title: PDSN09.H3K27ac, bulk ChIP-seq

data_processing:
The sequenced DNA reads from ChIP-seq libraries were mapped to human reference genome (hg19) using Burrows-Wheeler aligner (BWA)-mem (ver. 0.7.17, ‘-M’ option).
Reads with a low alignment quality (MAPQ < 10) were removed, and PCR duplicates were discarded using Picard (v2.6.0).
H3K27ac peaks were identified using MACS2 relative to the respective input control based on a significance threshold of P < 1 × 10-5.
We defined cis-regulatory elements (cREs) by merging H3K27ac peaks across the samples.
The number of ChIP-seq reads aligned to the cREs were computed by using bedtools (v2.29.1) coverage function.
The read counts were merged into a count matrix, quantile normalized using preprocessCore R package across the samples, and converted into reads per million (RPM) value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with quantile normalized RPM values for each sample

extract_protocol: ChIP-seq libraries were prepared manually by conducting DNA end repair (Epicentre, ER0720), adenosine addition at 3’ end (NEB, M0212), ligation of Illumina indexed adaptors (NEB, M2200), and PCR amplification (Thermo Fisher Scientific, F549).

value: H3K27ac (Active Motif, 39133)


title: NOSN01.HiC, in situ Hi-C

status: Public on Mar 05 2023

type: SRA

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: in situ Hi-C

library_source: genomic

data_processing:
The sequencing output from Hi-C libraries were mapped to the reference genome (hg19) using BWA-mem (‘–M’ option).
In-house scripts were used to remove low quality reads (MAPQ < 10), the reads that span ligation sites, chimeric reads, and self-interacting reads (two fragments located within 5kb).
The chimeric reads were removed since they are by-products of proximity ligation during Hi-C experiments, and cannot be properly processed by paired-end BWA-mem command.
The read-pairs were merged together as paired-end aligned BAM files, and PCR duplicates were removed with Picard (v2.6.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw Hi-C interaction frequencies between two 5kb bins within 1mb window

molecule: genomic DNA

organism: Homo sapiens

source_name: Substantia nigra

extract_protocol: Hi-C libraries were prepared manually by performing DNA end repair, removal of un-ligated ends, adenosine addition at 3’ end (NEB, M0212), ligation of Illumina indexed adapters (NEB, M2200), and PCR amplification (Thermo Fisher Scientific, F549). The number of cycles for PCR amplification was determined based on KAPA library quantification kit (KAPA, KK4854).

tag: tissue

value: Substantia nigra

tag: chip antibody

tag: genotype


title: NOSN03.HiC, in situ Hi-C

description: in situ Hi-C


title: NOSN02.HiC, in situ Hi-C

description: in situ Hi-C


title: Brain, Phe11KO, repC

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed with Trim Galore 42 (0.6.4_dev) using cutadapt 43 (1.18) (with parameters: --paired --fastqc --illumina, corresponding to cutadapt parameters: -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA).
Trimmed reads were aligned to the mouse genome downloaded from GENCODE (GRCm38.p6, primary assembly) masked for nuclear mitochondrial sequences with the vM24 GENCODE mouse gene annotation with STAR 44 (v2.7.8a) (--quantMode TranscriptomeSAM).
The transcriptome alignments produced by STAR were quantified with Salmon 45 (-l ISR --seqBias --gcBias) against a transcriptome fasta produced from the GENCODE gene annotation and genome sequence with gffread.
The output files were imported into R (https://www.R-project.org) with tximport and tRNA knockouts were analysed for differential expression against wild types with DESeq2 per tissue, utilising apeglm and a log fold change threshold of log2(1.5).
Assembly: GRCm38.p6
Supplementary files format and content: .txt files with DESeq2 output for each comparison
Supplementary files format and content: .txt files with normalised counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Heterozygous tRNA-Phe gene deleted transgenic mice on a C57BL/6N background were generated by the Monash Genome Modification Platform (MGMP) and the Australian Phenomics Network (APN). Male age- and littermate-matched wild-type (WT) and homozygous mutant mice were housed in standard cages (45 cm x 29 cm x 12 cm) under a 12-h light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 + 2 C and 50 + 10% relative humidity. Normal chow diet (NCD) and water were provided ad libitum.

extract_protocol:
3 mm x 3 mm tissue pieces (liver or brain) were homogenized in 200 l of cell extraction buffer (CEB; 100 mM Tris, 2 mM Na3VO4, 100 mM NaCl, 1% Triton X-100, 1 mM EDTA, 10% glycerol, 1 mM EGTA, 0.1% SDS, 1 mM NaF, 0.5% deoxycholate, 20 mM Na4P2O7), pH 7.4, containing PhosSTOP Phosphatase Inhibitor Cocktail (Roche) and EDTA-free Complete protease inhibitor cocktail (Roche). The homogenates were prepared using a bead beater and the homogenates were centrifuged at 9,000 g for 5 min at 4C. The previous steps were repeated until a clear tissue homogenate was produced. The tissue homogenate protein concentration was quantified using the bicinchoninic acid (BCA) assay using BSA as a standard. The tissues were snap frozen and stored at -80oC prior to RNA isolation and RNA was isolated using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA. RNA (2-5 g) was resolved on 1.2% agarose formaldehyde gels, then transferred to 0.45 m Hybond-N+ nitrocellulose membrane (GE Lifesciences) and hybridized with biotinylated oligonucleotide probes speci?c to nuclear tRNAs and 18S rRNA (probe sequences are listed in Table S4). Hybridizations were carried out overnight at 50C in 5x SSC, 20 mM Na2HPO4, 7% SDS and 100 g.ml-1 heparin, followed by washing. The signal was detected using streptavidin-linked infrared-labelled antibody (diluted 1: 10,000 in 3x SSC, 5% SDS, 25 mM Na2HPO4, pH 7.5) by the Odyssey Infrared Imaging System (LI-COR Biosciences).
RNA sequencing librarys were constructed using the Illumina TruSeq Sample Prep Kit according to the manufacturers instructions and sequenced on an Illumina NovaSeq 6000.

value: Brain


title: DDX58_1_unstimulated_rep3_24hr

city: Cambridge

first: Paul

last: Blainey

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Transcript counts were quantified using the command "kallisto quant" with default parameters and human reference hg19.annot.cdna and Sendai genome AB856846.1 (kallisto v0.45.0).
Genome_build: hg19
Supplementary_files_format_and_content: Transcript counts determined by kallisto are stored in a tab-delimited table with one row per transcript feature.

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100U/mL penicillin/streptomycin

extract_protocol: Cells were washed once with PBS and lysed in 1X TCL buffer (Qiagen, supplemented with 1% beta-mercaptoethanol). Smart-seq2 was performed as described (Trombetta et al., 2014).

treatment_protocol: Virus or hpRNA/Lyovec were added to culture medium

tag: cell line

value: HeLa

value: DDX58 sgRNA1

tag: stimulation

value: Unstimulated

tag: stimulation time


title: DDX58_1_unstimulated_rep1_24hr


title: Brain, Phe21KO, repA


title: DDX58_1_unstimulated_rep2_24hr


title: PDSN08.H3K27ac, bulk ChIP-seq


title: MAVS_1_hpRNA_rep2_24hr

value: MAVS sgRNA1

value: hpRNA


title: PDSN07.H3K27ac, bulk ChIP-seq


title: Brain, Phe11KO, repB


title: Brain, Phe11KO, repA


title: PDSN06.H3K27ac, bulk ChIP-seq


title: DDX58_1_SeV_rep4_6hr

value: SeV


title: Brain, wild type, repC

value: wild type


title: PDSN05.H3K27ac, bulk ChIP-seq


title: Brain, Phe21KO, repC


title: PDSN04.H3K27ac, bulk ChIP-seq


title: DDX58_1_SeV_rep4_15hr


title: PDSN03.H3K27ac, bulk ChIP-seq


title: Brain, wild type, repB


title: PDSN02.H3K27ac, bulk ChIP-seq


title: DDX58_1_SeV_rep3_6hr


title: PDSN01.H3K27ac, bulk ChIP-seq


title: DDX58_1_SeV_rep3_15hr


title: Brain, wild type, repA


title: Liver, Phe31KO, repC

source_name: Liver

value: Liver


title: Brain, Phe21KO, repB


title: NOSN05_2.H3K27ac, bulk ChIP-seq


title: NOSN05_1.H3K27ac, bulk ChIP-seq


title: NOSN03_1.H3K27ac, bulk ChIP-seq


title: DDX58_1_SeV_rep2_15hr


title: DDX58_1_SeV_rep1_6hr


title: DDX58_1_SeV_rep2_6hr


title: NOSN04.H3K27ac, bulk ChIP-seq


title: Liver, Phe31KO, repA


title: DDX58_1_SeV_rep1_15hr


title: NOSN02.H3K27ac, bulk ChIP-seq


title: NOSN03_2.H3K27ac, bulk ChIP-seq


title: NOSN01_2.H3K27ac, bulk ChIP-seq


title: NOSN01_1.H3K27ac, bulk ChIP-seq


title: Liver, Phe21KO, repC


title: Liver, Phe21KO, repB


title: PDSN09.RNA, bulk RNA-seq

data_processing:
Paired-end reads were aligned to the reference genome (hg19) using STAR software v2.7.5 with default parameters.
The raw read counts were quantified with RSEM based on a gene list obtained from GENCODE v38, selecting protein coding genes and long non-coding RNAs (lncRNAs) with confidence level 1 and 2 (n=22,090).
The count values were merged into a count matrix, quantile normalized using preprocessCore R package across the samples, and converted into transcripts per million (TPM) value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with quantile normalized TPM values for each sample

extract_protocol:
Total RNA was isolated from each sample using TRIzol (Thermo Fisher Scientific, 15596026)
RNA-seq libraries were prepared using TruSeq RNA Access Library Prep Kit (Illumina, 20020189).


title: sciPlexATAC3_A549_NIH3T3

city: Seattle

first: Gregory

middle: Thomas

last: Booth

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
The sequence processing strategy used here for sciATAC reads was based on procedures established for sciATAC-seq2 and sciATAC-seq3, and is described in previous publications (Cusanovich et al. Cell, 2018; Domcke et al. science 2020) as well as in our manuscript. each of the four barcodes associated with each read pair, together comprising a cell ID, was required to be within an edit distance of 2 from expected barcode sequences. Valid barcodes were corrected for any errors and read pairs were trimmed with Trimmomatic-0.36 to remove adapter sequences. Trimmed reads were then aligned to either a hybrid human/mouse (GRCh38/mm9) genome (for species mixed samples) or the human (GRCh38) genome alone using bowtie2 (Langmead and Salzberg, 2012) with options “-X 2000 -3 1”.  Properly aligned read pairs with a quality score of at least 10 were retained for downstream analysis using samtools with options “-f3 -F12 -q10”.
Bam files containing aligned barcoded chromatin fragments were processed into Arrow files using the ArchR (version 0.9.5) package (Granja et al., 2020) with the following arguments; filterFrags = 500 and filterTSS = 3 (Note that tNhe "fragments" files included with the processed data can also be used to create Arrow files for downstream analysis using ArchR). Likely-doublets were then identified based on chromatin profiles using a modified version of the scrublet algorithm, which has been described in detail previously (Domcke et al., 2020). Cells were also filtered to remove those with low hashing quality as described in the manuscript.
Sequenced nuclear barcode (hash) reads were processed either from separately sequenced hash libraries (sciPlex-ATAC-seq2), or the trimmed fastq files containing both ATAC and hash sequencing reads (sciPlex-ATAC-seq3), bonafide hash labels were retrieved for sample assignment if the first 10nt of read 2 were an exact match to one of the hash indices employed for a given experiment.  Hash reads were then grouped by their cell barcodes and collapsed based on UMIs within read 1.  Ultimately we obtain a vector of hash oligo UMI counts hi for each nucleus i in the experiment.
Genome_build: GRCh38 and mm9
Supplementary_files_format_and_content: Feature-by-cell (5KB windows, Peak, GeneScore) and peak-by-motif files are in matrix market exchange format and the cell (columns) and feature annotation (row) files that accompany these files are in tsv file format. Peak-by-cell,  gene score-by-cell, and peak-by-motif matrices were generated using ArchR (0.9.5), while the 5kb window matrices are output by our pipeline.  HashTable.out files are in tsv file format, where the columns represent: "experiment", "cell barcode", "hash Well", "axis", "UMIs".  The "hashCellAssignments" files are generated from the hashTable.out files and are in tsv file format with column headers describing the processed hash properties and assignments for each cell. "Fragments" files are included for the chemical screen and MLR experiments and contain tsv formated list of aligned fragments where columns represent: "chromosome", "frag_start", "frag_end", "cell_barcode", "count".  "Peak_cds" and "GeneScore_cds" files contain cds objects created using Monocle3 and formated as R data sets (RDS).  "Peakset" files are tsv formatted and included for the chemical screen and MLR experiments and describe non-overlaping 500bp sites of chromatin accessiblity identified using ArchR (0.9.5). "cellMetaData" files are tsv formated and included from the chemical screen and MLR experiments.  "cellMetaData" files describe all relevant information about the final cell sets used in each experiment, including quality metrics, hash assignments, celltype annotations, etc.

organism:
Homo sapiens
Mus musculus

source_name: A549 and NIH3T3 cells

growth_protocol: cell lines were cultured in RPMI supplemented with 10% FBS and 1% penn-strep.

extract_protocol:
For all experiments, cells were harvested following the sciPlex-ATAC-seq protocol as described in the methods section of our manuscript. Nuclei were isolated in-well and barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sciPlex-ATAC-seq library preparation.
Nucle were subjected to two- or three-level sciPlex-ATAC-seq following the protocols described in detail in the methods section of our manuscript. Briefly: Two-level library construction: To capture poly-adenylated hash molecules within the context of sciATAC-seq, we modified the original sciATAC-seq protocol (Cusanovich et al., Science, 2015), to include an indexed primer extension step. The indexed extension of the hash molecules is followed by indexed transposition within the reaction same well, creating a known pairing between well barcodes of hash and tagmented genomic DNA (gDNA). By design, extended hash molecules and tagmented gDNA possess nextera P5 and P7 PCR handles. After tagmentaiton, nuclei are pooled, stained with DAPI, and flow-sorted into 96 well plates for crosslink reversal and PCR. Amplification with indexed PCR primers adds an additional level of barcoding to both hash labels and accessible chromatin fragments. This protocol leverages unique combinations of well barcodes on hash and chromatin fragments to pair single cell chromatin profiles with their corresponding hash identifiers. Three-level library construction:  Accessible chromatin within all nuclei is tagmented using a single commercially-available transposome complex containing universal Nextera adaptors. Two separate splinted ligation reactions are then used to sequentially add well-specific barcodes separately to each side of the transposed DNA fragments, followed by a final PCR-based barcode addition (Domcke et. al. Science, 2020). In these three-level experiments, hash oligos bearing the universal Nextera P7 sequence are annealed to a capture oligo possessing the Nextera P5 sequence prior to ligation steps, and thus resemble transposed genomic DNA. Therefore, annealed nuclear labels and chromatin fragments can undergo the exact same indexing reactions as chromatin within each nucleus.

treatment_protocol: Untreated

tag: cell type

value: Human lung adenocarcinoma derived epithelial cells (A549) and mouse embryonic fibroblast (NIH3T3) cells.

tag: treatment

value: Untreated


title: DDX58_1_hpRNA_rep4_24hr


title: sS1_3

city: Xinxiang

first: xianyou

last: Wang

state: Henan

address: No.90 Hualan Avenue

country: China

institute: Henan Institute of Science and Technology

data_processing:
miRNAs of C. sinensis were predicted via bioinformatics analysis of the Solexa sequencing data.
The known miRNAs that were mapped to the database sequences were categorized into different miRNA families.
The software miRDeep2 (version 2.0.0.8) was used to map clean reads to the genome databases.
Unique reads were annotated using known miRNAs in the miRBase database.
GO and KEGG analyses were conducted on the target genes of the DEMs
Assembly: CSS and Tieguanyin genome database
Supplementary files format and content: Tab-separated values files and matrix files

organism: Camellia sinensis

source_name: Leaf

extract_protocol:
The Quick RNA Isolation Kit was used to extract total RNA per the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Leaf

tag: group


title: PDSN08.RNA, bulk RNA-seq


title: Liver, Phe21KO, repA


title: NOSN06.H3K27ac, bulk ChIP-seq


title: DDX58_1_hpRNA_rep3_24hr


title: sS1_2


title: Liver, Phe31KO, repB


title: PDSN07.RNA, bulk RNA-seq


title: PDSN06.RNA, bulk RNA-seq


title: Liver, Phe11KO, repB


title: sS1_1


title: DDX58_1_hpRNA_rep1_24hr


title: DDX58_1_hpRNA_rep2_24hr


title: Liver, wild type, rep C


title: Liver, Phe11KO, repA


title: PDSN05.RNA, bulk RNA-seq


title: sL2_2


title: PDSN04.RNA, bulk RNA-seq


title: sL2_1


title: sL2_3


title: sL1_3


title: CAPN15_1_unstimulated_rep3_24hr

value: CAPN15 sgRNA1


title: CAPN15_1_unstimulated_rep1_24hr


title: CAPN15_1_unstimulated_rep2_24hr


title: PDSN01.RNA, bulk RNA-seq


title: CAPN15_1_SeV_rep3_6hr


title: Liver, wild type, rep A


title: sL1_2


title: Liver, Phe11KO, repC


title: CAPN15_1_SeV_rep3_15hr


title: NOSN06_2.RNA, bulk RNA-seq


title: S30L_Phe31_liver

data_processing:
Sequenced reads were trimmed with Trim Galore (0.6.4_dev) using cutadapt (1.18) (with parameters: --paired --fastqc, corresponding to cutadapt parameters: -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA).
Trimmed reads were aligned to the mouse genome downloaded from GENCODE (GRCm38.p6, primary assembly) with Bowtie2 (2.4.1) (--very-sensitive --dovetail --no-discordant --no-mixed -k 20 -X 1000 --fr).
PCR duplicates in the resulting BAM files were marked and removed with Picard Tools (2.23.8) MarkDuplicates and filtered with SAMtools (1.10) (-q 30 -f 2 -F 256 -F 4), retaining only properly-paired primary alignments, removing low-quality alignments and those that fall within blacklisted regions (comprised of the ENCODE ENCFF547MET.bed blacklist and the mitochondrial chromosome).
Fragment size periodicity was estimated with the fast Fourier transform algorithm in the 01_calFragDist function of ATACgraph and used to segment the data into nucleosome-free, mono-, di- and trinucleosome-bound sets (based on the detected ~175 nt periodicity).
Nucleosome-free reads were subset with deeptools (3.5.0) alignmentSieve (--maxFragmentLength 175) and peak calling was performed with Genrich (0.6) (-E ENCFF547MET.bed -a 200 -m 30 -q 0.05 -j -r -e chrM,chrY -v) for each sample group.
Generation of a consensus peakset and differential accessibility analysis of nucleosome-free regions was performed with DiffBind (3.0.8) in R (4.0.3), applying the internal mouse genome blacklist and counting reads with the parameters: summits=FALSE, mapQCth=30, fragmentSize=0. The native DESeq2 method was used for testing changes in chromatin accessibility between the knockouts and wild types (no greylist applied).
Significant peaks were annotated with bedtools intersect and annotatePeaks.pl from the HOMER suite (4.11.1) against the mm10 (Dec 2011) gtRNAdb tRNA and GENCODE vM24 gene annotations.
Coverage profiles for each data subset were generated with deeptools bamCoverage (--extendReads --minFragmentLength [minlength] --maxFragmentLength [maxlength] --normalizeUsing CPM -bs 1 -of bigwig), after using the ATACshift function of deeptools alignmentSieve (--ATACshift) on the input BAMs, summarised with deeptools multiBigWigSummary (bins --outRawCounts -bs 1) and averaged per sample group. Coverage profiles were averaged over all samples in each sample group.
In addition to the genome-wide analysis, we also analysed tRNA regions specifically (using the gtRNAdb high-confidence set +/- 50 nt flanking regions), with the nucleosome-free BAMs using featureCounts (2.0.0) (-p -B -C -P -d 20 -D 1000 -Q 30 -f -t ‘exon’ -g ‘transcript_id’) to count reads mapping to these regions and DESeq2 (1.30.0) to test for changes, using apeglm for effect size shrinkage, returning s-values (significant at s < 0.01).
Assembly: GRCm38.p6
Supplementary files format and content: bigwig files containing normalised nucleosome-free ATAC-Seq coverage

source_name: liver

growth_protocol: Heterozygous tRNA-Phe gene deleted transgenic mice on a C57BL/6N background were generated by the Monash Genome Modification Platform (MGMP) and the Australian Phenomics Network (APN). Male age- and littermate-matched wild-type (WT) and homozygous mutant mice were housed in standard cages (45 cm x 29 cm x 12 cm) under a 12-h light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 + 2 °C and 50 + 10% relative humidity. Normal chow diet (NCD) and water were provided ad libitum. The feed was provided by Rat & Mouse Chow, Specialty Feeds, Glen Forrest, Western Australia.

extract_protocol:
Nuclei were isolated by dissociating 20 mg of fresh brain or liver tissue in 400 µl of lysis buffer (1M Tris-HCl, 1M MgCl2, 1M NaCl, 10% Nonidet-P40) by passing through a polished silanized Pasteur pipette. Samples were left to incubate at 4˚C for 5 min before repeated dissociation. Following an additional 5 min incubation, samples were treated with 2.5 ml of Wash buffer (1x PBS, 1% BSA), dissociated and filtered through a 30 µm cell strainer. Samples were centrifuged at 500 g for 5 min at 4˚C, with the remaining pellet resuspended in 110 µl Wash buffer. To estimate nuclei recovery efficiency, 10 µl of nuclei solution was combined with 10 µl of DAPI solution (1:5,000 in PBS) and loaded on a hematocytometer. The remaining nuclei suspension was treated with 180 µl of 1.8 M sucrose solution (2 M sucrose cushion solution (S9308-475ML), Nuclei PURE Sucrose Cushion Buffer (S9058-120ML)) and homogenized. The 280 µl of nuclei suspension was gently layered onto 1 ml of 1.3 M sucrose solution (S9308-475ML, Nuclei PURE Sucrose Cushion Buffer (S9058-120ML) and centrifuged at 3,000 g for 10 min. Nuclei pellets were suspended in 100 µl of wash buffer.
Assays for transposase-accessible chromatin using sequencing (ATAC-Seq) were performed on nuclei samples containing 50,000 nuclei. Isolated nuclei were centrifuged at 500 g for 10 min at 4˚C. The pellet was suspended in transposition reaction mix (Illumina Tagment DNA TDE1 Enzyme and Buffer Kit) and incubated at 37˚C for 30 min on a thermomixer (Eppendorf) at 1,000 rpm. DNA was then isolated with Zymo DNA Clean & Concentrator-5 Kit (Integrated Sciences) and DNA elutes were amplified by PCR with 25 µM of indexing primers. Library purification was performed by isolating amplified DNA with SPRIselect beads (Beckman Coulter Life Sciences) with an ethanol wash before suspension in nuclease-free water.

tag: strain

value: liver

tag: batch


title: S29L_Phe31_liver


title: NOSN06_1.RNA, bulk RNA-seq


title: sL1_1


title: CAPN15_1_SeV_rep2_6hr


title: NOSN05.RNA, bulk RNA-seq


title: sBud_3

value: sBud


title: S28L_Phe31_liver


title: Liver, wild type, rep B


title: sBud_2


title: CAPN15_1_SeV_rep1_6hr


title: NOSN04_1.RNA, bulk RNA-seq


title: PDSN02.RNA, bulk RNA-seq


title: sBud_1


title: CAPN15_1_SeV_rep2_15hr


title: NOSN04_2.RNA, bulk RNA-seq


title: S25L_WT_liver


title: S27L_WT_liver


title: NOSN03.RNA, bulk RNA-seq


title: S26L_WT_liver


title: NOSN02.RNA, bulk RNA-seq


title: CAPN15_1_hpRNA_rep3_24hr


title: PDX-R5, lung tumor PDX, sotorasib-resistant

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center (CNIO)

data_processing:
Nextpresso v1.9.2.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using bbduk, and pre-processed with Xenome to remove reads aligning to the mouse genome
Trimmed sequence reads were mapped to GRCm38 using tophat-2.0.10
Read count extraction was performed using HTSeq-count
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lung, patient-derived xenograft (PDX)

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for library construction.
Library construction was performed with the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, Cat.No. 015) and subsequently sequenced on an Illumina instrument according to manufacturer's protocols

value: lung, patient-derived xenograft (PDX)

value: sotorasib


title: S24_WT_liver


title: sciPlexATAC3_HumanPBMC_MLR_DrugScreen

data_processing:
The sequence processing strategy used here for sciATAC reads was based on procedures established for sciATAC-seq2 and sciATAC-seq3, and is described in previous publications (Cusanovich et al. Cell, 2018; Domcke et al. science 2020) as well as in our manuscript. each of the four barcodes associated with each read pair, together comprising a cell ID, was required to be within an edit distance of 2 from expected barcode sequences. Valid barcodes were corrected for any errors and read pairs were trimmed with Trimmomatic-0.36 to remove adapter sequences. Trimmed reads were then aligned to either a hybrid human/mouse (GRCh38/mm9) genome (for species mixed samples) or the human (GRCh38) genome alone using bowtie2 (Langmead and Salzberg, 2012) with options “-X 2000 -3 1”.  Properly aligned read pairs with a quality score of at least 10 were retained for downstream analysis using samtools with options “-f3 -F12 -q10”.
Bam files containing aligned barcoded chromatin fragments were processed into Arrow files using the ArchR (version 0.9.5) package (Granja et al., 2020) with the following arguments; filterFrags = 500 and filterTSS = 3 (Note that tNhe "fragments" files included with the processed data can also be used to create Arrow files for downstream analysis using ArchR). Likely-doublets were then identified based on chromatin profiles using a modified version of the scrublet algorithm, which has been described in detail previously (Domcke et al., 2020). Cells were also filtered to remove those with low hashing quality as described in the manuscript.
Sequenced nuclear barcode (hash) reads were processed either from separately sequenced hash libraries (sciPlex-ATAC-seq2), or the trimmed fastq files containing both ATAC and hash sequencing reads (sciPlex-ATAC-seq3), bonafide hash labels were retrieved for sample assignment if the first 10nt of read 2 were an exact match to one of the hash indices employed for a given experiment.  Hash reads were then grouped by their cell barcodes and collapsed based on UMIs within read 1.  Ultimately we obtain a vector of hash oligo UMI counts hi for each nucleus i in the experiment.
Assembly: GRCh38 and mm9
Supplementary files format and content: Feature-by-cell (5KB windows, Peak, GeneScore) and peak-by-motif files are in matrix market exchange format and the cell (columns) and feature annotation (row) files that accompany these files are in tsv file format. Peak-by-cell,  gene score-by-cell, and peak-by-motif matrices were generated using ArchR (0.9.5), while the 5kb window matrices are output by our pipeline.  HashTable.out files are in tsv file format, where the columns represent: "experiment", "cell barcode", "hash Well", "axis", "UMIs".  The "hashCellAssignments" files are generated from the hashTable.out files and are in tsv file format with column headers describing the processed hash properties and assignments for each cell. "Fragments" files are included for the chemical screen and MLR experiments and contain tsv formated list of aligned fragments where columns represent: "chromosome", "frag_start", "frag_end", "cell_barcode", "count".  "Peak_cds" and "GeneScore_cds" files contain cds objects created using Monocle3 and formated as R data sets (RDS).  "Peakset" files are tsv formatted and included for the chemical screen and MLR experiments and describe non-overlaping 500bp sites of chromatin accessiblity identified using ArchR (0.9.5). "cellMetaData" files are tsv formated and included from the chemical screen and MLR experiments.  "cellMetaData" files describe all relevant information about the final cell sets used in each experiment, including quality metrics, hash assignments, celltype annotations, etc.

source_name: Human PBMCs

growth_protocol: PBMCs were cultured and stimulated in cTCM (RPMI (Gibco), 10% FCS (Gibco), 1% Pen-Strep (Gibco), 1X GlutaMAX (Gibco), 1.85𝜇L BME (Sigma) per 500ml of media)

treatment_protocol: Whole blood was extracted by venipuncture using Sodium Heparin tubes (company) from four consenting volunteers (approved for experiments and genomic sharing under IRB: FWA #00006878). PBMCs were then isolated from whole blood using Ficoll Paque Plus. PBMCs from each donor were  divided into responder and stimulator pools. 2x10e5 responder cells were plated in each well of the allo and auto stim columns of a 96-well round-bottom plate, while 1x10e5 responder cells were deposited into bead stimulation wells.  For allo and auto stimulations, 2x10e5 irradiated stimulator cells were added to each well and all wells had a final volume of 200𝜇L with cTCM. Chemical treatments were initiated immediately after plating responders, stimulators and beads by adding 2𝜇L of the prepared compounds to each well to obtain the final target concentration (Extended Data Table 5). Cells from each well were harvested for SciPlex-ATAC3 six days after treatments using the approach described above.

value: Human peripheral blood mononuclear cells (PBMCs)

value: Fresh PBMCs were cultured with stimulator PBMCs, with T-cell Activation/Expansion beads, or otherwise unstimulated.


title: PDX-R6, lung tumor PDX, sotorasib-resistant


title: PDX-R4, lung tumor PDX, sotorasib-resistant


title: NOSN01.RNA, bulk RNA-seq

value: Substantia nigra


title: CAPN15_1_hpRNA_rep2_24hr

value: HeLa


title: CTCF_HiChIP_22Rv1_sgCtrl_rep1

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

data_processing:
library strategy: HiChIP
Pair-end HiChIP reads were mapped to hg19 human reference genome by Bowtie2 within HiCUP pipeline (v0.7.2). The digested reference genome was created by hiccup using the MboI cutting site. The resulting bam files from HiCUP pipeline were converted into valid fragment pairs by samtools and bedtools. The HiChIP valid pairs and matched ChIP-Seq peaks were then subjected to hichipper pipeline (v0.7.7) to generate bedpe files containing HiChIP loops. In this study, only the filtered intra-chromosome loops were used for downstream analyses.
To identify high confidence HiChIP loops, we considered that the mated PE reads could be located at any possible loop anchor pair by a binomial distribution and calculated the significance for each loop based on this model.
Genome_build: HG19
Supplementary_files_format_and_content: txt files contain the significant HiChIP loops.

source_name: 22Rv1 cells

growth_protocol: Prostate cancer cell lines were cultured at 37 °C with 5% CO2. The medium used for VCaP, 22RV1 and V16A cell culture was supplemented with 10% FBS (GIBCO, 10437-028), 1% streptomycin and 1% penicillin.

extract_protocol:
HiChIP was performed as previously described with a few modifications. Ten million cells were collected and pelleted and resuspended in 1% formaldehyde for 10 min with rotation at room temperature. The crosslinking was then quenched in 125 mM glycine for 5 min. The cells were washed twice by PBS and then resuspended in 500 μL ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1× protease inhibitor) followed by 30 min rotation at 4 °C. Nuclei were pelleted by 2500 rcf centrifugation for 5 min at 4 °C followed by washing once in Hi-C lysis buffer. The pelleted nuclei were resuspended in 100 μL 5% SDS and incubated at 62 °C for 10 minutes. To quench the SDS, 335 μL 1.5% Triton X-100 was then added and the mixture was incubated at 37 °C for 15 minutes. The chromatin was digested by adding 50 μL NEB buffer 2 and 375 U MboI restriction enzyme (NEB, R0147) and incubating at 37 °C for 20 minutes. MboI restriction enzyme was then inactivated by 62 °C incubation for 10 minutes. The fill-in master mix (1.5 μL of 10 mM dTTP, 1.5 μL of 10 mM dCTP, 1.5 μL of 10 mM dGTP, 37.5 μL of 0.4 mM biotin-dATP, 10 μL of 5U/μL DNA Polymerase I (NEB, M0210) was added and the tube was incubated at 37 °C for 1 hours with rotation. The ligation mix, containing 10 μL 400 U/μL T4 DNA Ligase (NEB, M0202), 150 μL 10X NEB T4 DNA ligase buffer with 10 mM ATP (NEB, B0202), 125 μL 10% Triton X-100, 3 μL 50 mg/mL BSA, 660 μL H2O, was added and the tube was incubated at room temperature for 4 hours with rotation. The nuclei was pelleted and then resuspended in 880 μL nuclear lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1× protease inhibitor). Nuclei was sonicated in a water bath sonicator (Diagenode bioruptor) to generate chromatin fragments at 300~800 bp. Immunoprecipitation was performed by adding protein A beads and appropriate antibodies (anti-H3K27ac, ab4729; anti-AR, 108341; anti-CTCF, ab70303) to sheared chromatin before incubation at 4 °C overnight with rotation. The ChIPed DNA was eluted from beads by 200 μL ChIP elution buffer (50 mM NaHCO3, 1% SDS) and purified by Zymo DNA Clean & Concentrator kit. The biotin-labelled DNA was captured by streptavidin C1 beads (Invitrogen, 65001) and subjected to tagmentation using 2.5 μL Tn5 (Illumina) for 50 ng DNA.
The HiChIP DNA was amplified by ~8 cycles using primers containing Illumina sequencing linkers. Each HiChIP library was sequenced by an Illumina HiSeq4000 system to generate ~150 million 2 ×150 bp paired-end reads.

treatment_protocol: For androgen stimulation treatment, cells were maintained in medium containing 5% charcoal-dextran stripped FBS for 48 hours and then treated by DHT for 2 or 24 hours.

value: Prostate cancer

value: Control sgRNA

value: Full FBS medium

value: anti-CTCF, ab70303


title: S21_Phe11_liver


title: CAPN15_0_unstimulated_rep3_24hr

value: CAPN15 sgRNA0

value: Unstimulated


title: S22_WT_liver

value: wild type


title: PDX-R2, lung tumor PDX, sotorasib-resistant


title: PDX-R3, lung tumor PDX, sotorasib-resistant


title: CAPN15_0_unstimulated_rep2_24hr


title: S20_Phe11_liver


title: CAPN15_0_unstimulated_rep1_24hr


title: PDX-R1, lung tumor PDX, sotorasib-resistant


title: S9_Phe21_liver


title: CTCF_HiChIP_22Rv1_sgDele_10Kb_rep1

value: Knockout of the -10Kb CTCF binding site


title: CAPN15_0_SeV_rep3_6hr

value: SeV


title: S8_Phe21_liver

value: liver


title: CTCF_HiChIP_22Rv1_sgCtrl_rep2


title: S7_Phe21_liver


title: CTCF_HiChIP_22Rv1_sgDele_10Kb_rep2


title: CAPN15_1_hpRNA_rep1_24hr

value: CAPN15 sgRNA1

value: hpRNA


title: H3K27ac_HiChIP_22Rv1_sgCtrl_rep1

value: anti-H3K27ac, ab4729


title: CAPN15_0_SeV_rep3_15hr


title: S4_Phe11_liver


title: S6_Phe11_liver


title: H3K27ac_HiChIP_22Rv1_sgCtrl_rep2


title: H3K27ac_HiChIP_22Rv1_sgDele_10Kb_rep1


title: PDX-C1, lung tumor PDX, control

value: lung, patient-derived xenograft (PDX)

value: control


title: CAPN15_0_SeV_rep2_6hr


title: CAPN15_0_SeV_rep2_15hr


title: CAPN15_1_SeV_rep1_15hr


title: S3_WT_liver


title: CAPN15_0_SeV_rep1_6hr


title: S1_WT_liver


title: sciPlexATAC3_HumanPBMC_MLR

treatment_protocol: Whole blood was extracted by venipuncture using Sodium Heparin tubes (company) from four consenting volunteers (approved for experiments and genomic sharing under IRB: FWA #00006878). PBMCs were then isolated from whole blood using Ficoll Paque Plus. PBMCs from each donor were  divided into responder and stimulator pools. responder PBMCs were seeded into round bottom 96-well plates and separately cultured in the presence of stimulator PBMCs from each individual,  T-cell activation/expansion beads,  or otherwise untreated. Culture wells containing only irradiated stimulators from each individual were also assayed.

value: Human peripheral blood mononuclear cells (PBMCs)

value: Fresh PBMCs were cultured with stimulator PBMCs, with T-cell Activation/Expansion beads, or otherwise unstimulated.


title: H3K27ac_HiChIP_V16A_S1_L001

source_name: V16A cells

value: Prostate cancer

value: Wild type


title: PDX-C3, lung tumor PDX, control


title: CDNRM RNA-seq replicate 3

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

description: RNA-seq performed on reporter gene barcode amplicons

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified using custom python scripts.
Demultiplexed reads were used to determine the read counts for each barcode. Read counts for each barcode were normalized by total reads in the sample (counts per million, cmp) and then dividing by the normlized DNA read counts to generate the activity scores, which are reported as log2 scores in the supplemental file. Data processing was performed using custom python scripts.
Assembly: mm10
Supplementary files format and content: Processed data are in the tab-delimited file cdnrm_mpra_library.txt. Column 1: synthetic cis-regulatory element name. Column 2: log2 activity scores (RNA/DNA)
Library strategy: Amplicon-seq

source_name: whole retina

growth_protocol: P0 mouse retinal explants were electroporated with plasmid library and cultured ex vivo for 8 days.

extract_protocol:
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript III.
Sequence barcodes from reporter genes were amplified by PCR and purified with Monarch PCR cleanup kit. Custom Illumina adapters were added by PCR.

value: whole retina

value: wild-type


title: H3K27ac_HiChIP_22Rv1_sgDele_10Kb_rep2

value: Full FBS medium


title: CAPN15_0_SeV_rep1_15hr

value: HeLa

value: CAPN15 sgRNA0


title: H3K27ac_HiChIP_22RV1_S2_L002


title: CAPN15_0_hpRNA_rep3_24hr


title: S16_WT_brain

source_name: brain

value: brain

value: wild type


title: S18_WT_brain


title: S14_Phe11_brain


title: CAPN15_0_hpRNA_rep1_24hr


title: PDX-C2, lung tumor PDX, control


title: CDNRM RNA-seq replicate 2


title: VCaP_AR_HiChIP_DHT_2hr

source_name: VCaP cells

value: VCaP

value: DHT stimulation for 2hr


title: CDNRM RNA-seq replicate 1


title: S13_Phe11_brain


title: ATP13A1_1_unstimulated_rep3_24hr

value: ATP13A1 sgRNA1

value: Unstimulated


title: VCaP_AR_HiChIP_Veh

value: Androgen starvation


title: VCaP_CTCF_HiChIP_DHT_24hr

value: DHT stimulation for 24hr

value: anti-CTCF, ab70303


title: sciPlexATAC2_A549_Transcription_Modulators

source_name: A549 cells

treatment_protocol: Cells were seeded at 25,000 cells per well in 96 well plates. 24 hours after seeding cells were exposed to increasing doeses of small molecules or dmso/ethanol vehicle control.

value: Human lung adenocarcinoma derived epithelial cells (A549)

value: Cells were treated with increasing doses of the small molecules BMS345541, dexamethasone, nutlin-3A, SAHA or vehicle control.


title: S11_Phe31_brain


title: S10_Phe31_brain


title: VCaP_H3K27ac_HiChIP_DHT_24hr

value: Prostate cancer

value: Wild type

value: anti-H3K27ac, ab4729


title: ATP13A1_1_SeV_rep3_6hr

value: SeV


title: VCaP_H3K27ac_HiChIP_DHT_2hr


title: ATP13A1_1_unstimulated_rep1_24hr

value: HeLa


title: S8_Phe21_brain


title: ATP13A1_1_SeV_rep2_6hr


title: S7_Phe21_brain


title: F. tularensis 2 hours post exposure to 0.016 µg/ml (1xMIC) Ciprofloxacin 2nd duplicate

city: Ness Ziona

first: Galia

last: Zaide

address: Reuven St.

department: Biochemistry and Molecular Genetics

country: Israel

institute: Israel Institute for Biological Research

description: Sample 6b

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped  to the reference genome Francisella tularensis subsp. tularensis Schu S4  (NC_006570) using bowtie2 (2.2.0) and htseq-count 0.6.1
Analysis of differentially expressed genes under various conditions was performed using the R package DESeq
Assembly: Francisella tularensis subsp. tularensis Schu S4  accession number NC_006570
Supplementary files format and content: txt files

organism: Francisella tularensis subsp. tularensis SCHU S4

source_name: WT Bacteria

growth_protocol: F. tularensis SchuS4 colonies isolated on Cyctine Heart Agar (CHA) plates at 37oC were inoculated into a 200 ml  HLMHI (cation- adjusted Muller-Hinton broth supplemented with 2% IsoVitaleX and 3 µM hematin) growth medium to a concentration of 5x105 CFU/ml and grew at 37oC, 200 rpm for 2 hours for the adjustment to HLMHI. The culture was then divided into three 50 ml culture samples followed by 2 hours of Ciprofloxacin/ Doxycycline exposure or no exposure (growth control sample).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen), residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Bacterial cultures were exposed to Cioprofloxacin/ Doxycycline at a concentration of 0.5/1 x  Minimal Inhibitory Concentration (MIC, [MIC values were determined by the standard microdilution susceptibility test, according to the CLSI guidlines]), at 37oC, 200 rpm, for 2 hours.  Untreated samples served for growth control. For total RNA extraction, cultures (40 ml each) were centrifuged (20 min., 4oC, 4,000xg), and the bacterial pellets were freezed by liquid nitrogen and stored at -70OC.

value: WT

value: Exposure to 0.016 µg/ml (1xMIC) Ciprofloxacin


title: CAPN15_0_hpRNA_rep2_24hr

value: CAPN15 sgRNA0

value: hpRNA


title: VCaP_H3K27ac_HiChIP_Veh

value: VCaP


title: ATP13A1_1_SeV_rep2_15hr

value: ATP13A1 sgRNA1


title: S12_Phe31_brain

value: brain


title: VCaP_AR_HiChIP_DHT_24hr


title: ATP13A1_1_unstimulated_rep2_24hr

value: Unstimulated


title: VCaP_CTCF_HiChIP_Veh

value: Androgen starvation


title: F. tularensis 2 hours post exposure to 0.016 µg/ml (1xMIC) Ciprofloxacin 1st duplicate

description: Sample 6a


title: S9_Phe21_brain


title: ATP13A1_1_SeV_rep1_6hr


title: Ice mouse I5

type: RNA

city: Tsu

first: Takehisa

last: Nakanishi

address: 2-174 Edobashi

country: Japan

institute: Mie university

description: Gene expression data from abdominal aorta of cutaneous inflammation mouse

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: the abdominal aorta of 4-month-old KCASP1Tg mouse

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Total RNA was extracted from 16 weeks old mice using Tri Reagent (Molecular Re-search Center, Cincinnati, OH, USA).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The RNA concentration was measured using a NanoDrop Lite spectrophotometer (Thermo Fisher Scientific), and one µg total RNA was converted to cDNA using High-Capacity RNA-to-cDNA Kit (Applied Bio-systems, Foster City, CA, USA).

value: dechorionated abdominal aorta


title: Ice mouse I4


title: F. tularensis 2 hours post exposure to 0.008 µg/ml (0.5xMIC) Ciprofloxacin 2nd duplicate

description: Sample 5b

value: Exposure to 0.008 µg/ml (0.5xMIC) Ciprofloxacin


title: Ice mouse I2


title: Ice mouse I3


title: ATP13A1_1_SeV_rep3_15hr


title: Ice mouse I6


title: Normal mouse N4

description: Gene expression data from abdominal aorta of wild type mouse

source_name: the abdominal aorta of 4-month-old WT mouse


title: S5_Phe11_brain


title: Ice mouse I1


title: Normal mouse N3


title: ATP13A1_1_SeV_rep1_15hr


title: Normal mouse N2


title: F. tularensis 2 hours post exposure to 0.008 µg/ml (0.5xMIC) Ciprofloxacin 1st duplicate

description: Sample 5a


title: S6_Phe11_brain


title: ATP13A1_1_hpRNA_rep3_24hr


title: F. tularensis 2 hours post exposure  to 0.25 µg/ml (1xMIC) Doxycycline 1st duplicate

description: Sample 4a

value: Exposure  to 0.25 µg/ml (1xMIC) Doxycycline


title: S2_WT_brain

value: wild type


title: S1_WT_brain


title: F. tularensis 2 hours post  exposure  to 0.25 µg/ml (1xMIC) Doxycycline 2nd duplicate

description: Sample 4b


title: ATP13A1_1_hpRNA_rep2_24hr


title: GL261-GFP_<0.1%O2_rep2_ATACseq

city: Warsaw

first: Monika

last: Dzwigonska

address: 3 Pasteur Street

country: Poland

institute: Nencki Institute of Experimental Biology, PAS

description: GL261 hypoxia <0.1% O2 16h rep2

data_processing:
Sequence reads were trimmed using Trimmomatic to remove adapter and transposase sequence with option “sliding window 5:20” and with cut off from 5’ and 3’ end set to 3 and 15, respectively. Then paired-end reads were aligned to mm10 using Bowtie2 aligner v2.2.5 with parameters set to –very sensitive and -X2000.
Duplicate reads were removed with Picard and reads mapping to the mitochondrial genome were also removed. Only proparly paired reads with high alignment quality (MAPQ>30) were kept for downstream analysis.
Peaks were called using MACS2 v.2.1.1.2 with parameters set to -f BAPME -q 0.001 –nomodel –shift 0.
Assembly: mm10
Supplementary files format and content: MACS2 narrow peaks files
Supplementary files format and content: Bigwig files were generated from BAM files using Deeptools (bamCoverage) and were normalized to genome coverage (RPGC).

source_name: Murine GL261 cells

growth_protocol: GL261 mouse glioma cells stably expressing either pEGFP-N1 were cultured in DMEM with 10% FBS.

extract_protocol:
ATACseq was performed as previously described with some modifications (Chen et al., 2016). GL261 cells were fixed with 1% formaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at room temperature. Cells were counted and 25,000 cells were washed and subsequently lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 5 min on ice. Cells were then centrifuged at 500xg for 8 min and cell pellets resuspended in transposition reaction according to the standard ATACseq protocol using 2.5 ul of Tn5 enzyme per 25 000 of cells (Buenrostro et al., 2015). After transposition cells were centrifuged and reverse crosslinked (50 mM Tris-Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 200 μg/ml proteinase K) at 65°C with an overnight shaking at 1000 rpm.  Zymo DNA Clean & Concentrator-5 columns (ZymoResearch) were used to purify DNA.
Sequencing libraries were prepared according to the original ATACseq protocol (Buenrostro et al., 2015). The ATACseq libraries were assessed for appropriate quality using Bioanalyzer 2100 and subjected to paired-end sequencing (2x76 bp) using NovaSeq 6000 (Illumina).

treatment_protocol: Cells were incubated at <0.1% or 1% O2 in a M35 Hypoxystation (Don Whitley) hypoxic chamber in the presence of 5% CO2.

value: glioma

value: GL261 stably expressing pEGFP-N1

value: hypoxia <0.1% O2 16h


title: ATP13A1_1_hpRNA_rep1_24hr

source_name: HeLa

value: HeLa


title: F. tularensis 2 hours post  exposure  to 0.125 µg/ml (0.5xMIC) Doxycycline 2nd duplicate

description: Sample 3b

value: WT

value: Exposure  to 0.125 µg/ml  (0.5xMIC) Doxycycline


title: ATP13A1_0_unstimulated_rep3_24hr

value: ATP13A1 sgRNA0


title: GL261-GFP_<0.1%O2_rep1_ATACseq

description: GL261 hypoxia <0.1% O2 16h rep1


title: ATP13A1_0_unstimulated_rep2_24hr


title: F. tularensis 2 hours post  exposure  to 0.125 µg/ml (0.5xMIC) Doxycycline 1st duplicate

description: Sample 3a


title: ChIP-on-ChIP in cut4 mutant strain with  anti H3-Lys9-me2 antibody

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: ChIP-on-ChIP for genome-wide localization of H3-Lys9-Me2 in cut4 mutant strain

hyb_protocol: Cy3-labeled WCE was combined with Cy5-labeled IP DNA samples , Agilent 10X Blocking agent (Part Number 5188-6416) and Hybridization buffer (Part Number 5188-6420) were added to it.  The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and incubated at 37oC for 30 minutes.

scan_protocol: Agilent Microarray Scanner G2505B

data_processing: Raw Data extraction from Images was done using Agilent Feature Extraction software

organism: Schizosaccharomyces pombe

label_protocol: Agilent Suretag Genomic DNA Labeling Kit (Part no : 5190-3399) was used for labeling. Protocol inclu random primers and the exo- Klenow fragment to differentially label genomic DNA samples with fluorescent- labeled nucleotides. Amplified WCE and IP DNA were mixed with 5µl of Random primers and incubated at 95oC for 3 minutes followed by  incubation  at 4oC for  5 minutes. Labeling master mix containing Cy5-dUTP(For IP samples) or Cy3-dUTP(For WCE samples), dNTP, Buffer and Klenow, were added to the denatured DNA sample and incubated at 37oC for 2 hours followed by enzyme inactivation at 65oC for 10 minutes

extract_protocol: Whole cell extract preparation, cross-linking, immunoprecipitation with specific antibody, reversal of cross-linking, DNA extraction and precipitation.

tag: genotype/variation

value: cut4 mutant

value: none, input DNA

source_name: Immunprecipitate of Whole cell extract of cut4 mutant strain

value: anti-H3-Lys9-me2 antibody


title: ChIP-on-ChIP in dts2 mutant strain with  anti Swi6 antibody

description: ChIP-on-ChIP for genome-wide localization of Swi6 in dts2 mutant strain

value: dts2 mutant

source_name: Immunprecipitate of Whole cell extract of dts2 mutant strain

value: anti-Swi6 antibody


title: F. tularensis without treatment with Ciprofloxacin 1st duplicate

description: Sample 2a

value: Growth control, no treatment


title: GL261-GFP_1%O2_rep2_ATACseq

description: GL261 hypoxia 1% O2 16h rep2

value: hypoxia 1% O2 16h


title: ATP13A1_0_unstimulated_rep1_24hr

value: Unstimulated


title: S3_WT_brain

value: brain


title: GL261-GFP_21%O2_rep2_ATACseq

description: GL261 normoxia 21% O2 rep2

value: normoxia 21% O2


title: F. tularensis without treatment with Doxycycline 2nd duplicate

description: Sample 1b


title: F. tularensis without treatment with Doxycycline 1st duplicate

description: Sample 1a


title: GL261-GFP_21%O2 rep1_ATACseq

description: GL261 normoxia 21% O2 rep1

value: glioma


title: GL261-GFP_1%O2_rep1_ATACseq

description: GL261 hypoxia 1% O2 16h rep1

value: GL261 stably expressing pEGFP-N1


title: ATP13A1_0_SeV_rep2_6hr

value: SeV


title: BM_Vehicle3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000 systems, with 151 bp paired-end reads obtained.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: CX3CR1-EGFP positive osteoclast precursors in vehicle-treated cells

extract_protocol:
Cells were digested in QIAZOL (Qiagen) to extract to total RNA, in accordance with the manufacturer’s instructions.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio). An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina) according to the SMARTer Kit instructions.

value: osteoclast precursors

value: vehicle-treated


title: DLD1 DAB2IP REP B

city: Boston

first: Abigail

middle: L

last: Miller

address: 77 Avenue Louis Pasteur NRB 466

institute: Mass General Brigham

data_processing:
FASTQ files were aligned using STAR. BAM files were sorted using samtools.  Sorted BAM files were then converted into count files using HtSeq to the hg19 genome.
Assembly: hg19
Supplementary files format and content: TPMs were generated using STAR methods.

source_name: cell line

growth_protocol: Cells were transduced with FB LACZ or FB DAB2IP.  After neomycin selection (3 days), recovery (1 day),  and further  propagation (2 days), cells were seed at 5x10^5 and collected 2 days later (70% confluency). .

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plus kit.
Kapa Hyper Prep

value: cell line

value: colon cancer


title: ATP13A1_0_SeV_rep2_15hr

value: HeLa

value: ATP13A1 sgRNA0


title: F. tularensis without treatment with Ciprofloxacin 2nd duplicate

description: Sample 2b

value: WT


title: ATP13A1_0_SeV_rep1_6hr


title: BM_Vehicle2


title: DLD1 DAB2IP REP A


title: ChIP-on-ChIP in swi7H4 mutant strain with  anti Swi6 antibody

description: ChIP-on-ChIP for genome-wide localization of Swi6 in swi7H4 mutant strain

value: swi7H4 mutant

value: none, input DNA

source_name: Immunprecipitate of Whole cell extract of swi7H4 mutant strain


title: Si-Setdb1-3

city: Guangzhou

first: Zhigang

state: GuangDong

address: 195 Dongfeng West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: KingMed School of Laboratory Medicine

institute: Guangzhou Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12)
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: AML12 cells, siSetdb1, Day3

growth_protocol: AML12 cells were  cultured in DMEM/F12 medium supplemented with 10% FBS and ITS-G (5 mg/ml insulin, 5 mg/l transferrin, 5 μg/l selenous acid) in humidified air containing 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: AML12 cells (5×105) were seeded in 6-well plates, after 24 hours, 50nm siRNA or scrambled RNA was transfected into AML12 with 5μl INTERFERin® (VWR International GmbH, Darmstadt, Germany) and 200 µL of DMEM/F12 medium without serum following manufacture’s instruction. Change the medium after 6 hours and continue transfection for 72 hours before using for subsequent experiments.

value: hepatocytes from a mouse  transgenic for human TGF alpha

value: AML12 cells were infected with Setdb1 siRNA for 72 hours


title: ChIP-on-ChIP with dts2 mutant strain with anti H3-Lys9-me2 antibody

description: ChIP-on-ChIP for genome-wide localization of H3-Lys9-Me2 in dts2 mutant strain

source_name: Whole cell extract of dts2 mutant strain

value: dts2 mutant

value: anti-H3-Lys9-me2 antibody


title: ChIP-on-ChIP in swi7H4 mutant strain with anti H3-Lys9-me2 antibody

description: ChIP-on-ChIP for genome-wide localization of H3-Lys9-Me2 in swi7H4 mutant strain

source_name: Whole cell extract of swi7H4 mutant strain


title: ChIP-on-ChIP in cut4 mutant strain with  anti Swi6 antibody

description: ChIP-on-ChIP for genome-wide localization of Swi6 in cut4 mutant strain

source_name: Whole cell extract of cut4 mutant strain

value: cut4 mutant

value: anti-Swi6 antibody


title: ChIP-on-ChIP with wt strain with  anti Swi6 antibody

description: ChIP-on-ChIP for genome-wide localization of Swi6 in wild type strain

source_name: Whole cell extract of wild type strain

value: Wild type strain

source_name: Immunprecipitate of Whole cell extract of wild type strain


title: ATP13A1_0_SeV_rep3_6hr

value: SeV


title: BM_Vehicle1

value: osteoclast precursors


title: ChIP-on-ChIP with wt strain with anti H3-Lys9-me2 antibody

description: ChIP-on-ChIP for genome-wide localization of H3-Lys9-Me2 in wild type strain

value: wild type strain


title: ATP13A1_0_SeV_rep3_15hr


title: ATP13A1_0_SeV_rep1_15hr


title: BM_JAK3

source_name: CX3CR1-EGFP positive osteoclast precursors in JAK inhibitor (JAKi)-treated cells

value: JAK inhibitor (JAKi)-treated cells


title: Si-NC3

source_name: AML12 cells, siControl, Day3

value: AML12 cells were infected with scrambled RNA for 72 hours


title: DLD1 LACZ REP C

value: cell line

value: colon cancer

value: LACZ


title: ATP13A1_0_hpRNA_rep3_24hr

value: HeLa

value: ATP13A1 sgRNA0

value: hpRNA


title: BM_JAK2


title: DLD1 LACZ REP B


title: ATP13A1_0_hpRNA_rep2_24hr


title: DLD1 LACZ REP A


title: Si-Setdb1-2

value: hepatocytes from a mouse  transgenic for human TGF alpha

value: AML12 cells were infected with Setdb1 siRNA for 72 hours


title: BM_JAK1


title: Si-NC1


title: ATP13A1_0_hpRNA_rep1_24hr


title: dKO_C3d.3

status: Public on Mar 04 2023

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 days, biological replicate-#3

growth_protocol: HEK293 cells and its derivatives (8KO, 19KO, dKO, dKO-V, dKO-8 and dKO-19) were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)  Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA prep kit (RS-122-2101/RS-122-2102)  Parental HEK293 (WT) cells, treated with vehicle control for 3 hrs, biological replicate-#1

treatment_protocol: Cells were treated with Vehicle control (0.1% DMSO) or 1microM Senexin B for different period of time (3hrs, 5hrs, 24hrs, 3 days and 5 days)

value: HEK293 (ATCC)

value: treated with 0.1 percent DMSO (vehicle control) for 3 days


title: dKO_S3d.2

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 days, biological replicate-#2

value: treated with 1microM Senexin B for 3 days


title: Si-Setdb1-1


title: dKO_S3d.3

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 days, biological replicate-#3


title: dKO_S3d.1

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 days, biological replicate-#1


title: dKO_C3d.2

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 days, biological replicate-#2


title: Normal mouse N1

source_name: the abdominal aorta of 4-month-old WT mouse

value: dechorionated abdominal aorta

value: WT


title: Si-NC2


title: TNBC Case 141

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

institute: Yonsei University

description: Gene expression data from tumor paraffin block

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human ST 2.0 Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT)

source_name: Triple-negative breast cancer

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT pico Terminal labeling kit.

extract_protocol: The RNA extraction of 147 FFPE tumor specimens was performed using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer's recommendations

tag: subclassification

value: B

tag: Sex

value: Female

tag: age

tag: tstage

tag: nstage

tag: mstage

tag: Stage


title: TNBC Case 147

value: LAR


title: TNBC Case 140

value: Mes


title: TNBC Case 139


title: TNBC Case 142


title: TNBC Case 145


title: TNBC Case 146

value: UNS


title: dKO_C3d.1

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 days, biological replicate-#1


title: TNBC Case 134


title: TNBC Case 144


title: TNBC Case 136


title: TNBC Case 138


title: TNBC Case 143


title: TNBC Case 131

value: IM


title: TNBC Case 129


title: TNBC Case 133


title: DLD1 DAB2IP REP C

source_name: cell line

tag: tissue

value: cell line

value: colon cancer

tag: genotype


title: TNBC Case 130


title: TNBC Case 126


title: TNBC Case 137


title: TNBC Case 127


title: TNBC Case 123


title: TNBC Case 128


title: TNBC Case 125


title: TNBC Case 135


title: TNBC Case 122


title: TNBC Case 124


title: TNBC Case 120


title: TNBC Case 119


title: TNBC Case 110


title: TNBC Case 117


title: TNBC Case 114


title: TNBC Case 102


title: TNBC Case 121


title: TNBC Case 99


title: TNBC Case 95


title: TNBC Case 108


title: TNBC Case 97


title: TNBC Case 105


title: TNBC Case 107


title: TNBC Case 104


title: TNBC Case 106


title: TNBC Case 96


title: TNBC Case 98


title: TNBC Case 118


title: TNBC Case 111


title: TNBC Case 101


title: TNBC Case 116


title: TNBC Case 92


title: TNBC Case 109


title: TNBC Case 112


title: TNBC Case 115


title: TNBC Case 103


title: TNBC Case 100


title: TNBC Case 94


title: TNBC Case 113


title: TNBC Case 132


title: TNBC Case 93


title: TNBC Case 89


title: TNBC Case 90


title: TNBC Case 91


title: RNA_seq_NPC_rep2

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
Adapters were trimmed using Cutadapt (v1.18)
RIBO-seq reads aligning to mitochondrial, ribosomal RNA, and tRNA sequences were filtered using Bowtie (v1.2)
Next, mRNA-seq and RIBO-seq reads were aligned to the human genome (hg38) with STAR (v2.7.1a)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38

source_name: Neural progenitor cell

growth_protocol: Human ESC line HUES8 was grown in Matrigel-coated plates (MATRIGEL MATRIX HESC-QUALIFIED, BD Bioscience, #354277) with mTeSR1 media (Stemcell Technologies, #1000023391) and passaged with Accutase (Stemcell Technologies, #A1110501) until the density reached roughly 80-90%. The medium was replaced every day. Dual SMAD inhibition was used for neural differentiation according to a previous protocol(Meng et al., 2021). Briefly, human ESCs were replated at a density of 5 x 104 cells per well in 24-well plates. After two days of cultivation in mTeSR1, neuroectoderm differentiation was triggered by neural induction media for 7 days (KnockOutTM DMEM/F12 (Gibco, #12660012), 0.5× N2 (Shanghai BasalMedia Technologies, #M430721), 0.5× B27 without vitamin A (Shanghai BasalMedia Technologies, #B430805), 1% Penicillin/Streptomycin (Thermo Fisher Scientific, #15140163), 1% 2-Mercaptoethanol (Gibco, #2121115), 1% GlutaMAXTM Supplement (Thermo Fisher Scientific, #35050061), 1% NEAA (Gibco, #11140-050), plus 2.5 uM SB431542 (Selleck, #S1067), and 0.05 uM LDN193189 (Selleck, #S7507)). The medium was changed daily, and the TGF-β inhibitor SB431542 was withdrawn from the neural induction media for the last 2 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neural progenitor cell

tag: cell line

value: NPC

tag: molecule type

value: rRNA depleted total RNA


title: RNA_seq_NPC_rep3

tag: cell type


title: TNBC Case 72


title: TNBC Case 87


title: TNBC Case 88


title: TNBC Case 86


title: TNBC Case 79


title: TNBC Case 83


title: TNBC Case 84


title: TNBC Case 82


title: TNBC Case 76


title: TNBC Case 78


title: TNBC Case 68


title: TNBC Case 70


title: TNBC Case 77


title: TNBC Case 80


title: TNBC Case 66


title: TNBC Case 81


title: TNBC Case 69


title: TNBC Case 75


title: TNBC Case 85


title: TNBC Case 71


title: TNBC Case 74


title: TNBC Case 67


title: RNA_seq_NPC_rep1


title: TNBC Case 73


title: HCT116-CPEB4

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

description: HCT-116 human colorectal cancer CPEB4 over-expressed cells

hyb_protocol: biotinylated fragmented-cDNA were hybridized with the Genechips.

scan_protocol: Arrays were washed and stained in the Affymetrix fluidics station and scanned in the 3000 7G scanner.

data_processing: Partek Genomics Suiteand the Bioconductor RankProd package were used for microarray data analysis.

label_protocol: Double-stranded cDNA was then used as template in an in vitro transcription reaction to prepared biotinylated cDNA.

growth_protocol: Complete growth medium RPMI-1640 which contains 10% FCS, 1% Penicillin-Streptomycin Solution was used for cell culture.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Both cell lines were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

value: colon cell line

value: CPEB4 over-expressed


title: HCT116-GFP

description: HCT-116 human colorectal cancer wild type cells

value: wildtype


title: RNA_seq_ESC_rep1

source_name: Embryonic stem cell

value: Embryonic stem cell

value: ESC


title: RNA_seq_ESC_rep2

value: WT


title: TNBC Case 65


title: TNBC Case 64


title: AHR-inhibited_DC-10_rep3 (RNA-Seq)

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Illumina software bcl2fastq-v2.19.0 used for base calling
Raw RNA sequences were trimmed (Cutadapt v 1.18) and aligned against the human reference genome GRChg19 using STAR (v 2.7.5a)
featureCounts (v. 2.0.1) was used to determine the total counts of transcripts per gene
Differential gene expression and clustering were performed in the R statistical environment using the DESeq2 package
Genome_build: hg19
Supplementary_files_format_and_content: deseq2IDC_DC10.csv:  Deseq2 IDC vs DC10
Supplementary_files_format_and_content: deseq2DC10CH_DC10.csv:  Deseq2 DC10CH vs DC10

source_name: peripheral blood

growth_protocol: CD14+ monocytes were isolated from PBMCs by positive selection using CD14 MicroBeads (Milteny Biotech) according to manufacturer’s instructions. CD14+ monocytes were differentiated into dendritic cells (DC) in RPMI 1640 medium (Lonza), 10% fetal bovine serum (FBS) (Euroclone), 100 U/ml penicillin/streptomycin (Lonza), and 2 mM L-glutamine (Lonza) at 10^6 cells/ml, in presence of 100ng/ml Recombinant Human GM-CSF (Miltenyi Biotech) and 10 ng/ml Recombinant Human IL-4 (Miltenyi). Biotech) for 7 days at 37°C with 5% CO2. Fresh medium with cytokines, at concentrations stated above, was added on day 3.

extract_protocol:
RNA was extracted by mirNeasy kit (Qiagen) following manufacturer’s instructions
library based on rRNA depletion were built and sequenced by 2x150 Illumina HiSeq or NovaSeq.

treatment_protocol: DC-10 were generated as previously described (Gregori et al. 2010). Briefly, CD14+ monocytes were cultured as described above fo DC differentiation, with the addition of Recombinant Human IL-10 (CellGenix) at 10 ng/ml. AHR-inhibited DC-10 were differentiated as described for DC-10, in presence of 20microM AHR specific antagonist CH223191 (Aurogene).

value: peripheral blood

value: Monocyte derived dendritic cells

tag: cell subset

tag: treatment

value: GM-CSF and IL4 and IL10 + CH223191


title: AHR-inhibited_DC-10_rep2 (RNA-Seq)


title: DC-10_rep2 (RNA-Seq)

value: GM-CSF and IL4 and IL10


title: RNA_seq_ESC_rep3


title: DC-10_rep1 (RNA-Seq)


title: Dendritic cells_rep2 (RNA-Seq)

value: Dendritic cells

value: GM-CSF and IL4


title: Dendritic cells_rep1 (RNA-Seq)


title: DC-10 - Multiple Scerosis patient_rep3 (RNA-seq)

data_processing:
Illumina software bcl2fastq-v2.20.0 used for base calling
Raw RNA sequences were trimmed (Cutadapt v 1.18) and aligned against the human reference genome GRChg19 using STAR (v 2.7.5a)
featureCounts (v. 2.0.1) was used to determine the total counts of transcripts per gene
Differential gene expression and clustering were performed in the R statistical environment using the DESeq2 package
Genome_build: hg19
Supplementary_files_format_and_content: deseq2_in_vitro_MS.csv:  Deseq2 MS vs HEALTHY

growth_protocol: CD14+ monocytes were isolated from PBMCs by positive selection using CD14 MicroBeads (Milteny Biotech) according to manufacturer’s instructions. CD14+ monocytes were differentiated into DC-10, as previously described (Gregori et al. 2010), in RPMI 1640 medium (Lonza), 10% fetal bovine serum (FBS) (Euroclone), 100 U/ml penicillin/streptomycin (Lonza), and 2 mM L-glutamine (Lonza) at 10^6 cells/ml, in presence of 100ng/ml Recombinant Human GM-CSF (Miltenyi Biotech), 10 ng/ml Recombinant Human IL-4 (Miltenyi. Biotech) and Recombinant Human IL-10 (CellGenix) at 10 ng/ml for 7 days at 37°C with 5% CO2. Fresh medium with cytokines, at concentrations stated above, was added on day 3.

extract_protocol:
RNA was extracted by mirNeasy kit (Qiagen) following manufacturer’s instructions
library based on polyA enrichment were built and sequenced by 2x150 Illumina HiSeq
low input RNA-Seq

tag: disease state

value: Multiple Scerosis

value: in vitro differentiated


title: DC-10 - Multiple Scerosis patient_rep2 (RNA-seq)


title: AHR-inhibited_DC-10_rep1 (RNA-Seq)


title: DC-10_rep3 (RNA-Seq)


title: TNBC Case 61

value: B

value: Female


title: DC-10 - HEALTHY_rep4 (RNA-seq)

value: Healthy


title: TNBC Case 58


title: DC-10 - HEALTHY_rep3 (RNA-seq)


title: TNBC Case 59


title: TNBC Case 62

value: UNS


title: DC-10 - HEALTHY_rep2 (RNA-seq)


title: Dendritic cells_rep3 (RNA-Seq)


title: TNBC Case 60


title: TNBC Case 63

value: LAR


title: TNBC Case 56

value: Mes


title: TNBC Case 54


title: DC-10 - HEALTHY_rep1 (RNA-seq)


title: TNBC Case 57

value: IM


title: TNBC Case 50


title: DC-10 - Multiple Scerosis patient_rep1 (RNA-seq)


title: TNBC Case 52


title: Ex vivo isolated DC-10 - Multiple Scerosis patient_rep4 (RNA-Seq)

data_processing:
Illumina software bcl2fastq-v2.20.0 used for base calling
Raw RNA sequences were trimmed (Cutadapt v 1.18) and aligned against the human reference genome GRChg19 using STAR (v 2.7.5a)
featureCounts (v. 2.0.1) was used to determine the total counts of transcripts per gene
Differential gene expression and clustering were performed in the R statistical environment using the DESeq2 package
Genome_build: hg19
Supplementary_files_format_and_content: deseq2_ex_vivo_MS.csv:  Deseq2 MS vs HEALTHY

extract_protocol:
[Isolation protocol]  DC-10 were FACSorted from PBMC as CD14+CD16+CD141+CD163+.
RNA was extracted by mirNeasy kit (Qiagen) following manufacturer’s instructions
library based on polyA enrichment were built and sequenced by 2x150 Illumina HiSeq
low input RNA-Seq

value: Ex vivo isolated


title: Ex vivo isolated DC-10 - Multiple Scerosis patient_rep3 (RNA-Seq)


title: Ex vivo isolated DC-10 - Multiple Scerosis patient_rep2 (RNA-Seq)


title: TNBC Case 49


title: TNBC Case 47


title: Ex vivo isolated DC-10 - Multiple Scerosis patient_rep1 (RNA-Seq)


title: Ex vivo isolated DC-10 - HEALTHY_rep4 (RNA-Seq)

value: healthy


title: TNBC Case 48


title: TNBC Case 44


title: Ex vivo isolated DC-10 - HEALTHY_rep2 (RNA-Seq)

value: peripheral blood


title: Ex vivo isolated DC-10 - HEALTHY_rep3 (RNA-Seq)


title: Ex vivo isolated DC-10 - HEALTHY_rep1 (RNA-Seq)


title: TNBC Case 55


title: AHR-inhibited_DC-10_rep2 (ATAC-Seq)

data_processing:
Illumina software RTA v.2.7.7 used for base calling
fastq reads were trimmed with trimmomatic (v 0.36) using the Nextera adapter library
Trimmed reads were then mapped on the hg19 version of the human genome using bwa-mem with default settings and duplicates were marked using samblaster (v 0.1.21).
Duplicates, blacklisted regions (ENCODE) and reads aligning with mitochondrial DNA were removed using samtools (v 0.1.19). Broad peaks were called using Macs2 (v. 2.1.1; --shift -100 --extsize 200 --broad)
The list of called peaks from each sample was used to assess the differentially open chromatin regions through the DiffBind package from the R statistical environment using edgeR and DESeq2 methods (FC>2 for in vitro data).
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak text files were generated using macs2
Supplementary_files_format_and_content: differential binding files were generated using DiffBind

extract_protocol:
DNA tagmentation and library preparation were performed concomitantly on 0.5-1x10^5 freshly isolated cells, according to FAST-ATAC protocol (Corces et al. 2017)
Library preparation was performed as previously described (Corces et al. 2017), with minor modifications, and sequenced by 2x150 Illumina HiSeq

value: Monocyte derived dendritic cells

value: GM-CSF and IL4 and IL10 + CH223192


title: TNBC Case 51


title: TNBC Case 46


title: TNBC Case 43


title: DC-10_rep5 (ATAC-Seq)

value: GM-CSF and IL4 and IL10


title: TNBC Case 53


title: TNBC Case 45


title: AHR-inhibited_DC-10_rep1 (ATAC-Seq)

value: GM-CSF and IL4 and IL10 + CH223191


title: DC-10_rep4 (ATAC-Seq)


title: DC-10_rep3 (ATAC-Seq)


title: DC-10_rep1 (ATAC-Seq)


title: Dendritic cells_rep3 (ATAC-Seq)

value: Dendritic cells

value: GM-CSF and IL4


title: DC-10_rep2 (ATAC-Seq)


title: TNBC Case 38


title: TNBC Case 40


title: TNBC Case 39


title: TNBC Case 41


title: TNBC Case 37


title: TNBC Case 34


title: TNBC Case 36


title: Dendritic cells_rep2 (ATAC-Seq)


title: Dendritic cells_rep1 (ATAC-Seq)


title: ex vivo isolated classical dendritic cells_rep3 (ATAC-Seq)

data_processing:
Illumina software RTA v.2.7.7 used for base calling
fastq reads were trimmed with trimmomatic (v 0.36) using the Nextera adapter library
Trimmed reads were then mapped on the hg19 version of the human genome using bwa-mem with default settings and duplicates were marked using samblaster (v 0.1.21).
Duplicates, blacklisted regions (ENCODE) and reads aligning with mitochondrial DNA were removed using samtools (v 0.1.19). Broad peaks were called using Macs2 (v. 2.1.1; --shift -100 --extsize 200 --broad)
The list of called peaks from each sample was used to assess the differentially open chromatin regions through the DiffBind package from the R statistical environment using DESeq2 methods (FC>4 for ex vivo data).
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak text files were generated using macs2
Supplementary_files_format_and_content: differential binding file generated using DiffBind

extract_protocol:
[Isolation protocol]  DC-10 were FACSorted from PBMC as CD14+CD16+CD141+CD163+, cDC as CD11c+CD14-CD1c+.
DNA tagmentation and library preparation were performed concomitantly on 0.5-1x10^5 freshly isolated cells, according to FAST-ATAC protocol (Corces et al. 2017)
Library preparation was performed as previously described (Corces et al. 2017), with minor modifications, and sequenced by 2x150 Illumina HiSeq

value: Dendritic Cells

value: classical dendritic cells

value: ex vivo isolated


title: ex vivo isolated classical dendritic cells_rep2 (ATAC-Seq)


title: ex vivo isolated classical dendritic cells_rep4 (ATAC-Seq)


title: TNBC Case 33

value: Female


title: ex vivo isolated classical dendritic cells_rep1 (ATAC-Seq)


title: ex vivo isolated DC-10_rep6 (ATAC-Seq)


title: TNBC Case 31


title: ex vivo isolated DC-10_rep5 (ATAC-Seq)


title: TNBC Case 30


title: TNBC Case 28


title: TNBC Case 35


title: ex vivo isolated DC-10_rep2 (ATAC-Seq)


title: TNBC Case 27

value: UNS


title: TNBC Case 23


title: TNBC Case 25

value: LAR


title: ex vivo isolated DC-10_rep3 (ATAC-Seq)


title: TNBC Case 29

value: Mes


title: TNBC Case 21

value: B


title: TNBC Case 26


title: ex vivo isolated DC-10_rep1 (ATAC-Seq)


title: TNBC Case 20

value: IM


title: 21-0107; #1592

city: New York

first: Oren

last: Becher

state: NY

address: 1468 Madison Ave 4th Fl,

department: Pediatric Hematology-Oncology

institute: Mount Sinai

description: Np53fl_H3.3G34R_vs_H3.3WT_results_deseq2, Np53fl;ATRXflfl_vs_Np53fl_H3WT_results_deseq2, ATRX KO H3.3G34R vs ATRX WT H3.3WT_results_deseq2

data_processing:
FASTQ files were aligned to the mm10 genome using RNA-STAR 2.7 .
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature with the following HTSeq-count parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
HTSeq-count files were imported into R (https://www.r-project.org/https://www.r-project.org/), and differential expression analysis was performed with the DESeq2 package using the DESeqDataSetFromHTSeqCount function with default settings. DESeq2 analyses were run comparing the following groups: ATRX KO H3.3G34R vs ATRX KO H3.3WT, ATRX WT H3.3G34R vs ATRX WT H3.3WT, ATRX KO H3.3WT vs. ATRX WT H3.3WT, ATRX KO H3.3G34R vs. ATRX WT H3.3G34R, and ATRX KO H3.3G34R vs. ATRX WT H3.3WT.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables in csv format containing DESeq2 output and DESeq2 normalized abundance measurements for each sample

source_name: frontal cortex

growth_protocol: Nestin Tv-a; p53 fl/fl and Nestin Tv-a; p53 fl/fl; ATRX fl/fl mice were injected with DF-1 cells transfected with RCAS-Cre, RCAS-PDGFA, and either RCAS-H3.3WT-GFP or RCAS-H3.3G34R-GFP. Mice were then allowed to reach a functional end point (erratic behavior, domed head, ataxia, 20% weight loss), euthanized and the tumor was collected from the frontal cortex.

extract_protocol:
Purified RNA was obtained by using Qiagen Rneasy extraction kit and protocol
TruSeq mRNA-Seq Library Prep

treatment_protocol: Mice were injected with DF-1 cells transfected with RCAS-Cre, RCAS-PDGFA, and either RCAS-H3.3WT-GFP or RCAS-H3.3G34R-GFP then allowed to reach a functional end point (erratic behavior, domed head, ataxia, 20% weight loss), euthanized and the tumor was collected from the frontal cortex.

value: frontal cortex

tag: strain

value: Cortical injection of Cre, PDGFA, H3.3WT-GFP

tag: h3.3 expression

value: wildtype


title: 21-0107; #1591


title: 21-0141; #1737


title: ex vivo isolated DC-10_rep4 (ATAC-Seq)

value: peripheral blood


title: 20-1225; #1488


title: 21-0109; #1731

description: Np53fl_H3.3G34R_vs_H3.3WT_results_deseq2, Np53fl;ATRXflfl_vs_Np53fl_H3G34R_results_deseq2

value: Cortical injection of Cre, PDGFA, H3.3G34R-GFP

value: G34R mutant


title: 21-0130; #1680


title: 21-0109; #1602


title: 21-0132; #1689

description: Np53fl;ATRXflfl_H3.3G34R_vs_H3.3WT_results_deseq2, Np53fl;ATRXflfl_vs_Np53fl_H3WT_results_deseq2


title: 21-0123; #1687


title: TNBC Case 19

tag: subclassification


title: TNBC Case 18

tag: Sex


title: TNBC Case 24

tag: age


title: 21-0124; #1695

description: Np53fl;ATRXflfl_H3.3G34R_vs_H3.3WT_results_deseq2, Np53fl;ATRXflfl_vs_Np53fl_H3G34R_results_deseq2, ATRX KO H3.3G34R vs ATRX WT H3.3WT_results_deseq2


title: TNBC Case 16

tag: tstage


title: TNBC Case 14

tag: nstage


title: 21-0120; #1645


title: TNBC Case 15

tag: mstage


title: TNBC Case 8

tag: Stage


title: TNBC Case 32


title: TNBC Case 17


title: TNBC Case 11


title: TNBC Case 9


title: TNBC Case 12


title: 21-0131; #1699

tag: tissue


title: TNBC Case 10


title: TNBC Case 22


title: TNBC Case 7


title: TNBC Case 13


title: 21-0127; #1649

tag: genotype


title: TNBC Case 6


title: 21-0124; #1693


title: ADTet_5uM_24hr_2

city: Hung Hom, Kowloon, Hong Kong

first: Ricky

last: Chan

address: 11 Yuk Choi Rd

country: Hong Kong

institute: The Hong Kong Polytechnic University

data_processing:
Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2
Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads.
Reads were aligned to Human genome version GRCh38 from Ensemble using HiSat2
Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: raw read counts for each sample in TSV format
Supplementary files format and content: normalized read counts for each sample in TSV format

source_name: HeLa

growth_protocol: Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 44 mM sodium bicarbonate (Sigma-Aldrich), 10 % v/v Fetal Bovine Serum (Gibco), 100 U/ml penicillin (Gibco) and 100 µg/ml streptomycin (Gibco), at 37°C with 5 % CO2

extract_protocol: Total RNA was extracted from cells using TRIzol extraction reagent (Millipore) according to the manufacturer's instructions.

treatment_protocol: Cells treated with DMSO or different concentration of Tetrandrine or AD-Tetrandrine for 24 hours.

tag: cell line

value: HeLa

value: Epithelial cell

value: WT

value: AD-Tetrandrine 5uM


title: ADTet_5uM_24hr_1


title: TNBC Case 5


title: 21-0117; #1658


title: P0-6 [miRNA-Seq]

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

state: PA

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

description: smRNA-seq

data_processing:
Sequenced reads were aligned to the mm10 genome using the Rsubread R package's align function (version 2.0.1; settings: type = 1, output_format = "BAM", nsubreads = 60, maxMismatches = 3, indels=0,sortReadsByCoordinate=TRUE,unique=FALSE,nBestLocations=10,minFragLength=21).
Reads were annotated to miRNA ussing features from miRBase (version 22) in GTF format with the Rsubread R package's featureCounts function (version 2.0.1; settings: isGTFAnnotationFile = TRUE, GTF.featuerType = "miRNA", GTF.attrType = "ID", allowMultiOverlap=TRUE, isPairedEnd = FALSE, strandSpecific=1).
Differential expression of miRNA was calculated with multiple testing corretion using the R package DESeq2 (version 1.26.0), with the fraction of aligned reads in the sample included as a cofactor and an adjusted p-value cutoff of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file containing miRNA counts as well as genomic locations and IDs from miRBase (version 22) and differential expression statistics from DESeq2.

source_name: P0 mouse nephron progenitor replicate 3

extract_protocol:
Up to 24 kidneys from each litter were pooled for progenitor isolation, while one kidney was retained as a whole-kidney qPCR control for confirming enrichment of progenitor cells relative to surrounding cell types. Pools of kidneys were subjected to limited (15 min) digestion at 37C with a mixture of collagenase A and pancreatin to collect cortical cells. Cells were then washed, and nephron progentors isolated through positive selection using magnetic beads biotinylated with antibodies for Itga8. A fraction containing 50,000 cells was immediately removed for ATAC-seq, and total RNA was extracted from the remaining cells using the Qiagen miRNeasy Mini Kit (Qiagen 217004).
Single-end smRNA libraries were prepared using the QIAseq miRNA library preparation kit (Qiagen 331502)

treatment_protocol: Litters were sacrificed at either 14 days post fertilization (E14.5) or the day of birth (P0).

value: Nephron progenitor

tag: embryonic day


title: ADTet_15uM_24hr_2

tag: cell type

value: AD-Tetrandrine 15uM


title: P0-4 [miRNA-Seq]

description: smRNA-seq

source_name: P0 mouse nephron progenitor replicate 2


title: TNBC Case 4

value: Female


title: P0-2 [miRNA-Seq]

description: smRNA-seq

source_name: P0 mouse nephron progenitor replicate 1


title: ADTet_15uM_24hr_1


title: TNBC Case 2

value: UNS


title: E14-6 [miRNA-Seq]

description: smRNA-seq

source_name: E14.5 mouse nephron progenitor replicate 3


title: TNBC Case 3


title: Tet_5uM_24hr_1

value: Tetrandrine 5uM


title: E14-5 [miRNA-Seq]

description: smRNA-seq

source_name: E14.5 mouse nephron progenitor replicate 2


title: TNBC Case 1

value: Mes


title: Tet_15uM_24hr_2

value: Tetrandrine 15uM


title: Tet_15uM_24hr_1


title: E14-2 [miRNA-Seq]

description: smRNA-seq

source_name: E14.5 mouse nephron progenitor replicate 1


title: P0-6

data_processing:
ATAC-seq data processing and IDR peak calling were performed using a custom Nextflow pipeline, available at https://bitbucket.org/clugstonA/mirna_enhancers/src/master/src/atacseq_pipeline/ATACseq_encode_pipeline_3.0.nf.
IDR peaks were annotated with overlapping enhancers from the FANTOM5 (available at https://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/) and Vista (available at https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=search&show=1&search.form=no&search.result=yes) using the R package GenomicRanges v1.38.0.
IDR peaks were annotated with overlapping genes, promoters, and exon annotations within the Ensemble R database package EnsDb.Mmusculus.v79 using the R package GenomicRanges v1.38.0.
IDR peaks were annotated with overlapping EnhancerAtlas 2.0 enhancer predictions (available at http://www.enhanceratlas.org/downloadv2.php) using the R package GenomicRanges v1.38.0.
Transcription factor footprints were detected using Regulatory Genomics' Hmm-based Identification of transcription factor footprints (HINT-RGT) ATAC-seq footprinting model, rgt-hint footprinting (settings: --organism=mm10 --atac-seq --paired-end).
Transcription factor footprints were annotated to known transcription factors using binding motifs from the HOCOMOCO11 DNA binding motif database (available at http://hocomoco11.autosome.ru/) using th HINT rgt-motifanalysis program (settings: --organism=mm10).
Genome_build: mm10
Supplementary_files_format_and_content: Bgzipped BED file containing mm10 IDR regions annotated with Tn5 insertion counts, differential accessibility statistics, transcription factor footprint results, and other genomic annotations.
Supplementary_files_format_and_content: Bgzipped BEDgraph files containing pileup scores for each sample.

extract_protocol:
Up to 24 kidneys from each litter were pooled for progenitor isolation, while one kidney was retained as a whole-kidney qPCR control for confirming enrichment of progenitor cells relative to surrounding cell types. Pools of kidneys were subjected to limited (15 min) digestion at 37C with a mixture of collagenase A and pancreatin to collect cortical cells. Cells were then washed, and nephron progentors isolated through positive selection using magnetic beads biotinylated with antibodies for Itga8. A fraction containing 50,000 cells was immediately subjected to suspension in ice-cold, non-ionic lysis buffer for 10 minutes to lyse cell membranes while maintaining the nuclear envelope. Nephron progenitor nuclei were washed and collected, then immersed in the sequencing library transposition reaction.
Libraries were prepared in accordance with that published by Buenrostro et. al (Nature Methods 2013). Nuclei were suspended in the Nextera DNA Flex Library Prep Kit (Illumina FC-121-1030) transposition reaction solution containing Tn5 transposase, and free DNA strands were collected and cleaned using the MinElute PCR Purification kit (Qiagen 28004). Forward (i7) and reverse (i5) Illumina indices were applied using PCR to add sample- and strand-specific molecular identifiers. The optimal number of amplification cycles for each sample was identified as the number of cycles required to  achieve 1/3 maximum fluorescence, measured in a 5uL PCR side reaction with a SYBR green reporter. Once determined, the remaining indexed DNA solutions were amplified using this many cycles. Libraries were then purified using Ampure XP magnetic beads (Beckman Coulter A63881).


title: DMSO_24hr_1

value: DMSO


title: RIBO_seq_NPC_rep2

value: Neural progenitor cell

value: NPC

tag: molecule type

value: ribosome bound total RNA


title: DMSO_24hr_2

tag: treatment


title: E14-6


title: P0-2


title: RIBO_seq_ESC_rep3

value: Embryonic stem cell

value: ESC


title: RIBO_seq_NPC_rep1


title: E14-2


title: Tet_5uM_24hr_2

value: HeLa


title: CD8+ D4-IgG4H-CD28TM CAR T cells stimulated with T3M4 cells, scRNA-seq

city: Bethesda

first: Mitchell

last: Ho

state: MD

address: 37 Convent Dr, Bldg 37 Rm 5002

department: Laboratory of Molecular Biology

institute: National Cancer Institute

description: Illumina

library_source: transcriptomic single cell

data_processing:
Raw Fastq Sequencing data was initially quality controlled with FASTQC version 0.11.9 to ensure reliable data quality.
Cutadapt version 3.4 was utilized to trim nucleotide bases from Read 1 that were not relevant for cell barcode identification.
Subsequently Alevin Salmon version 1.4.0 was utilized for cell barcode identification and gene expression quantification.
AlevinQC v. 1.10.0 was utilized to quality control the Alevin Salmon data processing step to ensure accurate estimation of cell barcodes identified.
Assembly: Human Reference - Release 36 (GRCh38.p13).

source_name: primary T cells

extract_protocol:
Cells were lysed in sealed microchambers and then mRNA was captured by barcoded microbeads
cDNA production occurs in the sealed micro chambers through action of reverse transcriptase.  cDNA amplification protocol was developed in-house using a commercially available polymerase. Illumina library preparation was done using the manufacturer’s protocol and Nextera XD library preparation kit (Illumina, FC-131-1096).

value: CD8+ T cell

value: stimulated with T3M4 cells


title: MZ 4.3hpf 1k

city: Beijing

first: Weimin

last: Shen

address: Tsinghuayuan park

institute: School of life science, Tsinghua University

description: fpkm table.txt

data_processing:
BGISEQ-500 platform was used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50, then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using software RSEM v1.2.8 from Langmead, B. et al., Nat. Methods, 2012, and Li, B. & Dewey, C. N., BMC Bioinformatics, 2011.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: whole mount embryo

extract_protocol:
total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard protocols

value: AB

value: whole mount embryo

tag: developmental stage

value: 4.3 hours post fertilization


title: MZ 7hpf Dome

description: fpkm table.txt

tag: strain

value: 7 hours post fertilization