title: Yeast Polysome Profiling R3, Fraction 23

city: Basel

first: Attila

last: Becskei

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

data_processing:
Sequence reads were trimmed for adaptor sequences using TrimGalore (TrimGalore v0.6.5) with --illumina parameter
Trimmed sequence reads were mapped and TPM values obtained with Salmon (Salmon v1.0.0)
Salmon index was created from NCBI's reference transcriptome (S288C, assembly R64) with Salmon index command
TPM quantification was performed with Salmon quant command
parameters: --validateMappings --seqBias --gcBias
Assembly: S288C, assembly R64
Supplementary files format and content: Microsoft excel spreadsheet with TPM values

organism: Saccharomyces cerevisiae

extract_protocol:
To start the cell lysis, cells were dissolved in 1X Polysome Lysis Buffer (PLB) [20mM Tris-HCl (ThermoScientific #AM9856), 10 mM MgCl2 (ThermoScientific #AM9530G), 1mM DTT (ThermoScientific #707265ML), 10 µg/mL cycloheximide (ThermoScientific #J66004-XF), 2 cOmplete EDTA free Protease Inhibitor (Sigma #COEDTAF-RO)/100mL, 8U/ml RNasIN (Promega #N2611), 1% v/v Triton X-100 (Fluka #93418)]. Lysis was carried out with Zirconia/Silica beads (Biospec #11079105z) with cell suspensions loaded in 1.5mL microfuge tubes on benchtop shaker/incubator set at 4°C. 15 cycles of interval shaking was carried out with each cycle consisting of 30s ON at 2000rpm and 30s OFF.
For the gradient, 10% and 50% w/v sucrose (ThermoScientific #036508-30) solutions were prepared in 1x Polysome Gradient Buffer (PGB) [as PLB but without Triton X-100]. The 10% sucrose was loaded on the centrifuge tubes (Beckman C14293/344059 Ultraclear 13.2ml [compatible with SW41Ti rotor]). With a 20ml syringe attached to long cannula, the 50% solution was layered at the bottom. The tubes were then covered with caps (BioComp #105-414-1) and the gradient was formed by high angle rotation, using the 10%-50% short cap (rate zonal) protocol in the BioComp™ Gradient Station machine.
To assess the volume of the cell lysate to be loaded, A254 was measured and a total of 10-50 A260 units was loaded onto the 10-50% sucrose gradient. Ultracentrifugation was carried out with a SW41Ti rotor (swing bucket) at 40000rpm for 2h at 4°C. The polysome profile was generated using the BioComp™ Gradient Station machine and 25 different fractions (450µL each) corresponding to different lengths in the centrifuge tube were collected. RNA from each fraction was purified by acid Phenol : Chloroform : Isoamyl Alcohol :: 25 : 24 : 1. Precipitation carried out with one volume of isopropanol at 4°C for 30 min to 1h with 2µL of GlycoBlue (ThermoScientific #AM9516) as co-precipitant. RNA was reconstituted with 20µL of nuclease free water (ThermoScientific #AM9932) containing RNasIN (Promega #N2611) at 1µL/mL (40U/mL).
Stranded SMART-Seq (Takara)


title: RH30 cells treated with Phosphoramide mustard

status: Public on Sep 28 2023

type: SRA

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

library_source: other

data_processing:
CRISPR KO screens were analyzed using Mageck-Vispr/0.5.7
Supplementary files format and content: Mageck default output describing resulting RRA scores

molecule: other

organism: Homo sapiens

source_name: Soft bone

extract_protocol: sgRNAs for the human CRISPR KO library were first designed using CRISPick . The top 30 sgRNAs for each gene then underwent an additional round of filtering using in-house off-target analysis to identify highly unique sgRNAs.  Up to 6 sgRNAs per gene were selected for the library along with non-targeting controls making up ~10% of the final library.

treatment_protocol: 72H treatments

tag: tissue

value: Soft bone

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

tag: genotype

tag: treatment

value: Phosphoramide mustard

tag: molecule type

value: gRNA


title: Yeast Polysome Profiling R3, Fraction 25

library_source: transcriptomic

molecule: total RNA


title: MOE, replicate 1, snATACseq

city: New York

first: Ariel

last: Pourmorady

state: NY

address: 3227 Broadway

department: Neurobiology and Behavior

institute: Columbia University

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10. "genes.gtf" file was used for snRNA alignment
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

organism: Mus musculus

source_name: main olfactory epithelium (MOE)

extract_protocol:
Nuclei must be purified under RNA clean conditions. A cell suspension of mouse MOE was obtained from an adult mouse following the dissociation conditions described in Monahan et al. 2017. Cells pellet were immediately resuspended in 300-uL of cold RNAse free lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), and nuclei were pelleted in a the Eppendorf 5810R Centrifuge at 1000-g, for 10-min at 4-˚C. Nuclei were resuspended in 500-uL of Homogenization Buffer (10x HB: 100-mM Trizma Base, 800 mM KCl, 100 mM EDTA, 10 mM spermidine trihydrochloride, 10 mM spermidine tetrahydrochloride in ddH2O, pH to 9-9.4 with NaOH, instructions for preparation of 1x HB can be found in Zhang et al. 2-12 50) with RNAse inhibitor (NEB MO314L), followed by 500-uL 82% Optiprep solution (4.1-mL Optiprep solution (Sigma Aldrich D1556-250ML), 25-uL 1M CaCl2, 15-uL 1M MgAc, 50-uL 1M Tris pH 8, 810-uL Water) then placed on ice. The 1-mL homogenate was carefully added onto 1-mL of 48% Optiprep solution (2.4-mL Optiprep solution, 800-uL 1M Sucrose, 25-uL 1M CaCl2, 15-uL 1M MgAc, 50-uL 1M Tris pH 8, 1710-uL Water), and was spun down in a pre-cooled swinging bucket centrifuge (Eppendorf 5810R) at 3200-g, for 20-min, at 4-˚C, acceleration 5/9, deceleration 0/9 (no break). The supernatant was aspirated and disposed, without dislodging the pellet. Air dry pellet and resuspend in 500-μL 1 x PBS diluted with 0.04% BSA with RNAse inhibitor. Cell concentration was measured for accurate loading into the 10x pipeline.
Joint scRNA- and scATAC-seq libraries were prepared in collaboration with the Columbia Genome Center using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions. Both GEX and ATAC libraries were sequenced to ~350M reads on an Illumina NextSeq550 100PE and Illumina NovaSeq 6000150PE, respectively.

value: main olfactory epithelium (MOE)

tag: age

value: adult


title: RH30 cells treated with Cisplatin

value: Cisplatin


title: P2-ImmFix-dipc-66

description: DipC on GFP+ cells from gg8tTAtetOP2/CAST hybrid mice

library_source: genomic

data_processing:
We excluded cells that had contacts < ~400,000 contacts, cells that had a low contact-to-read ratio, and cells that had high variability in 3D structure across computational replicates. Overall, the median number of contacts across nuclei was 715,690 contacts per cell for 74 cells for mor28-IRES-GFP Dip-C and 694,462 contacts per cell for 84 cells for gg8-tTA>tetO-P2-IRES-GFP Dip-C, for a total of 161 cells. 3D reconstruction of Dip-C models was performed exactly as described in (https://github.com/tanlongzhi/dip-c).
To characterize Greek Island and OR gene 3D relationships, we used the dip-c function 'dip-c pd' to generate symmetric matrices, measured in particle radii, of the pairwise distance relationships between these DNA elements. These processed data files end in "pd.txt".
To characterize Greek Island and OR gene genomic contacts, we used the haplotype imputed contacts file generated in the Dip-C pipelie "contacts.con.gz", to extract all contacts per cell at 50-kb resolution, normalized to contacts per million. Contacts for all male and female cells are compiled in separate text files ending in "50kb.contacts.haplotyped.txt".
Assembly: mm10
Supplementary files format and content: pd.txt: tab-delimited text files containing symmetric distance matrices.
Supplementary files format and content: "50kb.contacts.haplotyped.txt".: tab-delimited text files describing pairwise genomic contacts binned at 50-kb resolution.
Library strategy: Dip-C

source_name: olfactory sensory neurons

growth_protocol: Castaneous (Cas) mice were crossed to gg8-tTA>tetO-P2-IRES-GFP or mor28-IRES-GFP mice heterozygous F1 hybrids with SNPs to allow for downstream haplotype imputation.

extract_protocol:
Nuclei were extracted exactly as described in "Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice" (Bashkirova et al. 2023). Briefly, MOE was collected from at least 3 adult heterozygous mice resulting from this cross, and dissociated using the Worthing Dissociation Kit. GFP+ cells were sorted using FACs, and the sorted cells were fixed for 10 minutes in 2% formaldehyde and FAC-sorted to isolate GFP+ mOSNs. Dip-C was performed on 96 cells for each experiment.. Briefly, cells were lysed in Hi-C Lysis Buffer (10mM Tris pH8, 10mM NaCl, 0.2% NP40, 1x protease inhibitors) on ice for 15 minutes, nuclei were pelleted at 2500 rcf for 5 min at 4°C, then resuspended in 0.5% SDS and permeabilized 10 minutes at 62 °C then quenched in 1.1% Triton X-100 15min at 37 °C. Nuclei were digested in 1x DpnII buffer and 6U/ul DpnII enzyme and digested overnight at 37°C. Nuclei were then washed once in Ligation Buffer, and resuspended in Ligation buffer with 10U T4 DNA Ligase (Life Tech), and incubated for 4 hours at 16oC shaking at 600rpm. After ligation nuclei were pelleted and resuspended in cold PBS with DAPI to a final concentration of 300nM and GFP+ cells were FAC-sorted into a 96 well plate with 2ul lysis buffer (20mM Tris pH 8, 20mM NaCl, 0.15% Triton X-100, 25mM DTT, 1mM EDTA, 500nM Carrier ssDNA, and 15ug/mL Qiagen Protease) and lysed for 1 hour at 50°C and inactivated 15 minutes at 70°C.
DNA was transposed by adding 8ul transposition buffer (12.5 mM TAPS pH 8.5, 6.25mM MgCl2, 10% PEG 8000) with ~0.0125 uLTn5 (Vanzyme) and incubated at 55°C for 10 min, then stopped with transposome removal buffer (300nM NaCl, 45 mM EDTA, 0.01% Triton X-100 with 100ug/mL Qiagen Protease) and incubated at 50°C for 40 minutes and 70°C for 20 minutes. Libraries were amplified 14 cycles with i5 and i7 Nextera primers, with unique barcodes for each cell. Libraries from all cells were pooled and cleaned up with Zymo DNA Clean and Concentrate Kit.Libraries were sequenced 150PE on a full-lane of a Illumina NovaSeq2000.

value: olfactory sensory neurons

value: DipC


title: AC16 cells treated with JQAD1

source_name: Heart ventricle

value: Heart ventricle

value: Cardiomyocyte


title: DS-CD44-1

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

data_processing:
sequenced on the Illumina NextSeq 500
mapped to Mus_musculus_ensembl_v80 reference sequence, and quantified using CLC Genomics Workbench software (V22.0, Qiagen)
Fold changes were not calculated directly from RPKM values but from the generalized linear model, which corrects for differences in library size between the samples and the effects of confounding factors.
Assembly: Mus_musculus_ensembl_v80 reference sequence
Supplementary files format and content: .xlsx is count (RPKM and TPM) tables of mapped genes

molecule: polyA RNA

source_name: CD44+ CD8 T cells- spleen

growth_protocol: Adult Mice (>6wks) were held in SPF conditions and spleens were harvested.

extract_protocol:
fluorescence-activated cell sorting directly into lysis/stabilization media
Messenger RNA purification and fragmentation, complementary DNA synthesis and target amplification were performed with Smart-Seq v4 ultra Low input RNA sequencing preparation kit. Pooled complementary DNA libraries were sequenced on the Illumina NextSeq 500.

treatment_protocol: Magnetic Cd8 T cell enrichment then FACS sorted live CD44+ CD8 T lymphocytes

value: Spleen

value: CD44+ CD8 T cells

value: DS


title: RH30 cells treated with Veh72


title: PRFKO2

description: TCRa/b profiling

data_processing:
library strategy: TCR-seq
sequenced on the Illumina NextSeq 500
mapped to mmu (Mus Musculus)TCR V-, D-, and J-, and C- gene segments using MixCr
Supplementary files format and content: .txt is count tables of TCRa and TCRb V,D, J, and C rgenes

source_name: CD8 T cells- spleen

extract_protocol:
fluorescence-activated cell sorting directly into lysis/stabilization media
Messenger RNA purification and fragmentation, complementary DNA synthesis and target amplification were performed with TakaraBio SMARTer Mouse TCRa/b Profiling Kit. Pooled complementary DNA libraries were sequenced on the Illumina NextSeq 500.

treatment_protocol: Magnetic Cd8 T cell enrichment then FACS sorted live CD8 T cells

value: CD8 T cells- spleen

value: PRFKO


title: RH30 cells treated with Etoposide

value: Etoposide


title: Yeast Polysome Profiling R3, Fraction 22


title: AC16 cells treated with Retinoic acid

value: Retinoic acid


title: Yeast Polysome Profiling R3, Fraction 21


title: PRFKO3

description: TCRa/b profiling


title: P2-ImmFix-dipc-65


title: PRFKO1

description: TCRa/b profiling


title: Yeast Polysome Profiling R3, Fraction 19


title: P2-ImmFix-dipc-63


title: RH30 cells treated with Doxorubicin

value: Soft bone

value: Rhabdomyosarcoma

value: Doxorubicin


title: P2-ImmFix-dipc-64


title: Yeast Polysome Profiling R3, Fraction 20


title: 18TG3

description: TCRa/b profiling


title: AC16 cells treated with Vincristine

value: Vincristine

value: gRNA


title: 18TG2

description: TCRa/b profiling


title: Yeast Polysome Profiling R3, Fraction 18


title: P2-ImmFix-dipc-61

value: adult


title: Yeast Polysome Profiling R3, Fraction 17


title: DS-CD44-2


title: P2-ImmFix-dipc-62

value: olfactory sensory neurons


title: DSHET3

description: TCRa/b profiling

value: DSHET


title: AC16 cells treated with Topotecan

value: Heart ventricle

value: Topotecan


title: Yeast Polysome Profiling R3, Fraction 16


title: P2-ImmFix-dipc-60

value: DipC


title: AC16 cells treated with Doxorubicin

value: Cardiomyocyte


title: P2-ImmFix-dipc-59


title: DSHET1

description: TCRa/b profiling

value: Spleen


title: AC16 cells treated with Phosphoramide mustard

value: Phosphoramide mustard


title: P2-ImmFix-dipc-5


title: DSHET2

description: TCRa/b profiling

value: CD8 T cells- spleen


title: Yeast Polysome Profiling R3, Fraction 15


title: P2-ImmFix-dipc-57


title: AC16 cells treated with Veh144


title: Yeast Polysome Profiling R3, Fraction 13


title: DS2

description: TCRa/b profiling

value: DS


title: Yeast Polysome Profiling R3, Fraction 12


title: Yeast Polysome Profiling R3, Fraction 14


title: AC16 cells treated with Cisplatin

value: Cisplatin


title: 18TG1

description: TCRa/b profiling


title: P2-ImmFix-dipc-58


title: GIMEN cells treated with JQAD1

source_name: Peripheral Nervous System

value: Peripheral Nervous System

value: Neuroblastoma


title: AC16 cells treated with Veh72


title: AC16 cells treated with Etoposide

value: Etoposide


title: DS3

description: TCRa/b profiling


title: P2-ImmFix-dipc-56


title: Yeast Polysome Profiling R3, Fraction 11


title: GIMEN cells treated with Retinoic acid

value: Retinoic acid


title: Yeast Polysome Profiling R3, Fraction 10


title: DS1

description: TCRa/b profiling


title: GIMEN cells treated with Veh144

value: gRNA


title: P2-ImmFix-dipc-54

value: adult


title: P2-ImmFix-dipc-55

value: olfactory sensory neurons


title: GIMEN cells treated with Vincristine

value: Vincristine


title: TrackerSci-RNA, mouse brain

first: Ziyu

last: Lu

address: 1230 York Avenue

institute: The Rockefeller University

description: TrackerSci-RNA library

library_source: transcriptomic single cell

data_processing:
TrackerSci-RNA data processing: Read alignment and gene count matrix generation for the scRNA-seq were performed using the pipeline we developed before(“Cao, J. et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661–667 (2017)”). Briefly, base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) < 2). The RT barcode for each read was corrected to its nearest barcode (edit distance (ED) < 2), and reads with uncorrected barcodes (ED >= 2) were removed. Demultiplexed reads were then adaptor clipped using trim_galore/v0.4.1 with default settings. Trimmed reads were mapped to the mouse genome (mm39) using STAR/v2.5.2b with default settings. Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence, reverse transcription (RT) index, and read 2 end-coordinate (i.e. reads with identical UMI, RT index, and tagmentation site were considered duplicates). Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index. To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.18 HTseq package. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.     TrackerSci-ATAC data processing: Single-cell ATAC-seq data was performed using a published pipeline with mild modifications(“Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380–1385 (2018)”). Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) < 2). The indexed Tn5 barcode for each read was corrected to its nearest barcode (edit distance (ED) < 2), and reads with uncorrected barcodes (ED >= 2) were removed. Demultiplexed reads were then adaptor-clipped using trim_galore/0.4.1 with default settings. Trimmed reads were mapped to the mouse genome (mm39) using STAR/v2.5.2b with default settings. Duplicates were removed by picard MarkDuplicates/v2.25.2 per PCR sample. Deduplicated reads were split into constituent cellular indices by further demultiplexing reads using the Tn5 index.
Assembly: mouse reference genome (mm39)
Supplementary files format and content: Processed data files include a cell annotation csv file,  a gene annotation csv file,  and a gene count sparse matrix file for RNA data; a cell annotation csv file,  a peak annotation csv file,  a peak count sparse matrix file,  and a gene activity sparse matrix for ATAC data.
Supplementary files format and content: RNA_cell_annotation.csv: Cell annotation file, sample is cell id of each single cell with the reverse transcription barcode attached; UMAP_1 and UMAP_2 are cell coordinates after UMAP dimension reduction; Main_cluster_name contains the cell type annotation.
Supplementary files format and content: gene_annotation.csv: Gene annotation file including gene id, gene type and gene short name.
Supplementary files format and content: RNA_gene_count.txt: A sparse matrix file, each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.
Supplementary files format and content: ATAC_cell_annotation.csv: Cell annotation file, sample is cell id of each single cell with the Tn5 barcode attached; UMAP_1 and UMAP_2 are cell coordinates after UMAP dimension reduction; Main_cluster_name contains the cell type annotation.
Supplementary files format and content: ATAC_peak_annotation.csv: Peak annotation file including peak id, whether a peak overlaps with promoters and the corresponding gene information.
Supplementary files format and content: ATAC_peak_count.txt: A sparse matrix file, each row corresponds to peak id (with peak information in the peak_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to read count.
Supplementary files format and content: ATAC_gene_activity.txt: A sparse matrix file, each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to ATAC reads overlapping with the gene body.

source_name: Mouse brain

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory. All animal procedures were in accordance with institutional, state, and government regulations and approved under the IACUC protocol 21049.

extract_protocol:
Whole brains were extracted from mice, immediately snap-frozen in liquid nitrogen, and stored at -80°C upon further usage.  For nuclei isolations, thawed brains were cut into small pieces with fine scissors (Fine Science Tools, 14060-09) in 1 mL ice-cold PBS with 1% SUPERase•In™ RNase Inhibitor and 1% BSA, pelleted, resuspended in 1.5 mL Nuclei Isolation Buffer (EZ Lysis Buffer supplemented with 1% SUPERase•In™ RNase Inhibitor, 1% BSA and 1X cOmplete™ EDTA-free Protease Inhibitor Cocktail) for 5 minutes on ice, and homogenized through 40 µm cell strainers (VWR, 470236-276) with the rubber tips of syringes. Then, extracted nuclei were pelleted, fixed in 1% formaldehyde on ice for 10 minutes, washed twice with Nuclei Suspension Buffer (NSB) (10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848) supplemented with 0.1% SUPERase•In™ RNase Inhibitor (Thermo Fisher Scientific, AM2696), 1% BSA and 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001)),  and divided into two aliquots for both sci-RNA-seq and sci-ATAC-seq profiling. Nuclei subjected to sci-RNA-seq were briefly sonicated (Diagenode, low power mode for 12 seconds) to reduce clumping. Finally, nuclei were filtered through pluriStrainer Mini 20 µm filters (Pluriselect, 43-10020-70), resuspended in 100 µL NSB, snap frozen in liquid nitrogen, and stored at -80°C until further usage.
TrackerSci-RNA: EdU staining was performed on thawed nuclei using Click-iT Plus EdU Alexa Fluor™ 647 Flow Cytometry assay Kit (Thermo Fisher Scientific, 10634).  A 500 µL reaction buffer (prepared following the manufacturer’s protocol) supplemented with 1% SUPERase•In™ RNase Inhibitor was added directly to the nuclei suspension, mixed well and left in RT for 30 minutes. Then, nuclei were spun down for 5 minutes at 500g (4°C), washed once with 500 µL of 1X Click-iT saponin-based permeabilization and wash reagent, resuspended in 1 mL Nuclei Suspension Buffer (NSB) (10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848) supplemented with supplemented with 0.1% SUPERase•In™ RNase Inhibitor (Thermo Fisher Scientific, AM2696) and 1% BSA) with 1:20 dilution of 0.25 mg/ml 4',6-diamidino-2-phenylindole (DAPI, Invitrogen D1306) and FACS sorted. Alexa647 and DAPI positive nuclei were sorted into 96-well plates with each well (250~500 nuclei/well) containing 4 µL of NSB. Sorted plates were briefly centrifuged, mixed with 1 µL of 50 µM  oligo-dT primer  (5ʹ-ACGACGCTCTTCCGATCTNNNNNNNN[10bp-index]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3ʹ, where “N” is any base and “V” is either “A”, “C” or “G”, IDT) and 0.5 µL 10 mM dNTP mix (Thermo Fisher Scientific, R0194) and denatured at 55°C for 5 minutes and immediately placed on ice. 3.5 µL of first-strand reaction mix, containing 2 µL 5X SuperScript™ IV Reverse Transcriptase Buffer (Invitrogen, 18090200), 0.5 µL 100 mM DTT (Invitrogen, P2325), 0.5 µL SuperScript™ IV Reverse Transcriptase (Invitrogen, 18090200), 0.5 μL RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, 10777019) was then added to each well. Reverse transcription was carried out by incubating plates at the following temperature gradient: 4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes, and was stopped by adding 1 μL of 18 mM EDTA (VWR, 97062-656) to each well. All nuclei were then pooled, stained with DAPI at a final concentration of 3 μM, and sorted at 25 nuclei per well into 5 μL EB buffer. Cells were gated based on DAPI and Alexa647 such that singlets were discriminated from doublets and EdU+ cells were purified. 0.66 μL mRNA Second Strand Synthesis buffer and 0.34 µL mRNA Second Strand Synthesis enzyme (NEB, E6111L) were then added to each well. Second strand synthesis was carried out at 16°C for 1 hour. 6 μL tagmentation reaction mix (made by mixing 0.5 μL self-loaded Tn5 with 200 μL Tagmentation buffer containing 20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 20% Dimethylformamide (Fisher, AC327175000)) was added to each well and tagmentation was performed at 55°C for 5 minutes. After tagmentation, each well was mixed with 0.4 μL 1% SDS, 0.4 μL BSA (NEB, B90000S), and 2 μL of 10 μM P5 primer (5’-AATGATACGGCGACCACCGAGATCTACA[i5]CCCTACACGACGCTCTTCCGATCT-3’, IDT), and incubated at 55°C for 15 minutes. Then, 2 μL 10% Tween-20, 1.2 μL nuclease-free water and 2 μL of 10 μM indexed P7 primer (5’-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3’, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L) were added to each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 18-22 cycles of (98°C for 10 seconds, 66°C for 30 seconds, 72°C for 1 minute), and a final 72°C for 5 minutes. After PCR, samples were pooled and purified using 0.8 volumes of AMPure XP beads (Beckman Coulter, A63882) twice. Library concentrations were determined by Qubit (Invitrogen, Q33231), and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels (Invitrogen, G402022). All RNA-seq libraries were sequenced on the NextSeq 1000 platform (Illumina) using a 100 cycle kit (Read 1: 58 cycles, Read 2: 60 cycles, Index 1: 10 cycles, Index 2: 10 cycles). The TrackerSci RNA-seq library was sequenced to ~20,000 reads per cell.    TrackerSci-ATAC: EdU staining was performed on thawed nuclei using Click-iT Plus EdU Alexa Fluor™ 647 Flow Cytometry assay Kit (Thermo Fisher Scientific, 10634).  A 500 μL reaction buffer (prepared following the manufacturer’s protocol) supplemented with 1X cOmplete™ EDTA-free Protease Inhibitor Cocktail was added directly to the nuclei suspension, mixed well, and left in RT for 30 minutes. Then, nuclei were spun down for 5 minutes at 500g (4°C), washed once with 500 µL of 1X Click-iT saponin-based permeabilization and wash reagent, resuspended in 1 mL Nuclei Suspension Buffer (NSB) (10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848) supplemented with supplemented with 0.1% Tween-20 (Sigma, P9416-100ML), 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001) and 0.1% IGEPAL® CA-630 (VWR, IC0219859650)) with 1:20 dilution of 0.25 mg/ml 4',6-diamidino-2-phenylindole (DAPI) and FACS sorted. Alexa647 and DAPI positive nuclei were sorted into 96-well plates with each well (250~500 nuclei/well) containing 4 μL of NSB. Sorted plates were briefly centrifuged, mixed with 5 μL 2x TD buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 20% Dimethylformamide) and 1 μL barcoded Tn5. Tagmentation reaction was performed at 55°C for 30 minutes and stopped by adding 11 μL 2X Stop buffer (40 mM EDTA, 1 mM Spermidine (Sigma, S0266)) to each well. All nuclei were then pooled, stained with DAPI at a final concentration of 3 μM, and sorted at 25 nuclei per well into 5 μL EB buffer. Cells were gated based on DAPI and Alexa647 such that singlets were discriminated from doublets and EdU+ cells were purified. After sorting, each well was mixed with 0.25 μL 18.9 mg / mL proteinase K (Sigma, 3115828001), 0.25 µL 1% SDS and 0.5 µL nuclease-free water, and reverse crosslinking was performed at 65°C for 16 hours. Then, 2 μL 10% Tween-20 was added to each well to quench the SDS. Following on, 1 μL of 10 μM indexed P5 primer (5′-  AATGATACGGCGACCACCGAGATCTACA[i5]CCCTACACGACGCTCTTCCGATCT-3′, IDT), 1 μL of 10 μM indexed P7 primer (5’-CAAGCAGAAGACGGCATACGAGAT[i7]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’, IDT) and 10 μL NEBNext High-Fidelity 2X PCR Master Mix were added into each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 15-16 cycles of (98°C for 10 seconds, 66°C for 30 seconds, 72°C for 1 minute), and a final 72°C for 5 minutes. Final PCR products were pooled and purified by a Zymoclean DNA clean and concentration kit (Zymoresearch, D4014). Library concentrations were determined by Qubit, and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels. All ATAC-seq libraries were sequenced on the NextSeq 1000 platform (Illumina) using a 100 cycle kit (Read 1: 58 cycles, Read 2: 60 cycles, Index 1: 10 cycles, Index 2: 10 cycles). The TrackerSci ATAC-seq library was sequenced to ~50,000 reads per cell.

treatment_protocol: C57BL/6J mice of different age groups and 5XFAD transgenic mice (MMRRC Strain #034840-JAX) were obtained from The Jackson Laboratory. Mice were injected intraperitoneally with 50 mg/kg of EdU in PBS at 24-hour intervals for five days, and mouse brains were harvested 24 hours after the final injection.     C57BL/6J mice obtained from The Jackson Laboratory were labeled and harvested for pulse-chase labeling at various time points. Specifically, four mice (two male and two female) were injected intraperitoneally with 50 mg/kg of EdU in PBS for 3 days at 24-hour intervals, and brains were harvested 24 hours after the final injection. 12 mice were injected intraperitoneally with 50 mg/kg of EdU in PBS for five days at 24-hour intervals. In addition, for five-day injections, four mice (two male and two female) were harvested 1 day, 3 days, and 5 days after the final injection.

value: brain

tag: strain

value: C57BL/6 background


title: TrackerSci-ATAC, mouse brain

description: TrackerSci-ATAC library


title: Yeast Polysome Profiling R3, Fraction 9


title: GIMEN cells treated with Topotecan

value: Topotecan


title: Yeast Polysome Profiling R3, Fraction 8


title: ChIP-seq input for Kpr in Pcca-/- female 8-week-old mouse heart

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome (Bowtie2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads using Picard
Reference normalization by scaling read counts to mapped Drosophila reads (dm6) in IP and input samples
Assembly: mm10
Normalized bigWig generation using Homer v4.11

source_name: heart

growth_protocol: Mice were bred and housed in individually ventilated cages and all animals had ad libitum access to water and food (Teklad #2918 global 18% protein rodent diet). Mice used were either wild-types (Pcca+/+ A138T; amWT) for control experiments, or homozygous (Pcca-/- A138T; amPA). Only heterozygous or wild-type dams were used for breeding and genotyping by PCR was performed.

extract_protocol:
8-week-old mouse hearts were fixed for 10 min at room temperature with 1 % formaldehyde in modified AMVM isolation solution containing 0.5 mM EGTA (solution pH 7.4 at room temperature) in Langendorff mode. Fixed ventricles were minced and rinsed twice in PBS, then lysed in ChIP lysis buffer (1 % SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) by homogenisation (Qiagen TissueRuptor II). Lysates were pooled with fixed, sonicated Drosophila S2 cells at a ratio of 5:1 mouse:Drosophila cells, followed by IP.
DNA libraries were made using the NEBnext Ultra II DNA library preparation kit for Illumina (Cat no. E7645).

treatment_protocol: To harvest tissues, 8-week-old mice were killed humanely by i.p. injection of an appropriate volume adjusted for body weight of sodium pentobarbitone (stock 200 mg/ml) pre-mixed at a 2:1 ratio with sodium heparin (stock 5,000 I.U./mL).

value: FVB Pcca-/- A138T mutation

value: heart

tag: chip antibody

value: input


title: Kpr ChIP-seq in Pcca-/- female 8-week-old mouse heart

value: Kpr


title: Yeast Polysome Profiling R3, Fraction 7


title: GIMEN cells treated with Etoposide


title: ChIP-seq input for H3K27ac in Pcca-/- female 8-week-old mouse heart


title: Yeast Polysome Profiling R3, Fraction 6


title: GIMEN cells treated with Cisplatin


title: P2-ImmFix-dipc-53

value: DipC


title: ChIP-seq input for Kpr in wild-type female 8-week-old mouse heart

value: wild-type


title: P2-ImmFix-dipc-50


title: P2-ImmFix-dipc-51


title: GIMEN cells treated with Veh72 rep1

value: Peripheral Nervous System


title: H3K27ac ChIP-seq in Pcca-/- female 8-week-old mouse heart


title: GIMEN cells treated with Doxorubicin

value: Neuroblastoma

value: Doxorubicin


title: Yeast Polysome Profiling R3, Fraction 1-5


title: TGW cells treated with JQAD1


title: P2-ImmFix-dipc-52


title: Yeast Polysome Profiling R2, Fraction 22


title: Yeast Polysome Profiling R2, Fraction 25


title: P2-ImmFix-dipc-49


title: P2-ImmFix-dipc-4


title: TGW cells treated with Retinoic acid

value: Retinoic acid


title: H3K27ac ChIP-seq in wild-type female 8-week-old mouse heart


title: P2-ImmFix-dipc-48


title: ChIP-seq input for H3K27ac in wild-type female 8-week-old mouse heart


title: Yeast Polysome Profiling R2, Fraction 21


title: Kpr ChIP-seq in wild-type female 8-week-old mouse heart


title: Yeast Polysome Profiling R2, Fraction 23


title: TGW cells treated with Veh144

value: gRNA


title: Yeast Polysome Profiling R2, Fraction 20


title: TGW cells treated with Vincristine


title: Yeast Polysome Profiling R2, Fraction 19


title: TGW cells treated with Topotecan


title: Chlamydomonas reinhardtii liquid culture sRNA-seq r3

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
sRNA-seq; small RNA mapping in C.reinhardtii cells; Experiment SD45-2
C.reinhardtii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Chlamydomonas reinhardtii

source_name: liquid culture

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: liquid culture


title: P2-ImmFix-dipc-45

value: olfactory sensory neurons

value: adult


title: Chlamydomonas reinhardtii liquid culture sRNA-seq r1

description:
sRNA-seq; small RNA mapping in C.reinhardtii cells; Experiment SD792-1
C.reinhardtii-10.tss.txt


title: Chlamydomonas reinhardtii liquid culture sRNA-seq r2

description:
sRNA-seq; small RNA mapping in C.reinhardtii cells; Experiment SD795-2
C.reinhardtii-10.tss.txt


title: P2-ImmFix-dipc-46


title: TGW cells treated with Etoposide

value: Etoposide


title: Chlamydomonas reinhardtii liquid culture GRO-seq r1

description:
GRO-seq; nascent transcriptome profiling in C.reinhardtii; Experiment SD098
C.reinhardtii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: GRO-seq


title: P2-ImmFix-dipc-44


title: Yeast Polysome Profiling R2, Fraction 18


title: P2-ImmFix-dipc-47


title: P2-ImmFix-dipc-43


title: Yeast Polysome Profiling R2, Fraction 17


title: TGW cells treated with Phosphoramide mustard

value: Phosphoramide mustard


title: Chlamydomonas reinhardtii liquid culture csRNA-seq r3

description:
csRNA-seq; nascent TSS mapping in C.reinhardtii cells; Experiment SD24
C.reinhardtii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq


title: P2-ImmFix-dipc-41


title: Yeast Polysome Profiling R2, Fraction 15


title: Chlamydomonas reinhardtii liquid culture csRNA-seq r2

description:
csRNA-seq; nascent TSS mapping in C.reinhardtii cells; Experiment SD813-2
C.reinhardtii-10.tss.txt


title: Yeast Polysome Profiling R2, Fraction 14


title: Chlamydomonas reinhardtii liquid culture 5GRO-seq r2

description:
5'GRO-seq; nascent TSS mapping in C.reinhardtii cells; Experiment SD103
C.reinhardtii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: 5'GRO-seq


title: P2-ImmFix-dipc-40


title: Yeast Polysome Profiling R2, Fraction 13


title: SKMEL2 cells treated with JQAD1

source_name: Skin

value: Skin

value: Melanoma


title: P2-ImmFix-dipc-39


title: P2-ImmFix-dipc-3


title: TGW cells treated with Cisplatin

value: Cisplatin


title: SKMEL2 cells treated with Retinoic acid


title: P2-ImmFix-dipc-38


title: TGW cells treated with Doxorubicin


title: pif47_SH_3

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Rd

department: school of life sciences

country: China

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filitered reads were then mapped to Tair10 using Hisat2
Differential gene expression analysis was done using R package DESeq2
Assembly: Tair 10
Supplementary files format and content: all_genes_expression_FPKM.txt

organism: Arabidopsis

source_name: whole seedlings

growth_protocol: 6-day-old white light-grown Col-0, dvl1-1D,bsk36, and pif47 seedlings treated with 6hr shade.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel, and the RIN value was determined by Agilent 2100. Using magnetic beads with Oligo (dT) and ployA for A-T base pairing, mRNA can be isolated from total RNA for analysis of transcriptome information. Under the action of reverse transcriptase, six random primers were added to reverse synthesize a single strand of cDNA using mRNA as a template, followed by a two-strand synthesis to form a stable double-stranded structure. The structure of double-stranded cDNA is sticky end. Add End Repair Mix to repair it into a flat end, and then add an "A" base at the 3 'end to connect the Y-shaped connector.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With 6hr shade(R/FR=0.3) treatment

value: whole seedlings

value: pif47 mutant

value: shade


title: Chlamydomonas reinhardtii liquid culture 5GRO-seq r1

description:
5'GRO-seq; nascent TSS mapping in C.reinhardtii cells; Experiment SD102
C.reinhardtii-10.tss.txt


title: Yeast Polysome Profiling R2, Fraction 11


title: SKMEL2 cells treated with Veh144


title: P2-ImmFix-dipc-42

value: DipC


title: Yeast Polysome Profiling R2, Fraction 16


title: Yeast Polysome Profiling R2, Fraction 10


title: SKMEL2 cells treated with Vincristine

value: Vincristine


title: TGW cells treated with Veh72

value: Peripheral Nervous System

value: Neuroblastoma


title: pif47_SH_1


title: P2-ImmFix-dipc-36


title: Chlamydomonas reinhardtii liquid culture csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in C.reinhardtii cells; Experiment SD813-1
C.reinhardtii-10.tss.txt


title: Yeast Polysome Profiling R2, Fraction 9


title: SKMEL2 cells treated with Topotecan

value: Topotecan


title: pif47_WL_3

value: white light


title: P2-ImmFix-dipc-37


title: pif47_SH_2


title: Yeast Polysome Profiling R2, Fraction 8


title: Yeast Polysome Profiling R2, Fraction 12


title: pif47_WL_2


title: SKMEL2 cells treated with Etoposide

value: gRNA


title: P2-ImmFix-dipc-34

value: olfactory sensory neurons


title: P2-ImmFix-dipc-35

value: adult


title: Yeast Polysome Profiling R2, Fraction 7


title: pif47_WL_1


title: P2-ImmFix-dipc-33


title: P2-ImmFix-dipc-32


title: bsk36_SH_2

value: bsk36 mutant


title: SKMEL2 cells treated with Phosphoramide mustard

value: PM


title: SKMEL2 cells treated with Cisplatin

value: Skin


title: bsk36_SH_3


title: Yeast Polysome Profiling R2, Fraction 6


title: Yeast Polysome Profiling R2, Fraction 1- 5


title: SKMEL2 cells treated with Veh72

value: Melanoma


title: P2-ImmFix-dipc-31


title: P2-ImmFix-dipc-30


title: P2-ImmFix-dipc-2


title: bsk36_WL_3


title: bsk36_WL_2


title: SKNAS cells treated with Retinoic acid

value: Retinoic acid


title: SKMEL2 cells treated with Doxorubicin

value: Doxorubicin


title: bsk36_WL_1

value: whole seedlings


title: P2-ImmFix-dipc-29


title: SKNAS cells treated with Veh144


title: P2-ImmFix-dipc-27


title: P2-ImmFix-dipc-28


title: bsk36_SH_1

value: shade


title: dvl1-1D_SH_3

value: dvl1-1D mutant


title: dvl1-1D_SH_2


title: SKNAS cells treated with JQAD1


title: SKNAS cells treated with Etoposide

value: Etoposide


title: SKNAS cells treated with Vincristine

value: Peripheral Nervous System

value: Vincristine


title: P2-ImmFix-dipc-25

value: DipC


title: Sample.138.Maui Dolphin.206129790002_R02C02

type: genomic

city: Newport

first: Keith

last: Hernandez

state: OR

address: 2030 SE Marine Science Drive

department: Marine Mammal Institute

institute: Oregon State University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: SeSaME normalization as described in W. Zhou et al. 2018. PMID: 30085201

organism: Cephalorhynchus hectori maui

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: Genomic DNA was extracted from skin using a phenol-chloroform protocol modified for small skin samples as described in C. S. Baker et al. 1994. PMID: 7921358

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: species common name

value: Maui Dolphin

tag: female

tag: canbeusedforagingstudies

value: Yes


title: P2-ImmFix-dipc-26

value: olfactory sensory neurons


title: SKNAS cells treated with Doxorubicin

value: Neuroblastoma

value: gRNA


title: SKNAS cells treated with Topotecan

value: Topotecan


title: Sample.140.Maui Dolphin.206129790002_R05C02

value: Skin


title: dvl1-1D_WL_3

value: white light


title: dvl1-1D_SH_1


title: P2-ImmFix-dipc-24

value: adult


title: Sample.137.Maui Dolphin.206129790002_R06C01


title: dvl1-1D_WL_2


title: P2-ImmFix-dipc-23


title: SKNAS cells treated with Phosphoramide mustard

value: PM


title: SKNAS cells treated with Cisplatin

value: Cisplatin


title: Sample.141.Maui Dolphin.206129790002_R06C02


title: P2-ImmFix-dipc-22


title: Sample.134.Maui Dolphin.206129790002_R03C01


title: dvl1-1D_WL_1

value: whole seedlings


title: SKNAS cells treated with Veh72


title: P2-ImmFix-dipc-21


title: Col-0_SH_2

value: WT

value: shade


title: KELLY cells treated with JQAD1

value: Peripheral Nervous System


title: Col-0_SH_1


title: Col-0_SH_3


title: Col-0_WL_3


title: KELLY cells treated with Veh144


title: Sample.131.Maui Dolphin.206129790005_R06C02


title: Sample.133.Maui Dolphin.206129790002_R02C01


title: Sample.132.Maui Dolphin.206129790002_R01C01


title: Sample.139.Maui Dolphin.206129790002_R04C02


title: Sample.135.Maui Dolphin.206129790002_R04C01


title: KELLY cells treated with Retinoic acid

value: Retinoic acid


title: KELLY cells treated with Vincristine

value: Vincristine


title: P2-ImmFix-dipc-19

value: DipC


title: P2-ImmFix-dipc-20


title: Col-0_WL_2


title: P2-ImmFix-dipc-1


title: Sample.130.Maui Dolphin.206129790005_R05C02

value: Maui Dolphin

value: Yes


title: KELLY cells treated with Topotecan

value: Neuroblastoma


title: P2-ImmFix-dipc-16

value: olfactory sensory neurons


title: KELLY cells treated with Doxorubicin

value: Doxorubicin

value: gRNA


title: Col-0_WL_1

value: white light


title: Flp-In HEK293 RBMX iCLIP replicate 3

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_35 /5Phos/ WWW CGTAT NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'-NNNNATACGNNN, where N are random bases.

data_processing:
library strategy: iCLIP-seq
basecalling was done with bcl2fastq v2.19.1 and samples were demultiplexed with iCount v2.0.0 (https://github.com/tomazc/iCount)
Peaks were first derived on individual replicates of CLIP using iCount peaks on iMAPS at https://imaps.genialis.com. The crosslink positions were grouped by gene id.
Peaks were called using iCount version 2.0.1.dev with the significance FDR threshold of 0.05
The Cross-link sites (per sample) were all merged and peak calling was done. iCount clusters was used to cluster together the crosslink sites that were separated by 20 base pairs and merge them.
Assembly: GRCh38
Supplementary files format and content: tab deliminated text and peak height

source_name: kidney of a human embryo

growth_protocol: HEK293 cells were grown in DMEM, high glucose, pyruvate supplemented with 10% FBS, and maintained at 37°C with 5% CO2.

extract_protocol:
Cell pellets were resuspended in lysis buffer and sonicated in the Bioruptor (Diagenode) for 10 cycles with alternating 30 s on/off at low intensity. 1 mg/mL of the protein was treated with Turbo DNase I (Ambion) and high (2.5 U/mL) or low (0.8 U/mL) RNase I (Ambion)
Purified RNA was reverse transcribed into cDNA, using Superscript IV with distinct primers irCLIP_ddRT for each replicate. The PCR was amplified using Platinum™ II Hot-Start PCR Master Mix (Thermo Fisher Scientific). The final PCR libraries were purified by agarose gel electrophoresis on a 6% TBE gel, DNA in the range of 150-400nt was gel extracted using Costar SpinX column (Corning Incorporated, 8161) and submitted for sequencing.

treatment_protocol: HEK293 cells were crosslinked (150mJ/cm2) at 254 nm with a Bio-Rad Laboratories GS Gene Linker chamber

value: kidney of a human embryo

value: Flp-In HEK293

value: epithelial

tag: iclip antibody

value: anti-flag antibody (Sigma F1804)


title: P2-ImmFix-dipc-15

value: adult


title: KELLY cells treated with Etoposide

value: Etoposide


title: Flp-In HEK293 RBMX iCLIP replicate 2

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_34 /5Phos/ WWW CGATC NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'-NNNNGATCGNNN, where N are random bases.


title: Sample.128.Maui Dolphin.206129790005_R02C02

value: Skin


title: P2-ImmFix-dipc-17


title: KELLY cells treated with Cisplatin

value: Peripheral Nervous System

value: Cisplatin


title: P2-ImmFix-dipc-18

value: DipC


title: Sample.129.Maui Dolphin.206129790005_R04C02

value: Maui Dolphin


title: Sample.125.Maui Dolphin.206129790005_R02C01

value: Yes


title: Sample.127.Maui Dolphin.206129790005_R04C01


title: Sample.126.Maui Dolphin.206129790005_R03C01


title: 3565_GSC__INHEG_sg4_Ribo_rep2

city: Beijing

first: Lihui

last: Liu

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
A-3565sg4-2Ri
3565sg4VS3565NT_ribo_fpkm1.txt

data_processing:
For ribometh-seq, sdapters were removed by cutadapt v2.7 with parameters (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAAC). Trimmed reads were mapped to ribosome DNA sequence by bowtie v2.2.9 and then sorted by samtools v1.10. BAM files were converted to BED format by bamToBed (bedtools v2.26). Positions of 5' (beginnings) and 3' (ends) were extracted and converted to bedGraph using custom python script. The methylation level was further quantified by MethScore C2 calculation.
For RNA-seq, reads were aligned and counted by STAR with --quantMode GeneCounts option and differential expressed genes were identified by edgeR.
For ribosome profiling, adapter sequences were removed from raw sequencing data using cutadapt software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat2 and bowtie software separately. Read counts were calculated using featureCounts software. Raw counts were further normalized as RPKM values using fpkm function in edgeR package.
Assembly: NOP58_KO RNA-seq: hg19; INHEG-OE RNA-seq, Ribo-seq: hg38
Supplementary files format and content: for RNA-seq, the count table is the read counts for each sample calcualted from STAR with --quantMode GeneCounts mode. For ribometh-seq, methScore are provided for each nucleotide at each sample.
Library strategy: Ribo-seq

source_name: glioma stem cells

extract_protocol:
Cell culture medium were removed and RNA was harvested using Trizol reagent. For RiboMeth-seq, total RNA was fragmented in 50 mM sodium carbonate/bicarbonate buffer (pH 9.2) at 95°C. Next, Fragmented RNA was 3′-end dephosphorylated and purified with the RNA Clean & Concentrator-5 kit (Zymo Research). RNA was then 5′-end phosphorylated with T4 polynucleotide kinase (NEB) and purified again. For uvRIP-seq, RNA were harvested with Trizol reagent after NOP58 UV-crosslinked immunoprecipitaion.
For RiboMeth-seq, sequencing libraries were prepared with the VAHTSTM Small RNA Library Prep Kit for Illumina® (Vazyme) following the manufacturer's instruction. For RNA-seq, RNA libraries were prepared for sequencing using VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme) with total RNA. Ribo-seq: Ribosome profiling was performed using Ribosome Profiling Kit.  RPFs  was extracted using RNA clean&ConcentratorTM-5 kit.     EpiTM RiboRNA Depletion Kit  was used for rRNA depletion.  Sequencing libraries were constructed using QIAseq miRNA Library kit.

value: patient-derived glioma stem cell


title: HCT116 cells treated with JQAD1

source_name: Colorectal

value: Colorectal

value: colorectal carcinoma


title: Sample.124.Maui Dolphin.206129790003_R06C02


title: P2-ImmFix-dipc-11

value: olfactory sensory neurons


title: P2-ImmFix-dipc-13


title: Sample.123.Maui Dolphin.206129790003_R05C02


title: 3565_GSC__INHEG_sg4_Ribo_rep1

description:
A-3565sg4-1Ri
3565sg4VS3565NT_ribo_fpkm1.txt


title: P2-ImmFix-dipc-10


title: KELLY cells treated with Phosphoramide mustard

value: Neuroblastoma

value: PM

value: gRNA


title: HCT116 cells treated with Veh144


title: KELLY cells treated with Veh72


title: 3565_GSC__INHEG_sg2_Ribo_rep1

description:
A-3565sg2-1Ri
3565sg2VS3565NT_ribo_fpkm1.txt


title: P2-ImmFix-dipc-12


title: HCT116 cells treated with Vincristine

value: Vincristine


title: Sample.136.Maui Dolphin.206129790002_R05C01


title: 3565_GSC_EGFP_Ribo_rep1

description:
B-3565NT-1Ri
3565sg2VS3565NT_ribo_fpkm1.txt 3565sg4VS3565NT_ribo_fpkm1.txt


title: 3565_GSC__INHEG_sg2_Ribo_rep2

description:
A-3565sg2-2Ri
3565sg2VS3565NT_ribo_fpkm1.txt


title: Sample.122.Maui Dolphin.206129790003_R01C02


title: HCT116 cells treated with Retinoic acid

value: Retinoic acid


title: HCT116 cells treated with Topotecan

value: Topotecan


title: P2-ImmFix-dipc-14

description: DipC on GFP+ cells from gg8tTAtetOP2/CAST hybrid mice

value: adult


title: Sample.120.Maui Dolphin.206129790003_R03C01

value: Skin


title: 3565_GSC_EGFP_Ribo_rep2

description:
B-3565NT-2Ri
3565sg2VS3565NT_ribo_fpkm1.txt 3565sg4VS3565NT_ribo_fpkm1.txt


title: APM28DIP_9_

description: DipC on GFP+ cells from mor28iGFP/CAST hybrid mice


title: Sample.121.Maui Dolphin.206129790003_R05C01


title: HCT116 cells treated with Doxorubicin

value: Doxorubicin


title: Pevonedistat + VSVd51 2

city: Ottawa

first: Boaz

last: Wong

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Fastq files were checked for quality using FastQC (Babraham Bioinformatics, United Kingdom)
Pseudo alignment and transcript quantification were performed with KALLISTO
Differential expression was determined using SLEUTH
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

source_name: Kidney

growth_protocol: Human renal 786-0 carcinoma cells were maintained in DMEM supplemented with 10% FBS, seeded overnight in 12 well format

extract_protocol:
RNA extraction was performed 24 hours after infection for all conditions using the QIAGEN RNeasy kit (Qiagen) and quantified using a NanoDrop One Microvolume UV-Vis Spectrophotometer.
NEB NEBNext Ultra II Directional RNA library prep kit according to manufacturer’s protocol

treatment_protocol: Conditions treated with pevonedistat were treated for 4 hours with 1uM, then infected with VSVd51 (MOI 0.01).

value: Kidney

value: Carcinoma

value: WT

value: Pevonedistat (1uM) 4h + VSVd51 (MOI 0.01), 24h


title: VSVd51 2


title: APM28DIP_94_

value: DipC


title: HCT116 cells treated with Etoposide

value: Colorectal

value: Etoposide


title: APM28DIP_95_

value: olfactory sensory neurons


title: Sample.117.Maui Dolphin.205600840071_R06C02

value: Maui Dolphin

value: Yes


title: Pevonedistat + VSVd51 1


title: Sample.118.Maui Dolphin.206129790003_R01C01


title: Sample.119.Maui Dolphin.206129790003_R02C01


title: APM28DIP_93_


title: Pevonedistat 1

value: Pevonedistat (1uM) 24h


title: HCT116 cells treated with Veh72

value: colorectal carcinoma

value: gRNA


title: Sample.116.Maui Dolphin.205600840071_R05C02


title: Sample.115.Maui Dolphin.205600840071_R04C02


title: APM28DIP_96_


title: APM28DIP_90_


title: HCT116 cells treated with Phosphoramide mustard

value: PM


title: Pevonedistat 2


title: VSVd51 1


title: APM28DIP_91_

value: adult


title: Sample.114.Maui Dolphin.205600840071_R03C02

value: Skin


title: Sample.113.Maui Dolphin.205600840071_R02C02


title: APM28DIP_8_


title: R2-3

data_processing:
Quality assessment with FastQC Version 0.11.2
(samples 7-8, batch 1) Trimming - trimmomatic (v0.32). ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:12 TRAILING:1
(samples 7-8, batch 1) Reads were aligned to genome with STAR version 2.5.2b
(samples 7-8, batch 1) Gene counts were generated with HTSEQ-count. -f bam -r name -s reverse -a 4 -i gene_id -m union, using annotations from RefSeq
(samples 7-8, batch 1) Splicing changes were assessed with MAJIQ
(samples 1-6, batch 2) Reads were aligned to genome with STAR version 2.4.2a
(samples 1-6, batch 2) Reads were aligned to transcriptome with Salmon version 0.9.1 using annotations version 90 (GRCh38.90) from Ensembl
(samples 1-6, batch 2) Gene and transcript level abundances were made from the Salmon quant.sf files using tximport version 1.12.3 in R
(samples 1-6, batch 2) Splicing changes were assessed with SUPPA2
Genome_build: GRCh38 (primary assembly)
Supplementary_files_format_and_content: tab delimited text containing transcript level TPM abundances. Counts are not normalized
Supplementary_files_format_and_content: tab delimited text containing gene-level counts. Counts are not normalized

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 cells were maintained in DMEM (no phenol red) plus 10% fetal bovine serum and 1% penicillin Streptomycin.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen) following manufacturer’s instructions and re-suspended in nuclease-free water. RNA samples were DNase treated using DNA-free kit (Invitrogen).
Illumina's stranded mRNA kit
RNA-Seq 75 bp Paired-end reads

treatment_protocol: MDA-MB 231 cells were treated with an siRNA specific for RBMX, or a control siRNA, for 72 hours.

value: MDA-MB-231 cells

value: depleted for RBMX by siRNA

tag: batch


title: HEK293T cells treated with Retinoic acid

data_processing:
CRISPR KO screens were analyzed using Mageck-Vispr/0.5.7
Supplementary files format and content: Mageck default output describing resulting RRA scores

source_name: Embryonic kindey

value: Embryonic kindey

value: Epithelial

value: Retinoic acid


title: HEK293T cells treated with Veh144


title: HEK293T cells treated with JQAD1


title: Sample.112.Maui Dolphin.205600840071_R01C02


title: Mock 2

value: Kidney

value: Carcinoma

value: WT


title: HCT116 cells treated with Cisplatin

value: Colorectal

value: Cisplatin


title: Sample.111.Maui Dolphin.205600840071_R06C01

value: Maui Dolphin

value: Yes


title: APM28DIP_92_

value: olfactory sensory neurons

value: DipC


title: Mock 1


title: APM28DIP_89_


title: Sample.110.Maui Dolphin.205600840071_R05C01


title: HEK293T cells treated with Etoposide

value: Etoposide

value: gRNA


title: APM28DIP_86_

value: adult


title: HEK293T cells treated with Vincristine

value: Vincristine


title: TG_FD_Untreated_5905

city: Boston

first: Susan

last: Slaugenhaupt

state: MA

address: 185 Cambridge St

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
RNASeq reads were mapped against a custom referenceby STAR (version 2.5.22b) allowing 5% mismatch
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.36)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using HTSeq(v0.11.2) and DESeq2 (v1.34.0).
Assembly: human ELP1 gene (ENSG00000070061) Ensemble Human transcriptome reference GRCh37.75 to the Ensembl Mouse Transcriptome GRCm38.83
Supplementary files format and content: Supplementary Table S1 - DEG_stats.txt

source_name: Trigeminal Ganglion

growth_protocol: We developed a mouse model that faithfully recapitulates the the FD phenotype seen in patients using the TgFD9 hypomorphic mouse and human transgene.

extract_protocol:
RNA was harvested using QIAzol Reagent as per manufacturrers instructions. 100 ng of total RNA was used for the construction of sequencing libraries.
Tru-Seq Stranded® mRNA library Prep Kit (Illumina, 20020594) following manufacturer's protocols.

value: Trigeminal Ganglion


title: C1

value: MDA-MB-231 cells

value: control siRNA


title: Sample.107.Maui Dolphin.205600840071_R02C01

value: Skin


title: HEK293T cells treated with Topotecan

value: Embryonic kindey

value: Epithelial

value: Topotecan


title: Sample.108.Maui Dolphin.205600840071_R03C01


title: TG_FD_Untreated_5906

value: WT


title: HEK293T cells treated with Doxorubicin

value: Doxorubicin


title: APM28DIP_84_

data_processing:
We excluded cells that had contacts < ~400,000 contacts, cells that had a low contact-to-read ratio, and cells that had high variability in 3D structure across computational replicates. Overall, the median number of contacts across nuclei was 715,690 contacts per cell for 74 cells for mor28-IRES-GFP Dip-C and 694,462 contacts per cell for 84 cells for gg8-tTA>tetO-P2-IRES-GFP Dip-C, for a total of 161 cells. 3D reconstruction of Dip-C models was performed exactly as described in (https://github.com/tanlongzhi/dip-c).
To characterize Greek Island and OR gene 3D relationships, we used the dip-c function 'dip-c pd' to generate symmetric matrices, measured in particle radii, of the pairwise distance relationships between these DNA elements. These processed data files end in "pd.txt".
To characterize Greek Island and OR gene genomic contacts, we used the haplotype imputed contacts file generated in the Dip-C pipelie "contacts.con.gz", to extract all contacts per cell at 50-kb resolution, normalized to contacts per million. Contacts for all male and female cells are compiled in separate text files ending in "50kb.contacts.haplotyped.txt".
Assembly: mm10
Supplementary files format and content: pd.txt: tab-delimited text files containing symmetric distance matrices.
Supplementary files format and content: "50kb.contacts.haplotyped.txt".: tab-delimited text files describing pairwise genomic contacts binned at 50-kb resolution.
Library strategy: Dip-C

source_name: olfactory sensory neurons


title: HEK293T cells treated with Phosphoramide mustard

value: PM


title: APM28DIP_83_


title: APM28DIP_87_


title: TG_FD_Untreated_5881


title: Sample.106.Maui Dolphin.205600840071_R01C01

value: Maui Dolphin

value: Yes


title: TG_FD_Untreated_5877


title: APM28DIP_85_

value: olfactory sensory neurons

value: DipC


title: Sample.109.Maui Dolphin.205600840071_R04C01


title: Sample.104.Maui Dolphin.205600840091_R05C02


title: HEK293T cells treated with Veh72

value: gRNA


title: APM28DIP_81_

value: adult


title: Sample.105.Maui Dolphin.205600840091_R06C02


title: TG_FD_Untreated_5822


title: Flp-In HEK293 RBMX iCLIP replicate 1

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_33 /5Phos/ WWW GATGA NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'- NNNNTCATCNNN, where N are random bases.

value: kidney of a human embryo

value: Flp-In HEK293

value: epithelial

value: anti-flag antibody (Sigma F1804)


title: TG_FD_Untreated_5753

value: Trigeminal Ganglion


title: APM28DIP_80_


title: Sample.103.Maui Dolphin.205600840091_R04C02

value: Skin


title: Sample.102.Maui Dolphin.205600840091_R03C02


title: TG_FD_Untreated_5901


title: TG_FD_Untreated_5780


title: CHP212 cells treated with Veh144

value: Peripheral Nervous System

value: Neuroblastoma


title: APM28DIP_88_


title: CHP212 cells treated with Vincristine

value: Vincristine


title: Sample.101.Maui Dolphin.205600840091_R02C02


title: APM28DIP_78_


title: CHP212 cells treated with Retinoic acid

value: Retinoic acid


title: CHP212 cells treated with JQAD1


title: TG_FD_Untreated_5376

value: WT


title: APM28DIP_77_


title: APM28DIP_7_


title: Sample.97.Maui Dolphin.205600840091_R04C01

value: Maui Dolphin


title: APM28DIP_82_


title: HEK293T cells treated with Cisplatin

value: Embryonic kindey

value: Epithelial

value: Cisplatin


title: Sample.99.Maui Dolphin.205600840091_R06C01

value: Yes


title: TG_FD_Untreated_5374


title: Sample.98.Maui Dolphin.205600840091_R05C01


title: APM28DIP_76_

value: olfactory sensory neurons

value: DipC

value: adult


title: TG_FD_Untreated_5441


title: APM28DIP_79_


title: TG_FD_Untreated_5373


title: CHP212 cells treated with Phosphoramide mustard

value: PM

value: gRNA


title: APM28DIP_75_


title: Sample.96.Maui Dolphin.205600840091_R03C01


title: TG_Control_Untreated_5907

value: Trigeminal Ganglion


title: TG_Control_Untreated_5902


title: CHP212 cells treated with Doxorubicin

value: Doxorubicin


title: CHP212 cells treated with Topotecan

value: Peripheral Nervous System

value: Topotecan


title: APM28DIP_74_


title: TG_FD_Untreated_5378


title: Sample.93.Maui Dolphin.205600840087_R06C02

value: Skin


title: CHP212 cells treated with Cisplatin

value: Neuroblastoma


title: CHP212 cells treated with Etoposide

value: Etoposide


title: Sample.94.Maui Dolphin.205600840091_R01C01

value: Maui Dolphin


title: CHP212 cells treated with Veh72


title: SKNFI cells treated with JQAD1


title: Sample.95.Maui Dolphin.205600840091_R02C01


title: TG_Control_Untreated_5880

value: WT


title: APM28DIP_73_


title: Sample.92.Maui Dolphin.205600840087_R05C02


title: SKNFI cells treated with Retinoic acid

value: Retinoic acid


title: TG_Control_Untreated_5900


title: APM28DIP_70_


title: TG_Control_Untreated_5875


title: TG_Control_Untreated_5821


title: Sample.90.Maui Dolphin.205600840087_R03C02


title: APM28DIP_71_


title: APM28DIP_6_


title: Sample.91.Maui Dolphin.205600840087_R04C02


title: APM28DIP_72_


title: SKNFI cells treated with Topotecan


title: TG_Control_Untreated_5779


title: SKNFI cells treated with Vincristine

value: Vincristine


title: APM28DIP_69_


title: SKNFI cells treated with Veh144


title: TG_Control_Untreated_5752


title: Sample.89.Maui Dolphin.205600840087_R02C02

value: Yes


title: TG_Control_Untreated_5776


title: Sample.88.Maui Dolphin.205600840087_R01C02


title: TG_Control_Untreated_5377


title: APM28DIP_68_

value: olfactory sensory neurons


title: TG_Control_Untreated_5375


title: APM28DIP_65_

value: DipC


title: SKNFI cells treated with Cisplatin

value: Cisplatin


title: SKNFI cells treated with Etoposide


title: Sample.86.Maui Dolphin.205600840087_R05C01


title: APM28DIP_67_

value: adult


title: SC_FD_Untreated_5906

source_name: Spinal Cord

value: Spinal Cord

value: Familial Dysautonomia (FD)


title: SKNFI cells treated with Veh72

value: gRNA


title: Sample.85.Maui Dolphin.205600840087_R04C01


title: Sample.87.Maui Dolphin.205600840087_R06C01


title: NGP cells treated with JQAD1

value: Peripheral Nervous System


title: SKNFI cells treated with Doxorubicin

value: Doxorubicin


title: Sample.84.Maui Dolphin.205600840087_R03C01

value: Skin


title: APM28DIP_62_


title: Sample.81.Maui Dolphin.205600840069_R06C02


title: APM28DIP_66_


title: SC_FD_Untreated_5901


title: APM28DIP_61_


title: NGP cells treated with Veh144

value: Neuroblastoma


title: SKNFI cells treated with Phosphoramide mustard

value: PM


title: TG_Control_Untreated_5372

value: Trigeminal Ganglion


title: APM28DIP_64_


title: Sample.100.Maui Dolphin.205600840091_R01C02

value: Maui Dolphin


title: SC_FD_Untreated_5905


title: SC_FD_Untreated_5822


title: NGP cells treated with Etoposide

value: Etoposide


title: Sample.77.Maui Dolphin.205600840069_R02C02


title: NGP cells treated with Retinoic acid

value: Retinoic acid


title: APM28DIP_57_


title: SC_FD_Untreated_5753


title: SC_FD_Untreated_5881


title: NGP cells treated with Vincristine

value: Vincristine


title: Sample.82.Maui Dolphin.205600840087_R01C01

value: Yes


title: SC_FD_Untreated_5877


title: Sample.80.Maui Dolphin.205600840069_R05C02


title: Sample.83.Maui Dolphin.205600840087_R02C01


title: Sample.79.Maui Dolphin.205600840069_R04C02


title: APM28DIP_60_

value: olfactory sensory neurons

value: DipC


title: Sample.75.Maui Dolphin.205600840069_R06C01


title: APM28DIP_63_

value: adult


title: APM28DIP_5_


title: Sample.78.Maui Dolphin.205600840069_R03C02


title: APM28DIP_59_


title: Sample.74.Maui Dolphin.205600840069_R05C01


title: NGP cells treated with Phosphoramide mustard


title: APM28DIP_56_


title: NGP cells treated with Cisplatin

value: Cisplatin


title: SC_FD_Untreated_5378

value: Spinal Cord

value: Familial Dysautonomia (FD)


title: NGP cells treated with Doxorubicin

value: Peripheral Nervous System

value: gRNA


title: APM28DIP_58_


title: SC_FD_Untreated_5780


title: NGP cells treated with Veh72


title: APM28DIP_54_


title: Sample.76.Maui Dolphin.205600840069_R01C02

value: Skin


title: NGP cells treated with Topotecan

value: Neuroblastoma

value: Topotecan


title: BE2C cells treated with JQAD1


title: SC_FD_Untreated_5441


title: SC_FD_Untreated_5374


title: BE2C cells treated with Retinoic acid


title: APM28DIP_52_


title: Sample.71.Maui Dolphin.205600840069_R02C01


title: SC_FD_Untreated_5376


title: APM28DIP_55_


title: BE2C cells treated with Veh144


title: Sample.70.Maui Dolphin.205600840069_R01C01


title: SC_Control_Untreated_5907

value: WT


title: APM28DIP_51_


title: APM28DIP_50_


title: SC_FD_Untreated_5373


title: Sample.73.Maui Dolphin.205600840069_R04C01

value: Maui Dolphin


title: BE2C cells treated with Vincristine


title: BE2C cells treated with Topotecan


title: APM28DIP_53_


title: Sample.69.Maui Dolphin.205307780019_R06C02


title: SC_Control_Untreated_5900


title: Sample.72.Maui Dolphin.205600840069_R03C01


title: APM28DIP_4_


title: SC_Control_Untreated_5902


title: BE2C cells treated with Doxorubicin

value: Doxorubicin


title: APM28DIP_49_


title: Sample.68.Hector's Dolphin.205307780019_R05C02

organism: Cephalorhynchus hectori hectori

value: Hector's Dolphin


title: BE2C cells treated with Phosphoramide mustard

value: PM


title: SC_Control_Untreated_5875


title: BE2C cells treated with Etoposide

value: Etoposide


title: APM28DIP_47_

value: olfactory sensory neurons


title: SC_Control_Untreated_5821


title: BE2C cells treated with CX-5461


title: APM28DIP_46_

value: DipC


title: BE2C cells treated with Cisplatin


title: APM28DIP_45_

value: adult


title: BE2C cells treated with Veh72


title: SC_Control_Untreated_5752


title: SC_Control_Untreated_5880


title: APM28DIP_44_


title: Sample.65.Maui Dolphin.205307780019_R04C01

value: Yes


title: SC_Control_Untreated_5377

value: Spinal Cord


title: Sample.66.Maui Dolphin.205307780019_R05C01


title: APM28DIP_48_


title: Sample.64.Maui Dolphin.205307780019_R03C01


title: APM28DIP_43_


title: Sample.67.Maui Dolphin.205307780019_R06C01


title: Sample.63.Maui Dolphin.205307780019_R02C01


title: Sample.62.Maui Dolphin.205166520009_R06C02


title: Sample.61.Maui Dolphin.205166520009_R04C02


title: Sample.59.Maui Dolphin.205166520009_R02C02


title: SC_Control_Untreated_5375


title: SC_Control_Untreated_5779


title: APM28DIP_42_


title: SKES1 cells treated with Retinoic acid

source_name: Bone

value: Bone

value: Ewing Sarcoma

value: Retinoic acid


title: SKES1 cells treated with Veh144

value: gRNA


title: SC_Control_Untreated_5372


title: SC_Control_Untreated_5776


title: APM28DIP_41_


title: SKES1 cells treated with JQAD1


title: SKES1 cells treated with Vincristine

value: Vincristine


title: Sample.58.Maui Dolphin.205166520009_R01C02

value: Skin


title: MED_FD_Untreated_5906

source_name: Medulla

value: Medulla

value: Familial Dysautonomia (FD)


title: APM28DIP_40_


title: SKES1 cells treated with Topotecan

value: Topotecan


title: MED_FD_Untreated_5901


title: APM28DIP_3_


title: SKES1 cells treated with Doxorubicin

value: Doxorubicin


title: MED_FD_Untreated_5881


title: SKES1 cells treated with Phosphoramide mustard

value: PM


title: APM28DIP_38_


title: APM28DIP_39_


title: Sample.57.Hector's Dolphin.205166520009_R06C01

value: Hector's Dolphin


title: SKES1 cells treated with Etoposide

value: Etoposide


title: MED_FD_Untreated_5877


title: Sample.54.Maui Dolphin.205307780004_R05C02

value: Maui Dolphin


title: APM28DIP_37_

value: olfactory sensory neurons

value: DipC

value: adult


title: Sample.55.Maui Dolphin.205166520009_R02C01

value: Yes


title: SKES1 cells treated with CX-5461

value: Bone

value: Ewing Sarcoma


title: APM28DIP_35_


title: APM28DIP_36_


title: Sample.56.Maui Dolphin.205166520009_R03C01


title: MED_FD_Untreated_5905


title: SKES1 cells treated with Cisplatin

value: Cisplatin

value: gRNA


title: Sample.52.Maui Dolphin.205307780004_R03C02

value: Skin


title: APM28DIP_34_


title: MED_FD_Untreated_5753

value: Medulla


title: MED_FD_Untreated_5780

value: Familial Dysautonomia (FD)


title: MED_FD_Untreated_5441


title: GM12878 cells treated with JQAD1

source_name: Blood

value: Blood

value: B-lymphocyte


title: APM28DIP_33_


title: GM12878 cells treated with Retinoic acid

value: Retinoic acid


title: APM28DIP_32_


title: Sample.49.Maui Dolphin.205307780004_R04C01


title: Sample.60.Maui Dolphin.205166520009_R03C02


title: Sample.53.Maui Dolphin.205307780004_R04C02


title: Sample.50.Maui Dolphin.205307780004_R05C01


title: GM12878 cells treated with Veh144


title: MED_FD_Untreated_5822


title: MED_FD_Untreated_5378


title: MED_FD_Untreated_5376


title: Sample.51.Maui Dolphin.205307780004_R01C02


title: SKES1 cells treated with Veh72


title: APM28DIP_31_


title: Sample.47.Maui Dolphin.205166520007_R04C02


title: Sample.48.Maui Dolphin.205307780004_R01C01


title: MED_FD_Untreated_5374


title: GM12878 cells treated with Vincristine

value: Vincristine


title: APM28DIP_30_


title: GM12878 cells treated with Topotecan

value: Topotecan


title: Sample.46.Maui Dolphin.205166520007_R03C02

value: Maui Dolphin


title: MED_FD_Untreated_5373

value: WT


title: MED_Control_Untreated_5907


title: GM12878 cells treated with Phosphoramide mustard

value: PM


title: MED_Control_Untreated_5902


title: APM28DIP_2_

value: olfactory sensory neurons

value: DipC

value: adult


title: MED_Control_Untreated_5900


title: GM12878 cells treated with Etoposide

value: Etoposide


title: GM12878 cells treated with CX-5461


title: MED_Control_Untreated_5880


title: Sample.45.Hector's Dolphin.205138660001_R06C02

value: Hector's Dolphin

value: Yes


title: Sample.43.Hector's Dolphin.205138660001_R04C01

value: Skin


title: Sample.42.Hector's Dolphin.205138660001_R02C01


title: APM28DIP_27_


title: Sample.44.Hector's Dolphin.205138660001_R04C02


title: GM12878 cells treated with Cisplatin

value: Cisplatin

value: gRNA


title: MED_Control_Untreated_5875

value: Medulla


title: Sample.40.Hector's Dolphin.205128010011_R03C02


title: MED_Control_Untreated_5821


title: GM12878 cells treated with Doxorubicin

value: Blood

value: B-lymphocyte

value: Doxorubicin


title: Sample.41.Hector's Dolphin.205128010011_R05C02


title: APM28DIP_25_


title: APM28DIP_24_


title: APM28DIP_29_


title: SKNSH cells treated with JQAD1

source_name: Peripheral Nervous System

value: Peripheral Nervous System

value: Neuroblastoma


title: GM12878 cells treated with Veh72


title: APM28DIP_23_


title: MED_Control_Untreated_5779

value: WT


title: APM28DIP_28_


title: MED_Control_Untreated_5776


title: APM28DIP_26_


title: APM28DIP_22_


title: SKNSH cells treated with Veh144


title: Sample.38.Hector's Dolphin.205128010010_R03C02


title: MED_Control_Untreated_5752


title: APM28DIP_20_


title: Sample.37.Hector's Dolphin.205128010010_R01C02


title: Sample.39.Hector's Dolphin.205128010011_R04C01


title: SKNSH cells treated with Topotecan

value: Topotecan


title: SKNSH cells treated with Doxorubicin


title: MED_Control_Untreated_5377


title: APM28DIP_1_

value: olfactory sensory neurons


title: MED_Control_Untreated_5372


title: APM28DIP_21_

value: DipC


title: MED_Control_Untreated_5375


title: SKNSH cells treated with Retinoic acid

value: Retinoic acid


title: Sample.35.Hector's Dolphin.205128010010_R05C01


title: SKNSH cells treated with Phosphoramide mustard

value: PM


title: APM28DIP_18_

value: adult


title: DRG_FD_Untreated_5906

source_name: Dorsal Root Ganglion

value: Dorsal Root Ganglion

value: Familial Dysautonomia (FD)


title: Sample.34.Hector's Dolphin.205128010010_R03C01

value: Skin

value: Hector's Dolphin

value: Yes


title: DRG_FD_Untreated_5905


title: Sample.33.Hector's Dolphin.205128010010_R01C01


title: Sample.32.Hector's Dolphin.205128010033_R06C02


title: SKNSH cells treated with Etoposide

value: Etoposide

value: gRNA


title: Sample.31.Hector's Dolphin.205128010033_R01C02


title: APM28DIP_17_


title: SKNSH cells treated with Vincristine

value: Vincristine


title: Sample.36.Hector's Dolphin.205128010010_R06C01


title: DRG_FD_Untreated_5901


title: SKNSH cells treated with CX-5461

value: Peripheral Nervous System


title: APM28DIP_16_


title: Sample.30.Maui Dolphin.205128010033_R03C02

value: Māui Dolphin

value: Maui Dolphin


title: SKNSH cells treated with Cisplatin

value: Neuroblastoma

value: Cisplatin


title: APM28DIP_19_

value: olfactory sensory neurons

value: DipC


title: SKNSH cells treated with Veh72


title: DRG_FD_Untreated_5881


title: APM28DIP_15_


title: Sample.29.Hector's Dolphin.205128010010_R02C01


title: APM28DIP_14_


title: DRG_FD_Untreated_5877


title: DRG_FD_Untreated_5822


title: Sample.28.Hector's Dolphin.205128010011_R05C01


title: MHHNB11 cells treated with Retinoic acid

value: Retinoic acid


title: APM28DIP_12_

value: adult


title: APM28DIP_13_


title: Sample.26.Hector's Dolphin.205128010033_R02C02


title: MHHNB11 cells treated with Veh144


title: DRG_FD_Untreated_5753

value: Dorsal Root Ganglion


title: APM28DIP_11_


title: DRG_FD_Untreated_5441

value: Familial Dysautonomia (FD)


title: APM28DIP_10_


title: MHHNB11 cells treated with Vincristine


title: MHHNB11 cells treated with Topotecan

value: Topotecan


title: gg8tTAtetOP2, 60-min Pre-Digestion, r3

description: Liquid Hi-C with 60-minutes of pre-digesiton performed on an individual biological replicate of GFP+ OSNs sorted from adult mice

data_processing:
Reads were aligned to the mm10 genome using the distiller pipeline (https://github.com/mirnylab/distiller-nf), uniquely mapped reads (mapq > 30) were retained and duplicate reads discarded. Contacts were then binned into matrices using cooler 45. Analysis was performed on data pooled from two (HiChIP, Hi-C) or three biological replicates (Liquid Hi-C), after confirming that the results of analysis of individual replicates were similar.
Assembly: mm10
Supplementary files format and content: Genomic Contacts binned at 50-kb resolution
Library strategy: Hi-C/Liquid Hi-C/HiChIP

source_name: Olfactory Sensory Neurons

extract_protocol:
MOE were dissociated using the Worthington Papain Dissociation kit, and cells were fixed in 1% formaldehyde in 1x PBS either before or after sorting for GFP+ cells. For Liquid Hi-C, nuclei were digested with Dpn-II for various lengths of time, on a thermomixer shaking at 900 rpm at 37˚C, placed on ice for 10-minutes, then fixed in 1% formaldehyde in 1x PBS. After cross-linking, nuclei were processed for HiC exactly as described in "LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice" (Horta et al. 2019). Briefly nuclei were lysed, permeabilized, quenched, and then digested over night in DpnII . The next day we performed biotin-fill in with biotinylated dUTP, ligation with T4, and shearing. Cross-links were reversed overnight and DNA was purified with a 2x AMPure bead purification. Library prep was performed on MyOne Streptavidin beads to purify biotinylated contacts.
The HiChIP protocol was kindly given by the Chang Lab and integrated into our Hi-C protocol to perform H3K27ac HiChIP on olfactory sensory neurons. MOE from 5-7 gg8-tTA>tetO-P2 mice were dissociated to obtain 4M GFP+ cells per replicate, for a total of 2 replicates. Cells were processed according to the in situ Hi-C protocol with the following exceptions, nuclei were digested for only 2 hours instead of overnight; complete nuclei digestion was verified by running reverse cross-linked digested nuclei on a DNA Agarose gel. After ligation, nuclei were pelleted at 2500-g, for 5-min, at 4-˚C and stored overnight at -20 ˚C. The next day, nuclei were resuspended in 130-uL of HiChIP nuclear lysis buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1% SDS, 1X Protease Inhibitor in water), and sheared on a Covaris S220 with the following parameters: duty cycle – 2%, PIP – 140, cycles/burst – 200, time – 4 minutes. After shearing, samples were precleared and immunoprecipitation was performed with H3K27ac antibody (Abcam GR323193701),
Libraries were prepared using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit for HiC and Liquid HiC. For HiChIP, libraries were prepared using on-bead based tagmentation with Tn5 as described in "HiChIP: Efficient and sensitive analysis of protein-directed genome architecture" (Mumbach et al. 2016).

value: gg8-tTA >tetO-P2

value: Olfactory Sensory Neurons


title: Sample.25.Hector's Dolphin.205138660001_R01C02

source_name: Skin

value: Skin

value: Hector's Dolphin

value: Yes


title: MHHNB11 cells treated with JQAD1

value: Peripheral Nervous System

value: gRNA


title: DRG_FD_Untreated_5376


title: MHHNB11 cells treated with Doxorubicin

value: Doxorubicin


title: DRG_FD_Untreated_5780


title: Sample.24.Hector's Dolphin.205138660001_R05C01


title: gg8tTAtetOP2, 60-min Pre-Digestion, r2


title: MHHNB11 cells treated with Phosphoramide mustard

value: Neuroblastoma

value: PM


title: Sample.22.Hector's Dolphin.205128010011_R01C01


title: Sample.23.Hector's Dolphin.205128010010_R04C01


title: DRG_FD_Untreated_5374


title: gg8tTAtetOP2, 60-min Pre-Digestion, r1


title: Sample.27.Hector's Dolphin.205138660001_R01C01


title: MHHNB11 cells treated with Etoposide

value: Etoposide


title: Sample.21.Hector's Dolphin.205128010033_R04C02


title: DRG_FD_Untreated_5373


title: gg8tTAtetOP2, 30-min Pre-Digestion, r3

description: Liquid Hi-C with 30-minutes of pre-digesiton performed on an individual biological replicate of GFP+ OSNs sorted from adult mice


title: Sample.20.Hector's Dolphin.205128010011_R02C01


title: DRG_FD_Untreated_5378


title: MHHNB11 cells treated with CX-5461


title: MHHNB11 cells treated with Cisplatin

value: Cisplatin


title: DRG_Control_Untreated_5907

value: WT


title: MHHNB11 cells treated with Veh72


title: gg8tTAtetOP2, 30-min Pre-Digestion, r1


title: gg8tTAtetOP2, 30-min Pre-Digestion, r2


title: DRG_Control_Untreated_5902


title: gg8tTAtetOP2, 5-min Pre-Digestion, r3

description: Liquid Hi-C with 5-minutes of pre-digesiton performed on an individual biological replicate of GFP+ OSNs sorted from adult mice


title: Sample.19.Maui Dolphin.205128010033_R05C01

value: Māui Dolphin

value: Maui Dolphin


title: DRG_Control_Untreated_5900

value: Dorsal Root Ganglion


title: clonal CHP134 cells treated with Veh72


title: gg8tTAtetOP2, 5-min Pre-Digestion, r2


title: DRG_Control_Untreated_5880


title: Sample.16.Hector's Dolphin.205128010011_R03C01


title: Sample.17.Hector's Dolphin.205128010033_R05C02


title: clonal CHP134 cells treated with CX-5461 rep2


title: gg8tTAtetOP2, 5-min Pre-Digestion, r1


title: DRG_Control_Untreated_5821


title: clonal CHP134 cells treated with CX-5461 rep1


title: DRG_Control_Untreated_5875


title: Sample.15.Hector's Dolphin.205138660001_R06C01


title: pool CHP134 cells treated with CX-5461 rep2


title: Sample.18.Hector's Dolphin.205128010011_R06C02


title: DRG_Control_Untreated_5377


title: pool CHP134 cells treated with Veh72


title: gg8tTAtetOP2, control HiC, r1

description: Control Hi-C libraries performed on an individual biological replicate of GFP+ OSNs sorted from adult mice


title: DRG_Control_Untreated_5776


title: Sample.13.Hector's Dolphin.205128010033_R06C01


title: gg8tTAtetOP2, control HiC, r2


title: DRG_Control_Untreated_5752