title: mouse breast cancer scRNA-seq FAK knock-out

description: mouse allograft breast tumors from fak knock-out mice

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against either the Cell Ranger mm10 reference genome or GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample.
Cell barcodes representative of quality cells were differentiated from apoptotic cell barcodes or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 100,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin. Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis, normalized with a scale factor of 10,000 UMIs per cell, and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1) (Chen et al., 2013).
The first 15 principal components of the aggregated data were then used for uniform manifold approximation and projection (UMAP) analysis (Gulati et al., 2020). Cell annotations were ascribed using SingleR (version 3.11) against  the Mouse-RNAseq reference dataset, available at https://rdrr.io/github/dviraran/SingleR/man/mouse.rnaseq.html. Cell-type marker lists were generated using Seurat’s native FindMarkers function with a log fold change threshold of 0.25 using the ROC test to assign predictive power to each gene.

source_name: allograft breast tumor

growth_protocol: Cell lines used for allograft tumor experiments were Py8119. All cells were maintained under sterile conditions in a humidified incubator under 5% CO2 at 37ºC. A phase-contrast microscope (Leica) was used to image cells. Cells were grown to 70-80% confluence in DMEM-Glutamax after minimal passage prior to implantation in the mammary fat pad of mice.

extract_protocol:
Tumor tissue specimens from mousewere minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturer's protocol. Cells were counted and re-suspended for further processing.
Single-cell RNA-seq (scRNA-seq) was  performed at the Stanford Genomics Facility (SGF) for droplet-based microfluidics using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA). Droplets of the cellular suspensions, reverse transcription master mix, and partitioning oil were mixed, loaded onto a single cell chip, and processed on the Chromium Controller. Reverse transcription was performed, and cDNA was amplified using a BioRad C1000 Touch thermocycler, with cDNA size selected using SpriSelect beads (Beckman Coulter, USA). An Agilent Bioanalyzer High Sensitivity DNA chip was used to analyze cDNA for qualitative control purposes; cDNA was then fragmented using the proprietary fragmentation enzyme blend for 5min at 32°C, followed by end repair and A-tailing at 65°C for 30 min. DNA was double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

treatment_protocol: 10,000 cells were implanted per site under sterile conditions.

value: allograft breast tumor

value: all cells (unsorted)


title: mouse breast tumor early stage replicate 2

status: Public on Oct 21 2022

type: SRA

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

country: USA

institute: Stanford University

description: slice of mouse endogenous breast tumor harvested at early stage (replicate 2)

library_source: transcriptomic

data_processing:
The libraries were then sequenced using NextSeq (Illumina), and Bcl files were demultiplexed.
Raw FASTQ files and histology images were processed by sample with the Space Ranger software, which uses STAR v.2.5.1b (Dobin et al., 2013) for genome alignment, against the Cell Ranger mm10 reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/ (Dobin et al., 2013).
To analyze the spatial distribution of cell types in Visium data, pairwise cell-cell neighbor interactions were quantified by extracting a feature matrix, f, of the probability of cell type representation in each Visium spot. An adjacency matrix, j, was then used to identify neighboring Visium spots within k=5 nearest neighbors. For each possible cell-cell pairing, a pairing score was calculated as the dot product of individual cell type vectors in f with the adjacency matrix (i.e. f1⋅j⋅f2) using AdjacencyScore in R (Govek et al., 2021). Scores were averaged at the group-level, then subtracted between groups to quantify the magnitude of differential cell pairings in early tumor vs. native breast tissue and late tumor vs. early tumor.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: breast

extract_protocol:
Mouse tissue was processed according to the Visual Spatial Protocol-Tissue Preparation Guide by 10X Genomics.
In brief, we flash froze tissue samples in OCT using a Thermo Scientific Thermo-Flask benchtop container filled three quarters with liquid nitrogen and a small, round, metal bowl with 1-inch height worth of isopentane. A pair of sturdy needle-drivers was used to maneuver the isopentane bowl in and out of the Thermo-Flask. The isopentane bowl was incubated in liquid nitrogen for about 10 minutes. Tissue was completely frozen in approximately one minute, wrapped in aluminum foil, stored immediately in a box containing dry ice, and transferred to a -80°C freezer. Tumor tissues were cryosectioned at -20 degrees onto gene expression slides.
RNA-seq: The samples were uniquely barcoded, pooled, and sequenced on HiSeq (Illumina). scRNA-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform aiming for 50,000 reads per cell. scATAC-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform. In total, we generated scATAC-seq profiles from 5,353 cells, which yielded on average 13.0 × 10^3 unique fragments mapping to the nuclear genome. Spatial transcriptomics: The libraries were then sequenced using NextSeq (Illumina).
The Gene Expression Slide & Reagent kit was followed per protocol, and used to produce sequencing libraries.

tag: tissue

value: breast

tag: cell type

value: unsorted (all cells)

tag: genotype

value: black 6


title: mouse breast tumor early stage replicate 1

description: slice of mouse endogenous breast tumor harvested at early stage (replicate 1)


title: 3_2_GDX_Testo_sample40

city: San Francisco

first: Joni

last: Nikkanen

address: 555 Mission Bay Blvd S

institute: UCSF

data_processing:
Sequencing reads were aligned to mouse cDNA transcriptome using Kallisto with parameters: -b 50 --single -l 260 -s -20
scaled reads per base was calculated using Sleuth in gene mode.
Genome_build: Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: .csv file includes scaled reads per base and tpm values for each sample.

extract_protocol:
Total RNA was extracted from liver samples using TRIsure reagent (Bioline, #BIO-38033) and purified using RNA Mini Kit (Bioline #BIO-52073).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA kit (#20020594)

tag: strain background

tag: Sex

value: male

tag: gonads

value: gonadectomized

tag: treatment

value: testosterone infusion

tag: housing temperature

value: liver


title: FE1_Hydrazine_4hr_4mM_b

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

data_processing:
Fastq files were generated and uploaded to OmicSoft ArrayStudio (Qiagen)
Standard Internal ArrayStudio Mouse RNASeq Pipeline was run:
Raw data QC, Filtering NGS files, Align to Mouse.B38 and GeneModel Ensembl.R78, Raw Data QC and Post Alignment QC, Optional summarize Fusion, Exon Junctions, and Mutations, Perform Quantification, log2FPKM_UQ, Log2TPM, Trim UTRs by data, Generate BAS files. No default Land ALV files.
Assembly: OSA4 was used for alignment to Mouse B6.0 reference genome and the GeneModel Ensemble.R83 Build
supplementary file data content: counts

extract_protocol:
Qiazol extraction followed by DNaseI treatment
1 μg of total RNA per sample was subjected to library synthesis using the Illumina TruSeq V2 Stranded mRNA Library Prep Kit.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina dual indicess prior to 15 cycles of PCR. 1.3pM library pool was loaded on an Illumina HI OUTPUT flow cell and sequenced at 2 X75bp paired end on an Illumina NextSeq 500 instrument, approx 10 million reads per sample

tag: cell line

value: lung epithelial cells

value: 4 mM hydrazine

tag: time

value: 4 hr


title: 3_4_GDX_Testo_sample42


title: 3_1_GDX_Testo_sample39


title: mouse breast cancer scRNA-seq.

description: mouse allograft breast tumors from wild-type mice

library_source: transcriptomic single cell

value: black 6 (C57BL/6J)


title: 2_3_GDX_Veh_sample36

value: vehicle


title: 1_3_Sham_sample37

value: control


title: 3_3_GDX_Testo_sample41


title: FE1_Hydrazine_4hr plus 20hr washout_1mM_b

value: 1 mM hydrazine

value: 4hr plus 20 hr washout


title: FE1_Hydrazine_4hr_10mM_a

value: 10 mM hydrazine


title: 2_1_GDX_Veh_sample32


title: 1_1_Sham_sample34


title: 2_2_GDX_Veh_sample33


title: FE1_Hydrazine_4hr_1mM_b


title: 8_2_sample23

library_source: genomic

data_processing:
Reads were aligned to mm10 using bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files contains all peaks with peak score >50 identified in any of the experimental groups and the quantification of their acetylation status.

molecule: genomic DNA

source_name: Liver

extract_protocol:
Snap-frozen liver samples were used, and ChIP libraries prepared as described in the article.
Libraries were prepared according to Illumina's instructions for ChIP-seq libraries.

tag: infection

tag: antibody

value: +30 degree C


title: input_sample30 [set5]

value: uninfected

value: +22 degree C


title: 7_3_sample21


title: 1_4_Sham_sample38


title: 8_1_sample22


title: mouse breast tumor middle stage

description:
slice of mouse endogenous breast tumor harvested at middle stage
raw data not available for this sample.

value: breast

value: unsorted (all cells)

value: black 6


title: 7_2_sample20

value: male


title: 7_1_sample19


title: 8_3_sample24


title: 6_3_sample18

value: female


title: mouse breast cancer scATAC-seq

data_processing:
Raw base call (BCL) files were demultiplexed to fastq files using the 10x Genomics Cell Ranger tool cellranger-atac mkfastq. These files were then aligned to the mouse genome (mm10) using cellranger-atac count with default parameters.
Downstream analysis of scATAC-seq data were performed using ArchR, a novel tool developed by our collaborators (Granja et al., 2021).
Assembly: mm10
Supplementary files format and content: filtered peak matrix files and filtered transcription factor (tf) matrix files in 10X format

source_name: endogenous breast tumors

extract_protocol:
Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturer's protocol. Cells were counted and re-suspended for further processing.
Single-cell ATAC sequencing (scATAC-seq) was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines. Nuclei isolation was pursued as for scATAC-seq and multiome sequencing using 0.1x lysis buffer with 3-minute incubation.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: endogenous breast tumors

value: all cells (unsorted)


title: 6_2_sample17


title: 4_2_sample11


title: 5_3_sample15


title: 5_2_sample14


title: 2_3_sample6


title: 4_1_sample10


title: 5_1_sample13


title: 6_1_sample16


title: 2_1_sample4


title: 3_1_sample7


title: 3_2_sample8


title: 1_3_sample3


title: 2_2_sample5


title: 1_2_sample2


title: input_sample30

data_processing:
Reads were aligned to mm10 using bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files contains all peaks with peak score >70 identified in any of the experimental groups and the quantification of their acetylation status.

tag: age

value: 8 weeks


title: 1_1_sample1


title: 8_3_sample19


title: 8_1_sample4


title: Upf1FLAG_upf2Δ_CHX  rep2_RNAseq

city: Worcester

first: Robin

last: Ganesan

state: MA

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: UMass Chan Medical School

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5337

data_processing:
For RNA-Seq, RSEM (Li and Dewey, 2011; v 1.3.0) was used to map the sequence reads to the transcriptome and to quantify individual transcript abundance (rsem-calculate-expression --strandedness reverse --fragment-length-mean 200 --fragment-length-sd 50 --bowtie-m 10) without any pre-processing steps.
For ribosome profiling, pre-processing steps include adapter trimming of de-multiplexed sequences by cutadapt (Martin, 2011; v 1.9) to filter out low quality reads and read lengths shorter than 23 nt while trimming adapter sequences (cutadapt -a TGGAATTCTCGGGTGCCAAGG -q 10 --trim-n -m 23). Reads aligned to non-protein coding sequences and UPFs sequences were discarded (bowtie -m 100 -3 4 -5 4 -n 2 -l 15 --un) and PCR duplicates were removed based on the 4-mer barcodes on either end of the reads.
Processed ribosome profiling libraries were aligned to transcriptome using bowtie (Langmead et al., 2009; v 1.0.0) with settings -m 10 -n 2 -l 15 -S --best --strata. Desired read lengths were selected and transcript abundance were quantified using RSEM (Li and Dewey, 2011; v 1.3.0) with settings --strandedness forward --seed-length 15 --bowtie-m 10.
Genome_build: R64-2-1 S288C sacCer3 genome assembly (S288C_reference_genome_R64-2-1_20150113)
Supplementary_files_format_and_content: comma-delimited text files include read count (the "expected_count " column from RSEM output file isoforms.results) for each sample
Supplementary_files_format_and_content: comma-delimited text files include RPKM values (the "FPKM "column from RSEM output file isoforms.results) for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in selective media to OD600 ~0.6, diluted to OD600 ~0.15 into 6X1 liter YAPD medium and grown to OD600 ~0.6. Cells were harvested by rapid vacuum filtration, flash frozen in liquid nitrogen, and stored at -80°C until lysate preparation.

extract_protocol:
Cells were lysed in a cryomill (Retsch).  Frozen powder from a given sample was pooled, thawed and clarified by ultracentrifugation. For ribosome profiling, lysates were digested with RNaseI and ribosomes were isolated over 1 M sucrose cushion.  For immunopurified samples, ribosomes were subsequently immunopurified over α-FLAG M2 affinity gel (Sigma, #A2220). RNAs were isolated from ribosomes (for ribosome profiling) or from lysates (for RNA-seq) using the miRNeasy kit (QIAgen, #217004).
For ribosome profiling, ribosomal RNAs were depleted using the Yeast Ribo-Zero Gold rRNA removal kit (Illumina, #MRZY1324) or QIAseq FastSelect –rRNA Yeast Kit (#334215) and sequencing library was prepared using the NEXTFlex Small RNA-Seq Kit v3 (BIOO Scientific, #NOVA-5132-06). For RNA-seq, total RNAs were treated with BaselineZero DNase, depleted of rRNAs using the Yeast Ribo-Zero Gold rRNA removal kit (Illumina, #MRZY1324) or QIAseq FastSelect –rRNA Yeast Kit (#334215), then the sequencing library was prepared using the TruSeq Stranded mRNA sample prep kit (Illumina, #RS-122-2101)

treatment_protocol: When required, cycloheximide was added to the lysis buffer and culture immediately prior to vacuum filtration to 100μg/ml final concentration

tag: background

value: nmd2::HIS3, upf1::URA3

tag: plasmid

tag: source

value: cell lysate

value: cycloheximide

tag: rrna depletion

value: QIAseq FastSelect


title: 7_3_sample20


title: Upf1FLAG_upf2Δ_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5334


title: 7_2_sample7


title: DE572AAFLAG_CHX  rep3_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5035


title: Upf1FLAG_upf2Δ_CHX  rep3_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5338


title: 8_2_sample5


title: 1_2_Sham_sample35

value: control

tag: tissue

value: liver


title: DE572AAFLAG_CHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5034


title: 6_4_sample23

value: 4 weeks


title: DE572AAFLAG_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5033


title: Upf1FLAG_CHX  rep3_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5020


title: 7_1_sample6


title: Upf1FLAG_CHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5019


title: 5_2_sample15


title: 6_1_sample12


title: 5_3_sample24


title: 5_1_sample14


title: WT_EV_Cterm_CHX rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5041

value: Wild-type


title: chd8+/- 4dpf eNCC #3

city: Illkirch

first: Christelle

last: Golzio

state: Alsace

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations.
Genome_build: GRCz11
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

organism: Danio rerio

source_name: enteric Neural Crest Cells

extract_protocol:
chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2(phox2bb:EGFP) females, and the eggs were incubated at 28.5 °C.  At 4 days post-fertilization (dpf), the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube, all RPMI was removed and replaced with 1 ml of Trypsin-EDTA 1X (Sigma, ref 59417C-100ML).  The digestion was stopped after 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g, during 2 minutes at room temperature, the supernatant was removed and 100 µl of FACS Max medium were added (AMSBIO, ref T200100).  The larval bodies were then placed on a cell filter (diameter 40 µm, Dutscher, ref 141378C), previously moistened with 100 µL of FACS Max medium, and the cells were filtered, using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium, the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP-positive cells were immediately sorted, using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP-positive cells at -80 °C, in 10 µl of PBS-RNAsine 1 U/µl.
Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. 600 pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoresis.


title: 6_2_sample13

value: +22 degree C


title: 4_3_sample17


title: chd8+/- 4dpf eNCC #1


title: FLAGUpf1Upf2Upf3_CHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4903

value: Ribo-Zero Gold


title: chd8+/- 4dpf eNCC #4


title: 4_2_sample16


title: FLAGUpf1Upf2Upf3_CHX rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4902


title: 3_3_sample18


title: chd8+/- 4dpf eNCC #2


title: chd8+/+ 4dpf eNCC #2


title: 3_2_sample3


title: FLAGUpf3_CHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4881


title: chd8+/+ 4dpf eNCC #4


title: FLAGUpf3_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4880


title: chd8+/+ 4dpf eNCC #1


title: 3_1_sample2


title: WT_EV_Cterm_CHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5042


title: FLAGUpf2_CHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4821


title: Upf1FLAG_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5017


title: 2-NI-7D

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

data_processing:
Raw reads analyzed by FastQC for determine read quality information
Adaptors and low quality reads were removed using Trimmomatic
Filtered reads aligned against Gallus gallus genome by using Hisat2
featureCounts was applied to obtain gene counts
DESeq was used for obtainind lists of differentially expressed genes
Genome_build: GCA_000002315.5
Supplementary_files_format_and_content: normalized.counts and war.counts are in plain text format

organism: Gallus gallus

source_name: Gallus gallus embryo

extract_protocol:
Embryos were macerated then extracted using TRIzol® Plus RNA Purification kit
RNA libraries were prepared for sequencing using SureSelect Strand-specific RNA Library Prep for Illumina® Multiplexed Sequencing mRNA library (Agilent Technologies, Santa Clara, EUA), according to manufacturer.

value: Embryos cells

tag: timepoint

value: 7 days not infected


title: WT_EV_Nterm_CHX rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4869

tag: genotype


title: 2_2_sample8


title: 2_4_sample21


title: 4_1_sample1


title: FLAGUpf3_NoCHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4881minus

value: untreated


title: FLAGUpf1_NoCHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4819minus


title: 1_4_sample22

value: female


title: 2_3_sample9


title: 2-NI-3D

value: 3 days not infected


title: 2-NI-2D

value: 2 days not infected


title: WT_EV_Nterm_NoCHX rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4869minus


title: 2-IBDV-7D

value: 7 days post infection


title: FLAGUpf1_NoCHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4816minus


title: 2-NI-1D

value: 1 day not infected


title: chd8+/+ 4dpf eNCC #3


title: L_4_sample48

extract_protocol:
Total RNA was extracted from liver samples using TRIsure reagent (Bioline, #BIO-38033).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA kit (#20020594)

value: male

value: +30 degree C


title: 1_2_sample10


title: 1_3_sample11


title: 2-IBDV-5D

value: 5 days post infection


title: 2-IBDV-3D

value: 3 days post infection


title: Upf1FLAG_upf2Δ_CHX_IP  rep3_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5338

data_processing:
Library strategy: Ribo-seq
For RNA-Seq, RSEM (Li and Dewey, 2011; v 1.3.0) was used to map the sequence reads to the transcriptome and to quantify individual transcript abundance (rsem-calculate-expression --strandedness reverse --fragment-length-mean 200 --fragment-length-sd 50 --bowtie-m 10) without any pre-processing steps.
For ribosome profiling, pre-processing steps include adapter trimming of de-multiplexed sequences by cutadapt (Martin, 2011; v 1.9) to filter out low quality reads and read lengths shorter than 23 nt while trimming adapter sequences (cutadapt -a TGGAATTCTCGGGTGCCAAGG -q 10 --trim-n -m 23). Reads aligned to non-protein coding sequences and UPFs sequences were discarded (bowtie -m 100 -3 4 -5 4 -n 2 -l 15 --un) and PCR duplicates were removed based on the 4-mer barcodes on either end of the reads.
Processed ribosome profiling libraries were aligned to transcriptome using bowtie (Langmead et al., 2009; v 1.0.0) with settings -m 10 -n 2 -l 15 -S --best --strata. Desired read lengths were selected and transcript abundance were quantified using RSEM (Li and Dewey, 2011; v 1.3.0) with settings --strandedness forward --seed-length 15 --bowtie-m 10.
Genome_build: R64-2-1 S288C sacCer3 genome assembly (S288C_reference_genome_R64-2-1_20150113)
Supplementary_files_format_and_content: comma-delimited text files include read count (the "expected_count " column from RSEM output file isoforms.results) for each sample
Supplementary_files_format_and_content: comma-delimited text files include RPKM values (the "FPKM "column from RSEM output file isoforms.results) for each sample

value: nmd2::HIS3, upf1::URA3

value: immunopurified ribosomes

value: cycloheximide

value: QIAseq FastSelect


title: Upf1FLAG_upf2Δ_CHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5337


title: 2-NI-5D

value: 5 days not infected


title: 2-IBDV-2D

value: Embryos cells

value: 2 days post infection


title: Upf1FLAG_upf2Δ_CHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5334


title: L_2_sample46


title: L_1_sample45


title: K_4_sample44


title: DE572AAFLAG_CHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5034


title: 2-IBDV-1D

value: 1 day post infection


title: FLAGUpf3_NoCHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4880minus

value: cell lysate

value: untreated

value: Ribo-Zero Gold


title: Upf1FLAG_CHX  rep3_IP_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5020


title: 1-NI-7D

value: 7 days not infected


title: K_3_sample43


title: 1-NI-5D


title: WT_EV_Cterm_CHX rep3_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T5043

value: Wild-type


title: 1-NI-3D

value: 3 days not infected


title: Upf1FLAG_CHX  rep2_IP_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5019


title: L_3_sample47

value: male

value: +30 degree C


title: 1-NI-2D

value: 2 days not infected


title: K_2_sample42


title: 1-NI-1D

value: 1 day not infected


title: J_3_sample39

value: female


title: Upf1FLAG_CHX  rep1_IP_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5017

value: immunopurified ribosomes

value: cycloheximide


title: J_2_sample38


title: 1-IBDV-5D

value: 5 days post infection


title: 1-IBDV-3D

value: Embryos cells

value: 3 days post infection


title: FLAGUpf1Upf2Upf3_IP_CHX rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4903


title: J_4_sample40


title: FLAGUpf3_CHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4881


title: DE572AAFLAG_CHX_IP  rep3_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5035

value: QIAseq FastSelect


title: DE572AAFLAG_CHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
QU5033


title: 1-IBDV-7D

value: 7 days post infection


title: FLAGUpf1Upf2Upf3_IP_CHX rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4902


title: J_1_sample37


title: 1-IBDV-2D

value: 2 days post infection


title: FLAGUpf3_CHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4880

value: Ribo-Zero Gold


title: GOT1, Nonanoic acid (Na)

city: Gothenburg

first: Erik

last: Elias

address: Medicinaregatan 1G

department: Clinical Sciences

country: Sweden

institute: University of Gothenburg

data_processing:
Partek Flow Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using STAR - 2.7.3a in Partek Flow Software
Trimmed sequence reads were mapped to hg38 using STAR - 2.7.3a in Partek Flow Software
Read count extraction and normalization were performed using Partek Flow Software. Normalization methods:CPM (counts per million)
Assembly: hg38 - Ensembl Transcripts release 91
Supplementary files format and content: Excel file include, P-value (Nonanoic acid 300uM vs. DMSO), FDR step up (Nonanoic acid 300uM vs. DMSO), Ratio (Nonanoic acid 300uM vs. DMSO),
Supplementary files format and content: Fold change (Nonanoic acid 300uM vs. DMSO), LSMean(Nonanoic acid 300uM) (Nonanoic acid 300uM vs. DMSO), LSMean(DMSO) (Nonanoic acid 300uM vs. DMSO)

organism: Homo sapiens

growth_protocol: GOT1 cells was cultured in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 5 μg/mL insulin and 5 μg/mL transferrin

extract_protocol:
RNA extracted using RNeasy mini kit (Qiagen).
TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold

treatment_protocol: GOT1 cells were treated for 3 days with 300 µM nonanoic acid or medium with vehicle (0.1% DMSO).

tag: cell type

value: Small intestine neuroendocrine tumor cells

value: WT

value: Nonanoic acid (Na)


title: I_3_sample35

tag: Sex


title: FLAGUpf2_CHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4820


title: 1-IBDV-1D

value: 1 day post infection


title: FLAGUpf2_CHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4821


title: T24 cells, TGF-β treat2, Day2

city: Beijing

first: Yanlong

last: Zhang

address: 10th Tieyi Road, Haidian District

country: China

institute: Beijing Shijitan Hospital

data_processing:
Clean reads were aligned to the reference genome using HISAT2 (v2.0.5)
FeatureCounts (v1.5.0-p3) was performed to count the read numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: T24cells were maintained in MCC supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA quality and integrity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for the construction of sequencing libraries.
RNA libraries were prepared and sequenced using a 150 bp pairing end protocol by the Illumina NovaSeq 6000

treatment_protocol: T24 cells treated with or without TGF-β1 (10 ng/ml) for 48 h

value: Bladder Urothelial Carcinoma

value: TGF-B treat

value: Day 2


title: I_4_sample36

value: female

value: +30 degree C


title: H_4_sample32

value: male

value: uninfected


title: GOT1, Control (DMSO)

value: Control (DMSO)


title: T24 cells, TGF-β treat3, Day2


title: I_2_sample34


title: FLAGUpf1_CHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4816

value: immunopurified ribosomes

value: cycloheximide


title: K_1_sample41


title: FLAGUpf3_NoCHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4881minus

value: untreated


title: FLAGUpf2_NoCHX  rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4821minus

value: cell lysate


title: FLAGUpf1_CHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4819

value: Ribo-Zero Gold


title: FLAGUpf2_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4820


title: Isocortex307933

city: Hangzhou

first: Xin

last: Shao

state: Zhejiang

address: #866 Yuhangtang Rd.

institute: Zhejiang University

data_processing:
The raw sequencing data from Illumina® Xten were aligned and quantified using the FastQC (version 0.11.5) and Drop-seq Alignment Cookbook (version 2.0.0). The mouse genome mm10 was used as the reference genome.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: Brain

extract_protocol:
Hypothalamus and isocortex regions of the mouse brain were isolated by laser capture microdissection (LCM) and collected in 96-well plate containing barcoded magnetic beads. The tissue was lysed in the well, allowing mRNA to be captured by oligonucleotides on the surface of the magnetic beads. In detail, each well was loaded with 50 μL 2X lysis buffer (Tris-HCl(pH7.5) 120 μL, LiCl 80 μL, 10% SDS 120 μL, EDTA 16 μL, 500 mM DTT 12 μL, DNase and RNase-free water 852 μL). The tissue was lysed on ice for 12 minutes. The beads were washed with 6X SSC (Invitrogen, Cat#AM9770) and then the suspension was transfered to 1.5 mL centrifugal tube. The supernatant was removed. The beads were re-suspended with 500 μL 6X SSC, and the supernatant was removed after centrifugation. The beads were re-suspended with 300 μL 50 mM Tris(pH8.0, Beyotime Biotec., Cat#ST780) and then remove the supernatant. The beads were re-suspended with 20 μL RT Mix(DNase and RNase-free water 16.16 μL， 5X Superscript II first-strand buffer 8 μL, betaine (Sigma, Cat#B0300) 8 μL, 10 mM dNTPs 4 μL, DTT (Beyotime Biotec., Cat#ST041) 0.2 μL, MgCl2 (Invitrogen, Cat#AM9530G) 0.24 μL, 50 μM TSO primer 0.4 μL, PrimeScript II Reverse Transcriptase (Takara, Cat#2690A) 2 μL, and RNase Inhibitor 1 μL). The captured mRNA underwent reverse transcription (RT) at 42 ℃ for 90 min. Remove supernatant after centrifugation. The beads were washed with 200 μL TE-SDS (10% SDS and TE(pH8.0, Invitrogen, Cat#AM9849)), 200 μL TE-TW (10% Tween-20 (Sigma, Cat#P7949) and TE(PH8.0)), and 200 μL 10 mM Tris (pH8.0) in turn and remove the supernatant. The beads were re-suspended with 200 μL exonuclease mix (DNase and RNase-free water 170 μL, 10X Exol Buffer 20 μL, and Exol (Annoron, Cat#M0293L) 10 μL) and then incubated at 37 ℃ for 60 min. The beads were washed with 200 μL TE-SDS, 200 μL TE-TW and 200 μL 10 mM Tris (pH8.0) in turn and remove the supernatant.
Beads were distributed to 4 tubes. To every tube, 12.5 μL of PCR mix was added, which included 2X HiFi HotStart Readymix (Kapa Biosystems) and 0.5 μL 10 μM TSO-PCR primer. The PCR program was as follows: 98 ℃ for 3 min; 6 cycles of 98 ℃ 20 s, 65 ℃ 45 s, and 72 ℃ 6 min; 72 ℃  10 min and 4 ℃ hold. After pooling all PCR products, AMPure XP beads (Beckman Coulter) were used to purify the cDNA library. cDNA library was prepared following the guidance of Illumina Nextera XT DNA Library Preparation Kits.

tag: direction

value: Sagittal

tag: region

value: Isocortex

tag: organ

value: Brain


title: I_1_sample33

tag: housing temperature


title: T24 cells, TGF-β treat1, Day2

tag: cell line

value: WT

tag: treatment

tag: time


title: FLAGUpf1_CHX_IP rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4819


title: FLAGUpf1_CHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4816


title: FLAGUpf2_NoCHX_IP  rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4821minus


title: H_1_sample25

tag: infection


title: WT_EV_Nterm_CHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4870

tag: background

value: Wild-type


title: H_3_sample29


title: H_2_sample27


title: FLAGUpf3_NoCHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4880minus

tag: plasmid


title: T24 cells, Control1, Day2

value: Bladder Urothelial Carcinoma

value: control


title: FLAGUpf2_NoCHX  rep1_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4820minus

tag: source


title: G_4_sample31


title: FLAGUpf2_NoCHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4820minus

tag: rrna depletion


title: WT_EV_Nterm_NoCHX rep2_RNAseq

description:
RNAseq_RSEM_expected_count_isoforms.results.csv
RNAseq_RSEM_FPKM_isoforms.results.csv
T4870minus


title: FLAGUpf1_NoCHX_IP rep2_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4819minus


title: G_3_sample30


title: G_2_sample28


title: FLAGUpf1_NoCHX_IP  rep1_riboseq

description:
Riboseq_IP80S_RSEM_expected_count_isoforms.results.csv
Riboseq_IP80S_RSEM_FPKM_isoforms.results.csv
RU4816minus


title: T24 cells, Control3, Day2

value: Day 2


title: 2T

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

description: GFP

data_processing:
Illumina Casava1.7 software used for basecalling.
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Assembly: hg19
Supplementary files format and content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: liver cancer stem cells

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: liver cancer stem cells

value: TINCR knockdown


title: 1C

description: GFP


title: 1T

description: GFP


title: G_1_sample26

value: male

value: uninfected

value: +30 degree C


title: Upf1FLAG_upf2Δ_CHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5337

value: nmd2::HIS3, upf1::URA3

value: total ribosomes

value: cycloheximide

value: QIAseq FastSelect


title: Upf1FLAG_upf2Δ_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5334


title: F_3_sample23

value: female


title: F_2_sample21


title: Upf1FLAG_upf2Δ_CHX  rep3_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5338


title: DE572AAFLAG_CHX  rep3_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5035


title: 2D retina pericytes

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
fastq file was generated by NHLBI DNA Sequencing and Genomics Core
Count was generated in biowulf using 10x celll ranger-6.1.1 with default setting, matched genome GRCh30-2020-A
Read count extraction and normalization were performed using Seurat 3.0 pipeline with QC filter: nUMI >= 500, nGene>=200, log10GenesPerUMI >0.8, mitoRatio <0.2. Followed by running DoubletFinder3.0 R package to remove doublet
Separate cell types by identity
Scale data, PCA, TSNE, UMAP
[3D Bioprinted Tissues] Cluster cells, 0.9 resolution, group clusters by cell type
DE analysis to differentiate gene upregulation and downregulation in 2D culture, 3D bioprinted tissue, and 3D bioprinted tissue without RPE
Supplementary files format and content: xlsx file containing average expression data and DE analysis results per cell type included in the experiments, a large Seurat file containing processed sc-RNAseq data.

source_name: Angioproteomie Cat# cAP-0025

extract_protocol:
The digestion solution was created using 1.5 mg/mL Collagenase II (Gibco, Cat# 17101-015), 0.5 mg/mL DNAse I (Worthington Biochemical Corporation, Cat# 54D14897, Lakewood, NJ) and 0.2 mg/mL Dispase I (Sigma, Cat# D4818) in PBS.
Samples were washed in PBS, and manually homogenized with a disposable surgical scalpel. They were then were treated with digestion solution (~10mL per 6 tissues in 6 well format) and incubated at 37 degrees C for 20 minutes on an orbital shaker. Samples were then rescued with 10 mL of RPE-MM. Samples were centrifuged for 5 minutes at 1,000 RPM, had the supernatant removed, and were resuspended in PBS. Eye samples were filtered through a 0.2um filter and centrifuged (4 degrees, 5 mins, 1500rpm) to remove cell doublets and cell clumps
Samples were submitted to the Ilyas Singec Lab for library preparation.
Samples were submitted to NHLBI DNA Sequencing and Genomics Core for libriary construction using 10x genomics Single Cell 3' v3 kit

value: Angioproteomie Cat# cAP-0025

value: Pericyte

value: 2D Culture

value: Day 5


title: Yale Melanoma ITx2_4.10

type: RNA

city: New Haven

first: Ioannis

last: Vathiotis

address: 310 Cedar St

institute: Yale

hyb_protocol: Probes and target transcripts were hybridized at 67°C for 16–24 hours per manufacturer’s recommendations.

scan_protocol: Hybridized samples were run on the NanoString nCounter preparation station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge. The cartridge was scanned at maximum scan resolution on the nCounter Digital Analyzer

data_processing: Raw data counts were normalized using the geomean of 10 housekeeping genes included in the nCounter PanCancer IO 360™ Panel and each gene was adjusted based on the average of 2 panel standards across all data. Then, the housekeeper- and panel standard-normalized data were log2 transformed.

label: biotin

source_name: Malignant melanoma

label_protocol: Per sample, 250 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe and tagged with a fluorescent barcode from the custom gene expression code set.

extract_protocol: Total RNA was isolated from 5 μm-thick pretreatment FFPE sections of tumors fixed on positively charged slides using the High Pure FFPET RNA Isolation Kit (Roche) following the manufacturer’s protocols. RNA was quantified using the NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific).

tag: age

tag: bor

value: PR

tag: itx

value: IPI+NIVO

tag: prior checkpoint blockade

value: NO


title: 2D CDI-iCell Ecs

source_name: CDI Cat# R1112

value: CDI Cat# R1112

tag: cell type

value: Endothelial Cell

tag: genotype

value: WT


title: 2C

description: GFP

value: liver cancer stem cells

value: control


title: 2D D3C-iECs

source_name: Human iPSC D3C

value: Human iPSC D3C


title: Yale Melanoma ITx2_4.9

value: PD

tag: long-term benefit


title: F_4_sample24

tag: Sex

value: uninfected

value: +30 degree C


title: Yale Melanoma ITx2_4.7

value: CR

value: YES

value: NIVO


title: 3D tissue_CDI-iCell Ecs_iRPE_retina pericytes

source_name: Mixed Tissue

value: Mixed Tissue

value: Endothelial, Pericyte, Fibroblast, RPE

value: 3D Bioprinting

value: Week 6


title: F_1_sample18

value: female

tag: housing temperature


title: DE572AAFLAG_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5033

value: total ribosomes

value: cycloheximide

value: QIAseq FastSelect


title: Yale Melanoma ITx2_4.5

value: SD

value: NO

value: IPI+NIVO


title: 3D tissue_CDI-iCell Ecs_NO RPE_retina pericytes

tag: cell line

value: Endothelial, Pericyte, Fibroblast

value: WT


title: Yale Melanoma ITx2_4.4

value: PD


title: 3D tissue_D3C-iECs_D3C RPE_ retina pericytes

tag: treatment


title: Yale Melanoma ITx2_4.8

value: PEMBRO


title: Upf1FLAG_CHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5019


title: E_3_sample20

value: uninfected

value: +30 degree C


title: T24 cells, Control2, Day2

value: Bladder Urothelial Carcinoma

value: control

tag: time

value: Day 2


title: Yale Melanoma ITx2_4.3

value: PR

value: NIVO


title: 3D tissue_D3C-iECs_NO RPE_retina pericytes

value: Mixed Tissue

value: 3D Bioprinting

value: Week 6


title: E_1_sample17

value: female

tag: infection


title: Upf1FLAG_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5017

tag: background

value: total ribosomes

value: cycloheximide

value: QIAseq FastSelect


title: Yale Melanoma ITx2_4.6

value: SD

value: NO


title: 2D Placental pericyte

source_name: Angioproteomie Cat# cAP-0029

value: Angioproteomie Cat# cAP-0029

value: Pericyte

value: WT

value: 2D Culture

value: Day 5


title: 2D D3C

value: Human iPSC D3C

value: Retinal Pigment Epithelial Cell


title: 2D D3C fibroblasts

value: Fibroblast

value: Day 7


title: Yale Melanoma ITx2_4.2

value: PD

value: NIVO


title: Upf1FLAG_CHX  rep3_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5020

tag: plasmid


title: E_4_sample22

value: female

value: uninfected

value: +30 degree C


title: Yale Melanoma ITx2_3.12

value: PEMBRO


title: 8_4

data_processing:
Sequencing reads were aligned to mouse cDNA transcriptome using Kallisto with parameters: -b 100 --single -l 260 -s -20
scaled reads per base was calculated using Sleuth in gene mode.
Genome_build: Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: .csv file includes scaled reads per base and tpm values for each sample.

value: male

value: 8 weeks

value: +22 degreeC


title: 8_3


title: Yale Melanoma ITx2_4.1

value: NO

value: IPI+NIVO

value: YES


title: WT_EV_Cterm_CHX rep3_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5043

value: Wild-type

tag: source

value: total ribosomes

value: cycloheximide

value: QIAseq FastSelect


title: E_2_sample19


title: Yale Melanoma ITx2_3.10

value: CR


title: WT_EV_Cterm_CHX rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5041

tag: rrna depletion


title: 8_2

tag: age


title: FLAGUpf1Upf2Upf3_CHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4903

value: Ribo-Zero Gold


title: FLAGUpf1Upf2Upf3_CHX rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4902


title: 7_4


title: 8_1


title: PDAC 3 Bone Marrow

city: St. Louis

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

data_processing:
The generated libraries were sequenced using by MGI using a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50 K mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex the Illumina base call files to FASTQ files. All BM and PBMC files were demultiplexed with greater than 96% valid barcodes and greater than 93% q30 reads. Fastq files from each sample were then processed with Cellranger count and aligned to the human GRCh38 reference genome (Cellranger v3.1.0, 10X Genomics, Human reference genome GRCh38 from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz) to generate feature barcode matrix.
Assembly: GRCh38 from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

source_name: Bone Marrow

extract_protocol:
PBMCs were isolated from patients and healthy donors using Ficoll-Paque centrifugation (Cytiva, Marlborough, MA, USA), and then frozen. Prior to submission, samples were rapidly thawed at 37°C, stained, and sorted for live antigen presenting cells (7AAD-,CD45+, CD3/16/19/20-, and HLA-DR+) by using an Aria II Cell Sorter (BD Biosciences). For Bone marrow samples, BM was collected from patients, mononuclear cells were isolated via Ficoll-Paque centrifugation, and then frozen. Prior to submission, the samples were rapidly thawed at 37°C and lineage-depleted using MACS beads (Miltenyi) against CD3/15/16/20/56/235a.
Single-cell RNA-sequencing library preparation was then conducted by the Genome Technology Access Center at Washington University. Briefly, cells from each sample were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’v3 Reagent kits according to the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

tag: tissue

value: Bone Marrow

tag: disease state

value: PDAC

value: Lineage depleted (CD3/15/16/20/56/235a negative) BM cells


title: Yale Melanoma ITx2_3.9

tag: bor

value: PD

tag: itx

tag: prior checkpoint blockade


title: 2D iRPE

source_name: CDI Cat# 01279

value: CDI Cat# 01279

tag: cell type

value: Retinal Pigment Epithelial Cell

tag: genotype

value: WT

value: 2D Culture

value: Day 5


title: WT_EV_Cterm_CHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5042


title: Yale Melanoma ITx2_3.11

value: PR

tag: long-term benefit

value: NO

value: Pembro


title: FLAGUpf3_CHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4881

value: total ribosomes


title: PDAC 1 Bone Marrow


title: Yale Melanoma ITx2_3.7

value: UK

value: NIVO


title: 7_3

tag: Sex

value: male

value: 8 weeks

tag: housing temperature

value: +22 degreeC


title: 7_2


title: PDAC 2 Bone Marrow

value: Bone Marrow

value: PDAC


title: FLAGUpf3_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4880

tag: treatment

value: cycloheximide

value: Ribo-Zero Gold


title: Healthy Control 3 Bone Marrow

value: healthy

value: Lineage depleted (CD3/15/16/20/56/235a negative) BM cells


title: DE572AAFLAG_CHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
Q5034

value: QIAseq FastSelect


title: Healthy Control 2 Bone Marrow


title: Yale Melanoma ITx2_3.6

value: PD


title: 7_1


title: FLAGUpf2_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4820


title: FLAGUpf1_CHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4819


title: Yale Melanoma ITx2_3.5

value: SD

value: IPI+NIVO


title: Healthy Control 1 Bone Marrow


title: PDAC 3 PBMC

source_name: Blood

value: Blood

value: Antigen-presenting cells from PBMCs (7AAD-,CD45+, CD3/16/19/20-, and HLA-DR+)


title: 6_3

value: 4 weeks


title: Yale Melanoma ITx2_3.8

value: CR

value: YES

value: NIVO

value: NO


title: FLAGUpf1_CHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4816

value: total ribosomes


title: 6_2

value: male

value: +22 degreeC


title: PDAC 2 PBMC

value: PDAC


title: Yale Melanoma ITx2_3.2


title: Yale Melanoma ITx2_3.1


title: WT_EV_Nterm_CHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4870

value: Wild-type

value: cycloheximide

value: Ribo-Zero Gold


title: FLAGUpf2_CHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4821


title: WT_EV_Nterm_CHX rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4869


title: Healthy Control 3 PBMC

value: healthy


title: PDAC 1 PBMC


title: Healthy Control 2 PBMC


title: FLAGUpf3_NoCHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4881minus

value: untreated


title: Yale Melanoma ITx2_3.4

value: PR

value: PEMBRO


title: Yale Melanoma ITx2_3.3


title: Yale Melanoma ITx2_2.12


title: 5_4


title: 6_4


title: 6_1


title: 5_2


title: Healthy Control 1 PBMC

value: Blood

value: Antigen-presenting cells from PBMCs (7AAD-,CD45+, CD3/16/19/20-, and HLA-DR+)


title: FLAGUpf3_NoCHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4880minus


title: Yale Melanoma ITx2_2.9

value: CR

value: NIVO+EXPERIMENTAL


title: Yale Melanoma ITx2_2.10

value: IPI+NIVO


title: 4_4

value: female

value: 8 weeks


title: Yale Melanoma ITx2_2.11

value: SD

value: NO


title: FLAGUpf2_NoCHX  rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4821minus

value: total ribosomes


title: 4_3

value: +22 degreeC


title: FLAGUpf2_NoCHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4820minus


title: Human NASH Liver 9, snRNA-seq

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

description:
10x Genomics
humanNASH_9

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
40-60mg of total liver tissue  was chopped on ice in 1mL of 0.03% TST buffer (146mM NaCl, 10mM Tris-HCl pH 7.5, 1mM CaCl2, 21mM MgCl2 with freshly added 0.03% Tween-20, 0.01%BSA, and 0.4U/mL Ribolock RNase Inhibitor (Thermo Fisher Scientific FEREO0382, MA, USA)) [30] with Tungsten Noyes Spring Scissors (FST 15514-12, CA, USA). The resulting nuclei suspension was then filtered through 40mm cell strainers (Thermo Fisher Scientific 352340, MA, USA) into a fresh 50mL conical tube on ice. 1 more mL of 0.03% TST was used to rinse the cell strainer and 3mL of ST buffer was added to the nuclei suspension followed by briefly mixing by gentle flicking. The nuclei suspensions were spun at 500xg for 5 minutes at 4°C in a swing-bucket centrifuge. The final nuclei pellet is suspended in 200mL of 0.4% BSA in PBS by pipetting 30 times with a regular p1000 tip.
Nuclei preparations were processed by the Chromium 3′ Gene Expression V3 Kit according to the manufacturer’s guidelines. Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA.

value: NASH

value: Liver

value: F

value: 68 years


title: Human NASH Liver 8, snRNA-seq

description:
10x Genomics
humanNASH_8

value: M

value: 56 years


title: FLAGUpf1_NoCHX  rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4816minus

value: untreated

value: Ribo-Zero Gold


title: Yale Melanoma ITx2_2.8

value: PR

value: PEMBRO


title: 4_1


title: WT_EV_Nterm_NoCHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4870minus

value: Wild-type


title: 3_4

value: female


title: 5_3

value: male

value: 4 weeks


title: 4_2

value: 8 weeks


title: 5_1


title: Human NASH Liver 6, snRNA-seq

description:
10x Genomics
humanNASH_6

value: 62 years


title: ART (A09_post_6) ATAC fragments

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

data_processing:
ATAC libraries were demultiplexed using 10X Genomics cellranger-atac (v2.0) pipeline. NovaSeq-based sequences were filtered using 10X Genomics index-hopping-filter (v1.1).
ATAC libraries were processed (demultiplexing, alignment, and counting) using 10X Genomics cellranger-atac (v2.0) pipeline
ADT libraries were demultiplexed using bcl2fastq2 (v2.20.0.422)
ADT fastq files were mapped to the TotalSeaA cocktail catalog using kallisto (v0.46.2) and bustools (v0.40.0) as documented with the kite pipeline (https://github.com/pachterlab/kite)
Assembly: chimeric hg38 with viral genome (HXB2, SUMA, or autologous sequences)
Supplementary files format and content: fragment.tsv.gz output file from 10X Genomics cellranger-atac count for ATAC data
Supplementary files format and content: tar.gz folder of kallisto bus output for ADT data
Library strategy: single cell ASAPseq

source_name: peripheral blood

growth_protocol: Cells were thawed and rested in complete RPMI supplemented with DNaseI.

extract_protocol: Refer to Mimitou et al., Nature Biotechnology 2021 for ASAPseq protocol

treatment_protocol: For in vitro sample, bulk CD4+ T-cells were negatively enriched and were activated for infection with HIV-1 (SUMA clone). For ex vivo samples, memory CD4+ T-cells were negatively enriched.

tag: component

value: ATAC


title: Yale Melanoma ITx2_2.7

value: SD

value: NO

value: IPI+NIVO


title: WT_EV_Nterm_NoCHX rep1_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4869minus

tag: background

value: total ribosomes


title: Yale Melanoma ITx2_2.5


title: Yale Melanoma ITx2_2.6

value: PD


title: ART (A09_post_5) ATAC fragments


title: ART (A09_post_4) ATAC fragments


title: Yale Melanoma ITx2_2.4

value: CR

value: YES


title: endothelial cell  GC-PVOD#3

first: Baihui

last: Ma

address: 167 Beilishi Road

institute: Fuwai Hospital

data_processing:
Illumina  Nova S4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
High-quality reads were aligned to the human reference genome (GRCh38) using HISAT2 2.1.0. The raw counts for each of the genes were quantificated by StringTie 2.0.1 and prepDE.py (see manual of StringTie)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: endothelial cell

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles)

value: endothelial cell

value: gene-corrected


title: Yale Melanoma ITx2_2.2

value: PR


title: 3_2

source_name: Liver

value: +22 degreeC


title: Yale Melanoma ITx2_2.3


title: 3_3

value: female


title: ART (A09_post_3) ATAC fragments


title: FLAGUpf1_NoCHX rep2_riboseq

description:
Riboseq_Total80S_RSEM_expected_count_isoforms.results.csv
Riboseq_Total80S_RSEM_FPKM_isoforms.results.csv
R4819minus

tag: plasmid

value: untreated

value: Ribo-Zero Gold


title: Human NASH Liver 7, snRNA-seq

description:
10x Genomics
humanNASH_7

value: NASH

value: Liver

value: F

value: 72 years


title: endothelial cell  GC-PVOD#1


title: Yale Melanoma ITx2_2.1

value: NO

value: NIVO


title: 3_1

value: 8 weeks


title: endothelial cell  PVOD#3

value: mutation


title: ART (A09_post_2) ATAC fragments

value: ATAC


title: Yale Melanoma ITx2_1.12

value: CR


title: 2_4

value: 4 weeks


title: ART (A09_pre_6) ATAC fragments


title: endothelial cell  GC-PVOD#2

value: endothelial cell

value: gene-corrected


title: ART (A09_pre_5) ATAC fragments


title: 2_3

value: +22 degreeC


title: endothelial cell  PVOD#1


title: ART (A09_pre_4) ATAC fragments


title: Yale Melanoma ITx2_1.11

value: PD

value: PEMBRO


title: endothelial cell  PVOD#2


title: ART (A09_pre_3) ATAC fragments


title: 2_1

value: female


title: 1_4


title: mouse breast cancer scRNA-seq

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against either the Cell Ranger mm10 reference genome or GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample.
scRNA-seq: Hashtag oligos (HTOs) for human and mouse samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a ‘negative’ HTO distribution is calculated. For each HTO,  the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Since each of the five samples for this dataset contained exactly three pooled biological replicates (i.e., tumors from different mice or tumors from different humans), cells for which ambiguous HTO identity could not be clearly established were preserved and assigned to the hashtag for which it was most highly expressed.
Cell barcodes representative of quality cells were differentiated from apoptotic cell barcodes or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 100,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin. Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis, normalized with a scale factor of 10,000 UMIs per cell, and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1) (Chen et al., 2013).
The first 15 principal components of the aggregated data were then used for uniform manifold approximation and projection (UMAP) analysis (Gulati et al., 2020). Cell annotations were ascribed using SingleR (version 3.11) against either the Mouse-RNAseq reference dataset, available at https://rdrr.io/github/dviraran/SingleR/man/mouse.rnaseq.html, or human primary cell atlas dataset, available at https://rdrr.io/github/dviraran/SingleR/man/hpca.html. Cell-type marker lists were generated using Seurat’s native FindMarkers function with a log fold change threshold of 0.25 using the ROC test to assign predictive power to each gene.

source_name: endogenous breast tumors

extract_protocol:
Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturer's protocol. Cells were counted and re-suspended for further processing.
Cell suspensions from individual human and mouse samples were labeled with TotalSeq Series B hashtag oligonucleotide-labeled antibodies (BioLegend). Single-cell RNA-seq (scRNA-seq) was then performed at the Stanford Genomics Facility (SGF) for droplet-based microfluidics using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA). Droplets of the cellular suspensions, reverse transcription master mix, and partitioning oil were mixed, loaded onto a single cell chip, and processed on the Chromium Controller. Reverse transcription was performed, and cDNA was amplified using a BioRad C1000 Touch thermocycler, with cDNA size selected using SpriSelect beads (Beckman Coulter, USA). An Agilent Bioanalyzer High Sensitivity DNA chip was used to analyze cDNA for qualitative control purposes; cDNA was then fragmented using the proprietary fragmentation enzyme blend for 5min at 32°C, followed by end repair and A-tailing at 65°C for 30 min. DNA was double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: endogenous breast tumors

value: all cells (unsorted)

value: black 6


title: ART (A09_pre_2) ATAC fragments


title: Yale Melanoma ITx2_1.9

value: IPI+NIVO


title: ART (A09_pre_1) ATAC fragments


title: 1_3


title: human pancreas cancer scRNA-seq replicate 1

source_name: pancreatic adenocarcenoma

value: pancreatic adenocarcenoma

value: human


title: Yale Melanoma ITx2_1.8

value: NO

value: YES


title: human breast cancer scRNA-seq replicate 2


title: Yale Melanoma ITx2_1.7

value: PR


title: Yale Melanoma ITx2_1.6

value: SD

value: NIVO


title: ART (A09_pre_6) antibody derived tags

library_source: other

molecule: other

value: ADT


title: 1_2

value: 4 weeks


title: 2_2

value: +22 degreeC


title: human breast cancer scRNA-seq replicate 1


title: ART (A09_pre_5) antibody derived tags


title: 1_1


title: ART (A09_post_6) antibody derived tags


title: Yale Melanoma ITx2_1.10


title: MCF7/TGL/pQ CO 3

city: New York

first: Nancy

last: Du

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
FPKM.genes.xls
raw_counts.txt

data_processing:
Illumina bcl2fastq2 v2.19 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Read counts were calculated using HTSeq-count v0.6.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: excel file, normalized expression

source_name: ER+ breast cancer cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 0.2 mM L-glutamine, and 1% penicillin/streptomycin. In addition, 0.5 μgml-1 puromycin was added into the medium of MCF7/TGL/pQ cell lines.

extract_protocol:
Total RNA was extracted using the RNeasy Plus mini kit (Qiagen, 74134) and QIAshredder kit (Qiagen, 79654) according to the manufacturer’s protocol.
Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.
cDNA libraries were generated using the Illumina TruSeq RNA Sample preparation kit and sequenced with paired-end 50 bps on HiSeq4000 sequencer.

treatment_protocol: Cells were treated with CO at 250 ppm for 16 h. Control air condition was a regular cell culture incubator with 5% CO2.

tag: cell line

value: 250 ppm CO treated


title: ART (A09_pre_4) antibody derived tags


title: MCF7/TGL/pQ CO 2

description:
FPKM.genes.xls
raw_counts.txt


title: ART (A09_post_5) antibody derived tags


title: Yale Melanoma ITx2_1.5

value: PD


title: Yale Melanoma ITx2_1.4


title: ART (A09_pre_3) antibody derived tags


title: human pancreas cancer scRNA-seq replicate 2

last: Januszyk

address: 257 Campus Dr

institute: Stanford University


title: MCF7/TGL/pQ CO 1

description:
FPKM.genes.xls
raw_counts.txt


title: ART (A09_pre_2) antibody derived tags


title: Yale Melanoma ITx2_1.2


title: ART (A09_pre_1) antibody derived tags


title: ART (A09_post_4) antibody derived tags


title: CLL_211_D7

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

molecule: polyA RNA

source_name: PBMCs

growth_protocol: Blood samples were collected from the chronic lymphocytic leukemia (CLL) patients before and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

value: M

tag: cll-disease status

value: naive


title: Yale Melanoma ITx2_1.3

tag: age


title: ART (A09_post_2) antibody derived tags


title: Yale Melanoma ITx2_1.1


title: MDA-MB-231/TGL CO 3

description:
FPKM.genes.xls
raw_counts.txt

source_name: triple-negative breast cancer cell line


title: MCF7/TGL/pQ control 2

description:
FPKM.genes.xls
raw_counts.txt

value: untreated control


title: MCF7/TGL/pQ control 1

description:
FPKM.genes.xls
raw_counts.txt


title: Yale Melanoma ITx1_5.12


title: CLL_205_D7

value: frontline


title: MCF7/TGL/pQ control 3

description:
FPKM.genes.xls
raw_counts.txt


title: ART (A09_post_3) antibody derived tags


title: ART (B45_B2) antibody derived tags

data_processing:
ATAC libraries were demultiplexed using 10X Genomics cellranger-atac (v2.0) pipeline. NovaSeq-based sequences were filtered using 10X Genomics index-hopping-filter (v1.1).
ATAC libraries were processed (demultiplexing, alignment, and counting) using 10X Genomics cellranger-atac (v2.0) pipeline
ADT libraries were demultiplexed using bcl2fastq2 (v2.20.0.422)
ADT fastq files were mapped to the TotalSeaA cocktail catalog using kallisto (v0.46.2) and bustools (v0.40.0) as documented with the kite pipeline (https://github.com/pachterlab/kite)
Assembly: chimeric hg38 with viral genome (HXB2, SUMA, or autologous sequences)
Supplementary files format and content: fragment.tsv.gz output file from 10X Genomics cellranger-atac count for ATAC data
Supplementary files format and content: tar.gz folder of kallisto bus output for ADT data

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for ASAPseq protocol
OTHER: single cell ASAPseq


title: CLL_211_D0


title: MDA-MB-231/TGL CO 1

description:
FPKM.genes.xls
raw_counts.txt


title: MDA-MB-231/TGL CO 2

description:
FPKM.genes.xls
raw_counts.txt


title: ART (B45_B1) antibody derived tags


title: CLL_205_D0


title: Yale Melanoma ITx1_5.11

value: PEMBRO


title: ART (B45_A3) antibody derived tags


title: MDA-MB-231/TGL control 2

description:
FPKM.genes.xls
raw_counts.txt


title: CLL_105_D0

value: F

value: remission


title: CLL_213_D34


title: Yale Melanoma ITx1_5.10

value: NO

value: IPI+NIVO


title: CLL_105_D7


title: ART (A08_2) ATAC fragments

value: ATAC


title: Yale Melanoma ITx1_5.9

value: PR

value: YES


title: ART (A08_4) ATAC fragments


title: MDA-MB-231/TGL control 1

description:
FPKM.genes.xls
raw_counts.txt


title: ART (A08_1) ATAC fragments


title: Yale Melanoma ITx1_5.7

value: SD

value: NIVO


title: ART (B45_A2) antibody derived tags

value: ADT


title: Yale Melanoma ITx1_5.6

value: CR


title: chd8_KO

data_processing:
Alignment, barcode and UMI filtering and counting were performed with Cell Ranger 3.1.0 count, using GRCz11 assembly and Ensembl release 98 annotations.
Genome_build: GRCz11
Supplementary_files_format_and_content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary_files_format_and_content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Intestinal cells

extract_protocol:
chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 µg/ml tricaine solution. The fish were dissected, their guts were harvested and placed in RPMI at room temperature. The guts were rolled on paper moistened with RPMI to remove the fat residue, then placed in RPMI with 10% fetal calf serum and cut into small pieces that were placed in 1 ml of digestion medium (1 ml of RPMI - 12 µl of activated fetal calf serum - 10 mg of dispase collagenase) for 15 minutes, at 37 °C, under agitation at 500 rpm. The cells were then filtered on a cell filter (diameter 40 µm, Dutscher, ref 141378C), using the plunger of 1 ml syringe.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of > 90 % viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). 10,000 total cells were loaded per well to yield approximately 6,500 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). Single cell 3’ mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell 3’ Reagent Kits (v3 Chemistry). Briefly, GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEMs were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR with 14 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).


title: MDA-MB-231/TGL control 3

description:
FPKM.genes.xls
raw_counts.txt


title: ART (A08_4) antibody derived tags


title: CLL_213_D0


title: Yale Melanoma ITx1_5.3

source_name: Malignant melanoma


title: Yale Melanoma ITx1_5.4


title: chd8_WT


title: Yale Melanoma ITx1_5.8


title: GIM-024 C3

city: Lund

first: Vivien

last: Horvath

address: Sölvegatan 17

institute: Lund University

description:
small RNA (17-30bp)
replica 3

data_processing:
We obtained 771 million single-end reads for all the 36 samples in total (three tolerant, three sensitive strains in treated and control conditions and in three biological replicates).
Fastq sequence quality was assessed using FastQC (v0.11.9) (www.bioinformatics.babraham.ac.uk/projects/fastqc).
Then, the Illumina sequencing reads were filtered using BBduk (parameters: minlen=15 qtrim=rl ktrim=r k=21 hdist=2 mink=8, http://jgi.doe.gov/data-and-tools/bb-tools/) to remove adapters and ribosomal RNA sequences.
The trimmed reads were then analyzed using SPORTS 1.0. (Shi et al 2018): an annotation pipeline designed to optimize the annotation and quantification of canonical and non-canonical small RNAs including tRNA derived fragments (tRFs) in small RNA sequencing data (https://github.com/junchaoshi/sports1.0).
Next, to identify the genes that could be targeted by the tRFs, we mapped the tRF sequences – taken from SPORTS output file –against the full transcripts of the D. melanogaster r6.15 transcriptome using RNAhybrid (Krüger et al 2006). RNA hybrid was used with the following parameters: (-u 1, -m 18500, -b 1, -v 1). Only the first 12nt of each sequence —containing the seed region—was used for the query sequences (Karaiskos et al 2015). While two minimum free energy (MFE) cut off points were explored (MFE -20 and -30), we chose a stringent method and used MFE -30 cut off as also used in Seong et al 2019. Transcripts with at least 10 tRF mapped reads in at least two replicates per sample were used for further analysis.
Genome_build: dm6.15

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: Flies were collected in 2015 from different European locations by members of the DrosEU consortium. Flies were inbred for 20 generations, . Fly stocks were kept at 25 °C and 65% relative humidity with 12h day and night cycles.

extract_protocol:
Total RNA was isolated using Trizol (Thermo Fisher Scientific) from three replicates of 4-7 day-old flies after desiccation stress and in control conditions. For the extraction 30 whole female flies were used per replicate. RNA samples were treated with DNAse I (Thermo Fisher Scientific) following manufacturer’s instructions. small RNAs were obtained by gel size selection from total RNA using 10% TBE urea gel (Thermo Fisher Scientific). Fragments between 17 and 30 nucleotides were carefully cut from the gel and were eluted for subsequent sequencing (Quiagen elution kit). Quality check was performed using Bioanalyzer small RNA kit. Libraries were sequenced using Illumina 50 bp single-end reads.
Libraries were done using standard Illumina library prep kits.

treatment_protocol: In treated conditions,  flies were placed in empty vials and between the cotton and the parafilm, three grams of silica gel (Merck) were placed, so they were starved and desiccated. Control vials were prepared similarly, except that it contained 1mL of 1% agar on the bottom of the vial to prevent desiccation. Agar in the tubes provides hydration but not food source for the control flies (Sinclair et al 2007).

tag: condition

value: Control

value: Female


title: ART (A08_2) antibody derived tags


title: ART (A08_1) antibody derived tags


title: CLL_212_D2


title: Yale Melanoma ITx1_5.5

tag: bor


title: CLL_212_D0


title: Yale Melanoma ITx1_5.2

tag: itx


title: CLL_213_D7

value: naive


title: GIM-024 C2

description:
small RNA (17-30bp)
replica 2


title: GIM-024 C1

description:
small RNA (17-30bp)
replica 1


title: ART (A01_4) antibody derived tags


title: CLL_210_D31

value: M

value: relapsed


title: Yale Melanoma ITx1_5.1

value: PEMBRO

tag: prior checkpoint blockade


title: CLL_210_D7


title: ART (A01_3) antibody derived tags


title: CLL_210_D1


title: GIM-024 T3

description:
small RNA (17-30bp)
replica 3

value: Desiccation treated


title: ART (A01_1) antibody derived tags


title: Yale Melanoma ITx1_4.11

value: PD


title: ART (A01_2) antibody derived tags


title: Yale Melanoma ITx1_4.10

value: NO


title: Yale Melanoma ITx1_4.12

value: IPI+NIVO


title: in vitro ATAC fragments

value: ATAC


title: GIM-024 T2

description:
small RNA (17-30bp)
replica 2


title: CLL_212_D7

value: F

value: remission


title: CLL_209_D30


title: CLL_209_D8


title: in vitro antibody derived tags


title: GIM-012 C3

description:
small RNA (17-30bp)
replica 3


title: Yale Melanoma ITx1_4.8


title: GIM-012 C2

description:
small RNA (17-30bp)
replica 2


title: Yale Melanoma ITx1_4.9

value: PR


title: CLL_209_D2


title: Yale Melanoma ITx1_4.7

value: SD

value: YES


title: GIM-012 C1

description:
small RNA (17-30bp)
replica 1


title: CLL_209_D0


title: CLL_208_D7


title: GIM-024 T1

description:
small RNA (17-30bp)
replica 1


title: GIM-012 T3

description:
small RNA (17-30bp)
replica 3


title: Yale Melanoma ITx1_4.6

value: CR


title: Yale Melanoma ITx1_4.5


title: CLL_208_D0


title: COR-023 C3

description:
small RNA (17-30bp)
replica 3

value: Control


title: CLL_206_D33


title: Yale Melanoma ITx1_4.4


title: GIM-012 T1

description:
small RNA (17-30bp)
replica 1

value: Female


title: Yale Melanoma ITx1_4.3

value: NIVO


title: Yale Melanoma ITx1_4.2


title: COR-023 C2

description:
small RNA (17-30bp)
replica 2


title: Yale Melanoma ITx1_4.1


title: Yale Melanoma ITx1_3.12


title: CLL_206_D2

value: M


title: CLL_206_D7


title: Comparison with AP and cortex replication 4

city: Nagoya

first: Hirokazu

last: Takahashi

state: Aichi

address: Furo-cho, Chikusa

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description:
Biological replicate 4 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep4

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent).  cRNA was hybridized to microarray using hybridization oven G2531A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505C  according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 10.5.1.1 (Agilent).

organism: Glycine max

source_name: AP and cortex were isolated from hypocotyl

label_protocol: Total RNAs (10 ng each) were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Plastic pots (300 mL) were filled with 200 mL silica sand. A 2 cm deep hole was dug in each pot, into which a single soybean seed was sown and covered with a small amount of the silica sand. Seedlings were grown at 25 °C under 14 h light/10 h dark conditions for approximately 10 until the unifoliate leaves were fully expanded (approximately 10-day-old).

extract_protocol: Total RNA was extracted from each LM-isolated tissue by Picopure RNA isolation kit (Thermo Fisher Scientific)

treatment_protocol: The soil was waterlogged by raising the deionized water (DI), and water levels were maintained at 3 cm above the soil surface for 5d.

tag: culivars

value: Enrei

tag: Stage

value: about 10 days (the unifoliate leaves were fully expanded )

value: Waterlogging

tag: tissue

value: Cortex (CO)

value: AP


title: Comparison with AP and cortex replication 6

description:
Biological replicate 6 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep6


title: Comparison with AP and cortex replication 3

description:
Biological replicate 3 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep3


title: Comparison with AP and cortex replication 5

description:
Biological replicate 5 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep5


title: Comparison with AP and cortex replication 1

description:
Biological replicate 1 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep1


title: CLL_208_D1

value: relapsed


title: CLL_206_D0


title: Yale Melanoma ITx1_3.11

tag: long-term benefit

value: NO

value: IPI+NIVO


title: Comparison with AP and cortex replication 2

description:
Biological replicate 2 of 6. AP and CO were isolated from waterlogged hypocotyl using LCM
AP vs CO_Rep2


title: Comparison with phellogen and cortex replication 6

description:
Biological replicate 6 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep6

source_name: PH and cortex were isolated from hypocotyl

value: Phellogen (PH)


title: GIM-012 T2

description:
small RNA (17-30bp)
replica 2

value: Desiccation treated

tag: Sex


title: COR-023 T3

description:
small RNA (17-30bp)
replica 3


title: CLL_203_D7

value: F

value: frontline


title: Yale Melanoma ITx1_3.10

value: PD


title: CLL_203_D0


title: Comparison with phellogen and cortex replication 5

description:
Biological replicate 5 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep5

tag: treatment


title: CLL_201_D35


title: COR-023 C1

description:
small RNA (17-30bp)
replica 1

value: Control


title: Yale Melanoma ITx1_3.9

value: YES


title: CLL_203_D34


title: COR-023 T1

description:
small RNA (17-30bp)
replica 1

value: Female


title: MUN-013 C3

description:
small RNA (17-30bp)
replica 3


title: MUN-013 C2

description:
small RNA (17-30bp)
replica 2


title: Yale Melanoma ITx1_3.8

value: PEMBRO


title: Yale Melanoma ITx1_3.7


title: CLL_201_D7

value: M


title: MUN-013 C1

description:
small RNA (17-30bp)
replica 1


title: Comparison with phellogen and cortex replication 4

description:
Biological replicate 4 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep4

value: Enrei

value: about 10 days (the unifoliate leaves were fully expanded )


title: CLL_201_D2


title: Comparison with phellogen and cortex replication 2

description:
Biological replicate 2 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep2

value: Waterlogging

value: Cortex (CO)


title: Comparison with phellogen and cortex replication 3

description:
Biological replicate 3 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep3


title: CLL_201_D0

value: relapsed


title: Yale Melanoma ITx1_3.4

value: PR

value: NO

value: NIVO


title: Yale Melanoma ITx1_3.5

value: SD


title: Yale Melanoma ITx1_3.6

value: CR

value: IPI+NIVO


title: MUN-013 T3

description:
small RNA (17-30bp)
replica 3

value: Desiccation treated


title: siRNA_2_CUTnTAG

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description: 100-bp read length

data_processing:
library strategy: Cut&Tag
reads exhibiting 3’ contamination by this sequence, which was removed prior to alignment using Trimmomatic version 0.39
Read alignment was performed using Bowtie2 version 2.4.460 in end-to-end and very sensitive modes using the GRCh37 reference sequence
Peak finding was accomplished using Homer version 4.11
Assembly: GRCh37
Supplementary files format and content: bed files of read alignments

source_name: monocyte-derived macrophages

growth_protocol: CD14+ monocytes were cultured at 37°C and 5% CO2 in RPMI medium supplemented with 10% fetal calf serum (FCS) and 50 ng/mL macrophage colony-stimulating factor (M-CSF, Peprotech)

extract_protocol: Cleavage Under Targets and Tagmentation (CUT&Tag) is a method to investigate genomic localization of histone modifications and some transcription factors to reveal interactions between proteins and DNA or identifying DNA binding sites for proteins of interest. CUT&Tag is based on the same principles as ChIP-Seq but with several changes to the protocol, where fresh cells are bound to concanavalin A beads and the antibody incubation is performed with cells in their native state. Directly following antibody binding, the chromatin is sheared, tagmentation performed using the protein A-Tn5 (pA-Tn5) transposome and NGS libraries are prepared. CUT&Tag-IT™ Assay Kits (Catalog No. 53160Active Motif North America) were used for tagmentation and library preparation as per kit procedures. Briefly, 50,000 to 100,000 cells were harvested and washed with 1X wash Buffer supplemented with Protease Inhibitor Cocktail. Then the cells were bound to Concanavalin A beads and incubated with 1ry antibody overnight at 4°C with orbital mixing. This was followed by 2 hours incubation with Guinea Pig Anti-Rabbit Antibody secondary antibody 1:100 in Dig-Wash Buffer. Cells were incubated for 60 minutes with pA-Tn5 Transposomes diluted to 1:100 in Dig-300 buffer. Then 50 μl of Tagmentation Master Mix was added to each sample and incubated at 37°C for 30 minutes in a thermomixer set at 800 rpm. This was followed by extraction and amplification of tagmented DNA with library preparation using unique combinations of i7/i5 primers which are based on Illumina’s Nextera adapters. Finally, the library was purified by SPRI bead clean-up.

treatment_protocol: Small interfering RNA (siRNA)  transfection was performed with Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions using 50 nM of the specific siRNA or non-targeting control for 48 hours

value: monocyte-derived macrophages

tag: cell type

value: primary cells

tag: antibody


title: siRNA_1_CUTnTAG

description: 100-bp read length


title: MUN-013 T2

description:
small RNA (17-30bp)
replica 2

value: Female


title: Scramble_1_CUTnTAG

description: 100-bp read length


title: CLL_107_D26

value: F


title: Comparison with phellogen and cortex replication 1

description:
Biological replicate 1 of 6. PH and CO were isolated from waterlogged hypocotyl using LCM
PH vs CO_Rep1

value: Phellogen (PH)


title: Yale Melanoma ITx1_3.3


title: CLL_107_D7


title: LUN-07 C2

description:
small RNA (17-30bp)
replica 2

value: Control


title: CLL_107_D0


title: siRNA_1_ATAC

description: 100-bp read length

data_processing:
reads exhibiting 3’ contamination by this sequence, which was removed prior to alignment using Trimmomatic version 0.39
Read alignment was performed using Bowtie2 version 2.4.460 in end-to-end and very sensitive modes using the GRCh37 reference sequence
Peak finding was accomplished using Homer version 4.11
Assembly: GRCh37
Supplementary files format and content: bed files of read alignments

extract_protocol: In the assay, intact nuclei are treated with a hyperactive Tn5 transposase mutant which is able to simultaneously tag the target DNA with sequencing adapters to fragment the DNA in a process termed “tagmentation”. The ATAC-Seq Kit (Catalog No. 53150 Active Motif North America) was used for tagmentation and library preparation as per kit procedures. Briefly, cells were counted and aliquots of 50,000 to 100,000 cells were centrifuged at 500 x g for 5 minute at 4°C. Then the pellet was resuspended in 100 μl ice-cold ATAC Lysis Buffer. 50 μl of Tagmentation Master Mix was added to each sample and incubated at 37°C for 30 minutes in a thermomixer set at 800 rpm. This was followed by extraction and amplification of the tagmented DNA with library preparation using unique combinations of i7/i5 primers which are based on Illumina’s Nextera adapters. Finally, the library was purified using SPRI bead clean-up.

tag: methodology

value: tagmentation


title: Yale Melanoma ITx1_3.1

value: YES


title: Yale Melanoma ITx1_2.12

value: PD


title: Scramble_2_ATAC

description: 100-bp read length

source_name: primary monocyte-derived macrophages

tag: cell line

value: primary monocyte-derived macrophages


title: siRNA_2_ATAC

description: 100-bp read length


title: CLL_106_D28

tag: gender

value: relapsed


title: Scramble_2_CUTnTAG

description: 100-bp read length


title: Scramble_1_ATAC

description: 100-bp read length


title: Yale Melanoma ITx1_2.11

value: PEMBRO

value: NO


title: COR-023 T2

description:
small RNA (17-30bp)
replica 2


title: LUN-07 C1

description:
small RNA (17-30bp)
replica 1


title: LUN-07 T3

description:
small RNA (17-30bp)
replica 3


title: CLL_106_D7

tag: cll-disease status


title: MUN-013 T1

description:
small RNA (17-30bp)
replica 1


title: siRNA_Cont_5

description: 100-bp read length

data_processing:
Read alignment and junction mapping to genome build GRCh37 were accomplished using STAR version 2.7.6a
Known splice junctions from the University of California Santa Cruz (UCSC) hg19 genome annotation were supplied to the aligner and de novo junction discovery was also permitted
Differential gene expression analysis and statistical testing were performed using Cuffdiff2 version 2.2.158, employing the hg19 genome annotation
Transcript expression was calculated as gene-level relative abundance in fragments per kilobase of exon model per million mapped fragments and employed correction for transcript abundance bias
Assembly: hg19
Supplementary files format and content: csv,FPKM of expression level

extract_protocol:
Total RNA was isolated from MDMs transfected with MBOAT7 siRNA or control with and without LPS using the RNA mini kit (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer. Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina). Briefly, mRNA was purified, fragmented, and used for first- and second-strand cDNA synthesis followed by adenylation of 3′-ends. Samples were ligated to unique adaptors and subjected to PCR amplification. Libraries were validated using the 2100 BioAnalyzer (Agilent), normalized and pooled for sequencing. RNA-seq libraries prepared from three biological replicates for each condition were sequenced on the Illumina HiSeq 2000 using barcoded multiplexing and a 100-bp read length.
Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina)

tag: replicate


title: LUN-07 C3

description:
small RNA (17-30bp)
replica 3

tag: condition


title: CLL_106_D0

tag: age


title: Yale Melanoma ITx1_2.10

tag: bor

value: SD

tag: itx


title: LUN-07 T2

description:
small RNA (17-30bp)
replica 2


title: LUN-07 T1

description:
small RNA (17-30bp)
replica 1


title: siRNA_Cont_3

description: 100-bp read length


title: siRNA_Cont_4

description: 100-bp read length


title: siRNA_Cont_2

description: 100-bp read length


title: Yale Melanoma ITx1_2.9

value: PR

tag: prior checkpoint blockade


title: CLL_104_D34

value: M


title: Yale Melanoma ITx1_2.8

value: IPI+NIVO


title: TOM-08 C3

description:
small RNA (17-30bp)
replica 3


title: CLL_104_D7


title: TOM-08 C2

description:
small RNA (17-30bp)
replica 2


title: Yale Melanoma ITx1_2.7


title: TOM-08 C1

description:
small RNA (17-30bp)
replica 1


title: siRNA_Cont_0

description: 100-bp read length

value: monocyte-derived macrophages


title: CLL_104_D0


title: Yale Melanoma ITx1_2.6


title: CLL_106_D1


title: CLL_104_D2


title: CLL_103_D28


title: TOM-08 T2

description:
small RNA (17-30bp)
replica 2

value: Desiccation treated


title: Scram_Cont_5

description: 100-bp read length

value: primary cells


title: TOM-08 T3

description:
small RNA (17-30bp)
replica 3

value: Female


title: Scram_Cont_4

description: 100-bp read length


title: Yale Melanoma ITx1_2.4

value: CR


title: CLL_103_D7


title: TOM-08 T1

description:
small RNA (17-30bp)
replica 1


title: Yale Melanoma ITx1_2.3

value: NIVO


title: Scram_Cont_2

description: 100-bp read length


title: Yale Melanoma ITx1_2.2


title: CLL_103_D0


title: ART (B45_B2) ATAC fragments

tag: component

value: ATAC


title: Yale Melanoma ITx1_2.1

value: YES


title: Scram_Cont_1

description: 100-bp read length


title: Yale Melanoma ITx1_1.12

value: PD


title: Zar -/- GV oocyte, biol rep 3

city: Göttingen

first: Shiya

last: Cheng

address: Am Fassberg 11

department: Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
Basecalling with bcl2fastq v2.20.0.422
Adapter trimming with cutadapt v2.8 using the “-q 20 -m 35 -j 15” parameters
Read mapping with STAR v2.7.8a using the default settings
Read counting with HTSeq v0.13.5
Assembly: mm39
Supplementary files format and content: A table with counts for each feature

source_name: GV oocyte

extract_protocol:
Libraries and polyA mRNA were extracted and prepared from 10 oocytes using the QIAseq FX Single Cell RNA Library Kit
Libraries and polyA mRNA were extracted and prepared from 10 oocytes using the QIAseq FX Single Cell RNA Library Kit

tag: tissue

value: GV oocyte

value: C57BL/6N strain background

tag: genotype

value: Zar1 knockout