.

organism: Danio rerio

source_name: 30 pooled larvae (5dpf)_triptolide for 6 h

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5 °C

extract_protocol:
Total RNA was extracted from pooled zebrafish larvae (30 larvae per sample) for qPCR and RNA-sequencing. Larvae were fixed in Qiazol after which they were disrupted using a tissue disruptor. Subsequently, total RNA was extracted using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) eluted in 30 µl RNAse free water.
RNA libraries were prepared for each sample with the Truseq Stranded Total RNA Sample Prep LT Kit. Libraries were checked for size, purity and concentration with a high sensitivity DNA chip on the Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: 5 dpf larvae (N = 30) were treated per 50 ml dish for 6 h with a TP concentration of 0 µM (8 dishes) or 1.6 µM (8 dishes)

value: WIK

tag: developmental stage

value: triptolide (1.6μM) for 6 h

value: 30 pooled larvae

tag: molecule subtype

value: small RNA


title: Hu4_ret_nuclei_RNA

description:
total nuclear RNA
Hu4_ret_nuclei_RNA

tag: donor apparent sex

value: caucasian


title: K4

source_name: Left liver lobes

value: 56Fe Irradiated

value: 1 month


title: Hu4_retina_1_snRNA

description:
single nucleus polyA RNA
Hu4_retina_1_snRNA
Hu1_Hu4_Hu8_single_nuclei_rawcount_matrix.txt


title: Hu3_rpe_ChIP_H3K27ac

source_name: Adult human retinal pigment epithelium and choroid


title: col0_mock_rep1

source_name: wild type H2O treatment, rep1

tag: age

value: 14 days

value: seedlings

tag: genotype


title: exp11: CRISPRi multiplexing target enrichment (lane 1-16)

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

data_processing:
Fastq.gz files were generated from raw Illumina BCL files using bcl2fastq.
BAM files were generated from the fastq.gz files using 10X Genomics Cellranger version 3.0.0 with default paramaters (cellranger count).
Reads from multiple channels (ie. lanes, gemgroups) of the 10X platform were combined using 10X Genomics Cellranger version 3.0.0 (cellranger aggr) with normalization by number of mapped reads.
Gene-barcode matrices were determined using 10X Genomics Cellranger version 3.0.0 with default parameters.
Guide or guide barcode identities were determined as described in the paper.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: BAM files were generated by cellranger and contain raw reads for single-cell RNAseq, including cell identity, UMI information, and gemgroup id (referred to in guide barcode filenames). Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger. These are provided in the format outputted by cellranger: the matrix itself is in matrix market exchange format, with the rows (cell barcodes) and columns (gene identities) labels given in TSV format as described in the cellranger documentation. Guide or guide barcodes were specifically amplified from the RNA-seq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper.

source_name: K562 cells

growth_protocol: RPMI-1640 with 25mM HEPES, 2.0 g/L NaHCO3, 0.3 g/L L-Glutamine supplemented with 10% FBS, 2 mM glutamine, 100 units/mL penicillin and 100 µg/mL streptomycin was used to grow K562 cells. K562 cells were maintained at a density between 250,000 cells per mL and 1,000,000 cells per mL throughout the course of the experiments.

extract_protocol:
All samples were processed for single-cell RNA-sequencing on 10x genomics plaforms.
Droplet-based single-cell RNA sequencing

treatment_protocol: Cells were FACS sorted to maximize guide positive cells (>80% for all samples) on the day of single-cell RNA sequencing.

tag: cell line

tag: scrna-seq platform

tag: number of 10x lanes/gemgroups

tag: l1000 target enrichment?

value: yes

tag: molecule

value: RNA (L1000 target enriched mRNA)


title: JD17 [miRNA-seq]


title: Hu3_rpe_nuclei_RNA

description:
total nuclear RNA
Hu3_rpe_nuclei_RNA

tag: donor age


title: exp10: Cholesterol/DNA repair target enrichment (lane 1)


title: JD15 [miRNA-seq]


title: exp9: Cholesterol/DNA repair deep sequencing (lane 1)

value: no

value: RNA (poly-A mRNA)


title: JD16 [miRNA-seq]


title: H23

tag: treatment type

value: Non-Irradiated Control

tag: time

value: 12 months

tag: biological replicate


title: JD14 [miRNA-seq]

tag: tissue


title: Hu3_ret_ChIP_H3K27ac

source_name: Adult human retina

value: Male

tag: donor apparent race

tag: postmortem interval

tag: chip_seq antibody


title: H22

tag: strain


title: exp7: CRISPRi multiplexing

value: RNA (poly-A mRNA and sgRNA)


title: K2


title: JD13 [miRNA-seq]

value: WIK

tag: developmental stage

tag: treatment

tag: molecule subtype


title: exp8: CRISPRa multiplexing

tag: cell line


title: Hu3_ret_ChIP_CRX

tag: donor apparent sex

value: Santa Cruz Biotechnology cat# sc_30150 (H_120) X; Lot# A2113; RRID:AB_2276566


title: Hu3_ret_nuclei_RNA

description:
total nuclear RNA
Hu3_ret_nuclei_RNA


title: H21


title: K3


title: JD12 [miRNA-seq]

value: triptolide (1.6μM) for 6 h

value: 30 pooled larvae


title: exp6: Cholesterol/DNA repair

tag: scrna-seq platform

tag: number of 10x lanes/gemgroups


title: exp5: UPR 5' sgRNAcs1

tag: l1000 target enrichment?

tag: molecule


title: JD11 [miRNA-seq]

value: small RNA


title: H17

tag: treatment type

value: 9 months


title: Hu3_ret_ATAC

tag: donor age

value: caucasian


title: exp3: UPR 3' sgRNAcs2


title: JD08 [miRNA-seq]

source_name: 30 pooled larvae (5dpf)_vehicle

value: vehicle


title: H13

tag: time

value: 4 months

tag: biological replicate


title: FT Normal Organoid 1

source_name: FT OC1-O

tag: donor

tag: sourcetype

value: Organoid

tag: condition

value: Normal

tag: medium

value: StandardFT


title: exp2: UPR 3' sgRNAcs1

value: no


title: Hu2_RPE_ChIP_H3K27ac

value: Female

tag: donor apparent race

tag: postmortem interval

tag: chip_seq antibody


title: Hu2_rpe_nuclei_RNA

description:
total nuclear RNA
Hu2_rpe_nuclei_RNA


title: H12

value: Non-Irradiated Control

tag: strain


title: exp1: UPR GBC

tag: cell line

value: RNA (poly-A mRNA and GBC)


title: JD05 [miRNA-seq]

tag: developmental stage

tag: treatment

tag: tissue

tag: molecule subtype


title: JD04 [miRNA-seq]


title: H9

tag: treatment type

value: 2 months


title: JD06 [miRNA-seq]

value: WIK


title: JD03 [miRNA-seq]


title: YAC-iEPCs

city: Nagoya

first: Hiromasa

last: Aoki

address: 3-1 Tanabe-dori, Mizuho-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Nagoya City University

data_processing:
After cleaning, the reads were mapped to hg19 using TopHat 2.0.9. Paired mates that were uniquely mapped were applied for downstream analysis.
Per-gene read counts obtained using HTSeq 0.6.1 were converted to FPKM.
For differential gene expression analysis, the read counts were adjusted by edge R and then analyzed using the DEGSeq R package (1.12.0). The p-values were adjusted using the Benjamini & Hochberg (BH) method for controlling the False Discovery Rate (FDR).
Genome_build: hg19
Supplementary_files_format_and_content: Results of counts and differential gene expression analysis (excel file)

source_name: endothelial progenitor cells

extract_protocol:
Total RNAs from Cont-iEPCs and YAC-iEPCs were purified using an Agencourt RNAdvance Tissue Total RNA Purification Kit (Beckman Coulter, Brea, CA, USA).
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.
The library were preparated using NEBNext Ultra RNA Library Prep Kit for Illumina.

tag: cell type

value: hiPS-derived endothelial progenitor cells

tag: time point

value: day 14

value: YAC (day 8–14)


title: H8

tag: time

tag: biological replicate


title: Hu3_mac_nuclei_RNA

first: Timothy

last: Cherry

institute: Seattle Children's Research Institute

description:
total nuclear RNA
Hu3_mac_nuclei_RNA

data_processing: QUANTIFICATION AND STATISTICAL ANALYSIS: Sequence read data processing (ATAC_Seq, ChIP_Seq): Read processing and alignment: Demultiplexed FASTQ files were trimmed with Trimmomatic (version 0.33) using the parameter SLIDINGWINDOW:5:30 (Bolger et al., 2014). Trimmed reads were indexed and aligned to the human or mouse genomes (Human GRCh38/hg38 assembly December 2013; Mouse GRCm38/mm10 assembly, December 2011) using the Burrows_Wheeler Aligner (bwa) tool (Li and Durbin, 2010) with the parameters: bwa aln  _q 0  _t 4  _n 2  _k 2  _l 32  _e _1  _o 0 and bwa samse  _n 5. Tag directories of reads were created using HOMER (version 4.6) makeTagDirectory (Heinz et al., 2010). Peak calling: High confidence peaks across concordant biological replicates were identified via ENCODE’s Irreproducible Discovery Rate (IDR) pipeline using a 1% IDR threshold (Landt et al., 2012). For each set of replicates, bam files of reads were pooled and 2 pseudoreplicate files were generated by samtools view with the parameters _h _b _s 1.5 and _h _b _2.5. Peaks in biological replicate, pooled replicate, and pseudoreplicate samples were called over pooled input samples using MACS2 (version 2.1.1) (Zhang et al., 2008) with the parameters –nomodel _g <hs or mm> _p 1e_1 –extsize 200, where hs or mm refers to human or mouse genomes. An optimal final set of IDR_filtered peaks was obtained from the peak caller and used as the final high_confidence peak set for further analyses and the centers of these peaks were used as summits for analyses with HOMER. Sequence read data processing (Total RNA Nuc_Seq): Read processing and alignment: Reads were trimmed to 70bp and aligned to the human genome (Human GRCh38/hg38 assembly December 2013) using the Burrows_Wheeler Aligner (bwa) tool. Two sets of target sequences were provided and incorporated into the bwa index in addition to the usual 23 chromosomal targets: (1) the human mitochondrial genome (GenBank accession NC_012920.1); and (2) a set of ~10 million short (≤138bp) exon_exon splice_junction sequences (see below). For RNA_seq data, a third set of 92 short (< 2.1kb) spike_in oligos representing a wide range of reference concentrations (ERCC RNA Spike_In Mix, Life Technologies; Mix 2) was also incorporated into the index. Typically ~90% of all reads were mappable, allowing up to 2 mismatches, and of these ~70_85% were mapped uniquely. Multiple reads whose 5ʹ ends were assigned to the same locus were not flattened to a single count. The splice_junction target sequences were based on the NCBI RefSeq database for GRCh38. For each annotated transcript, we noted all subsets of two or more exons, not necessarily adjacent, that could be spliced together to produce a sequence at least as long as the read length. Each of these sequences were then trimmed to the maximum number of bases such that a read mapping to the sequence would necessarily cross these ordered exons’ splice junction(s). This procedure produced a library of all unique sets of exons whose intragenic splice junctions could possibly be covered by a read of the given length, based on the RefSeq annotation of exonic loci. Aligned reads thus had the opportunity to align either to genomic (chromosomal) sequences or to exon_junction_crossing sequences found only in mature mRNA. Expression level quantification: An in_house software tool, MAPtoFeatures (Gray et al., 2014), was used to quantify expression levels for individual genes as follows. A database of genic features (CDSs and UTRs) was constructed from ~103,000 genomic transcripts annotated in RefSeq for GRCh38. Merged genes were constructed by unioning all exons in all transcripts assigned to each distinct gene; the resulting segments defined the gene’s exonic coordinates used here (with the gaps between them defining introns). Genes with zero CDS exons were labeled ‘‘noncoding’’. These 24,644 genes were supplemented with 37 mitochondrial genes and 1,752 additional noncoding genes specified by the loci of all ribosomal RNA genes obtained from RepeatMasker (where the options Variations and Repeats, rmsk.repFamily=‘‘rRNA’’ yielded 414 LSU_rRNA_Hsa; 74 SSU_rRNA_Hsa; ,1264 5S). The purpose of this step was to allow the filtering out of reads stemming from transcription of repeats and rRNA genes, which tend to get populated to inconsistent degrees from sample to sample depending on the variable quality of rRNA depletion. Reads that aligned uniquely were then queried for their intersection with the exonic ranges of any of the above 26,433 genes, including exon_exon splice junctions. The total number of read bases that overlapped an exonic range was divided by the range’s length to give an average exonic read density (i.e., coverage). All reads were assigned to genes or to intergenic regions. However, only those reads not assigned to noncoding genes counted towards the total normalization count N, which ultimately afforded a more stable comparison of expression levels between samples than simply using the total number of reads. All read densities were normalized to a reference total of 10 million reads and a reference read length of 35 bp through multiplication by the factor (107/N)*(35 bp/70 bp). (Division of these normalized densities by 0.35 yields expression levels in alternative units of reads per kilobase of transcript per million mapped reads, RPKM.) For downstream analyses, genes with a normalized exon density value of 0 in any replicate at any timepoint were discarded to remove lowly expressed genes. Sequence read data processing (Single_nucleus RNA_Seq): inDrops sequencing_data processing: Transcripts were processed according to a previously published pipeline (Hrvatin et al., 2018; Klein et al., 2015). Briefly, this pipeline was used to build a custom transcriptome from the Ensembl GRCh38 genome and annotation with Bowtie 1.1.1 (Langmead et al., 2009), after filtering the annotation gtf file (gencode.v17. annotation.gtf filtered for feature_type=‘gene’, gene_type=‘protein_coding’ and gene_status=‘KNOWN’). Read quality control and mapping against this transcriptome were then performed. Finally, unique molecular identifiers were used to reference sequence reads back to individual captured molecules, thus yielding values denoted UMIFM counts. All steps of the pipeline were run with default parameters unless explicitly specified. Quality control for cell inclusion: Our initial dataset contained ~30,000 cells with more than 1,000 reads assigned to each cell. All mitochondrially encoded genes were removed from the dataset. Cells with fewer than 400 or more than 15,000 unique_molecular_identifier counts were next excluded, thus yielding 4,763 high quality cells isolated from three donors. Dimensionality reduction and clustering: All 4,763 cells were combined into a single dataset. The Seurat R package (Macosko et al., 2015; Satija et al., 2015) was used to cluster cells. The data were log normalized and scaled to 10,000 transcripts per cell. Variable genes were identified with the MeanVarPlot() function, which calculates the average expression and dispersion for each gene, then bins genes and calculates a z score for dispersion within each bin. The following parameters were used to set the minimum and maximum average expression and the minimum dispersion: x.low.cutoff=0.0125, x.high.cutoff=3, y.cutoff=0.5. Next, PCA was carried out, and the top 20 principal components were retained. The clustering resolution was set to 0.6. This method resulted in 14 initial clusters across 4,763 cells. Quantifying bioreplicate correlations: To validate the reproducibility of our epigenomic and transcriptomic assays, we compared the correlation of bioreplicates performed on distinct samples for ATAC_Seq/DNase_Seq, H3K27ac ChIP_Seq and total RNA Nuc_Seq experiments. For each assay, we found a high degree of correlation between samples of the same tissue type (Figure S1A). As expected, retinal and macular samples

extract_protocol:
METHOD DETAILS: DNA accessibility: ATAC_Seq: Flash_frozen tissue was thawed by addition of 700ul of lysis buffer (10 mM Tris_HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP_40), homogenized by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, and transferred back to original 1.5mL LoBind tube (Eppendorf). Dounce was washed with an additional 700ul ice cold lysis buffer and buffer was transferred to tube with sample for a final volume of 1.4mL. Sample was then centrifuged in a microcentrifuge at 4C for 10min at 500 rcf. The pellet was re_eluted in 1.4mL ice cold lysis buffer, transferred to a pre_chilled dounce, homogenized again 12x with tight pestle, and transferred back to 1.5mL LoBind tube. Nuclei were counted on a hemocytometer and the volume of lysis buffer/nuclei suspension needed for 20,000 nuclei was aliquoted into a separate 1.5mL LoBind tube. Samples were centrifuged along with tube containing remaining nuclei (for nuclear localized RNA) at 4C for 5min at 500g (RCF). The supernatant was removed from samples and remaining nuclei. Subsequent ATAC libraries were generated with 20,000 nuclei per sample using the Nextera DNA library prep kit (FC_121_1030; Illumina, San Diego, CA USA) according to the protocol described in (Buenrostro et al., 2013; Buenrostro et al., 2015). DNase I_Seq: Sequence files from the ENCODE Consortium (Consortium, 2012) for human retinal pigment epithelium (ENCBS420ENC, ENCBS893GDP), embryonic human retina (ENCSR820ICX, ENCSR474GZQ, ENCSR621ENC), and 8 week mouse retina (ENCSR000CNW) described in (Wilken et al., 2015) were analyzed in parallel with ATAC_Seq data. Chromatin immunoprecipitation: Crosslinking: Flash frozen human or mouse tissue was homogenized in crosslinking buffer (10 mM HEPES_NaOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) containing 1% formaldehyde (added immediately before crosslinking) by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, transferred back to original 1.5mL LoBind tube (Eppendorf), and incubated while rotating gently at room temperature for 10 min. Crosslinks were quenched by addition of glycine to a final concentration of 0.125 M and incubated while rotating gently at room temperature for 5 min. Cells were pelleted by centrifugation 5 min at 1,350 g at 4C. Cell pellets were resuspended once with cold PBS and re_spun for 5 min at 1,350 g at 4C. Nuclei prep: Crosslinked cell pellets were resuspended in cold 5mL L1 buffer (50 mM HEPES_NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X_100, 0.5% NP_40, 10% glycerol, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) by pipetting and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 5mL L2 by pipetting (10mM Tris_HCl pH 8.0, 200mM NaCl, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 1.5 mL LB3 (10mM Tris_HCl pH 8.0, 100mM NaCl, 1mMEDTA, 0.5mMEGTA, 0.1% sodium deoxycholate, 0.5% N_lauroylsarcosine, protease inhibitors; 10mM sodium butyrate added for H3K27ac ChIPs) by pipetting and transferred to polystyrene tubes (Thermo Fisher 352099) for sonication. Sonication: Nuclei pellets were sonicated (Bioruptor Plus, Diagenode) in polystyrene tubes on high power with 36 cycles of 30 sec ‘‘on’’, 45 sec ‘‘off’’. After sonication, Triton X_100 was added to 1% final concentration and sonicated chromatin was centrifuged at 16,000 g for 5 min at 4C. The supernatant was used for preclearing and ChIP. All subsequent steps were performed using DNA LoBind tubes (Eppendorf). Preclearing and antibody_bead coupling: Protein A Dynabeads (Life Technologies) were washed twice with blocking buffer (0.1% BSA in LB3 + 1% Triton X_100) and aliquoted for preclearing and antibody_bead coupling. Antibodies were coupled to beads in 1.8 mL of blocking buffer by vertical rotation at 4C for 4 hr. In parallel, each sample of sonicated chromatin was incubated with an equivalent volume of washed bead slurry for preclearing. Each ChIP was performed in 1.8 mL LB3 + 1% Triton X_100 and rotated vertically at 4C for 16 hr. For input samples, 1% of sample was saved for de_crosslinking and DNA purification. Washes and elution: For each wash, beads were rotated vertically in wash buffer at 4C for 5 min. Beads were washed twice with low salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 500 mM NaCl), twice with lithium chloride wash buffer (0.25 M LiCl, 1% NP_40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris_HCl pH 8.0), and once with TE (50 mM Tris, 10 mM EDTA). Beads were then incubated at 65C in 200 mL of TE + 1% SDS per sample for 30 min with vortexing every 10 min. Eluted protein_DNA complexes were separated from the beads and incubated at 65C for 16 hr to reverse crosslinks. Purification of immunoprecipitated DNA: Elutions were incubated with 10mg RNase A for 1 hr at 37C, followed by 140 mg proteinase K for 2_3 hr at 55C with shaking. DNA was extracted with 1 volume of 25:24:1 phenol_chloroform_isoamyl alcohol and purified with a Qiagen PCR purification kit. ChIP DNA concentrations were determined by Qubit dsDNA HS Assay Kit (Thermo Fisher). Gene expression: Total RNA Nuc_seq: To determine RNA expression in adult human retina, macula and RPE nuclei, RNA was extracted from excess nuclei (~80M) from the ATAC nuclear preparation protocol using Trizol (ThermoFisher; 15596026). Prior to RNA extraction, an equal amount of ERCC spike_in control RNA (Mix 2) was added to each sample, following the manufacturer’s specifications. RNA was extracted using the Qiagen RNeasy Mini Kit with on_column DNase I digestion (Qiagen 79254). Single Nucleus RNA_seq: Generation of single_nucleus suspensions were prepared by isolating nuclei from flash frozen human retina as described above and purified using an iodixanol gradient (Optiprep; Sigma_Aldrich, St. Louis, MO, USA) with RNase_inhibitor. After gradient centrifugation, the nuclei were washed in dissociation solution (Hrvatin et al., 2018; Klein et al., 2015) containing 0.04% BSA and were resuspended in dissociation solution containing 0.04% BSA and 15% Optiprep for single_nucleus RNA sequencing using a modified inDrops protocol (Klein et al., 2015).
Library preparation and sequencing: ATAC_seq: ATAC_Seq libraries were prepared as described above and sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads. ChIP_seq: 2_40 ng of each ChIP sample was used to prepare libraries with the NuGEN Ovation Ultralow Library System v2 kit per manufacturer’s protocol. Libraries were sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads.Total RNA Nuc_seq: RNA_seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (E7420L, NEB) and either NEB rRNA depletion kit (E6310, NEB) or Qiagen GeneRead rRNA Depletion Nano kit (180211, Qiagen). Spike_in RNA (Fisher 4456740) were used for sample_to_sample normalization. Samples were then sequenced on the Illumina NextSeq 500 platform with 2x 150 bp paired_end reads. Single_nucleus RNA_seq: Single_nucleus RNA sequencing (inDrops): One or two libraries of approximately 3,000 cells were collected from each donor retina. inDrops was performed as previously described (Klein et al., 2015; Zilionis et al., 2017), generating indexed libraries that were then pooled and sequenced on the NextSeq 500 (Illumina) platform.

tag: donor apparent sex

value: Male

tag: donor age


title: Cont-iEPCs

value: DMSO (day 8–14)


title: Hu2_ret_ATAC

value: caucasian


title: exp4: UPR 5' standard sgRNA

tag: scrna-seq platform

tag: number of 10x lanes/gemgroups

tag: l1000 target enrichment?

tag: molecule

value: RNA (poly-A mRNA and sgRNA)


title: Hu3_mac_ATAC

tag: donor apparent race

tag: postmortem interval

tag: chip_seq antibody


title: Hu2_mac_nuclei_RNA

description:
total nuclear RNA
Hu2_mac_nuclei_RNA


title: H16

value: 9 months

tag: strain


title: Hu2_ret_nuclei_RNA

description:
total nuclear RNA
Hu2_ret_nuclei_RNA


title: Hu2_ret_ChIP_H3K27ac


title: JD07 [miRNA-seq]

tag: developmental stage

tag: treatment

value: vehicle

tag: tissue

value: 30 pooled larvae

value: small RNA


title: myco_STF_4

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4).
Trimmed reads were mapped to mm10 and hg19 using STAR aligner (version 2.6) separately; then, ambiguous reads which mapping to both mm10 and hg19 were assigned to mm10, hg19 or discarded using tool –“Disambiguate"
Subread featureCounts (version 1.4.6) was applied for gene quantification based on GENCODE annotation release (GRCh37,p13)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count and log2 transformed DESeq2 normalized counts for each sample

source_name: tumor

growth_protocol: Clean (no bacteria) or M. hyorhinis-infected HCT116 cells were grown in RPMI1640 with 10% FBS and pen/strep.

extract_protocol:
RNA was extracted using RNAeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA with Ribo-Zero kit.

treatment_protocol: 2*10e6 clean (no bacteria) or M. hyorhinis-infected (Mycoplasma) HCT116 cells were xenografted into nude mice.  Treatment with 15 mg/Kg STF118804 or vehicle control twice daily by subcutaneous injections was initiated when the tumor reached 200 mm3 and continued for two weeks or till tumor reached 1000 mm3. Then mice were sacrificed, tumor RNA isolated and analyzed by RNAseq.

tag: cell line

tag: cancer type

value: colon adenocarcinoma

tag: infection

value: Mycoplasma Hyorhinis

tag: protocol

value: xenografted into nude mice

value: xenograft tumor


title: Hu2_mac_ATAC

city: Seattle

tag: donor apparent sex

value: Female


title: myco_STF_5


title: H7

tag: treatment type

value: Non-Irradiated Control

tag: time

value: 2 months

tag: biological replicate


title: H11

value: 4 months


title: JD01 [miRNA-seq]

value: WIK

tag: molecule subtype


title: JD18

data_processing:
The raw sequences were quality assessed using fastqc; no primer removal was required.
Zebrafish transcripts details and sequences were obtained from Ensembl release (Rel84, March 2016); a total of 57264 transcript models were obtained.
Alignments (end-to-end, --very-sensitive settings) to the reference transcript set were performed using bowtie2, with a requirement for concordant read pair mapping was applied, and all other alignments discarded.  Alignments were stored in indexed BAM files, and transcript counts extracted for each transcript using samtools idxstats.
Raw "tag counts" per sample were scale normalised to the sample with the lowest number of alignments, and counts converted to log2; "abundance normalised" data were not further quantile normalised for linear model fitting purposes.
Pairwise comparisons of the two sample groups (e.g. cases relative to controls) were performed on the normalised tag counts using linear modeling (Bioconductor limma package).
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text of annotated raw transcript counts

value: triptolide (1.6μM) for 6 h


title: myco_STF_2


title: H3

value: 1 month


title: H4


title: Hu1_rpe_nuclei_RNA

description:
total nuclear RNA
Hu1_rpe_nuclei_RNA

value: Male

tag: donor age

value: caucasian


title: Hu1_RPE_ChIP_H3K27ac

tag: donor apparent race


title: myco_STF_1


title: H2