title: KO_low_5

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Halobacterium salinarum NRC-1 genome (RefSeq GCF_000006805.1) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset)
Count files were input into DeSeq2 to generate normalised counts, exclude outlier samples, and generate lists of differentially expressed genes in pairwise comparisons. (The normalised count file with all 24 samples is included in this GEO dataset)
Genome_build: GCF_000006805.1_ASM680v1
Supplementary_files_format_and_content: tab-delimited text file with raw counts for each gene
Supplementary_files_format_and_content: comma-separated values file with noramlised counts for each gene; all samples in a single file; rRNA genes removed.

source_name: Δura3 ΔhpyA_Reduced (3.4M NaCl)_archaeal cells

growth_protocol: 6 biological replicates of strains MDK407 (WT) and KAD100 (KO) were pre-cultured in rich media for ~96 hours, and diluted down to OD600 ~0.02. Identical replicates were grown in both optimal and reduced salt rich media (4.2M and 3.4M NaCl) and allowed to reach mid-exponential phase (~31-34 hours, OD~0.1-0.4). A 4mL cell pellet was flash frozen using liq N2 and kept overnight before RNA extraction.

extract_protocol:
Agilent Absolutely RNA Miniprep kit was used to to extract total RNA, following manufacturer's protocol. DNase digestion step was extended to 45 mins. gDNA contamination was ruled out using PCR amplification. Nucleic acid concentration measured using Nanodrop and Bioanalyzer (RNA 6000 Nano chip). rRNA was removed using the NEBNext Bacterial rRNA depletion kit; for replicates 1-3 of all conditions manufacturer-supplied probes were used, while for replicates 4-6, custom-designed probes targeted to Haloferax volcanii rRNA were used. rRNA depletion was verified using Bioanalyzer.
NEBNext Ultra II Directional RNA Library Prep kit was used to generate cDNA libraries from the rRNA-depleted samples. Library quality and concentration was checked using Bioanalyzer using High Sensitivity DNA chip. Samples were pooled (replicates 1-3 from all conditions in batch 1, replicates 4-6 in batch 2) and run in a single lane on Illumina NovaSeq 6000 paired-end sequencing at the Duke Sequencing Core.

value: {delta}ura3 {delta}hpyA

tag: salt concentration

value: Reduced (3.4M NaCl)

value: archaeal cells


title: V13_HJ7M2BBXX

status: Public on Aug 25 2021

type: SRA

city: San Diego

first: Amin

last: Haghani

state: CA

address: 5510 Morehouse Dr

country: USA

institute: Altos labs

description:
gene counts.csv
gene map.csv

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality checked with FastQC
adapter sequences were trimmed from the reads using Trimmomatic
Reads were aligned to the mm10 genome using the HISAT2 splice-aware aligner
alignments overlapping genes were counted using featureCounts version 1.5.0-p3 relative to Gencode version M11
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv files count values for each gene

molecule: total RNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Samples were homogenized and disrupted with pestles, 22-gauge needles, pipetting and QIA shredders (Qiagen #79654).  DNA was extracted using QIAzol (Qiagen #79306) from the organic layer for genotyping. RNA was extracted following the QIAGEN RNeasy plus universal protocol (Qiagen #73404). Extracted RNA was used to determine sex of mouse pups by qPCR for the Y-chromosome Sry gene.
RNA (600ng) was made into RNA-seq libraries using the Illumina RiboZero Gold library preparation kit and sequenced on an Illumina HiSeq 3000 sequencer at the Lieber Institute for Brain Development

treatment_protocol:
Prenatal transcriptome changes of air pollution were examined by exposing pregnant C57BL/6 dams to 300 mg/m3 nano-sized particulate matter (nPM) for 5 hr/day, 3 days/weeks beginning at gestational day 2 until birth.
A random number of 3 pups per sex of each group were euthanized at day 5 age for collection of blood and cerebral cortex

tag: Sex

value: M

tag: tissue

value: Cortex

tag: treatment

value: Exposed

tag: age (days)

value: 3 to 5

tag: strain

tag: rin

tag: lane


title: KO1-1

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

country: China

institute: Sun Yat-sen university

description: differentaited cells at day 7 (sample1)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

organism: Homo sapiens

source_name: SOX10 KO1 hiPSC-derived cells at day 7 (sample1)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

tag: genotype

value: SOX10 KO


title: Jurkat RB1-KO-Palbo 72h_rep 2 [10_RNAseq_in_vitro_Jurkat]

city: Melbourne

first: Emily

middle: Jane

last: Lelliott

state: VIC

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (from the Subread package, v1.5.0) prior to differential gene expression analysis using Voom/Limma.
Gene set enrichment analyses were performed using GSEA software (Broad Institute) and barcode plots were plotted using ReplotGSEA.R (part of the Rtoolbox R package).
Genome_build: Hg19

source_name: Jurkat cell line

growth_protocol: Jurkat cells were cultured in RPMI 1640 containing 10% FBS and 1% GlutaMAX

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions
Sequencing libraries were prepared using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria)
Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Cell cultures were treated with DMSO or 1uM palbociclib for 72h

tag: drug

value: Palbociclib 1uM

tag: treatment time

tag: cell line

value: Jurkat


title: V11_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: F


title: KO_low_4

city: Durham

first: Amy

last: Schmid

state: NC

address: 3242 French Family Science Center

institute: Duke University

organism: Halobacterium salinarum

tag: cell type


title: Jurkat RB1-KO-Palbo 72h_rep 1 [10_RNAseq_in_vitro_Jurkat]


title: Worm_EnGliaInf_1

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. Cells were sorted directly into Trizol. Total RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies). A total of 7 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies). The libraries were then normalized to 2,5 nM, pooled and loaded onto a HiSeq4000 (Illumina) to generate 75bp single-end reads.

treatment_protocol: All mice were injected with tamoxifen on two consecutive days 10 days prior cell isolation and some mice were infected with H. poly 7 days prior cell isolation.

value: Small intestine tunica muscularis

value: Enteric Glia

tag: age

value: Adult

tag: disease state

value: H. poly


title: KO_low_6


title: Worm_EnGliaCtrl_3

value: Naive


title: Worm_EnGliaCtrl_4


title: sample3_Marginal EAT

type: RNA

city: Yufu

first: Ichitaro

last: Abe

state: Oita

address: 1-1 Idaigaoka, Hasama

department: Department of Cardiology and Clinical Examination

country: Japan

institute: Oita University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: sample3, Marginal EAT

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions.

value: epicardial adipose

tag: location

value: marginal

tag: patient diagnosis

value: Atrial fibrillation (AF)


title: Worm_EnGliaCtrl_2


title: KO_low_1

value: {delta}ura3 {delta}hpyA

tag: salt concentration

value: Reduced (3.4M NaCl)

value: archaeal cells


title: Worm_EnGliaCtrl_1


title: Jurkat RB1-KO-DMSO 72h_rep 2 [10_RNAseq_in_vitro_Jurkat]

value: Dimethyl Sulfoxide (DMSO) (Vehicle)


title: V10_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

tag: Sex

value: Cortex

value: Unexposed

value: 3 to 5


title: Jurkat RB1-KO-DMSO 72h_rep 1 [10_RNAseq_in_vitro_Jurkat]

value: Jurkat


title: Jurkat WT-Palbo 72h_rep 3 [10_RNAseq_in_vitro_Jurkat]

value: Palbociclib 1uM


title: KO_optimal_6

source_name: Δura3 ΔhpyA_Optimal (4.2M NaCl)_archaeal cells

value: Optimal (4.2M NaCl)


title: sample2_Marginal EAT

source_name: sample2, Marginal EAT

tag: tissue


title: V09_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: F

tag: treatment

value: Exposed


title: sample1_Central EAT

source_name: sample1, Central EAT

value: central


title: sample2_Central EAT

source_name: sample2, Central EAT


title: Jurkat RB1-KO-DMSO 72h_rep 3 [10_RNAseq_in_vitro_Jurkat]


title: sample3_Central EAT

source_name: sample3, Central EAT


title: KO_low_3


title: sample1_Marginal EAT

source_name: sample1, Marginal EAT


title: KO_optimal_5


title: Jurkat WT-Palbo 72h_rep 1 [10_RNAseq_in_vitro_Jurkat]


title: KO_optimal_4


title: PA_normoxia

city: New Haven

first: Edward

middle: Paul

last: Manning

state: CT

address: TAC 440 South, 300 Cedar St

institute: Yale School of Medicine, West Haven VA

data_processing:
Raw sequencing reads were demultiplexed based on sample index adaptors, which were added during the last step of cDNA library preparation. Possible adaptor and/or primer contamination were removed using Cutadapt. We processed the RNA-sequence data using the scRNA-seq implementation of STAR (STARsolo), where reads were mapped to the murine reference genome GRCm38 release M22 (GRCm38.p6), collapsed and counted, and summarized to a gene expression matrix. Data were analyzed and visualized using the R packages Seurat
Genome_build: GRCm38 release M22 (GRCm38.p6)
Supplementary_files_format_and_content: RDS

source_name: pulmonary arterial cells

extract_protocol: The pulmonary arteries were chopped mechanically and placed in 1mg/ml collagenase (Roche) and 3 U/ml elastase (Worthington). Following cellular dissociation, we barcoded unique mRNA molecules of each cell using our 10x Genomics Chromium platform (3’ v3.1 kit), a droplet-based microfluidic system, and performed reverse transcription, cDNA amplification, fragmentation, adaptor ligation, and sample index PCR according to the manufacturer’s protocol. High sensitivity DNA bioanalyzer traces of cDNA after barcoding and of the final cDNA library were evaluated for quality control. The final cDNA libraries were sequenced on a HiSeq 4000 Illumina platform in our core facility aiming for 150 million reads per library.

value: arterial

value: male


title: PA_hypoxia


title: Jurkat WT-Palbo 72h_rep 2 [10_RNAseq_in_vitro_Jurkat]


title: KO_low_2


title: Jurkat WT-DMSO 72h_rep 3 [10_RNAseq_in_vitro_Jurkat]


title: KO_optimal_3


title: Jurkat WT-DMSO 72h_rep 2 [10_RNAseq_in_vitro_Jurkat]


title: KO_optimal_2


title: Jurkat WT-DMSO 72h_rep 1 [10_RNAseq_in_vitro_Jurkat]


title: Lewis Y CAR T Palbo_rep 2 [9_RNAseq_in_vitro_human_LeY_CAR]

source_name: Human Lewis Y CAR T cells CD3--activated in vitro

growth_protocol: Human peripheral blood mono- nuclear cells (PBMCs) were isolated from normal donor buffy coats and retrovirally transduced with an anti-human LeY chimeric receptor. PBMCs were stimulated with anti-human CD3 (OKT3 30 ng/ml, Ortho Biotech) and IL-2 (600 units/ ml), followed 3 and 4 days later by incubation with supernatant from the PG13 retroviral producer cell line on a Retronectin (Takara Bio, Otsu, Japan) matrix as per the manufacturer’s instructions. Briefly, Retronectin was coated at a concentration of 6 mg/cm2 in non-tissue culture six-well plates (Becton Dickinson, Franklin Lakes, NJ, USA) and incubated with 5 ml of retroviral supernatant. After 4 h, supernatant was removed and 2.5 x106 T cells in 5 ml of complete media added for 12 h. Cells were maintained in RPMI 1640 plus 20 mM HEPES containing 10% ABS, 1% GlutaMAX, 1 mM Sodium Pyruvate, 1 mM MEM Non-Essential Amino Acids, 0.1% 2-mercaptoethanol and Antibiotic-Antimitotic and cultured at 37 °C in 5% CO2

treatment_protocol: 8d post-activation, transduced CAR T cell cultures were treated with DMSO or 1uM palbociclib for 7d

tag: culture & treatment protocol

value: CAR T cells treated 8d post-activation and analysed 15d post-activation

value: Lewis Y CAR T cells


title: KO_optimal_1

tag: strain

value: {delta}ura3 {delta}hpyA


title: WT_low_5

source_name: Δura3_Reduced (3.4M NaCl)_archaeal cells

value: Reduced (3.4M NaCl)


title: WT_low_6

value: archaeal cells


title: Lewis Y CAR T DMSO_rep 2 [9_RNAseq_in_vitro_human_LeY_CAR]

value: Dimethyl Sulfoxide (DMSO) (Vehicle)


title: MCMV_CD27- CD62L- cells derived from transferred CD27+ CD62L- Ly49H+ NK cells_d8pi_1

city: München

first: Sophie

last: Flommersfeld

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University of Munich

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 11

data_processing:
The gene expression count matrix was obtained using Salmon (version 0.9.1; Genome Reference Consortium Mouse Build 38).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table, in csv format, with raw gene counts.
Supplementary_files_format_and_content: Matrix table, in csv format, with size factor normalized gene counts.

source_name: splenic NK cells

extract_protocol:
500 cells were sorted of each population. Arcturus Pico Pure Isolation Kit was used for RNA isolation and SMART Seq V4 Ultra low input RNA Kit (Takara) was used for cDNA generation according to the manufacture's protocol.
Nextera XT DNA Kit (Illumina) was used according to the manufacturer's protocol for library contruction.

value: spleen

value: Ly49H+ NK cells


title: MCMV_CD27- CD62L+ cells derived from transferred CD27- CD62L+ Ly49H+ NK cells_d8pi_1

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 13


title: Ly49H+ NK cells_spleen_steady state

description: scRNAseq

data_processing:
Cell Ranger (version 2.1.0; 10x Genomics) was used for demultiplexing and alignment (resulting in the bam file) as well as counting (resulting in the mtx and tsv files) using default parameters.
velocyto 27 (version 0.17.17) performed counting of spliced and unspliced RNA molecules (based on bam file) to create loom file.
Python software package SCANPY (version 1.4.4) was used for downstream analysis.
Cells with more than 5% mitochondrial counts were filtered out (7 cells); additionally, one cell for which total counts exceeded those of the other cells by a factor of three was excluded from further analysis. Genes with less than 20 counts were filtered out.
Genome_build: Mouse reference genome GRCm38
Supplementary_files_format_and_content: Output of the Cell Ranger Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized).
Supplementary_files_format_and_content: Unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts.

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics).
Chromium Single Cell 3′ Library Construction Kit (10x Genomics).
Paired-end, single indexing.


title: hippocampus_Control_rep2

city: Shanghai

first: Kexin

last: Zou

address: 131 Dongan Rd.

department: School of Medicine

institute: Fudan University

description: SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using GenomeStudio (1.9.0) following the manufacturer's protocol

source_name: hippocampus,Control

label_protocol: Standard Illumina Labelling protocol

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) kit, following the manufacturer's protocol.

value: ICR

value: hippocampus

tag: gender

tag: generation

value: Control


title: MCMV_CD27- CD62L- cells derived from transferred CD27+ CD62L- Ly49H+ NK cells_d8pi_2

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 12


title: Lewis Y CAR T Palbo_rep 1 [9_RNAseq_in_vitro_human_LeY_CAR]

value: Palbociclib 1uM


title: MCMV_CD27- CD62L- cells derived from transferred CD27- CD62L+ Ly49H+ NK cells_d8pi_2

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 16


title: MCMV_CD27- CD62L+ cells derived from transferred CD27- CD62L+ Ly49H+ NK cells_d8pi_2

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 14


title: MCMV_CD27- CD62L- cells derived from transferred CD27- CD62L+ Ly49H+ NK cells_d8pi_1

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 15


title: hippocampus_Control_rep3

description: SAMPLE 13


title: hippocampus_Control_rep4

description: SAMPLE 14


title: hippocampus_Control_rep5

description: SAMPLE 15


title: MCMV_CD27+ CD62L- cells derived from transferred CD27+ CD62L- Ly49H+ NK cells_d8pi_2

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 10


title: WT_low_3

tag: genotype


title: MCMV_CD27+ CD62L- cells derived from transferred CD27+ CD62L- Ly49H+ NK cells_d8pi_1

description:
bulkRNA-Seq of 500 progeny cells
rawCounts_d8pi_Fig_5G.csv
normalizedCounts_d8pi_Fig_5G.csv
Sample 9


title: Lewis Y CAR T DMSO_rep 1 [9_RNAseq_in_vitro_human_LeY_CAR]

tag: drug


title: Melanoma sc-seq - VDJ [02_patient_samples]

data_processing:
Cell Ranger: Reads were aligned to the hg38 reference genome, cellular barcodes were de-multiplexed and unique molecular identifiers (UMI) and antibody capture (Antibody Derived Tags (ADT) and Hashtag oligos (HTO)) were quantified using 10x Genomics' Cell Ranger software (version 3.1.0). Cell barcodes containing RNA or antibody counts from cells from more than one sample (inter-sample doublets) were identified using Seurat's HTODemux function. Barcodes containing counts from more than one cell within the same sample (intra-sample doublets) were identified using the Scrublet python package (version 0.2.1) . A cutoff of more than one median absolute deviation (MAD) value above the median Scrublet score was chosen. Cells identified as either type of doublet were removed from the analysis. Relative transcription factor activity in each cell was estimated using the Single-Cell Regulatory Network Inference And Clustering (SCENIC) method. Area-under-curve (AUC) scores for transcription factors were calculated based on inferred gene regulatory networks using the pyscenic python package (version 0.9.19). Gene expression and antibody count matrices were processed in R (version 3.6.1) using the Seurat R package (version 3.1.0) . RNA transcript counts for barcodes identified as cells by Cell Ranger were normalized using sctransform via Seurat's SCTransform function. The counts were first transformed with no covariates in the sctransform model then cell cycle phase scores were estimated using Seurat's CellCycleScoring function with mouse homologues of the cell cycle gene sets provided by Seurat. The sctransform normalization was then rerun with the cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell as variables to be regressed out in the model. Principal component analysis (PCA) was then performed on the sctransform scaled RNA expression values for genes with residual variance in the sctransform model greater than 1.3. A shared-nearest-neighbours (SNN) network was calculated using the top 10 principal components using the FindNeighbors function with k-nearest neighbors set to 50 and cosine distance metric. The SNN network was then used to identify cell populations using the FindClusters function using the Louvain algorithm with resolution parameter 0.6. Uniform Manifold Approximation and Projection (UMAP) values were also calculated using the RunUMAP function with the top 10 principal components as input and parameters n.neighbors=50 and metric="cosine". Monocle3 was utilized for pseudotime analysis using default setting.
Genome_build: hg38

source_name: Melanoma patient - peripheral T cells

growth_protocol: PBMC were isolated from a melanoma patient during the course of their treatment

extract_protocol:
PBMC were thawed and T cells were isolated by FAC sorting. Isolated cells were then labelled with ADT and HTO, followed by droplet encapsulation for single cell sequencing using 10xGenomics platform
TCR-sequencing and Hashing/CITE-Seq were performed using the 10x Single Cell V(D)J kit with Feature Barcoding (enabled for 5′ Gene Expression, TCR and Feature Barcoding for Cell Surface Protein) protocol following the manufacturer’s instructions. TCR libraries were prepared using the 10x Chromium Single Cell V(D)J Enrichment Kit, Human (or Mouse) T Cell. 5’ HTO/ADT (one library) was prepared using Chromium Single Cell 5' Feature Barcode Library Kit and indexed using the Chromium i7 Multiplex Kit N, Set A.

treatment_protocol: with combination palbociclib and binimetinib (palbo/bini) for one month, followed by a switch to ipilimumab and nivolumab (ipi/nivo). Samples were collected and cryopreserved prior to and 2 weeks into treatment with palbo/bini, and prior to and 1 month into treatment with ipi/nivo

tag: target/sample (oligo barcode)

value: Melanoma


title: hippocampus_F2-GDM_rep4

description: SAMPLE 9


title: ILC1_1

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 7

data_processing:
The gene expression count matrix was obtained using Salmon (version 0.9.1; Genome Reference Consortium Mouse Build 38).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table, in csv format, with raw gene counts.
Supplementary_files_format_and_content: Matrix table, in csv format, with size factor normalized gene counts.

source_name: splenic ILC1s

extract_protocol:
500 cells were sorted of each population. Arcturus Pico Pure Isolation Kit was used for RNA isolation and SMART Seq V4 Ultra low input RNA Kit (Takara) was used for cDNA generation according to the manufacturer's protocol.
Nextera XT DNA Kit (Illumina) was used according to the manufacturer's protocol for library construction.


title: ILC1_2

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 8


title: Melanoma sc-seq - ADT/HTO [02_patient_samples]

value: ADT [CD4 (GAGGTTAGTGATGGA); CD8 (GCGCAACTTGATGAT); CD279 (ACAGCGCCGTATTTA); CD366 (TGTCCTACCCAACTT); IL7R (GTGTGTTGTCCTATG); CD7 (TGGATTCCCGGACTT); CD183 (GCGATGGTAGATTAT); CD62L(GTCCCTGCAACTTGA )]; HTO [Baseline (palbo/bini) (Hash#1 - GTCAACTCTTTAGCG); 2wk palbo/bini (Hash#2 - TGATGGCCTATTGGG); Baseline (ipi/nivo) (Hash#3 - TTCCGCCTCTCTTTG); 1m ipi/nivo (Hash#4 - AGTAAGTTCAGCGTA)]


title: CD27+ CD62L- Ly49H+ NK_spleen_steady state_2

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 6

tag: cell markers


title: WT_low_1

tag: cell type


title: Melanoma sc-seq - GEX [02_patient_samples]


title: WT_optimal_6

source_name: Δura3_Optimal (4.2M NaCl)_archaeal cells

value: Optimal (4.2M NaCl)


title: WT_low_4


title: hippocampus_F2-GDM_rep5

description: SAMPLE 10

tag: age


title: hippocampus_F2-GDM_rep3

description: SAMPLE 8


title: CD27+ CD62L- Ly49H+ NK_spleen_steady state_1

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 5


title: hippocampus_Control_rep1

description: SAMPLE 11


title: hippocampus_F2-GDM_rep2

description: SAMPLE 7


title: siRBM10 pulldown  with Anti-StarPAP Antibody

city: Trivandrum

first: Rakesh

middle: S

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

data_processing:
Quality report checked with FastQC galaxy version 0.72+galaxy1, Adapter removal by CutAdapt version 1.14
Filtered and trimmed using CLIP Tool Kit
BWA version 0.7.12 with parameters bwa aln -t 4 -n 0.06 -q 20 used for mapping
Peak calling was then performed using Model-based Analysis of ChIP-Seq (MACS2) version 2.1.1.20160309.6 parameters threshold 0.05 and mFold  minimum 5 and maximum 50
Genome_build: hg19
Supplementary_files_format_and_content: peak called .bed files

source_name: HEK293 Cell lines

growth_protocol: HEK 293 cells were obtained from American Type Cell Culture Collection.HEK 293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (Himedia) with 10% Foetal Bovine Serum (Gibco) and 50 U/ml Pencillin Streptomycin (Gibco) at 37°C in 5% CO2

extract_protocol:
HEK 293 cells grown on 15 cm plates were UV crosslinked with 400 mJ/cm2 . Cells were then harvested and lysed by sonication in the lysis buffer. Immunoprecipitation was carried out from the supernatant using anti-Star-PAP antibody conjugated with pre-incubated Dynabeads Protein A (Invitrogen) in the presence of bridging anti-rabbit IgG antibody. Protein-RNA complexes were subjected to Proteinase K (Sigma) digestion the released CLIP RNA fragments were extracted by acid Phenol:Chloroform:Isoamyl alcohol.
Library preparation and sequencing was carried out at Genotypic Technologies (http://www.genotypic.co.in).
The library was prepared using NEBNext Ultra directional RNA Library Prep kit as per manufacturer’s instruction and sequenced on an Illumina platform.

treatment_protocol: After reaching 60% of confluency, HEK 293 cells was transfected with siRNA oligos using Oligofectamine reagent and cells were harvested 48-hours post-transfection.

tag: cell line

tag: antibody

value: Anti-StarPAP

tag: genotype/variation

value: siRBM10 pulldown


title: WT_optimal_4

tag: salt concentration


title: WT_low_2


title: hippocampus_F1-GDM_rep4

description: SAMPLE 4

value: male


title: hippocampus_F1-GDM_rep3

description: SAMPLE 3


title: CD27+ CD62L+ Ly49H+ NK_spleen_steady state_2

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 4


title: WT_optimal_3


title: siStar-PAP pulldown with Anti-StarPAP Antibody

value: siStar-PAP pulldown


title: StarPAP pulldown  with Anti-StarPAP Antibody

value: StarPAP pulldown


title: hippocampus_F1-GDM_rep2

description: SAMPLE 2


title: WT_optimal_2


title: CD27- CD62L+ Ly49H+ NK_spleen_steady state_2

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 2


title: WT_optimal_1


title: cardiac_non neural crest cells_1

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

institute: The First Affiliated Hospital, Sun Yat-sen University

hyb_protocol: Hybridize arrays at 48ºC for 16 hrs at 60rpm

scan_protocol: Transfer clean arrays to the Scanner 3000 Autoloader and initiate the scanner using the AGCC Scanner Control functions of Command Console

data_processing:
The microarray signals were analyzed with Affymetrix Expression Console Software
The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: E10.5 mouse non neural crest cells

label_protocol: Biotinylated RNA were prepared according to the standard GeneChip miRNA Array Target Protocol from 1 ug total RNA

growth_protocol: E10.5 Rosa-mT-mG/Wnt1-Cre EGFP positive embryos were collected. The 3rd, 4th and 6th pharyngeal arches and outflow tract were dissected out.

extract_protocol: Cell total RNA was isolated using Trizol reagent.

treatment_protocol: Collected tissues were digested and sorted for both EGFP+ cranial NCCs and EGFP- control cells by FACS sorting

tag: developmental stage

value: non neural crest cells


title: CD27- CD62L+ Ly49H+ NK_spleen_steady state_1

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 1

tag: tissue


title: IgG control

value: IgG


title: hippocampus_F1-GDM_rep5

description: SAMPLE 5


title: Neg

city: Beijing

first: Anming

last: Meng

state: Beijing

address: Tsinghuayuan Street

department: School of Life Science

institute: Tsinghua University

library_source: genomic

data_processing:
library strategy: ssDRIP-seq
For small RNA sequencing data processing: adaptors were cut off by Cutadapt, and only reads that lay between 18-40 nt were kept. Ns on the beginning of each reads were removed by Trimmomatic. Three databases were used: GRCz10 reference genome, tRNA database scanned from zv8 zebrafish genome (GtRNAdb) and Danio rerio miRBase_v21. The reads of each sample were first aligned to the GRCz10 reference genome by using Bowtie2, then to the tRNA database and to the miRNA database.
For ssDRIP-seq data processing: the adaptors were trimmed off by Cutadapt. Low-quality bases and first 7 bases of each ends were discarded from all reads. And only reads longer than 50 bp were kept. Then, the zebrafish GRCz11 reference genome was used for reads alignment, which was accomplished by Bowtie2 with default parameters. SAMtools was used to remove reads with low mapping quality, and Picard tools (http://broadinstitute.github.io/picard) was used to remove duplicated reads.  Mapped reads were split into forward and reverse R-loop reads by SAMtools according to their orientation on chromosomes. Forward reads mean that the ssDNAs in the R-loop structure locate on the Watson strand, which makes it also name as wR-loop; on the contrary, reverse reads, also called as cR-loop, indicate ssDNAs located on the Crick strand. The aligned reads files (BAM) were converted to normalized coverage files (bigWig) with 5 bp bins using bamCoverage from deepTools. Normalization was performed using bamCoverage from deepTools, with read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content). Integrative Genomic Viewer (IGV) was used for visualization. MACS2 was used to identify peaks in individual replicates, and peaks < 100 bp were discarded to reduce the noise during data analysis. Metaplots were generated with deepTools and R scripts. Normalized R-loop signal on genes and differential R-loop genes were identified by DESeq2.
Genome_build: For small RNA sequencing: zebrafish GRCz10 reference genome, tRNA database scanned from zv8 zebrafish genome (GtRNAdb) and Danio rerio miRBase_v21. For ssDRIP-seq: zebrafish GRCz11 reference genome and  tRNA database scanned from GRCz11 zebrafish genome (GtRNAdb) were used.
Supplementary_files_format_and_content: For small RNA sequencing data: tab-delimited text files include Raw counts or RPM values for each Sample. For ssDRIP-seq:  bigwig files were generated by deepTools, and the matix files in excel were generated by DeSeq2, which contain the counts and normalized signal of sense and antisense R-loop of each sample.

molecule: genomic DNA

organism: Danio rerio

source_name: Embryo

extract_protocol:
For small RNA sequencing: About 50-100 zebrafish eggs or embryos at a desired stage were collected to extract total RNA, and dechorionated by Pronase digestion. Embryos were then transferred to 1.5-ml eppendorf tube, and lysed in 1 ml Trizol Reagent (Thermo Fisher Scientific, 15596018). The lysate was centrifuged at 12,000 rpm for 10 min, and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. After centrifugation at 12,000 rpm for 10 min at 4℃, the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min, followed by thorough mix and centrifugation at 12,000 rpm for 10-20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at -80℃ until all samples were collected.
For ssDRIP-seq:  Embryos were collected at desired stages, of which 2 biological replicates were kept, and lysed in genome extraction buffer (200 mM NaCl, 10 mM Tris-HCl pH 8.0,10 mM EDTA, 0.5% SDS, and 200 μg /ml freshly added Proteinase K) at 37℃ for 8-12 h. Then, 1/2 volume of 3 M potassium acetate solution (pH 5.2) was added to the lysate and mixed gently, followed by incubation on ice for 20 min. Following extraction with equal volume of phenol: chloroform: isoamyl alcohol (25:24:1, pH 7.8) and chloroform sequentially, genomic DNA, which include RNA:DNA hybrids, was precipitated by addition of equal volume of isopropanol for 10 min at room temperature. The precipitate was washed by 70% ethanol for once and then air-dried.
For small RNA sequencing: RNA pellets were dissolved by nuclease free water, and treated with T4 Polynucleotide Kinase (NEB) for 30 min at 37℃ to remove the 2'3'-cyclicphosphate group on the 3'end of tRNA derived fragments. Small RNA libraries, using 1 μg RNA each, were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column (Zymo Research), then bands of 135-160 bp, about the length of 15-40 nt RNA ligated with both adaptors, were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc, pH4.5, followed by precipitation by adding 2.5 volumes of ethanol.
For ssDRIP-seq:  Genomic DNA fragmentation was performed by digestion at 37℃ for 4-6 h with a set of restriction enzymes, including AluI, MboI, DdeI and MseI (NEB). For negative control sample, genomic DNA was digested by RNase H (NEB) at 37℃ overnight in advance. After digestion, the fragmented genomic DNA was purified by phenol-chloroform extraction and quantified by Qubit 3.0 (Invitrogen). To immunoprecipitate RNA:DNA hybrids, 5 μg genomic DNA was diluted to 440 μl with nuclease free water, then to it 50 μl 10x DRIP binding buffer (100 mM NaPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 10 μg S9.6 antibody (ATCC, HB-8730) were added. The mixture was incubated on a vertical rotator for 12-14 h at 4℃. After addition with 50 μl Protein G Dynabeads (Invitrogen), the mixture was incubated for 4 h further. Then, beads with its conjugates were spun down, and washed by 1x DRIP binding buffer for 4 times at room temperature. Elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and Proteinase K was added to the beads, and incubated for 40 min at 55°C. DNA was purified by phenol: chloroform: isoamyl alcohol (25:24:1, pH 7.8) extraction, and then subjected to library construction using Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences)

value: Tubingen

value: Shield stage

tag: treatement

value: RNaseH treated before DRIP

value: Embryo


title: 6h-2

description:
processed data file:
antisense_counts.txt
antisense_norm.txt
sense_counts.txt
sense_norm.txt


title: The skin tissue of cashmere is taken from scapularis of healthy Liaoning cashmere goats 2

city: Shenyang

first: Ying

middle: Ze

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District, Shenyang

institute: 沈阳农业大学

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）. Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger，version 5.0.1) and scRNA-seq data were aligned to Ensembl genome GRCh38/GRCm38 reference genome, a total of 30,000 single cell captured from 5 healthly donors and 5 patients were processed using 10X Genomics Chromium Single Cell 3’Solution. The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Overall, 25,000 cells passed the quality control threshold : all genes expressed in less than three cells （default parameters：1 cell）were removed、number of genes expressed per cell > 500 as low and <5000 as high cut-off、UMI counts less than 500、the percent of mitochondrial-DNA derived gene-expression <25%.
To visualize the data, we further reduced the dimensionality of all 18,339 cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes:1、Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2、PCA (Principal component analysis) analysis was performed using the normalized expression value, Within all the PCs, the top 10 PCs were used to do clustering and t-SNE analysis；3、To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method. Marker genes for each cluster were identified with the Wilcoxon rank-sum test （default parameters is"bimod" : Likelihood-ratio test）with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 10% of the cells in a cluster and average log(Fold Change) of greater than 0.25（default parameters：0.26）.

organism: Capra hircus

source_name: skin tissue

growth_protocol: Skin tissue was obtained from healthy Liaoning Cashmere Goats.Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers.Tissue s were dissociated into single cells in dissociation solution  in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, then pipetting 5-10 times with a Pasteur pipette。The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells  using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.

extract_protocol: Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

tag: growth cycle

value: anagen


title: cardiac_neural crest cells_1

source_name: E10.5 mouse cardiac neural crest cells

value: The 3rd, 4th and 6th pharyngeal arches and outflow tract

value: cardiac neural crest cells


title: CD27+ CD62L+ Ly49H+ NK_spleen_steady state_1

description:
bulkRNA-Seq of 500 cells
rawCounts_steadyState_Fig_3_S3A_S4.csv
normalizedCounts_steadyState_Fig_3_S3A_S4.csv
Sample 3

tag: strain

value: spleen

value: Ly49H+ NK cells


title: The skin tissue of cashmere is taken from scapularis of healthy Liaoning cashmere goats 1


title: 4h-1

value: Sphere stage


title: 4h-2


title: 6h-1


title: RNA-Seq Alkbh5 cell_rep3

city: Nashville

first: James

middle: G.

last: Patton

state: TN

address: 2325 Stevenson Center

department: Department of Biological Sciences

institute: Vanderbilt University

description: Alkbh5 cell_rep3

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
STAR was used to map reads to the human reference genome.
DESeq2 was used to detect differential expression between conditions.
Genome_build: hg38
Supplementary_files_format_and_content: A count table that provides complete data with values for all features and all samples

source_name: Colorectal cancer cell line

growth_protocol: Cell lines were grown in DMEM in the presence of 10% fetal bovine serum, 1% L-glutamine, 1% non-essential amino acids and antibiotics

extract_protocol:
RNA was harvested using Trizol reagent. Libraries were generated using NextFlex small RNA library preparation kit v3 with modified step F.
Libraries were size-selected using Pippin Prep and quality was assessed by 2100 Bioanalyzer. Libraries were sequenced using the Illumina NextSeq500 system.

treatment_protocol: Stable cell lines were generated expressing shRNAs against Mettl3 and Alkbh5.

tag: phenotype

value: knockdown

value: KRAS mutant colorectal cancer


title: PhADT overexpressor A9 - Rep 3

city: Madison

first: Stuti

last: Shrivastava

state: WI

address: 430 Lincoln Drive

department: Botany

institute: University of Wisconsin, Madison

data_processing:
The RNA-seq filtered Illumina reads were pre-processed using FastQC (v 0.11.2) and FASTX toolkit (v 0.0.13.2) retaining reads with a Phred33 score ≥ 30 and length ≥ 50 bases. The quality trimmed reads were mapped to the tomato transcriptome (v ITAG2.4) using bowtie2 (v 2.2.6) with the default parameters.
Differentially expressed contigs (DECs) were identified using the FPKM measure (FDR corrected p-value <= 0.05) as normalized contig expression level, calculated using CummeRbund package (Trapnell et al., 2013) in R (R core team, 2014). A custom script generated using gtools (v 3.5.0) package in R added another constraint of 1.5-fold change on the DECs. The clean assembled contigs were validated by mapping to the coding sequences of tomato (Solanum lycopersicum, ITAG2.4; Mueller et al., 2009) reference genome using BLASTx (E < 1e-3), by the Bioinformatics facility at Purdue University.
Supplementary_files_format_and_content: Matrix table with FPKM vaules for all contigs for all samples

organism: Petunia x hybrida

source_name: Corolla

growth_protocol: Petunia hybrida cv. Mitchell overexpressor for PhADT were grown under standard greenhouse conditions with a light period from 6 AM to 9 PM.

extract_protocol:
Total RNA was isolated from at least eight petunia corollas harvested at 20:00 h on day 2 post-anthesis using the RNeasy Plant Mini Kit (Qiagen), treated with DNase I to eliminate genomic DNA using the TURBODNA-free kit (Ambion, Foster City, CA, USA) and was reverse-transcribed to cDNA using the High Capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Corolla

tag: mutation site

tag: tag

value: PhADT overexpressor A9


title: RNA-Seq Mettl3 cell_rep3

description: Mettl3 cell_rep3


title: RNA-Seq Mettl3 cell_rep2

description: Mettl3 cell_rep2


title: RNA-Seq Mettl3 cell_rep1

description: Mettl3 cell_rep1


title: RNA-Seq Alkbh5 cell_rep2

description: Alkbh5 cell_rep2


title: PhADT overexpressor A9 - Rep 2


title: Ly6c+ c-kit+ cells_rep3

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The ATACseq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATAC-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 with following command “-q 0.05 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by bedGraphtoBigwig and visualized in Integrated genome viewer (IGV) v2.8.3.

source_name: FACS-sorted Ly6c+c‑kit+ precursor cells

growth_protocol: B16F10 tumors were implanted bilaterally in the upper anterior thigh of C57BL/6 mice (Jackson).

extract_protocol:
Cells were isolated by rapid mechanical disaggregation of TDLNs from established (day 14) untreated B16F10 tumors.  LNs were pooled and stained for CD11c, Ly6c and c-kit (CD117), then the CD11cNEGLy6c+c-kit+ precursor population was sorted and used for ATAC-seq.
For each sample, 50,000 nuclei prepared from FACS-sorted Ly6c+c‑kit+ precursor cells were incubated with 2.5 mL Nextera Tn5 transposase (Illumina) in 50mL 1X transposition reaction mixture in a thermocycler at 37 °C for 1hr. The transposition reaction mixtures were purified with a DNA Clean and Concentrator kit (Zymo Research), and amplified for 11-13 cycles using NEBNext High-Fidelity 2X Master Mix (New England Biolabs) and Nextera Index primers (Illumina). The amplified libraries were size-selected by two rounds of AMPure beads purification (0.5X and 1.2X).

tag: surface markers

value: Tumor draining lymph node


title: Ly6c+ c-kit+ cells_rep1


title: Ly6c+ c-kit+ cells_rep2


title: hippocampus_F1-GDM_rep1

description: SAMPLE 1

value: ICR

value: hippocampus

tag: gender

value: male

tag: generation


title: PhADT overexpressor A9 - Rep 1


title: 256-1

value: Tubingen

value: 256c stage


title: RNA-Seq Alkbh5 cell_rep1

description: Alkbh5 cell_rep1

tag: cell type


title: RNA-Seq DKO-1 cell_rep3

description: DKO-1 cell_rep3

value: control


title: PhADT overexpressor A4 - Rep 3

value: PhADT overexpressor A4


title: tRNA_Shield

description: Enriched 60-100nt RNA

data_processing:
Adaptor trimming and quality control were done by FastP (Version 0.19.5) and Cutadapt (Version 3.4), then 60-100 nt length reads were preserved for down-stream analysis.
Reads were first mapped to genome (GRCz11) by Bowtie2 (Version 2.4.2) with very-sensitive-local mode (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50). Then aligned reads were further mapped to tRNA database (GtRNAdb, GRCz11).
The counts of reads aligned to each tRNAs were calculated and normalized to all reads mapped to genome for down-stream analysis.
Genome_build: GRCz11
Genome_build: tRNA database from GtRNAdb, GRCz11
Supplementary_files_format_and_content: tab-delimited text files include tRNA RPM values for each sample

source_name: Whole Embryo

extract_protocol:
About 50-100 zebrafish eggs or embryos at a desired stage were collected to extract total RNA, and dechorionated by Pronase digestion. Embryos were then transferred to 1.5-ml eppendorf tube, and lysed in 1 ml Trizol Reagent (Thermo Fisher Scientific, 15596018). The lysate was centrifuged at 12,000 rpm for 10 min, and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. After centrifugation at 12,000 rpm for 10 min at 4℃, the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min, followed by thorough mix and centrifugation at 12,000 rpm for 10-20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at -80℃ until all samples were collected.
Total RNA was placed on ice for 30 min with 10% PEG8000 and 0.5 M NaCl, then centrifuged at 14,000 rpm for 15 min at 4℃. Supernatant (low molecular weight, LMW RNA) was collected and precipitated  by addition of ethanol. The LMW RNA was separated by 8% 8 M Urea PAGE gel, then the bands correspond to 60-120 nt length were cut and crunched into small pieces. RNA was eluted from the gel by 0.3 M NaOAc overnight on a vertical rotator at 4℃. Then the supernatant was precipitated at -20℃ after addition with 2 μl of Glycoblue and 2.5 volume of ethanol. After centrifuged at 12,000 rpm for 30 min and washed by 75% ethanol, the RNA precipitant was dissolved in RNase free water.  There are three pretreatment steps before library preparation. 60-120nt RNA enriched in the previous step was first incubated in 100 mM Tris-HCl pH 9.0 at 37℃ for 30 min to be deacylated, then the RNA was treated with T4 PNK to repair ends at 37℃ for 30 min. Modifications on tRNAs were removed by ALKB treatment [1 μg purified RNA was treated by ALKB protein mixture (wt ALKB, 160 pmol; ALKB D135S, 200 pmol; and ALKB D135S/L118V, 200 pmol) in reaction buffer (300 mM KCl, 2 mM MgCl2, 50 μM (NH4)2Fe(SO4)2, 300 μM α-ketoglutarate, 2 mM vitamin C, 50 μg/ml BSA, 50 mM MES pH 5.0, 40 U RNase Inhibitor, 1x Protease Inhibitor) for 2 h at room temperature]. Purification was needed after each pre-treatment step. 100 ng RNA was then subjected for RNA library preparation. tRNA library was prepared by VAHTS Small RNA Library Prep Kit for Illumina (Vazyme, NR801). RNA was heat denatured at 80℃ for 2 min in the first step, then every steps were done followed the manual in kit. The libraries were first concentrated by DNA concentrator spin column (Zymo), then separated on 6% native PAGE gel. Bands correspond to 180-240 bp (60-120 nt RNA ligated with both adaptors) length were cut and DNA libraries were eluted from gels.

tag: genotype

value: WT

value: TU

value: Shield


title: tRNA_Sphere

description: Enriched 60-100nt RNA

value: Sphere


title: PhADT overexpressor A4 - Rep 2


title: RNA-Seq DKO-1 cell_rep2

description: DKO-1 cell_rep2


title: PhADT overexpressor A4 - Rep 1


title: RNA-Seq DKO-1 cell_rep1

description: DKO-1 cell_rep1


title: tRNA_256c

description: Enriched 60-100nt RNA


title: tRNA_1cell

description: Enriched 60-100nt RNA


title: Wild-type petunia flowers - Rep 2

value: Wild-type


title: tRNA_24hpf

description: Enriched 60-100nt RNA


title: 256-2

value: Embryo


title: 24hpf-ncRNA-seq

data_processing:
For data processing, reads were quality checked by FastQC(Version 0.11.8), and adaptors were cut off by Cutadapt (Version 1.16), and only reads that lay between 18-40 nt were kept.
The reads of each sample were first aligned to different database by using Bowtie2  (Version 2.3.4.1), count table was generated by featureCounts.
Genome_build: GRCz11 genome and cDNA,  tRNA database (GtRNAdb, GRCz11)

source_name: embryo

extract_protocol:
For small RNA sequencing: About 50-100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5-ml eppendorf tube, and lysed in 1 ml Trizol Reagent (Thermo Fisher Scientific, 15596018). The lysate was centrifuged at 12,000 rpm for 10 min, and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. After centrifugation at 12,000 rpm for 10 min at 4℃, the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min, followed by thorough mix and centrifugation at 12,000 rpm for 10-20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at -80℃ until all samples were collected. Two pretreatment steps were included: First, purified total RNAs were treated with T4 Polynucleotide Kinase (NEB, M0201S) with ATP for 30 min at 37℃, then purified by phenol: chloroform extraction. The aim of this step is removing the 2,3’-cyclic phosphate group from the 3’end of 5’tRFls, and add phosphate group to the 5’end of 3’tRFs. In the second step, total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation.
For small RNA sequencing:  Small RNA libraries, using 1 μg RNA each, were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column (Zymo Research), then bands of 135-160 bp, about the length of 15-40 nt RNA ligated with both adaptors, were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc, pH 4.5, followed by precipitation by adding 2.5 volumes of ethanol.

value: 24-hpf stage

value: no


title: Wild-type petunia flowers - Rep 1

value: Corolla


title: Wild-type petunia flowers - Rep 3


title: Smartseq_htseq_counts_matrix 2

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'.  Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-Seq: htseq count matrix with raw counts for all individual cells; scATAC-Seq: fragments file with fragments for all individual cells; Omni-ATAC: bigwig files generated using the nf-core ATAC pipeline; CUT&Tag: bigwig files

source_name: Multiple myeloma cell line MOLP2

growth_protocol: MMCLs were cultured cultured in RPMI-1640 media with 10% of heat-inactivated fetal bovine serum, 100 μM penicillin/streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 1x NEAA, 20 mM HEPES and 0.5 mM 2-mercaptoethanol.

extract_protocol:
Single cells were directly sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

treatment_protocol: Cells were treated for 72h with PVD/DMSO.

value: Bone marrow


title: tRNA_Egg

description: Enriched 60-100nt RNA

source_name: Mature Egg

value: Mature egg


title: MOLP2_PVD_CUTTAG_H3K27ac_R1

description: Bone marrow

data_processing:
Library strategy: CUT&Tag
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10  --alignSJstitchMismatchNmax 5  -1  5  5'. Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-Seq: htseq count matrix with raw counts for all individual cells; scATAC-Seq: fragments file with fragments for all individual cells; Omni-ATAC: bigwig files generated using the nf-core ATAC pipeline; CUT&Tag: bigwig files

growth_protocol: MMCLs were cultured in RPMI-1640 media with 10% of heat-inactivated fetal bovine serum, 100 μM penicillin/streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 1x NEAA, 20 mM HEPES and 0.5 mM 2-mercaptoethanol.

extract_protocol: Libraries were prepared using the Bench top CUT&Tag V.3 protocol (dx.doi.org/10.17504/protocols.io.bcuhiwt6).

tag: cell line

tag: treatment

value: PVD


title: MOLP2_DMSO_CUTTAG_H3K27ac_R1

description: Bone marrow

value: DMSO

tag: antibody


title: Shield-ncRNA-seq

value: Tubingen

value: Shield stage


title: SKOV3 shGNAi2 Hypoxia

city: Oklahoma City

first: Muralidharan

last: Jayaraman

state: Oklahoma

address: 975 NE 10th Street BRC1401

department: Cell Biology

institute: University of Oklahoma Health Sciences Center

description: Agilent SurePrint G3 Human GE V2 array, 8x60K Microarray

hyb_protocol: Hybridization was done overnight with Gene Expression hybridization kit (Agilent Catalog #5188-5242)

scan_protocol: The scanning was done on an Agilent SureScan Scanner, using the GE2_1100_2_no_spike protocol for 2 channels. Only green laser signal was this experiment dataset.

data_processing: Agilent Feature extraction version 11.0.1.1 was used to extract the data from the slides.

source_name: SKOV3 ovarian cancer cells

label_protocol: Labeling the cRNA was done with Agilent Quick Amp Labeling kit (Agilent Catalog# 5190-0444) and Cleaned with Qiagen RNeasy mini kit

growth_protocol: SKOV3 cells were grown in DMEM media added with 10% FBS.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit

treatment_protocol: The cells were serum starved and treated with 10 µM LPA for 16 h under normoxic or hypoxic conditions

tag: stable cell line

value: Stable cells


title: Smartseq_htseq_counts_matrix

source_name: Bone marrow

tag: library strategy

value: Single cell RNA


title: SKOV3 shGNAi2 Normoxia


title: scATAC fragments file

extract_protocol:
2000-5000 plasma cells were bulk sorted using the following antibodies: CD38 FITC (multi-epitope, Cytognos), CD138 PE (44F9, Miltenyi), SLAMF7 APC (162.1 , Biolegend), BCMA PE-Cy7 (19F2, Biolegend). Following tagmentation, single cells were sorted into 96 well plates containing 4 μl of lysis buffer and Nextera XT indexes.
Single cell RNA-seq libraries were prepared using the protocol described by Chen et al., 2018.

tag: tissue

value: Single cell ATAC


title: 256c-ncRNA-seq

tag: developmental stage

value: 256c stage

tag: treatement


title: Sphere-ncRNA-seq

tag: strain

value: Sphere stage


title: MOLP2_DMSOtreated_72h_OmniATAC_rep1

extract_protocol: Libraries were prepared using the Omni-ATAC protocol as described by Corces et al. 2017.

value: Omni-ATAC


title: Egg-ncRNA-seq

source_name: mature oocyte

value: Mature Oocyte


title: IRES_6742_Relocate

city: St. Louis

first: Chun-Kan

last: Chen

state: MO

address: 660 S Euclid Ave

department: Cell Biology and Physiology

institute: Washington University in St. Louis

description:
Purified circRNA
M2Seq_rdat.rar

data_processing:
IRES screening and polysome profiling: Single-end reads in the length of 90-nt were trimmed to 37-nt containing the unique oligo variable region using fastx_trimmer module (-f 54). Trimmed reads were mapped to the synthetic library sequences using Bowtie2 with default settings. Multi-mappers were excluded from the subsequent analysis by excluding the reads with the "XS" flag in the .sam files (grep -v). The number of reads for each designed oligo was counted in each bin respectively using bedtools multiBamCov module.
M2-seq: Single-end reads in the length of 300-nt were trimmed to 174-nt containing the unique oligo sequence using fastx_trimmer module (-f 39 -l 212). ShapeMapper was used to align the trimmed reads to reference sequences and record mutations, and the results were converted to M2-seq data and mutation spectra using scripts available at https://github.com/ribokit/m2seq. The M2-net analysis, mutate-and-map visualization, RNA structural analysis, and RNA structure visualization were performed as described in Cheng et al. (PNAS, 2017).
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: IRES screening: .xlsx file that contains the synthetic oligo index, sequence, and cap-independnet translation activity.
Supplementary_files_format_and_content: Polysome profiling: .xlsx file that contains the number of (poly)ribosome-enriched oligos
Supplementary_files_format_and_content: M2-seq: .rdat file for 2nd structure determination

organism: synthetic construct

source_name: Designed oligonucleotides

extract_protocol:
IRES screening: Total DNA from each expression bin was extracted using Quick-DNA Microprep Plus Kit (Zymo Research).Synthesis (NEB BioLabs), and purified with DNase digestion (TURBO DNase; Thermo Fisher Scientific) and RNase R digestion (MACLAB; 20 U RNase R per 20 μg of RNA).
Polysome profiling: The total RNAs of each fraction were purified respectively using RNeasy Mini Kit (Qiagen) with DNase treatment (Qiagen). The RNAs were then treated with RNase R and purified using RNA Clean & Concentrator-25 (Zymo Research).
M2-seq: The circRNA of oligo of interest was produced with in vitro transcription using HiScribe™ T7 High Yield RNA
IRES screening: Three rounds of PCR using NEBNext Ultra II Q5 Master Mix (NEB BioLabs) were performed to generate the library for next-generation sequencing. For the first PCR, oligo library sequence was amplified using the following primer set – Fw: GGGATCACTCTCGGCATGGA; Rv: GCTCCTCGCCCTTGCTCAC. Each 50 μL PCR reaction contained 200 ng total DNA, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 24 cycles of 98°C for 30 s, 65°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the second PCR, adapter priming sequences were added to the oligo library using the following primer set – Fw: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGGATCACTCTCGGCATGGA; Rv: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTCCTCGCCCTTGCTCAC (underlined sequence represents the sequence for illumina adapters priming). Each 50 μL PCR reaction contained 1.25 μL of the first PCR product, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 18 cycles of 98°C for 30 s, 70°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the third PCR, custom barcodes adapters were used for the reaction. Each 50 μL PCR reaction contained 1 μL of 1:20 diluted second PCR product, 1 μM Ad1 adapter, and 1 μM Ad2 adapter. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 72°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. The PCR product was then separated on a 2% E-Gel™ EX Agarose Gel (Invitrogen) and the DNA fragments with expected size were purified using Zymoclean Gel DNA Recovery Kit (Zymo Research).
Polysome profiling: The oligo sequences from each sample were amplified by RT-PCR with SuperScript™ IV One-Step RT-PCR System (Thermo Fisher Scientific) using primers flanking the oligo sequence (Fw: GGGATCACTCTCGGCATGGA; Rv: GCTCCTCGCCCTTGCTCAC). cDNA libraries were generated and sequenced with HiSeq 4000 using the library generation method as for IRES screening.
M2-seq: The complimentary single-stranded DNA of the circRNA was generated by reverse transcription using SuperScript™ IV (Thermo Fisher Scientific) with oligo sequence specific primer (TCTTTTGTTGGAGTCTACTCGACTCCTTT) and purified with DNA Clean & Concentrator-5 (Zymo Research). Three rounds of PCR using NEBNext Ultra II Q5 Master Mix (NEB BioLabs) were performed to generate the cDNA library for next-generation sequencing. For the first PCR, oligo library sequence was amplified using the following primer set – Fw: GAACGACTCGAGTAGAGTCGAAAA; Rv: TCTTTTGTTGGAGTCTACTCGACTCCTTT. Each 50 μL PCR reaction contained 200 ng total DNA, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 67°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the second PCR, sequences for adapters priming were added to the oligo library using the following primer set – Fw: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGAACGACTCGAGTAGAGTCGAAAA; Rv: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTTTTGTTGGAGTCTACTCGACTCCTTT (underline represents the sequence for illumina adapters priming). Each 50 μL PCR reaction contained 1.25 μL of the first PCR product, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 12 cycles of 98°C for 30 s, 67°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the third PCR, custom barcodes adapters were used for the reaction. Each 50 μL PCR reaction contained 1 μL of 1:20 diluted second PCR product, 1 μM Ad1 adapter, and 1 μM Ad2 adapter. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 72°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. The PCR product was then separated on a 2% E-Gel™ EX Agarose Gel (Invitrogen) and the DNA fragments with expected size were purified using Zymoclean Gel DNA Recovery Kit (Zymo Research).
IRES screening: DNA-seq.
Polysome profiling: RNA-seq
M2-seq: RNA-seq

tag: functional assay

value: In vitro transcription

tag: master plasmid

value: oligo-circRNA


title: SKOV3 shGNA13 Normoxia


title: SKOV3 shGNA12 Normoxia


title: IRES_6742_Comp

description:
Purified circRNA
M2Seq_rdat.rar


title: SKOV3 shGNA12 Hypoxia


title: SKOV3 shControl Hypoxia


title: MOLP2_DMSOtreated_72h_OmniATAC_rep2


title: MOLP2_PVDtreated_72h_OmniATAC_rep2


title: IRES_6742_Single

description:
Purified circRNA
M2Seq_rdat.rar


title: SKOV3 shControl Normoxia


title: SKOV3 shGNA13 Hypoxia


title: at-endosperm.RNAseq.wt.replicate3

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana endosperm of wt (Columbia-0) during germination

data_processing:
RNA-seq: For each replicate, the 150 bp long reads were trimmed by removing the 20 bp from the 5’ end and 30 bp from the 3’ and mapped in single-end mode to the Arabidopsis (TAIR10) genome, masked for rRNA genes, using TopHat v2.1.0 (Trapnell et al. 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130). Mapped reads were counted and normalized to reads per kilobase per million mapped reads (RPKM) for chromosmic protein coding genes using GFOLD (Feng et al, 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for protein coding genes in the five chromosomes of TAIR10 for each condition and replicate.

organism: Arabidopsis thaliana

source_name: AT endosperm in germinating seeds

growth_protocol: Seeds were sterilized using 5% sodium hypochlorite. They were sown on half-strength Murashige and Skoog medium and treated with stratification (4°C) for three days. After the treatment, seeds were imbibed under long-day conditions (16 h light/8h darkness) at  21°C and a light intensity of 150 µE.

extract_protocol:
Total RNA from endosperm was extracted using MagMAX™ Plant RNA Isolation Kit (Thermo Fisher Scientific) according to the supplier’s instructions for RNA extraction from plant seeds.
mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB) and cDNA libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB).
Libraries were sequenced on Illumina NovaSeq platforms with paired-end 150 bp read length through Novogene mRNA sequencing services.

treatment_protocol: Endosperm were manually dissected from seeds that were imbibed for 24 hours under a microscope using tweezers and syringe needle.

value: endosperm

value: wt (Col-0)


title: MOLP2_PVDtreated_72h_OmniATAC_rep1


title: at-endosperm.RNAseq.wt.replicate2


title: IRES_6742_dis

description:
Purified circRNA
M2Seq_rdat.rar


title: IRES_6742_MS2

description:
Purified circRNA
M2Seq_rdat.rar


title: Peripheral blood mononuclear cell-PM

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: PBMC-PM

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files, which were subsequently used to generate feature-barcode matrices using Cell Ranger RNA v3.1 (10x Genomics). PM sample was run through the Single cell RNA-seq app on BaseSpace. Briefly, reads were aligned against a reference genome using Spliced Transcripts Alignment to a Reference (STAR), followed by barcode tagging and BAM indexing. Count file was generated using gene UMI counter and with cells passing quality filter based on cells above background and passing knee filter.
Initial single-cell analysis was performed using Seurat v3.1.0 (2). Cells containing less than 200 genes were removed, and log-normalized expression of 2,000 variable genes were used to reduce the data into two-dimensional space.
Cells from all 9 biopsies were combined using FindIntegrationAnchors and IntegrateData functions. Cell identities were manually assigned using highly expressed genes. To retain the highest number of cells for subsequent analyses, no additional filters were initially applied.
Genome_build: hg19
Supplementary_files_format_and_content: filtered_feature_bc_matrix, UMI count file in CSV format

source_name: Peripheral blood

growth_protocol: Organoids were maintained in growth factor-reduced matrigel and grow in progenitor tumor organoid media (PaTOM)

extract_protocol:
Biopsies were minced with sterile surgical scalpels to 0.5-1 mm fragments in approximately 1 ml of media. After centrifugation for 5 minutes at 125 g, cells were resuspended in DMEM with 0.5 mg/ml Liberase TH (Sigma-Aldrich) and 1% penicillin-streptomycin (Corning) and incubated in an orbital shaker for 15 min at 37°C. Liberase was quenched with equal volume of 1% BSA in DMEM followed by centrifugation for 5 minutes at 125 g. Cells were resuspended in 2 ml Accutase (Sigma-Aldrich) and incubated in an orbital shaker for 15 minutes at 37°C. Organoids were dissociated by incubating with TrypLE Express (Thermo Fisher) for 5-15 minutes at 37°C followed by manual disruption. Dissociated cells were passed through a 40 μm strainer and centrifuged for 5 minutes at 125 g. Isolated cells were resuspended in 0.04% BSA in phosphate buffered saline (Corning) for subsequent viability analysis and counting.
Single-cell transcriptomic amplification and library preparation was performed using the 5’ or 3’ Library Construction Kit (10x Genomics) following the manufacturer’s recommendations. Amplification and library prep of the PM sample was performed using the SureCell WTA 3’ Library Prep Kit for the ddSEQ System following the manufacturer’s recommendations (Illumina, Cat# 20014279).
single cell RNA sequencing

value: Peripheral blood


title: at-endosperm.RNAseq.wt.replicate1


title: at-endosperm.RNAseq.wt.replicate6


title: Peripheral blood mononuclear cell-LuM

description: PBMC-LuM


title: 1cell-ncRNA-seq

value: 1cell stage

value: no


title: hippocampus_F2-GDM_rep1

description: SAMPLE 6

data_processing: Data was processed using GenomeStudio (1.9.0) following the manufacturer's protocol

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) kit, following the manufacturer's protocol.

value: ICR

tag: age

value: hippocampus

value: male


title: IRES_6742_BoxB

description:
Purified circRNA
M2Seq_rdat.rar


title: Peripheral blood mononuclear cell-LiM

description: PBMC-LiM


title: Peripheral blood mononuclear cell-VM

description: PBMC-VM


title: V12_HJ7M2BBXX

city: San Diego

first: Amin

last: Haghani

state: CA

address: 5510 Morehouse Dr

institute: Altos labs

description:
gene counts.csv
gene map.csv

data_processing:
Raw sequencing reads were quality checked with FastQC
adapter sequences were trimmed from the reads using Trimmomatic
Reads were aligned to the mm10 genome using the HISAT2 splice-aware aligner
alignments overlapping genes were counted using featureCounts version 1.5.0-p3 relative to Gencode version M11
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv files count values for each gene

source_name: Cortex

extract_protocol:
Samples were homogenized and disrupted with pestles, 22-gauge needles, pipetting and QIA shredders (Qiagen #79654).  DNA was extracted using QIAzol (Qiagen #79306) from the organic layer for genotyping. RNA was extracted following the QIAGEN RNeasy plus universal protocol (Qiagen #73404). Extracted RNA was used to determine sex of mouse pups by qPCR for the Y-chromosome Sry gene.
RNA (600ng) was made into RNA-seq libraries using the Illumina RiboZero Gold library preparation kit and sequenced on an Illumina HiSeq 3000 sequencer at the Lieber Institute for Brain Development

tag: Sex

value: F

value: Cortex

value: Unexposed

tag: age (days)

value: 3 to 5

tag: rin

tag: lane


title: IRES_43704

description:
Purified circRNA
M2Seq_rdat.rar


title: at-endosperm.RNAseq.wt.replicate4

tag: genotype


title: Peripheral blood mononuclear cell - P4


title: IRES_35001

description:
Purified circRNA
M2Seq_rdat.rar

tag: cell line


title: at-endosperm.RNAseq.suvh456.replicate2

description: Arabidopsis thaliana endosperm of suvh456 (Columbia-0) during germination

value: suvh456 (Col-0)


title: at-endosperm.RNAseq.suvh456.replicate3


title: IRES_41767

description:
Purified circRNA
M2Seq_rdat.rar


title: IRES_19420

description:
Purified circRNA
M2Seq_rdat.rar


title: Peripheral blood mononuclear cell - P2


title: at-endosperm.RNAseq.suvh456.replicate1


title: IRES_6885_add

description:
Purified circRNA
M2Seq_rdat.rar


title: IRES_18377

description:
Purified circRNA
M2Seq_rdat.rar


title: at-endosperm.RNAseq.ref6-1.replicate3

description: Arabidopsis thaliana endosperm of ref6-1 (Columbia-0) during germination


title: WT_optimal_5

city: Durham

first: Amy

last: Schmid

state: NC

address: 3242 French Family Science Center

institute: Duke University

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Halobacterium salinarum NRC-1 genome (RefSeq GCF_000006805.1) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset)
Count files were input into DeSeq2 to generate normalised counts, exclude outlier samples, and generate lists of differentially expressed genes in pairwise comparisons. (The normalised count file with all 24 samples is included in this GEO dataset)
Genome_build: GCF_000006805.1_ASM680v1
Supplementary_files_format_and_content: tab-delimited text file with raw counts for each gene
Supplementary_files_format_and_content: comma-separated values file with noramlised counts for each gene; all samples in a single file; rRNA genes removed.

source_name: Δura3_Optimal (4.2M NaCl)_archaeal cells

extract_protocol:
Agilent Absolutely RNA Miniprep kit was used to to extract total RNA, following manufacturer's protocol. DNase digestion step was extended to 45 mins. gDNA contamination was ruled out using PCR amplification. Nucleic acid concentration measured using Nanodrop and Bioanalyzer (RNA 6000 Nano chip). rRNA was removed using the NEBNext Bacterial rRNA depletion kit; for replicates 1-3 of all conditions manufacturer-supplied probes were used, while for replicates 4-6, custom-designed probes targeted to Haloferax volcanii rRNA were used. rRNA depletion was verified using Bioanalyzer.
NEBNext Ultra II Directional RNA Library Prep kit was used to generate cDNA libraries from the rRNA-depleted samples. Library quality and concentration was checked using Bioanalyzer using High Sensitivity DNA chip. Samples were pooled (replicates 1-3 from all conditions in batch 1, replicates 4-6 in batch 2) and run in a single lane on Illumina NovaSeq 6000 paired-end sequencing at the Duke Sequencing Core.

tag: salt concentration

value: Optimal (4.2M NaCl)

tag: cell type

value: archaeal cells


title: at-endosperm.RNAseq.wt.replicate5


title: Peripheral blood mononuclear cell - P1


title: IRES_9128

description:
Purified circRNA
M2Seq_rdat.rar

value: In vitro transcription


title: at-endosperm.RNAseq.ref6-1.replicate2


title: IRES_6885

description:
Purified circRNA
M2Seq_rdat.rar

value: oligo-circRNA


title: Lung metastasis

description: LuM

source_name: Lung

value: Lung


title: Vaginal metastasis

description: VM

source_name: Vaginal apex

value: Vaginal apex


title: IRES_6742

description:
Purified circRNA
M2Seq_rdat.rar


title: at-endosperm.RNAseq.ref6-1.replicate1

value: endosperm


title: IRES_Screening_Rep2_Bin7

description:
Total DNA
Oligo_eGFP_expression.xlsx

value: circRNA cap-independent translation

value: oligo-split-eGFP-circRNA


title: Peripheral blood mononuclear cell - P3

value: Peripheral blood


title: Fine needle aspiration - P3

source_name: Pancreas

value: Pancreas


title: IRES_Screening_Rep2_Bin5

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: Fine needle aspiration - P4


title: IRES_Screening_Rep2_Bin4

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: IRES_Screening_Rep2_Bin6

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: Fine needle aspiration - P1


title: IRES_Screening_Rep2_Bin3

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: Peritoneal metastasis

description: PM

source_name: Peritoneum

value: Peritoneum


title: IRES_Screening_Rep2_Bin2

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: IRES_Screening_Rep2_Bin1

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: Hippocampus_AD_NR_REPLICATE5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were filtered to remove undetected and array control probes, before computing log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

extract_protocol: RNA was purified with Nucleospin RNA isolation kit following manufacturer’s protocol (Macherey-Nagel, #740955.250).

treatment_protocol: All animal experiments were performed and approved by NIA Animal Care and Use Committee. All the animals were maintained at the National Institute on Aging under standard conditions and fed standard animal chow. The APP/PS1 mouse strain (#stock number 004462 in Jackson’s laboratory) was from Prof. Mark Mattson’s laboratory. APP/PS1 mice and their WT littermates were used for experiments. The APP/PS1 mice were treated with NR (12 mM) in drinking water starting from 7 months (the age at which Aβ plaques appear) to 12 months. The NR treatment was performed as previously reported. From 9-month-old, the mice were subsequently evaluated for behavioral endpoints.

tag: genotype/variation

value: APP/PS1 AD

value: Brain

tag: brain region

value: Hippocampus

tag: treatment

value: NR

tag: treatment duration

value: 5 months

value: 12 months


title: IRES_Screening_Rep1_Bin6

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: IRES_Screening_Rep1_Bin7

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: CB06_DL1_ILC2_CD5p

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: in vitro generated

data_processing:
The unstranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: Derived from CD34+ progenitors from CB

extract_protocol:
CD34+ hematopoetic progenitors were sorted and plated on OP9 or OP9-DL1. Media was supplemented with 10% human AB serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and cytokine mix. Cytokine mix consisted of SCF, Flt3L, IL-7, and IL-15 when stated (all 20 ng/ml) and IL-3 (all cultures: 5 ng/ml). After one week IL-3 supplementation was dropped. After two weeks Flt3L was reduced to 5 ng/ml. Medium and cytokines were refreshed every 3-4 days by replacing half of the media containing 1x concentration of cytokines. At day 7, 14 and 21 cells were replated onto fresh OP9 or OP9-DL1 onto flat bottom plates. To replate, cells were collected by forceful pipetting and passed through a 50µm filter to remove OP9/OP9-DL1 cells, wells and filter were washed 2x with PBS, cells were counted and up to 50000 cells/well were replated. Cells were harvested at day 30 and RNA was isolated.
RNA was isolated using RNeasy Plus Micro Kit (QIAGEN) when cell numbers were < 5x105 and Nucleospin RNAII kit (Macherey-Nagel) when cell numbers were > 5x105. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions

tag: donor

tag: condition


title: CB06_DL1_ILC2_CD5n

description: in vitro generated


title: IRES_Screening_Rep1_Bin5

description:
Total DNA
Oligo_eGFP_expression.xlsx

tag: functional assay


title: Hippocampus_AD_NR_REPLICATE4

tag: tissue


title: Fine needle aspiration - P5


title: CB06_DL1_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: Hippocampus_AD_NR_REPLICATE3

tag: age


title: Hippocampus_AD_REPLICATE6

value: CTR


title: Hippocampus_AD_REPLICATE7


title: CB06_DL1_IL-15_NK/ILC1_CD94n

description: in vitro generated


title: Hippocampus_AD_NR_REPLICATE1


title: Hippocampus_AD_REPLICATE4


title: Hippocampus_AD_NR_REPLICATE2


title: CB06_OP9_IL-15_ILC3

description: in vitro generated


title: Hippocampus_AD_REPLICATE5


title: CB06_DL1_CD161n_CD5p

description: in vitro generated


title: IRES_Screening_Rep1_Bin4

description:
Total DNA
Oligo_eGFP_expression.xlsx

tag: master plasmid


title: IRES_Screening_Rep1_Bin3

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: CB06_OP9_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: CB05_DL1_ILC2_CD5p

description: in vitro generated


title: CB05_DL1_ILC2_CD5n

description: in vitro generated


title: Hippocampus_AD_REPLICATE3


title: CB05_DL1_IL-15_NK/ILC1_CD94n

description: in vitro generated


title: Hippocampus_AD_REPLICATE1


title: Hippocampus_WT_NR_REPLICATE6

value: WT


title: CB05_OP9_IL-15_ILC3

description: in vitro generated


title: Hippocampus_AD_REPLICATE2


title: Hippocampus_WT_NR_REPLICATE5


title: LOXP 11 bio rep5

city: Muenster

first: Timofey

middle: S.

last: Rozhdestvensky

state: NRW

address: Von-Esmarch-Str. 56

department: University of Muenster

institute: Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM)

description:
total RNA/5-Ht2cr pre-mRNA
The raw data only include reads from 5-HT2c mRNA isoforms.

data_processing:
Sequncing: Ion Torrent technology, Instrument PROTON
Read trimming and aligment: Torrent suite 4.0.2, default parameters
Analysis of diffrential isoform expression via t-tests and custom designed R scripts. All statistics were computed with functions and routines based on the statistical computing systems S+ and R (TIBCO® Spotfire S+ 8.1 for Windows, R version 3.3.2 (2016-10-31), Copyright (C) 2016)).  R is the freely available implementation of the S-programming language and runs on UNIX, MAC and Windows systems (https://www.cran.r-project.org). Functions and R-routines are available on demand. For fast computation of large datasets, we vectorised standard statistical tests (Student’s t-test and correction for multiple testing) in our functions. P-values for t-tests of analyzed isoforms with RPKM ≥10 were adjusted for multiple testing via the step-up procedure for correction of the ‘False Discovery Rate’ (FDR).   For all manipulations on BAM files (BAM to SAM conversion, indexing, IDX-statistics), we used the 32-Bit Windows version of the freely available samtools (http://samtools.sourceforge.net) .
Genome_build: All reads were mapped to two splice variants of the 5-Ht2c receptor; (i) 5-Ht2cr-sequence : 209nt and (ii) 5-Ht2cr-tr-sequence: 114 nt. FASTA is available on the series record.
Supplementary_files_format_and_content: Isoform expression: Excel file with quantified expression values for analysed isoforms.

source_name: choroid plexus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) accoding to manufacture instruction.
cDNA synthesis was performed with total RNA samples 100ng each using 200 pmol of 5ht2cRTrev oligonucleotide and 10 U of Transcriptor Reverse Transcriptase (Roche) in a 20 µl reaction as described above. Five µl aliquots of the RT-reactions were subjected to 10 cycles of PCR amplification with 5-Ht2cr exons IV and VI specific oligonucleotides: 5ht2cF and 5ht2cRTrev. PCR products were purified using High Pure PCR cleaning Micro Kit (Roche) and eluted in 20 µl of ddH2O. Ten µl of purified reactions were used for 15 cycles of PCR amplification to introduce  PGM adapters with barcodes. Twelve cDNA libraries (6 per genotype) were generated. Choroid plexuses from 24 male mice (12 animals from each genotype) at postnatal day 21 were isolated; two choroid plexuses per library were pooled and subjected to total RNA extraction.

tag: background strain

value: Hybrid (129SV x C57BL6/J) > 90% C57BL6/J

value: choroid plexus

value: postnatal day 21


title: IRES_Screening_Rep1_Bin1

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: LOXP 10 bio rep4


title: IRES_Screening_Rep1_Bin2

description:
Total DNA
Oligo_eGFP_expression.xlsx


title: LOXP 9 bio rep3


title: LOXP 8 bio rep2


title: CB04_DL1_ILC2_CD5p

description: in vitro generated


title: CB04_DL1_CD161n_CD5p

description: in vitro generated


title: CB04_DL1_ILC2_CD5n

description: in vitro generated


title: Hippocampus_WT_NR_REPLICATE4


title: Hippocampus_WT_NR_REPLICATE3


title: total NK cells_lymph nodes_steady state

city: München

first: Sophie

last: Flommersfeld

address: Trogerstr. 30

institute: Technical University of Munich

description: scRNAseq

data_processing:
Cell Ranger (version 5.0.1; 10x Genomics) was used for demultiplexing and alignment using default parameters.
velocyto 27 (version 0.17.17) performed counting of spliced and unspliced RNA molecules to create loom file.
Python software package SCANPY (version 1.4.4) was used for downstream analysis.
Spleens: cells filtered out that express < 700 and >1800 genes, <1800 and >4500 counts,  > 0.05% or <0.01 mitochondrial genes, >0.25 or <0.1 ribosomal genes. Genes were filtered out that were present in < 3 cells.
LN: cells filtered out that express < 750 and >1500 genes,<2000 and >5000 counts, > 0.05%  mitochondrial genes, >0.25 ribosomal genes. Genes were filtered out that were present in < 3 cells.
Gene counts were per-cell normalized and (log+1)-transformed.
Cell cycle, percent mito, n_genes and n_counts were regressed out.
Genome_build: Mouse reference genome GRCm38 release 84
Supplementary_files_format_and_content: Output of the Cell Ranger Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized).
Supplementary_files_format_and_content: unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts.

source_name: lymph node NK cells

extract_protocol:
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics).
Chromium Next GEM Single Cell 3' Library Kit v3.1 (10x Genomics), Chromium Single Cell 3' Feature Barcode Library Kit (10x Genomics).
Paired-end, single indexing.

treatment_protocol:
Cells were stained with TotalSeq-B anti-mouse Hashtag Antibodies (Biolegend, Clone: M1/42, 30-F11) prior to sorting of NK cell populations. Equal numbers of Ly49H+ and Ly49H- NK1.1+ Eomes GFP+ cells were sorted from each organ marked by distinct Hashtags.
The following Hashtags were used:   Hashtag 1: Spleen, Ly49H- NK cells sorted;   Hashtag 2: Spleen, Ly49H+ NK cells sorted;   Hashtag 4: LN peripheral, Ly49H- NK cells sorted;   Hashtag 5: LN peripheral, Ly49H+ NK cells sorted;   Hashtag 6: LN mesenteric, Ly49H- NK cells sorted;   Hashtag 7: LN mesenteric, Ly49H+ NK cells sorted.

tag: strain

value: mesenteric, inguinal, axillary and brachial lymph nodes

value: NK cells (CD3- NK1.1+ Eomes GFP+)


title: Hippocampus_WT_NR_REPLICATE1


title: Hippocampus_WT_NR_REPLICATE2


title: LOXP 12 bio rep6


title: LOXP 7 bio rep1


title: total NK cells_spleen_steady state

description: scRNAseq

source_name: splenic NK cells

value: spleen


title: CB04_DL1_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: WT 6 bio rep6

value: wildtype


title: CB04_DL1_IL-15_NK/ILC1_CD94n

description: in vitro generated


title: Alb-R3 48h ccl4 rep3

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment of reads was performed using Kallisto software, version 0.44.0 using the following parameters: quant -t 8 --bias --bootstrap-samples 10 --seed 42 --single --rf-stranded --fragment-length 150 --sd 70, and reference genome version GRCm38.p6 from GENCODE project with gene model annotation version M23
For differential expression analysis, the edgeR software, version v3.28.0 was used with the following parameters: Normalization  method - TMM (trimmed mean of m-values), data modelling -  glm (generalised linear model), statistical test - QL (quasi likelihood), Benjamini Hochberg (BH) multiple testing correction. Prior to differential expression analysis, data were filtered by estimated counts with the threshold of 20 to avoid inclusion of genes that are expressed at extremely low levels.
Genome_build: GRCm38.p6, gene model annotation version M23
Supplementary_files_format_and_content: Matrix file with normailzed counts and FPKM

source_name: Primary hepatocytes

extract_protocol:
Hepatocytes were isolated after perfusion with Liberase  following differential centrifugation and Percoll gradient purification. RNA was isolated using the Total RNA Mini Kit (IBI Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight- to ten-week-old male mice were injected intraperitoneally (i.p.) with a single dose of CCl4 (0.4 mg/g body weight diluted in olive oil) between 8 a.m. and 12 p.m. Vehicle-injected (oil) served as controls.

value: Primary hepatocytes

value: 48h ccl4


title: WT 5 bio rep5


title: Hippocampus_WT_REPLICATE5


title: CB04_OP9_IL-15_ILC3

description: in vitro generated


title: Hippocampus_WT_REPLICATE4


title: Alb-R3 48h ccl4 rep1


title: Hippocampus_WT_REPLICATE6


title: CB04_OP9_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: Hippocampus_WT_REPLICATE3


title: Alb-Cre 48h ccl4 rep2

value: Alb-Cre


title: WT 3 bio rep3


title: CB03_DL1_CD161n_CD5p

description: in vitro generated


title: WT 2 bio rep2


title: WT 1 bio rep1


title: Hippocampus_WT_REPLICATE2

value: Brain


title: Alb-Cre 48h ccl4 rep1


title: Alb-R3 48h oil rep3

value: 48h oil


title: CB03_DL1_ILC2_CD5n

description: in vitro generated


title: Hippocampus_WT_REPLICATE1

value: Hippocampus


title: Cortex_AD_NR_REPLICATE5

value: APP/PS1 AD

value: Cortex

value: NR

value: 5 months


title: Cortex_AD_NR_REPLICATE4

value: 12 months


title: Alb-R3 48h ccl4 rep2


title: WT 4 bio rep4

value: Hybrid (129SV x C57BL6/J) > 90% C57BL6/J

value: choroid plexus


title: CB03_DL1_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: Alb-R3 48h oil rep2


title: Alb-R3 48h oil rep1


title: Alb-Cre 48h ccl4 rep3


title: CB03_DL1_IL-15_NK/ILC1_CD94n

description: in vitro generated


title: Alb-Cre 48h oil rep3


title: Cortex_AD_NR_REPLICATE2


title: Cortex_AD_NR_REPLICATE3


title: CB03_OP9_IL-15_ILC3

description: in vitro generated