title: RMB148


title: Black 6 TCT Colitis B6_TCT_3

status: Public on Aug 08 2022

type: SRA

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

description: Black 6 TCT Colitis

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed and filtered to remove adaptor contamination and poor-quality bases using trimmomatic.
The resulting read files were mapped to the GRCm38 genome assembly using Hisat2 with default parameters.
The number of reads mapping to the genomic features annotated in Ensembl with a MAPQ score higher than or equal to 10 was calculated using htseq-count with default parameters.
Assembly: GRCm38
Supplementary files format and content: Text file in comma-separated value format with the raw counts of read pairs uniquely and concordantly mapped to each gene

molecule: total RNA

organism: Mus musculus

source_name: colon

extract_protocol:
Colon segments were taken from mice after confirmation of death, and placed into 1 ml of RNA later. RNA was extracted from colon segments or purified cells with Qiazol reagent (Invitrogen). In this method, distilled solutions of RNA were purified using chloroform and isopropanol and eluted with ethanol before being resuspended in RNAse free water. RNA was cleaned up using the Qiagen RNeasy Microkit and performing the DNA clean up protocol as listed in the manufacturer’s guidelines. RNA samples were then checked for the quality, contamination and concentration using a NanoDrop, Qubit spectrophotometer and Bioanalyzer. RNA with only a RIN score of above 7 were used for RNA sequencing. RNA was then stored at -80°C awaiting further analysis.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: 3% DSS (MW 36,00-50,000, MP Biomedicals, LLC) was administered orally in drinking water for 5 days, DSS was then removed and put back on normal water and mice were culled at day 10 upon recovery. 200μl of 3mg DNBS (Sigma-Aldrich) resolved in 50% EtOH were administered rectally while mice were under isoflurane anaesthesia. 50ug of anti-CD40 (2bScientific, UK) agonist was injected intraperitoneally and mice were culled after 7 days. CD4+ T cells with naive markers (CD4+ CD25- CD44low CD62Lhigh) were sorted using a FACS Aria to a purity of >95%. Rag2-/- mice were injected intraperitoneally with 0.5x10^6 CD4+ cells per mouse and humanely culled after 6-8 weeks. 750ug of anti-IL-10R (2bScientific, UK) were injected into mice intraperitoneally and mice were culled after 4 weeks (unless signs of colitis were seen before).

tag: cell line

value: colon

tag: genotype

tag: treatment

value: Naive CD4 T-cell transfer

tag: identifier in_raw_counts.csv


title: Black 6 TCT Colitis B6_TCT_5

description: Black 6 TCT Colitis


title: RMB147

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 downloaded from GENCODE using RSEM program version 1.2.19 with default parameters.
Gene expression values in transcripts per million (TPM) were calculated using the RSEM program and the mouse GENCODE gene annotation version M4.
Quality control and outlier cell detection was performed using Seurat R package.
Assembly: GRCm38
Supplementary files format and content: tab delimited TPM table

extract_protocol:
single cells were captured on Fluidigm C1 mRNA Seq IFC and lysed and reverse-transcribed in situ
Nextera XT

tag: age

value: Adult


title: M_C0_iNKT_cell_2

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: mm10
Supplementary files format and content: The detected copy number of RNA moelcules per tube (i.e., 200 cells) for each gene is listed.

growth_protocol: Freshly isolated

extract_protocol:
RNAs from cell lysate was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 200 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Two hundred cells were isolated from thymus or blood using FACS cell sorter

tag: cell type

value: Thymus iNKT cell

tag: cell subset

value: TCRbeta+NK1.1+CD1d tet+CD244-CXCR6-


title: RMB146


title: M_C0_iNKT_cell_1


title: M_C1_iNKT_cell_2

value: TCRbeta+NK1.1+CD1d tet+CD244-CXCR6+


title: M_C0_iNKT_cell_3


title: RMB145


title: M_C1_iNKT_cell_4


title: Black 6 TCT Colitis B6_TCT_1

description: Black 6 TCT Colitis


title: M_C1_iNKT_cell_3


title: M_C1_iNKT_cell_1


title: untreated Black 6 Rag1 B6_R1C_4

description: untreated Black 6 Rag1


title: untreated Black 6 Rag1 B6_R1C_3

description: untreated Black 6 Rag1


title: RMB144


title: RMB150


title: M_C2_iNKT_cell_4

value: TCRbeta+NK1.1+CD1d tet+CD244+CXCR6+


title: M_C2_iNKT_cell_3


title: M_C2_iNKT_cell_2


title: RMB143


title: Susd2-/- CD8 TILs, biological replicate 4, scRNAseq

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

country: USA

institute: The Ohio State University Wexner Medical Center

description:
10x Genomics
SusD2KO_raw_expression.zip

library_source: transcriptomic single cell

data_processing:
For each dataset, a cell was considered as low quality or abnormal and removed based on (i) less than 200 expressed genes, (ii) fewer than 200 or higher than 4,000 total features, and (iii) mitochondria content higher than 90%. We then performed the integrative analysis using the Seurat (v3.0) pipeline. Data integration was performed on the top 2,000 highly variable genes in each sample via canonical correlation analysis. Cell clusters were identified using the top five principal components (PCs) with a resolution of 0.5 in Louvain clustering. All cell clusters were manually annotated according to the expression of curated marker genes. Differentially expressed genes (DEGs) were identified in each cell cluster using the Wilcoxon rank test built in Seurat, with log-fold change as 0.25 and adjusted p-value as 0.05.
Assembly: mm10
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for each cell

source_name: s.c. tumor

extract_protocol:
8 weeks old WT and Susd2-/- C57BL/6 mice were inoculated subcutaneously with 1 x 10^6 MC38 tumor cells. On Day 18 post inoculation, single cell suspensions were prepared from the tumors after mechanical disruption and enzymatic digestion with 1 mg/mL Type IV Collagenase. Cells were strained through a 70 µM filter. Live tumor infiltrating lymphocytes (CD45+ 7-AAD-) were sorted on a BD FACSAria Ilu Cell Sorter and immediately processed for scRNA-seq.
Experimental procedures for scRNA-seq followed established techniques using the Chromium Single Cell 3’ Library V3 Kit (10x Genomics).  Briefly, FACS-sorted Live CD45+ cells were processed using the inDrops V3 scRNA-seq platform. inDrops Libraries were sequenced on the NextSeq Illumina Platform, paired-end mode.The raw sequences (FASTQ format; four WT and four KO) were aligned and quantified using the CellRanger (v3.0.2) pipeline against the pre-built 10X mouse reference genome (mm10)

tag: tissue

value: s.c. tumor

value: colorectal cancer

value: Susd2-/- C57BL6

value: 6-8 weeks old


title: RMB142


title: M_C2_iNKT_cell_1


title: Black 6 Rag1 treated with anti-CD40 B6_R1a_8

description: Black 6 Rag1 treated with anti-CD40

value: Anti-CD40 antibodies


title: untreated Black 6 Rag1 B6_R1C_2

description: untreated Black 6 Rag1


title: RMB141


title: Black 6 Rag1 treated with anti-CD40 B6_R1a_6

description: Black 6 Rag1 treated with anti-CD40


title: Susd2-/- CD8 TILs, biological replicate 1, scRNAseq

description:
10x Genomics
SusD2KO_raw_expression.zip


title: OL_RNA_repl2

city: Baltimore

first: Jeff

last: Coller

address: 725 N. Wolfe St PCTB 505

institute: Johns Hopkins University

data_processing:
Library strategy: RNA-Seq (QuantM-seq)
Reads were trimmed off the adapter with fastx_clipper (FASTX-Toolkit).
Reads were mapped to GRCm38 (mm10) genome using hisat2 v2.1.0.
Sequence annotation gff3 files were generated for the mouse canonical transcripts and coding sequence
FPKM were tabulated using stringtie v.1.3.5 and ballgown
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt file that contains FPKM for OPCs and OLs for Ribosome protected RNA fragments and total RNA seq, for each replicate

source_name: Oligodendrocytes

growth_protocol: OPCs were grown onto nunclon plates coated with poly-L-ornithine (PO) (Sigma, P3655-50MG) and laminin (Sigma, L2020-1MG), in OPC growth media consisting of DMEM/F12 supplemented with N2 Max (R&D Systems, AR009), B27 (Thermo Fisher, 12587010), 20ng/mL bFGF (R&D Systems, 23-3FB-01M), and 20ng/mL PDGFA (R&D Systems, 221-AA). Media was changed every 48 hours and cultures were maintained in 37°C with 5% CO2.

extract_protocol:
RNA (total and ribosome footprints) was isolated by phenol chloroform extraction and treated with DNAse I before ribosomal RNA depletion. Total RNA samples were fragmented by alkaline treatment.
After PAGE purification, RNA was dephosphorylated and ligated to a preadenylylated linker (Universal miRNA Cloning Linker) before performing reverse transcription with Superscript III (Thermo Fisher Scientific). The cDNAs were precipitated, PAGE purified and circularized with CircLigase. Libraries were obtained by 12 cycles of PCR using primers adapted to Illumina sequencing, and sequenced on an Illumina HiSeq 2500 using single read 50 cycles runs.

treatment_protocol: OLs were differentiated from OPCs in OL differentiation media that consisted of DMEM/F12 supplemented with N2 Max, B27, 100ng/mL noggin (R&D, 3344NG050), 100ng/mL IGF-1 (R&D, 291G1200), 10uM cyclic AMP (Sigma, D0260-100MG), 10ng/mL NT3 (R&D, 267N3025) and 40ng/mL T3 (Thyroid hormone, Sigma, T-6397). OPCs and differentiated OLs were flash-frozen then collected in lysis buffer containing emetine. For ribosome protected fragments, the lysates were treated with micrococcal nuclease (nuclease S7) and the monosomes isolated by sucrose density gradient.

value: OLs differentiated from OPCs

tag: strain

tag: treatment of cell

value: Differentiated with T3

tag: treatment of lysate

value: No treatment

tag: molecule

value: RNA


title: Susd2-/- CD8 TILs, biological replicate 2, scRNAseq

description:
10x Genomics
SusD2KO_raw_expression.zip


title: Melanocyte hSN-CM RGMB-Depleted 1

city: Meguro

first: Yoshiho

last: Ikeuchi

state: Tokyo

address: 4-6-1 Komaba

department: Institute of Industrial Science

institute: The University of Tokyo

data_processing:
Sequenced reads were trimmed for adaptor sequence. STAR aligner (version. 2.5.2b)(Dobin et al., 2013) was used to map the reads to human reference genome hg38 (quantmode).
Mapped reads were quantified using featureCounts(Liao et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Read counts

organism: Homo sapiens

source_name: Melanocyte

growth_protocol: Melanocytes were cultured in 254 Medium supplemented with Human Melanocyte Growth Supplement (HMGS)

extract_protocol:
Cells were harvested using TriPure Isolation Reagent. RNA was extracted using Direct-Zol RNA Microprep Kits (Zymo Research)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Melanocytes were changed to 20% HMGS medium (minus bovine pituitary extract and insulin) 24 hours after plating and treated with either RGMB, IgG control medium, or RGMB depleted medium.

tag: developmental stage

value: Neonatal

tag: pigmentation

value: Highly pigmented

value: Treated (RGMB depleted hSN-CM)


title: Melanocyte hSN-CM IgG 2

value: Treated (IgG incubated hSN-CM)


title: RMB139

value: Adult


title: WT CD8 TILs, biological replicate 4, scRNAseq

description:
10x Genomics
B6a_raw_expression.zip

value: WT C57BL6


title: Melanocyte hSN-CM RGMB-Depleted 2


title: RMB140


title: OL_RNA_repl1


title: RMB138


title: OL_FP_repl2

data_processing:
Library strategy: Ribosome profiling
Reads were trimmed off the adapter with fastx_clipper (FASTX-Toolkit).
Reads were mapped to GRCm38 (mm10) genome using hisat2 v2.1.0.
Sequence annotation gff3 files were generated for the mouse canonical transcripts and coding sequence
FPKM were tabulated using stringtie v.1.3.5 and ballgown
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt file that contains FPKM for OPCs and OLs for Ribosome protected RNA fragments and total RNA seq, for each replicate

value: MNase digestion

value: RNA (ribosome protected)


title: Melanocyte Recombinant RGMB 2

value: Treated (RGMB)


title: RMB137


title: untreated Balb/C Control_2

description: untreated Balb/C

value: colon

value: Balb/C


title: Melanocyte Recombinant RGMB 1


title: WT CD8 TILs, biological replicate 3, scRNAseq

description:
10x Genomics
B6a_raw_expression.zip

value: s.c. tumor

value: colorectal cancer

value: 6-8 weeks old


title: OL_FP_repl1

value: OLs differentiated from OPCs

value: Differentiated with T3


title: WT CD8 TILs, biological replicate 2, scRNAseq

description:
10x Genomics
B6a_raw_expression.zip


title: RMB136


title: Black 6 Rag1 treated with anti-CD40 B6_R1a_7

description: Black 6 Rag1 treated with anti-CD40

value: Anti-CD40 antibodies


title: OPC_RNA_repl2

source_name: Oligodendrocyte Progenitor Cells

value: Epiblast stem cells-derived OPCs

value: No treatment

value: RNA


title: WT CD8 TILs, biological replicate 1, scRNAseq

description:
10x Genomics
B6a_raw_expression.zip


title: Melanocyte hSN-CM IgG 1

value: Neonatal

value: Highly pigmented

value: Treated (IgG incubated hSN-CM)


title: Melanocyte Control

value: Untreated


title: D10_5443_g_pLN

city: Boston

first: Xuan

last: He

state: MA

address: 3 Blackfan Circle,  E/CLS 1024-B8

institute: BIDMC

description: TMP matrix.csv

data_processing:
All samples were processed using an RNA-Seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis. Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos).
Trimmed reads were aligned to the Macaca mulatta genome (https://www.unmc.edu/rhesusgenechip/index.htm) using STAR v2.7.3. Alignments will be checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools.
Counts of reads aligning to known genes are generated by featureCounts. In parallel, Transcripts Per Million (TPM) measurements per isoform were generated using Salmon (Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference). We used DESeq2 (Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) internal filtering algorithm called "independentFiltering" that sets a threshold on the mean of normalized counts of all samples (baseMean > 10) in order to maximize the number of tests that pass multiple test correction.
A corrected P value cut-off of 0.05 was used to assess significant genes that were up-regulated or down-regulated on days 3, 7, and 10 using an adjusted P of<0.05 and the Benjamini-Hochberg (BH) correction method.
Genome_build: Macaca mulatta genome (https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: TMP matrix.csv

organism: Macaca mulatta

source_name: CD4 T cells from genital LNs

extract_protocol:
CD4 T cells from mesenteric LNs and pelvic LNs in monkeys necropsied on day 0, 3, 7 and 10 following infection were enriched by negative selection through EasySep™ Non-Human Primate Custom Enrichment Kit (STEMCELL Technologies).  The enriched cells were further stained with viability dyes and flow cytometric antibodies including CD45, CD3, CD4, CD8, and CD4 T cells were sorted by BD FACSAria flow cytometer. RNA extraction was carried out using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions. A Low-Input mRNA library (Clontech SMARTer) v4 was applied and samples were sequenced on Illumina NS500 Paired-End 75 bp (PE75) at the Molecular Biology Core Facility at Dana-Farber Cancer Institute.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD4 T cells

tag: tissues

value: genital LNs

tag: days post siv infection


title: Susd2-/- CD8 TILs, biological replicate 3, scRNAseq

description:
10x Genomics
SusD2KO_raw_expression.zip

value: Susd2-/- C57BL6


title: RMB134

value: Adult


title: OPC_RNA_repl1


title: RMB133


title: OPC_FP_repl2

value: MNase digestion

value: RNA (ribosome protected)


title: RMB132


title: D7_5358_g_pLN

description: TMP matrix.csv


title: OPC_FP_repl1


title: D10_5441_g_pLN

description: TMP matrix.csv


title: D10_5440_g_pLN

description: TMP matrix.csv


title: RMB131


title: D7_5355_g_pLN

description: TMP matrix.csv


title: RMB130


title: Control + STZ rep 2 (mouse 13+14)

city: Kiel

first: Eileen

last: Dahlke

state: Schleswig-Holstein

address: Otto-Hahn-Platz 8

department: Anatomisches Institut

country: Germany

institute: Christian-Albrechts-Universität Kiel

data_processing:
our in-house RNA-Seq pipeline to map and align the sequenced data (https://github.com/nf-core/rnaseq)
processed the raw data from the sequencer with FastQC v0.11 and Trimgalore v0.4. aligned the reads with STAR v2.5.2b and generated gene counts with featurecounts v1.5.2 and StringTie v1.3.3b
Quality control was assessed throughout with RSeqQC dupRadar, Preseq and MultiQC v1.4
Differentially expressed genes were identified by comparing expression profiles of the different genotypes.
Statistical analysis preformed using R v3.6.3.To identify differentially expressed genes between groups and time points, we used DESeq2 R package v1.26.0. DESeq2 was used for executing pairwise comparisons between genotypes.
Assembly: Genome Reference Consortium Mouse Build 38 and GenBank Assembly ID: GCA_000001635.8
Supplementary files format and content: merged gene counts as tab delimited text file

source_name: kidney

extract_protocol:
RNA was harvested using NucleoSpin(Macherey-Nagel). 0.5 ug of total RNA was used for the construction of sequencing libraries.
TrueSeq stranded mRNA

value: kidney

value: WT

value: STZ


title: VHL knockout rep 2 (mouse 9+10)

value: VHL knockout


title: Control +STZ rep 1 (mouse 11+12)


title: VHL knockout + STZ rep 2 (mouse 17+18)


title: VHL knockout rep 1 (mouse 7+8)


title: OL_repl2_6hr

data_processing:
Library strategy: RNA-Seq (5-EU Decay-seq)
Reads were trimmed off the adapter with fastx_clipper (FASTX-Toolkit).
Reads were mapped to GRCm38 (mm10) genome using hisat2 v2.1.0.
Sequence annotation gff3 files were generated for the mouse canonical transcripts and coding sequence
FPKM were tabulated using stringtie v.1.3.5 and ballgown
The raw FPKM numbers at each time-point were normalized to the relative number of reads aligning to the spike-ins, and half-lives were estimated by fitting a least absolute deviations regression model to an exponential decay equation
Genome_build: mm10
Supplementary_files_format_and_content: Txt files that contain FPKM for OPCs or OLs at every-time point, and txt files with the half-lives values for each replicate.

extract_protocol:
RNA was extracted with Trizol. A spike-in 5-EU labeled control was added to each time point prior to library preparation.
Samples were DNAse treated, depleted of ribosomal RNAs and fragmented by alkaline treatment. After precipitation, biotinylation of the 5-EU labelled RNA was performed following the Click-iT nascent RNA capture kit protocol, using 0.5 mM biotin azide. After PAGE purification, pull-down was performed with C1 myOne streptavidin beads (Thermo Fisher). RNA was dephosphorylated on the beads, and ligated to a preadenylylated linker (Universal miRNA Cloning Linker) before performing reverse transcription on the beads. The cDNA was eluted from the beads, PAGE purified, circularized with CircLigase, and PCR was performed for 14 to 16 cycles. Libraries were sequenced on an Illumina HiSeq 2500 using single read 76 cycles runs.

treatment_protocol: OLs were differentiated from OPCs in OL differentiation media that consisted of DMEM/F12 supplemented with N2 Max, B27, 100ng/mL noggin (R&D, 3344NG050), 100ng/mL IGF-1 (R&D, 291G1200), 10uM cyclic AMP (Sigma, D0260-100MG), 10ng/mL NT3 (R&D, 267N3025) and 40ng/mL T3 (Thyroid hormone, Sigma, T-6397). OPCs and 40-hr differentiating OLs were incubated in the presence of 5-ethynyl uridine (5-EU) for 24 hours. Following, 5-EU was removed from the media and replaced by uridine. Time points of 1 hr, 2 hr, 4 hr and 6 hr were then collected during the ensuing chase.

value: OLs differentiated from OPCs

tag: treatment for cell type

value: Differentiated with T3

tag: treatment for decay

value: 5-EU metabolic labeling for 24hr then uridine chase for 6hr

value: 5-EU labeled RNA (click-iT, streptavidin pull-down)


title: RMB135


title: OL_repl2_4hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 4hr


title: D7_5354_g_pLN

description: TMP matrix.csv


title: OL_repl2_2hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 2hr


title: RMB129


title: Control rep 3 (mouse 5+6)

tag: genotype


title: RMB128


title: VHL knockout +STZ rep 1 (mouse 15+16)

tag: treatment


title: D7_5353_g_pLN

description: TMP matrix.csv


title: OL_repl2_1hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 1hr


title: OL_repl2_0hr

value: 5-EU metabolic labeling for 24hr


title: RMB127


title: Control rep 1 (mouse 1+2)


title: RMB126


title: RMB125


title: D7_5442_g_pLN

description: TMP matrix.csv

value: CD4 T cells

value: genital LNs


title: OL_repl1_6hr


title: D7_5438_g_pLN

description: TMP matrix.csv


title: D7_5439_g_pLN

description: TMP matrix.csv


title: D7_5070_g_pLN

description: TMP matrix.csv


title: RNA-seq spleen CD8 L1/L2 DKO #2

city: St. Louis

first: Brian

middle: Todd

last: Edelson

state: MO

address: 660 S. Euclid Ave., Box 8118

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM in tab-delimitted text format

source_name: Spleen CD8 T cells

growth_protocol: Not applicable

extract_protocol:
Quick DNA/RNA Microprep Plus Kit
Clontech SMARTer Ultra Low RNA

treatment_protocol: see column related to "activation"

value: Spleen CD8 T cells

tag: mouse genotype

value: L1/L2 DKO

tag: activation

value: Non-activated


title: OL_repl1_4hr

tag: cell type


title: D3_5359_g_pLN

description: TMP matrix.csv


title: RNA-seq spleen CD8 36/L2 DKO #2

value: 36/L2 DKO


title: RMB124

tag: age

value: Adult


title: OL_repl1_2hr


title: D3_5349_g_pLN

description: TMP matrix.csv


title: OL_repl1_1hr


title: RNA-seq spleen CD8 36/L2 DKO #1


title: D3_5348_g_pLN

description: TMP matrix.csv


title: RNA-seq spleen CD8 36/L1 DKO #2

value: 36/L1 DKO


title: OL_repl1_0hr


title: Control rep 2 (mouse 3+4)

tag: tissue

value: kidney

value: WT


title: wt_cga_mono_r1

first: Anthony

middle: John

last: Veltri

state: Maryland

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

data_processing:
Library strategy: Ribo-seq
Raw reads from FASTQ files were deduplicated based on a unique molecular identifier to remove PCR artifacts by dedupe.sh (BBtools 38.44).
UMI and adapter sequences were removed by  bbduk.sh (Bbtools 38.44).
Noncoding sequence reads were removed via alignment by STAR 2.6.1c to a reference genome containing only noncoding RNA
Surviving coding-RNA reads were aligned by STAR 2.6.1c to a yeast reference genome excluding HIS3 and including the reporter sequence.
Correct shifts to represent ribosomal A sites were calculated from aligned read 5' ends and read distributions at each position of the reporter were calculated by custom Python scripts.
Genome_build: SacCer3 R64-1-1 with translation reporter
Supplementary_files_format_and_content: CSV files include calculated A site shifted ribosome footprint RPMs at each position of the reporter. The seq column contains the sequence of the reporter at each position

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were grown to OD 0.4-0.6

extract_protocol:
Frozen yeast cultures were lysed mechanically in liquid nitrogen using a freezer mill and thawed into lysis buffer
Ribosomes were pelleted through a sucrose cushion then separated into monosomes or disomes by centrifugation through a sucrose gradient and fractionated. Complexes were treated with RNase I and RNA footprints were extracted by phenol/chloroform. Footprint size selection (monosome: 15-35 nt, disome: 40-70 nt) was performed by gel extraction, followed by dephosphorylation, linker ligation, and reverse transcription. Ribosomal cDNA was depleted by subtracted with a pool of biotinylated oligonucleotides. Finally, cDNA was circularized and amplified by PCR with barcode-containing primers.

treatment_protocol: Yeast cultures were filter harvested and flash frozen in liquid nitrogen

tag: reporter

value: minCGA

value: wild type

tag: footprint library type

value: monosome


title: wt_non_mono_r1

value: minNONOPT


title: wt_opt_mono_r1

value: minOPT


title: OPC_repl3_6hr

value: Epiblast stem cells-derived OPCs

tag: strain

value: 5-EU metabolic labeling for 24hr then uridine chase for 6hr

value: 5-EU labeled RNA (click-iT, streptavidin pull-down)


title: D0_5841_g_pLN

description: TMP matrix.csv

value: CD4 T cells

value: genital LNs


title: RNA-seq spleen CD8 36/L1 DKO #1

value: Spleen CD8 T cells


title: RNA-seq spleen CD8 Control #4

value: Control

value: Non-activated


title: OPC_repl3_4hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 4hr

tag: molecule


title: D0_5835_g_pLN

description: TMP matrix.csv


title: OPC_repl3_2hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 2hr


title: D10_5443_mLN

description: TMP matrix.csv

source_name: CD4 T cells from mesenteric LNs

value: mesenteric LNs


title: HEK293T cells WT rep 4

city: Indianapolis

first: Evan

last: Cornett

address: 980 West Walnut Street

institute: Indiana University

data_processing:
Illumina's bcl2fastq software was used for basecalling and sequencing data were assessed using FastQC (v.0.11.5).
All sequenced libraries were mapped to the human genome (UCSC hg38) using STAR RNA-seq aligner (v.2.5) with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils (v.0.5.9) (from ngsutils).
Uniquely mapped sequencing reads were assigned to hg38 refGene genes using featureCounts (v.1.5.1) (from subread) with the following parameters: “-s 2 –p –Q 10”.
Quality control of sequencing and mapping results were summarized using MultiQC (v.0.11.5). Genes with read count per million (CPM) < 1 in more than 4 of the samples were removed.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated and purified using the QIAGEN RNeasy Plus Mini Kit.
500 nanograms of RNA per sample were used to prepare a single-indexed strand-specific cDNA library using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: cell line

value: WT


title: RNA-seq spleen CD8 L1/L2 DKO #1

value: L1/L2 DKO


title: RNA-seq spleen CD8 Control #3


title: HEK293T cells WT rep 2


title: D10_5083_mLN

description: TMP matrix.csv


title: HEK293T cells WT rep 1


title: D10_5441_mLN

description: TMP matrix.csv


title: RNA-seq spleen CD4 L1/L2 DKO #2

source_name: Spleen CD4 T cells

value: Spleen CD4 T cells


title: RNA-seq spleen CD4 L1/L2 DKO #1


title: OPC_repl3_0hr

value: 5-EU metabolic labeling for 24hr


title: HEK293T cells SETMAR KO#2 rep 4

value: SETMAR KO#2


title: OPC_repl2_6hr


title: D10_5440_mLN

description: TMP matrix.csv


title: RNA-seq spleen CD4 36/L2 DKO #2

value: 36/L2 DKO


title: D7_5442_mLN

description: TMP matrix.csv


title: OPC_repl2_4hr

value: Epiblast stem cells-derived OPCs


title: HEK293T cells SETMAR KO#2 rep 3


title: RNA-seq spleen CD4 36/L2 DKO #1


title: OPC_repl2_2hr


title: D7_5438_mLN

description: TMP matrix.csv


title: HEK293T cells SETMAR KO#2 rep 2


title: HEK293T cells WT rep 3


title: RNA-seq spleen CD4 36/L1 DKO #2

value: 36/L1 DKO


title: HEK293T cells SETMAR KO#2 rep 1


title: RNA-seq spleen CD4 36/L1 DKO #1


title: D7_5439_mLN

description: TMP matrix.csv


title: OPC_repl2_1hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 1hr

value: 5-EU labeled RNA (click-iT, streptavidin pull-down)


title: HEK293T cells SETMAR KO#1 rep 4

value: SETMAR KO#1


title: D7_5354_mLN

description: TMP matrix.csv

value: CD4 T cells


title: OPC_repl3_1hr


title: RNA-seq spleen CD4 Control #4

value: Control


title: OPC_repl2_0hr


title: HEK293T cells SETMAR KO#1 rep 3


title: RNA-seq spleen CD4 Control #3

value: Non-activated


title: D7_5074_mLN

description: TMP matrix.csv


title: HEK293T cells SETMAR KO#1 rep 2


title: HEK293T cells SETMAR KO#1 rep 1


title: OPC_repl1_4hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 4hr


title: D7_5355_mLN

description: TMP matrix.csv


title: mRNA decay-seq TKO #3 time120

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM in tab-delimitted text format

source_name: Spleen CD44hi CD4 T cells

extract_protocol:
E.Z.N.A. MicroElute Total RNA Kit (OMEGA Bio-Tek R6831)
Clontech SMARTer Ultra Low RNA

value: Spleen CD44hi CD4 T cells

value: TKO

value: 24h plate-bound anti-CD3/CD28; 120 min post-ActD


title: D7_5358_mLN

description: TMP matrix.csv

value: mesenteric LNs


title: OPC_repl1_6hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 6hr


title: OPC_repl1_2hr

value: 5-EU metabolic labeling for 24hr then uridine chase for 2hr


title: OPC_repl1_1hr


title: mRNA decay-seq TKO #3 time60

value: 24h plate-bound anti-CD3/CD28; 60 min post-ActD


title: mRNA decay-seq TKO #3 time30

value: 24h plate-bound anti-CD3/CD28; 30 min post-ActD


title: D7_5353_mLN

description: TMP matrix.csv


title: IL9: IL9 treated colonoid donor 4

data_processing:
Fastq files were firstly processed with in-house Perl scripts to discard reads with adaptor contamination, or at least 10% of uncertain bases (N), or at least 50% of nucleotides with a Phred quality score less than 20
Read pairs were then aligned to the human genome (GRCh37/hg19) using TopHat v2.0.12
HTSeq v0.6.1 was used to count the read pairs mapped uniquely and concordantly to each gene
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: files in tab-separated value format report the raw counts of read pairs uniquely and concordantly mapped to each gene

source_name: colonic organoid

growth_protocol: Establishment of human colonoids was performed as previously described by Fujii et al.(2015). The crypts were cultured in growth medium containing advanced Dulbecco’s modified Eagle’s medium/F12, penicillin/streptomycin (100 units/mL), 10 mM HEPES, 2 mM Glutamax, supplements N2 (1x) and B27 (1x), 50 ng/mL mouse epidermal growth factor (all from Life Gibco), 1 mM N-acetylcysteine (Sigma-Aldrich), 50% v/v Wnt3a conditioned medium, 10% v/v R-spondin-1 conditioned medium, 100 ng/mL murine recombinant noggin protein (Peprotech),10 nM gastrin (Sigma-Aldrich), 500 nM A83-01 (Bio-techne), 10 μM SB202190 (Sigma-Aldrich) and 10 mM Nicotinamide (Sigma-Aldrich). 10 μM Y-27632 (Sigma-Aldrich) was added to the culture medium for the initial 3 days. Medium was changed every 2 days. Differentiation towards a mature epithelium in human colonoids was achieved with reduction of Wnt3a to 15% v/v and withdraw of SB202190 and nicotinamide for 5-7 days.

extract_protocol:
Total RNA was isolated from human colonoids (released from Matrigel with Cell Recovery solution (Corning)) using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. On-column DNase digestion was performed to remove any residual genomic DNA (Qiagen).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: During the last 24h in differentiation medium human colonoids were treated with human recombinant IL13 (10 ng/mL) or IL9 (10ng/mL).

tag: disease state

value: healthy

value: colonic organoid

value: IL9 10ng/mL

tag: treatment duration

value: 24 hours

tag: donor

tag: experiment


title: mRNA decay-seq TKO #3 time0

value: 24h plate-bound anti-CD3/CD28; no ActD


title: OPC_repl1_0hr

value: Epiblast stem cells-derived OPCs

tag: treatment for cell type

tag: treatment for decay

value: 5-EU metabolic labeling for 24hr

value: 5-EU labeled RNA (click-iT, streptavidin pull-down)


title: D3_5359_mLN

description: TMP matrix.csv

value: CD4 T cells

tag: tissues

tag: days post siv infection


title: D7_5070_mLN

description: TMP matrix.csv


title: mRNA decay-seq TKO #2 time120

value: Spleen CD44hi CD4 T cells

tag: mouse genotype

tag: activation


title: D3_5349_mLN

description: TMP matrix.csv

tag: cell type


title: CTL: untreated colonoid donor 4

tag: tissue

tag: treatment

value: untreated


title: mRNA decay-seq TKO #2 time60

value: TKO


title: IL13: IL13 treated colonoid donor 6

value: IL13 10ng/mL


title: D3_5348_mLN

description: TMP matrix.csv

value: mesenteric LNs


title: ESCs, Ago12_KO2

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP52

data_processing:
Library strategy: Ribo-Seq
Sequenced reads were trimmed for adaptor sequence using trimmomatic
read were then sequentially mapped using unmapped reads for the next step. Reads were mapped first to fly and then mouse rRNA, tRNA and cDNA annotations using the ensmebl mm10 (GRCm38.91) and dm6 (BDGP6.22.78) annotations using bowtie2
non-ambiguous reads were then summed up on the gene level and mouse samples normalized by the corresponding fly spike-in reads
Genome_build: mm10, dm6
Supplementary_files_format_and_content: tab-delimited text file with spike-in normalized read count

source_name: Embyronic stem cells

growth_protocol: mESCs were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on 0.2% gelatine coated plates.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 5 ug of total RNA for the construction of sequencing libraries.
5 µg of total RNA were used for rRNA depletion using the Ribo-Zero Magnetic Kit from epicentre-Illumina. Drosophila spike-ins were added and followed by by a 12 cycle PCR amplifcation

treatment_protocol: Cells were treated with cycloheximide (0.1 mg/mL) for 2 min at 37°C to arrest translation elongation, and immediately harvested, followed by lysate preparation. For the generation of ribosome-protected fragments, cell lysates were treated with 5 units RNase I (ART-Seq) per OD260, and monosomes were purified in MicroSpin S-400 columns (GE Healthcare)

value: 129/Ola background

value: Blastocyst

value: Embyronic stem cells

tag: genotype

value: Ago1&Ago2 double knockout


title: ESCs, Ago12_KO1

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP40

tag: strain


title: mRNA decay-seq TKO #2 time30

value: 24h plate-bound anti-CD3/CD28; 30 min post-ActD


title: ESCs, Dicer_KO2

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP38

value: Dicer knockout


title: CTL: untreated colonoid donor 6

value: healthy

value: colonic organoid

value: 24 hours


title: mRNA decay-seq TKO #2 time0

value: 24h plate-bound anti-CD3/CD28; no ActD


title: D0_T475_mLN

description: TMP matrix.csv


title: IL9: IL9 treated colonoid donor 5

value: IL9 10ng/mL


title: D0_5835_mLN

description: TMP matrix.csv

value: CD4 T cells


title: IL13: IL13 treated colonoid donor 4


title: mRNA decay-seq TKO #1 time120

value: Spleen CD44hi CD4 T cells

value: 24h plate-bound anti-CD3/CD28; 120 min post-ActD


title: IL13: IL13 treated colonoid donor 5


title: C1, iNKT, 4

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the hg38 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clustered by molecular barcode
The number of cluster for each gene was counted, which provides the number of molecules detected for each gene
Assembly: hg38
Supplementary files format and content: RNA_expression.txt (The detected copy number of RNA moelcules per tube (i.e., 200 cells) for each gene is listed.)

source_name: Blood iNKT cell

growth_protocol: Isolated from human blood

treatment_protocol: Two hundred cells were isolated from peripheral blood of human using FACS cell sorter

value: peripheral blood

value: iNKT cells

tag: cell subset

tag: cell surface markers

value: CD3+CD1d tet+CD244-CXCR6+


title: mRNA decay-seq TKO #1 time60

value: TKO

value: 24h plate-bound anti-CD3/CD28; 60 min post-ActD


title: IL9: IL9 treated colonoid donor 6

tag: disease state


title: C1, iNKT, 3


title: ESCs, Drosha_KO1

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP30

value: 129/Ola background

value: Blastocyst

value: Embyronic stem cells

tag: cell line

value: Drosha knockout


title: ESCs, Dgcr8_KO2

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP39

value: Dgcr8 knockout


title: TNF treated colonoid donor 4 [TNFa_4]

data_processing:
Fastq files were firstly processed with in-house Perl scripts to discard reads with adaptor contamination, or at least 10% of uncertain bases (N), or at least 50% of nucleotides with a Phred quality score less than 20
Read pairs were then aligned to the human genome (GRCh37/hg19) using TopHat v2.0.12
HTSeq v0.6.1 was used to count the read pairs mapped uniquely and concordantly to each gene
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: file in tab-separated value format with the raw counts of read pairs uniquely and concordantly mapped to each gene

extract_protocol:
Total RNA was isolated from human colonoids (released from Matrigel with Cell Recovery solution (Corning)) using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. On-column DNase digestion was performed for removing any residual genomic DNA (Qiagen).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: During the last 24h in differentiation medium human colonoids were treated with human recombinant IL17A (50ng/mL), TNFα (10ng/mL), IFNγ (20ng/mL), IL22 (10ng/mL) or combination of IL17A & IL22.

tag: tissue/cell type

value: colonic organoid

value: TNF 10ng/mL

tag: treatment duration

tag: donor id


title: C1, iNKT, 2


title: mRNA decay-seq TKO #1 time0

value: 24h plate-bound anti-CD3/CD28; no ActD


title: ESCs, Dgcr8_KO1

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP28


title: C1, iNKT, 1


title: TNF treated colonoid donor 3 [TNFa_3]

value: 24 hours

tag: experiment


title: ESCs, WT_2

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP37

value: Wild Type


title: TNF treated colonoid donor 2 [TNFa_2]


title: mRNA decay-seq Control #3 time120

value: Spleen CD44hi CD4 T cells

value: Control


title: C2, iNKT, 4

value: peripheral blood

value: CD3+CD1d tet+CD244+CXCR6+


title: ESCs, Dicer_KO1

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP31

value: Dicer knockout


title: ESCs, WT_1

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP29


title: ESCs, Drosha_KO2

description:
Single stranded ArtSeq Ribosome Profiling Illumina library Protocol
Processed file column: RP41


title: C2, iNKT, 3

value: iNKT cells


title: mRNA decay-seq Control #3 time0


title: C2, iNKT, 2


title: mRNA decay-seq Control #3 time30

value: 24h plate-bound anti-CD3/CD28; 30 min post-ActD


title: mRNA decay-seq Control #3 time60

value: 24h plate-bound anti-CD3/CD28; 60 min post-ActD


title: mRNA decay-seq TKO #1 time30

value: TKO


title: CTL: untreated colonoid donor 5

value: healthy

value: untreated

tag: donor


title: TCR_lsmc2_4

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

country: South Korea

institute: GENOME INSIGHT

description: 10x Genomics

data_processing:
library strategy: CITE-seq / TCR-seq
Libraries were constructed and sequenced at a depth of approximately 20,000 reads per cell for gene, antibody-derived tags (ADTs), and TCR sequence expression using the Nextseq 550 or Novaseq 6000 platform (Illumina). The sequenced data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v3.0.1) to generate fastq files. Demultiplexed fastq files of gene and ADT expression were aligned to the reference human genome (GRCH38; 10X Cell Ranger reference GRCh38 v3.0.0) and the barcode sequence of each ADT, and filtering, barcode counting, and UMI counting were performed to generate feature-barcode matrices using the count function (Cell Ranger, v3.0.1).
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv

molecule: polyA RNA

source_name: liver sinusoid

extract_protocol:
Livers were perfused with Custodiol HTK (Essential Pharmaceuticals) solution during bench preparation of the liver from living donors. The first 500 ml of 1000 ml of total perfusate was discarded, and the second 500 ml was collected and filtered. Liver sinusoidal mononuclear cells (LSMCs) were separated by density gradient centrifugation using Lymphocyte separation medium (Corning).
Single-cell CITE-seq and TCR-seq libraries were generated using the Chromium Single Cell 5′ Library & Gel Bead Kit (PN-10000006), 5’ Feature Barcode Library Kit (PN-1000020), and V(D)J Kit, Human T Cell (PN-1000005) (10X Genomics) following the manufacturer’s instructions.

value: liver sinusoid

value: mononuclear cell

tag: library type

value: mRNA


title: IL22 treated colonoid donor 4 [IL22_4]

value: colonic organoid

value: IL22 10ng/mL


title: IL22 treated colonoid donor 3 [IL22_3]

value: 24 hours


title: C2, iNKT, 1


title: TCR_lsmc2_2

description: 10x Genomics


title: mRNA decay-seq Control #2 time120

value: Spleen CD44hi CD4 T cells

tag: mouse genotype

value: 24h plate-bound anti-CD3/CD28; 120 min post-ActD


title: IL22 treated colonoid donor 2 [IL22_2]


title: TCR_lsmc2_1

description: 10x Genomics


title: mRNA decay-seq Control #2 time60

value: Control

tag: activation


title: U937-EG_EG_12h

city: Shanghai, China

first: Yifan

last: Zhang

address: Ruijin Hospital

country: China

institute: Shanghai Institute of Hematology

library_source: genomic

data_processing:
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1
Alignmented SAM files were handled using samtools(1.7)
Peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set
BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: U937 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
U937-AE and U937-EG were cross-linked with 1% formaldehyde for 10min and stopped by 125mM glycine. After lysis and sonication, 30μL of anti-HA magnetic beads (MCE, HY-K0201) was incubated with chromatin samples overnight at 4℃ for immunoprecipitation. The DNA were purified with the MinElute PCR Purification Kit (QIAGEN) and subjected to library construction and next-generation sequencing with Illumina systems.
ChIP-seq libraries were used the VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (ND607).

treatment_protocol: AML1-ETO or ETO2-GLIS2 was induced by treatment with 5ug/ml doxycycline (Sigma) for 48h.

tag: cell type

value: monocytic cell line

value: EG over-expressed

value: doxycycline 12h


title: TCR_lsmc1_2

description: 10x Genomics

tag: tissue


title: U937-EG_Input_12h

tag: treatment


title: mRNA decay-seq Control #2 time30

value: 24h plate-bound anti-CD3/CD28; 30 min post-ActD


title: TNF treated colonoid donor 1 [TNFa_1]

value: TNF 10ng/mL


title: TCR_lsmc1_1

description: 10x Genomics


title: U937-AE_Input_12h

tag: genotype

value: AE over-expressed


title: mRNA decay-seq Control #2 time0

value: 24h plate-bound anti-CD3/CD28; no ActD


title: IL17A+IL22 treated colonoid donor 4 [IL2217_4]

value: IL17A 50ng/mL + IL22 10ng/mL


title: TCR_lsmc2_3

description: 10x Genomics

value: liver sinusoid


title: ADT_lsmc2_4

library_source: other

molecule: protein

value: mononuclear cell

value: ADT

tag: antibodies/tags

value: anti-CD45RA-TotalSeq™-C, anti-CD45RO-TotalSeq™-C, anti-CD14-TotalSeq™-C, anti-CD19-TotalSeq™-C, anti-CD56-TotalSeq™-C , anti-TCRα/β -TotalSeq™-C, anti-CD4-TotalSeq™-C, anti-CD8-TotalSeq™-C, anti-CD25-TotalSeq™-C, anti-CD27-TotalSeq™-C, anti-CD28-TotalSeq™-C , anti-CD127-TotalSeq™-C, anti-CCR7-TotalSeq™-C, anti-CD69-TotalSeq™-C, anti-CD103-TotalSeq™-C , anti-CXCR3-TotalSeq™-C, anti-PD-1-TotalSeq™-C , anti-CTLA-4-TotalSeq™-C , anti-TIGIT-TotalSeq™-C, anti-HVEM-TotalSeq™-C, anti-CD39-TotalSeq™-C, anti-DNAM-1-TotalSeq™-C, anti-PD-L1-TotalSeq™-C , anti-ICOS-TotalSeq™-C , anti-CD38-TotalSeq™-C, anti-OX40-TotalSeq™-C , anti-4-1BB-TotalSeq™-C , anti-NKG2D-TotalSeq™-C, Hashtag1-TotalSeq™-C, Hashtag2-TotalSeq™-C, Hashtag3-TotalSeq™-C, Hashtag4-TotalSeq™-C, Hashtag5-TotalSeq™-C , anti-CD45-TotalSeq™-C, anti-CD16-TotalSeq™-C, anti-TCR Vδ2 -TotalSeq™-C, anti-CD161-TotalSeq™-C, anti-CD57-TotalSeq™-C, anti-CD154-TotalSeq™-C, anti-CD272-TotalSeq™-C, anti-CD58-TotalSeq™-C, anti-TIM-3-TotalSeq™-C, anti-GITR-TotalSeq™-C


title: mRNA decay-seq Control #1 time120


title: IL17A+IL22 treated colonoid donor 2 [IL2217_2]

value: colonic organoid


title: ADT_lsmc2_2


title: IL17A+IL22 treated colonoid donor 1 [IL2217_1]

value: 24 hours


title: IL22 treated colonoid donor 1 [IL22_1]

value: IL22 10ng/mL


title: IL17A treated colonoid donor 4 [IL17_4]

value: IL17A 50ng/mL


title: mRNA decay-seq Control #1 time60

value: Spleen CD44hi CD4 T cells

value: Control

value: 24h plate-bound anti-CD3/CD28; 60 min post-ActD


title: mRNA decay-seq Control #1 time30


title: mRNA decay-seq Control #1 time0


title: CC15 - FFPE healthy colon

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

description: 10X Visium

data_processing:
Demultiplexing, barcode processing, and raw counts were generated using Space Ranger v1.3.0 from 10X Genomics (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Downstream sample processing was carried out in R using the Seurat package.
Assembly: GRCh38 (using 10X probe set: Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv)
Supplementary files format and content: Tab-separated raw count matrix with genes in rows and barcodes in columns.
Supplementary files format and content: Supplementary metadata file is a tab-delimited matrix matching samples to barcodes and tissue descriptions.

source_name: FFPE healthy colon

extract_protocol:
Allprep DNA/RNA FFPE kit (Qiagen, Cat. # 80234), following manufacturer's protocols
Visium 10x Genomics, following manufacturer's protocols

value: FFPE healthy colon


title: CC14 - FFPE healthy colon

description: 10X Visium


title: ADT_lsmc1_2

value: anti-CD45RA-TotalSeq™-C, anti-CD45RO-TotalSeq™-C, anti-CD14-TotalSeq™-C, anti-CD19-TotalSeq™-C, anti-CD56-TotalSeq™-C , anti-TCRα/β -TotalSeq™-C, anti-CD4-TotalSeq™-C, anti-CD8-TotalSeq™-C, anti-CD25-TotalSeq™-C, anti-CD27-TotalSeq™-C, anti-CD28-TotalSeq™-C , anti-CD127-TotalSeq™-C, anti-CCR7-TotalSeq™-C, anti-CD69-TotalSeq™-C, anti-CD103-TotalSeq™-C , anti-CXCR3-TotalSeq™-C, anti-PD-1-TotalSeq™-C , anti-CTLA-4-TotalSeq™-C , anti-TIGIT-TotalSeq™-C, anti-HVEM-TotalSeq™-C, anti-CD39-TotalSeq™-C, anti-DNAM-1-TotalSeq™-C, anti-PD-L1-TotalSeq™-C , anti-ICOS-TotalSeq™-C , anti-CD38-TotalSeq™-C, anti-OX40-TotalSeq™-C , anti-4-1BB-TotalSeq™-C , anti-NKG2D-TotalSeq™-C, Hashtag1-TotalSeq™-C, Hashtag2-TotalSeq™-C, Hashtag3-TotalSeq™-C, Hashtag4-TotalSeq™-C, Hashtag5-TotalSeq™-C


title: RNA-seq kidney CD8 TKO #2

description: Sample 16

source_name: Kidney CD8 T cells

value: Kidney CD8 T cells

value: TKO

value: Non-activated


title: IL17A treated colonoid donor 2 [IL17_2]


title: IL17A+IL22 treated colonoid donor 3 [IL2217_3]

value: IL17A 50ng/mL + IL22 10ng/mL


title: ADT_lsmc1_1

value: liver sinusoid


title: CC10 - FFPE healthy colon

description: 10X Visium


title: CC3 - FFPE healthy colon

description: 10X Visium


title: CC6 - FFPE healthy colon

description: 10X Visium


title: mRNA_lsmc2_4

description: 10x Genomics

value: mononuclear cell

value: mRNA


title: ADT_lsmc2_3

value: ADT

value: anti-CD45RA-TotalSeq™-C, anti-CD45RO-TotalSeq™-C, anti-CD14-TotalSeq™-C, anti-CD19-TotalSeq™-C, anti-CD56-TotalSeq™-C , anti-TCRα/β -TotalSeq™-C, anti-CD4-TotalSeq™-C, anti-CD8-TotalSeq™-C, anti-CD25-TotalSeq™-C, anti-CD27-TotalSeq™-C, anti-CD28-TotalSeq™-C , anti-CD127-TotalSeq™-C, anti-CCR7-TotalSeq™-C, anti-CD69-TotalSeq™-C, anti-CD103-TotalSeq™-C , anti-CXCR3-TotalSeq™-C, anti-PD-1-TotalSeq™-C , anti-CTLA-4-TotalSeq™-C , anti-TIGIT-TotalSeq™-C, anti-HVEM-TotalSeq™-C, anti-CD39-TotalSeq™-C, anti-DNAM-1-TotalSeq™-C, anti-PD-L1-TotalSeq™-C , anti-ICOS-TotalSeq™-C , anti-CD38-TotalSeq™-C, anti-OX40-TotalSeq™-C , anti-4-1BB-TotalSeq™-C , anti-NKG2D-TotalSeq™-C, Hashtag1-TotalSeq™-C, Hashtag2-TotalSeq™-C, Hashtag3-TotalSeq™-C, Hashtag4-TotalSeq™-C, Hashtag5-TotalSeq™-C , anti-CD45-TotalSeq™-C, anti-CD16-TotalSeq™-C, anti-TCR Vδ2 -TotalSeq™-C, anti-CD161-TotalSeq™-C, anti-CD57-TotalSeq™-C, anti-CD154-TotalSeq™-C, anti-CD272-TotalSeq™-C, anti-CD58-TotalSeq™-C, anti-TIM-3-TotalSeq™-C, anti-GITR-TotalSeq™-C


title: RNA-seq kidney CD8 Control #2

description: Sample 14


title: U937-AE_AE_12h

value: monocytic cell line

value: AE over-expressed

value: doxycycline 12h


title: IL17A treated colonoid donor 1 [IL17_1]

value: colonic organoid

value: IL17A 50ng/mL

value: 24 hours


title: RNA-seq kidney CD8 TKO #1

description: Sample 15


title: CC2 - FFPE healthy colon

description: 10X Visium

value: FFPE healthy colon


title: mRNA_lsmc2_3

description: 10x Genomics


title: CC13 - FFPE healthy colon

description: 10X Visium


title: IFNG treated colonoid donor 4 [IFNg_4]

value: IFNG 20ng/mL


title: IL17A treated colonoid donor 3 [IL17_3]


title: IFNG treated colonoid donor 2 [IFNg_2]


title: CC1 - FFPE healthy colon

description: 10X Visium


title: ADT_lsmc2_1


title: RNA-seq kidney CD8 Control #1

description: Sample 13

value: Kidney CD8 T cells

value: Control


title: mRNA_lsmc2_2

description: 10x Genomics


title: C10 - FFPE colon irAE

description: 10X Visium

source_name: FFPE colon irAE

value: FFPE colon irAE


title: IFNG treated colonoid donor 3 [IFNg_3]


title: RNA-seq kidney CD4 TKO #2

description: Sample 12

source_name: Kidney CD4 T cells

value: Kidney CD4 T cells

value: TKO

value: Non-activated


title: mRNA_lsmc2_1

description: 10x Genomics

value: liver sinusoid

value: mononuclear cell

value: mRNA


title: IFNG treated colonoid donor 1 [IFNg_1]


title: C9 - FFPE colon irAE

description: 10X Visium


title: mRNA_lsmc1_2

description: 10x Genomics


title: RNA-seq kidney CD4 Control #2

description: Sample 10


title: Untreated colonoid donor 4 [Control_4]


title: RNA-seq kidney CD4 Control #1

description: Sample 9


title: Untreated colonoid donor 3 [Control_3]


title: mRNA_lsmc1_1

description: 10x Genomics


title: Cell and GD955-38 and TSN-3

city: Guangzhou

first: Xinheng

address: No.483, Wushan Road, Tianhe District

institute: South China Agricultural University

description: PAMs cells ASFV infection plus TSN treatment group (CeViDrug)

data_processing:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was   purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis   Reaction Buffer(5X).
First strand cDNA was synthesized using random hexamer primer and   M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA   synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining   overhangs were converted into blunt ends via exonuclease/polymerase activities.
After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to   prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in   length, the library fragments were purified with AMPure XP system (Beckman Coulter,   Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase,   Universal PCR primers and Index (X) Primer.
At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Sus scrofa

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Lung

value: Porcine alveolar macrophages

value: primary cell

value: WT

value: ASFV-infected PAMs incubated with TSN for 24 h


title: RNA-seq spleen CD8 TKO #2

description: Sample 8

value: Spleen CD8 T cells


title: C6 - FFPE colon irAE

description: 10X Visium


title: Untreated colonoid donor 2 [Control_2]

value: colonic organoid

value: 24 hours


title: Cell and GD955-38 and TSN-2


title: RNA-seq kidney CD4 TKO #1

description: Sample 11


title: C2 - FFPE colon irAE

description: 10X Visium


title: RNA-seq spleen CD8 Control #2

description: Sample 6


title: Cell and GD955-38-3

description: PAMs cells  viral (ASFV) infection group (cellViru)

value: PAMs were infected with ASFV


title: RNA-seq spleen CD8 Control #1

description: Sample 5

value: Control


title: Untreated colonoid donor 1 [Control_1]


title: Cell and GD955-38-2

description: PAMs cells  viral (ASFV) infection group (cellViru


title: Cell and GD955-38 and TSN-1

description: PAMs cells  ASFV infection plus TSN treatment group (CeViDrug)


title: P2 - FFPE Psoriasis

description: 10X Visium

source_name: FFPE Psoriasis

value: FFPE Psoriasis


title: C1 - FFPE colon irAE

description: 10X Visium

value: FFPE colon irAE


title: RNA-seq spleen CD4 TKO #2

description: Sample 4

value: Spleen CD4 T cells

value: TKO


title: C8 - FFPE colon irAE

description: 10X Visium


title: P1 - FFPE Psoriasis

description: 10X Visium


title: Cell and GD955-38-1

description: PAMs cells viral (ASFV) infection group (cellViru)


title: RNA-seq spleen CD4 TKO #1

description: Sample 3

value: Non-activated


title: CNOT6-MDM4

first: Elizabeth

last: Cohen

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
BAM files preprocessed by the Broad Institute were reverted to unmapped BAMs and converted to fastq files, using Picard (v1.11.5) functionalities.
Candidate somatic fusions were called by three fusion callers, STAR Fusion (v1.2.0), FusionCatcher (v1.00) and ChimPipe (v0.9.6) with default parameters.
STAR Fusion was run with the Trinity Cancer Transcriptome Analysis Toolkit (CTAT) genome library (vNov012017), FusionCatcher was run with FusionCatcher’s human database (v90), and ChimPipe was run with the GENCODE annotation library (v19).
The candidate fusion calls indicated by each caller were normalized and consensus fusions were identified for each sample.
Discordant reads were identified using SAMtools (v0.1.19) using the “-F 1294” flag. A BED file of the discordant reads was created using the “bamtobed” function of BEDTools (v2.25.0), with the “-bedpe” argument included to facilitate further analysis of the discordant read pairs.
To produce the BigWig files appropriate for visualizing in the IGV browser, read coverage was calculated using BAM files and the “bamCoverage” function of deepTools (v3.5.0) with default parameters.
Genome_build: GRCh37

source_name: lung adenocarinoma tumor

extract_protocol:
RNA was extracted from tissue at Broad Institute
Library was prepared at Broad Institute for Transcriptome Capture or Whole Transcriptome assays and processed on Illumina HiSeq 2500 sequencers.

value: lung

tag: sample type

value: clinical sample

value: lung adenocarcinoma


title: FGFR1-intergenic (sample 11)


title: FGFR1-intergenic (sample 10)


title: SYNDIG1-GNAS


title: C5 - FFPE colon irAE

description: 10X Visium


title: Cell and TSN-3

description: PAMs cells drug (TSN) treatment group (cell Drug)

value: Lung

value: Porcine alveolar macrophages

value: PAMs incubated with TSN for 24 h


title: cirAE08 - FFPE skin irAE

description: 10X Visium

source_name: FFPE skin irAE

value: FFPE skin irAE


title: RNA-seq spleen CD4 Control #2

description: Sample 2


title: RNA-seq spleen CD8 TKO #1

description: Sample 7

value: Spleen CD8 T cells


title: RNA-seq spleen CD4 Control #1

description: Sample 1


title: Cell and TSN-2

value: primary cell

value: WT


title: EBF2-NRG1


title: FCypSC_4: female Cyp KO sc435 rep4

city: Atlanta

first: Paul

last: Dawson

state: GA

address: 1760 Haygood Drive

institute: Emory University

data_processing:
Clustering: Clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool since Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantifaction: FeatureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene. The FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the read counts, and is currently the most commonly used method for estimating gene expression levels.
Differential analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provides statistical routines for determining differential expression of digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment Analysis: We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected P-values less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected P-values less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected P-values less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Alternative Splicing: Alternative Splicing is an important mechanism for regulation of gene expression. rMATS(4.1.0) software was used for analysis of AS events.
SNP analysis: GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP < 10).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: Mice were sacrificed at 12 weeks

extract_protocol:
Livers were removed at time of sacrafice, flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Mice in experimental group were switched to SC-435 containing diet (0.006%, ~11mg/kg/day) 3 weeks after weaning.

tag: strain

value: liver

tag: age

value: 12 week adult mouse

tag: Sex

value: female


title: 20099HC

city: Leipzig

first: Diana

last: Le Duc

address: Deutscher Platz 6

department: Department of Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

data_processing:
RNA-Seq reads were mapped to the human genome assembly hg38 with STAR (version 2.6.1d).
Count with Htseq and followed by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: HTseq count
Supplementary_files_format_and_content: DESeq Result

source_name: whole blood

extract_protocol:
RNA was extracted from PAXgene blood samples using PAXgene Blood RNA Kit (Qiagen).
RNA sequencing libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA) and sequenced on an Illumina NovaSeq platform with paired-end reads.

value: whole blood

value: male

value: 52 years

tag: disease

value: control


title: Cell-3

description: PAMs cells control group （cell)

tag: cell line

value: PAMs incubated at 37 C for 24 h


title: BCL6-intergenic

value: lung

value: clinical sample


title: 20101CC

value: 51 years


title: Cell and TSN-1

value: Lung

value: Porcine alveolar macrophages


title: DLG1-BRAF

value: lung adenocarcinoma


title: FCypSC_2: female Cyp KO sc435 rep2


title: FCypSC_3: female Cyp KO sc435 rep3


title: SLC4A4-GNAS


title: 19893TS

value: 27 years

value: 15q13.3 microdeletion


title: FWTSC_4: female WT sc435 rep4

value: wild type


title: 18786BP

value: 63 years


title: FKBP5-ESR1


title: TMEM196-ABL1


title: Cell-2

description: PAMs cells control group （cell)

value: primary cell

value: WT


title: 17411GS

value: whole blood

value: female

value: 20 years


title: Cell-1

description: PAMs cells control group （cell)


title: OPC - No biotin control

source_name: Oligodendrocyte Progenitor Cells

value: Epiblast stem cells-derived OPCs

tag: treatment for cell type

tag: treatment for decay

value: 5-EU metabolic labeling for 24hr, no biotin azide reaction for negative control

tag: molecule

value: 5-EU labeled RNA (click-iT, streptavidin pull-down)


title: 17412MS

value: male

value: 49 years

value: control


title: mdmSol_replicate3

city: Lowell

first: Matthew

last: Gage

state: Massachusetts

address: 265 Riverside St

department: Chemistry

institute: University of Massachusetts Lowell

data_processing:
Post sequencing read quality was checked using the FastQC quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for high throughput sequence data.
If the per-base quality score was below 20 at any position along the 75 bp length stretch, those samples were processed using sliding window quality filtering (window size = 4 bp) in Trimmomatic v0.32. After filtering, only the paired-end reads collected from the read-trimming were used for downstream data analysis
After filtering, only the paired-end reads collected from the read-trimming were used for downstream data analysis (Table S3). Original samples that showed a satisfactory per base quality score (>20) were used without filtering. Sequencing adapters were trimmed while converting initial BCL data to fastq files from the sequencing center prior to receiving the data files and no adaptor contamination was detected in FASTQC analysis.
Prepared fastq files were aligned to the Mus musculus GRCm38.p4 genome annotation using the Tophat alignment tool. In order to calculate the insert sizes between paired-end reads,  a subset of 250,000 reads from each sample was aligned using the BWA-aln short read alignment tool available on the Galaxy web platform. The built-in reference mouse genome (mm10) was used to carry out the alignment under default settings.
Alignment statistics for the pre-alignments were generated using CollectInsertSizeMetrics Picard tool (http://broadinstitute.github.io/picard/), and average insert sizes and standard deviations were fed into subsequent complete read alignments generated with Tophat v2.1.1
Assembly: GRCm38.p4
Supplementary files format and content: tab delimited count file (.txt)

source_name: Soleus

extract_protocol:
Total RNA from the collected muscles was extracted according to the recommended protocol in the Qiagen Fibrous Tissue Total RNA extraction mini kit. RNA concentration was measured using a Qubit RNA Broad-Range assay, and RNA integrity number (RIN) was assessed with Agilent 2100 Bioanalyzer RNA 6000 Nano assay. Samples with a concentration >20ng/ul, RIN>7 were chosen for the subsequent cDNA library preparation.
cDNA libraries from the selected samples were prepared with Illumina TruSeq Stranded Total RNA Library Prep Kit. Quality of the cDNA libraries was assessed with KAPA Library Quantification qPCR Kit for Illumina sequencing platforms, and library fragment sizes were tested using an Agilent 2100 Bioanalyzer High Sensitivity dsDNA quantification assay. The mean library sizes of the samples were between 256-323bp. Prepared cDNA libraries were sequenced in an Illumina NextSeq 500 high throughput sequencer following sequencing guidelines recommended by Illumina. Short 75 bp paired-end reads were generated from each library, and the samples were sequenced using a total of five sequencing runs. The sequenced library coverage varies between 9.5 - 100 million reads with a median of 23 million reads.

value: Soleus

value: mdm

tag: condition


title: mdmEDL_replicate5

source_name: EDL

value: EDL


title: 17820FH

value: 15q13.3 microdeletion


title: mdmPso_replicate5

source_name: Psoas

value: Psoas


title: cirAE20 - FFPE skin irAE

description: 10X Visium

value: FFPE skin irAE


title: FCypSC_1: female Cyp KO sc435 rep1

value: liver

value: 12 week adult mouse


title: FWTSC_3: female WT sc435 rep3

value: wild type


title: RET-intergenic

value: lung

value: clinical sample

value: lung adenocarcinoma

value: RET-intergenic


title: FWTSC_1: female WT sc435 rep1

value: female


title: NPM1-FGFR2


title: mdmPso_replicate4


title: FWTSC_2: female WT sc435 rep2


title: mdmEDL_replicate4


title: hel2_cga_di_r2

tag: reporter

value: minCGA

tag: footprint library type

value: disome


title: TAZ knock Down HTS cell (replicate 4) [HTS_TAZKD-3_S48_L002]

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the subread-2.0.3
count values containg file were obtained using featureCounts of subread-2.0.3
differential expression was obtained using DESeq2
mean insert length and standdard deviation calculated using picard 2.26.6
Genome_build: UCSC hg38(iGenomes illumina)
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample

source_name: cell line

growth_protocol: Cell culture protocol was published earlier (Saha et al. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17864-17875. doi: 10.1073/pnas.2002449117)

extract_protocol:
For RNA extraction we used Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol. For each experimental conditions, 1 million cells were used to isolate total RNA.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell.  For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

tag: tissue source

value: Placenta

tag: cell type

value: trophoblast stem cells

tag: genotype/variation

value: TAZ knock Down


title: hel2_cga_di_r1

tag: genotype


title: FCypCh_3: female Cyp KO chow rep3

tag: tissue

tag: treatment

value: chow


title: FCypCh_4: female Cyp KO chow rep4

tag: strain


title: TAZ knock Down HTS cell (replicate 1) [HTS_TAZKD-1_S46_L001]


title: mdmSol_replicate2

value: Soleus

value: mdm

value: Male

tag: age


title: TAZ knock Down HTS cell (replicate 2) [HTS_TAZKD-1_S46_L002]


title: FCypCh_2: female Cyp KO chow rep2

value: liver

tag: Sex


title: wt_cga_di_r2


title: wt_cga_di_r1


title: wt_non_di_r2

value: minNONOPT


title: mdmSol_replicate1


title: wt_non_di_r1

value: wild type


title: mdmPso_replicate3

value: Psoas

value: Female


title: wt_opt_di_r2

value: minOPT


title: FCypCh_1: female Cyp KO chow rep1

value: 12 week adult mouse


title: Control HTS cell (replicate 4) [HTS_ctrl-3_S3_L002]

value: Control


title: Control HTS cell (replicate 3) [HTS_ctrl-3_S3_L001]


title: Control HTS cell (replicate 2) [HTS_ctrl-1_S1_L002]


title: FWTCh_2: female WT chow rep2

value: female


title: mdmEDL_replicate3

value: EDL


title: mdmPso_replicate1


title: syh1_cga_mono_r3

value: minCGA

value: monosome


title: mdmPso_replicate2


title: TAZ knock Down HTS cell (replicate 3) [HTS_TAZKD-3_S48_L001]

value: Placenta

value: trophoblast stem cells

value: TAZ knock Down


title: wt_opt_di_r1

value: disome


title: syh1_cga_mono_r2


title: FWTCh_3: female WT chow rep3

value: chow


title: Control HTS cell (replicate 1) [HTS_ctrl-1_S1_L001]


title: FWTCh_1: female WT chow rep1

value: liver


title: mdmEDL_replicate2

value: mdm

value: Male


title: mdmEDL_replicate1


title: syh1_cga_mono_r1


title: MCypSC_4: male Cyp KO sc435 rep4

value: male


title: FWTCh_4: female WT chow rep4

value: wild type


title: Sample gonad from 13GW female1 (10x genomics)

city: Nanning

first: wang

last: yifu

state: Guangxi

address: Shuangyong Road 22

department: Center for Genomic and Personalized Medicine

institute: guangxi medical univercity

description: a sample from aborted human fetal gonad tissue

data_processing:
Raw data were demultiplexed using mkfastq application (Cell Ranger v3.1.0) to make Fastq files. Fastq files were then run with count application (Cell Ranger v3.1.0) using default settings, which performs alignment (using STAR aligner, aligned to the GRCh38 human reference genomic data), filtering and UMI counting. The UMI count tables were used for further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.h5 file with raw gene counts for every gene and every cell

source_name: human fetal gonad tissue

extract_protocol:
The fresh samples of human fetal adrenal glands or gonads were placed into RPMI 1640 medium (GIBCO, C11875500BT), which containing 5% Fetal Bovine Serum (FBS; HyClone, SH30070.03) and 1% penicillin-streptomycin (Gibco, 15140-122) and quickly transported to laboratory on ice. Then the fetal adrenal glands and gonads were separated under stereomicroscope (Nikon) and collected in DNA LoBind tubes (Eppendorf) with the cold RPMI 1640 solution containing 5% FBS. Then, washed in cold D-PBS (WISENT, 311-425-CL), and sliced into approximately 1-2mm3 pieces. The tissues were transferred to digestion solution (0.1mg/ml Liberase TL (Roche, 5401020001) and 1mg/ml DNase I (Roche, 10104159001) in RPMI 1640), and digested at 37 °C with gentle shaking throughout, adrenal glands for 20 min and gonads for 30 min, respectively, then filtered through a 100μm cell strainer (Falcon, 352360), centrifuged and resuspended in 5 ml of 1X red blood cell (RBC) lysis buffer (BioLegend, 420301) for 5 min on ice. The suspensions were washed twice with D-PBS containing 1% FBS, and then filtered by a 40 μm cell strainer (Falcon, 352340), centrifuged and resuspended in DPBS with 1% FBS. The cell number and viability were assessed by Trypan blue (Gibco, 15250-061) staining and counting in a counting chamber.   Except for above, some steps were adjusted to get Aorta-gonad-mesonepheros region (AGM) at 6-7 gestation weeks (GW) —AGM suspension was passed through a 70μm cell strainer directly after digestion and didn’t need to lysis RBC.
For 10x Genomics single-cell RNA sequencing,reverse transcription and library preparation were performed using the 10x Genomics Single Cell v3 kit following the 10x Genomics protocol. Briefly, we added the single cell suspension, gel beads and partitioning oil to 10x Genomics Chromium chip B and ran the Chromium Controller. After water-in-oil generation, samples were transferred into a PCR tube and reverse transcription was performed using T100 Thermal Cycler (Bio-Rad). Then cDNA purification and library preparation were performed as the user guide. cDNA librarys were send to company Genergy Biotech (Shanghai) and sequenced by Novaseq 6000 (Illumina).    For Smart-seq2, Single cells were acquired and picked into cell lysis buffer by mouth pipette. Transcriptomes of the single cells were amplified refer to the previous method 4,5. Briefly：We reverse transcribed RNA molecules using 25 nt oligo (dT) primer anchored with 8-bp unique molecular identifiers (UMIs). After the first-strand and second-strand cDNA were synthesized, and the cDNA were amplified by 15 cycles of PCR. Absorbed 4μL amplified cDNA for further step. The cDNAs were biotinylated pre-indexed primers to further amplify the PCR product. The product was fragmented into ~300-bp fragments using sonicator (Covaris M220) and was captured by Dynabeads-MyOne Streptavidin C1 beads (Invitrogen,65002). The RNA-seq library was constructed using a Kapa HyperPrep kit (Kapa Biosystems, kk8504). The libraries were subjected to 150 bp paired-end sequencing on an Novaseq 6000 (Illumina) platform in Genergy Biotech company (Shanghai).

value: 13 gestational weeks

value: fetal gonad tissue


title: MCypSC_2: male Cyp KO sc435 rep2

value: 12 week adult mouse


title: spleen M-MDSCs WT replicate 1

city: Athens

first: Maria

last: Grigoriou

state: Papagou

address: Soranou Efesiou 4

country: Greece

institute: BRFAA

description:
WT replicate 1
Spleen WT2 Ly6C

data_processing:
Fastq files were downloaded from Illumina-BaseSpace and mapped to mm10 genes (iGenomes UCSC/mm10) using hisat2 version 2.1.0 (--score-min L 0,-0.5)
Gene counts were computed with htseq-count (-s yes, version 0.11.2)
Further processing was performed with the R Bioconductor package edgeR v.3.14.0. Reads were normalized for intra- and inter-sample variances using the functions “calcNormFactors” and “estimateTagwiseDisp”, and further by the gene-length as per Ensembl V103 Genes annotations, resulting in fragments-per-kilobase-per-million (FPKM) for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: spleen M-MDSCs

growth_protocol: The murine melanoma cancer cell line B16.F10 was used for the solid tumor induction. B16.F10 cells were cultured at 37°C under 5% CO2 in RPMI medium supplemented with 10% heat inactivated fetal bovine serum, 1% penicillin-streptomycin and 0,1% 2-Mercaptoethanol.

extract_protocol:
M-MDSCs and G-MDSCs were sorted from spleens of B16.F10 melanoma bearing Wild Type and Nrlp3-/- mice, and total RNA was extracted using Macherey-Nagel NucleoSpin RNA kit as described by manufacturer’s protocol (NucleoSpin® RNA). Each RNA sample was representative of one mouse.
NGS libraries were generated using 300 ngr total RNA as input on average with the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit from Lexogen according to manufactures protocol, using 15 or 17 cycles of amplification. Libraries were sequenced on Illumina Nextseq 500 on 1 x 75 High flowcell.
QuantSeq 3′ mRNA-Seq Library

treatment_protocol: Mice were implanted subcutaneously, in the intradermal layer of the back, with 3×10^5 B16.F10 melanoma cells.

value: M-MDSCs

value: B16.F10 bearing wild type mice


title: spleen G-MDSCs Nlrp3-/- replicate 4

description:
Nlrp3-/- replicate 4
Spleen KO5 Ly6G

source_name: spleen G-MDSCs

value: G-MDSCs

value: B16.F10 bearing Nlrp3-/- mice


title: MCypSC_3: male Cyp KO sc435 rep3


title: spleen G-MDSCs Nlrp3-/- replicate 3

description:
Nlrp3-/- replicate 3
Spleen KO3 Ly6G


title: Sample adrenal from 13GW female1 (10x genomics)

description: a sample from aborted human fetal adrenal tissue

source_name: human fetal adrenal tissue

value: female

value: fetal adrenal tissue


title: hel2_cga_mono_r2

city: Baltimore

institute: Johns Hopkins University

data_processing:
Library strategy: Ribo-seq
Raw reads from FASTQ files were deduplicated based on a unique molecular identifier to remove PCR artifacts by dedupe.sh (BBtools 38.44).
UMI and adapter sequences were removed by  bbduk.sh (Bbtools 38.44).
Noncoding sequence reads were removed via alignment by STAR 2.6.1c to a reference genome containing only noncoding RNA
Surviving coding-RNA reads were aligned by STAR 2.6.1c to a yeast reference genome excluding HIS3 and including the reporter sequence.
Correct shifts to represent ribosomal A sites were calculated from aligned read 5' ends and read distributions at each position of the reporter were calculated by custom Python scripts.
Genome_build: SacCer3 R64-1-1 with translation reporter
Supplementary_files_format_and_content: CSV files include calculated A site shifted ribosome footprint RPMs at each position of the reporter. The seq column contains the sequence of the reporter at each position

extract_protocol:
Frozen yeast cultures were lysed mechanically in liquid nitrogen using a freezer mill and thawed into lysis buffer
Ribosomes were pelleted through a sucrose cushion then separated into monosomes or disomes by centrifugation through a sucrose gradient and fractionated. Complexes were treated with RNase I and RNA footprints were extracted by phenol/chloroform. Footprint size selection (monosome: 15-35 nt, disome: 40-70 nt) was performed by gel extraction, followed by dephosphorylation, linker ligation, and reverse transcription. Ribosomal cDNA was depleted by subtracted with a pool of biotinylated oligonucleotides. Finally, cDNA was circularized and amplified by PCR with barcode-containing primers.

value: minCGA

value: monosome


title: Sample gonad from 13GW male1 (10x genomics)


title: MCypSC_1: male Cyp KO sc435 rep1


title: MWTSC_4: male WT sc435 rep4


title: wt_cga_mono_r3


title: spleen G-MDSCs Nlrp3-/- replicate 1

description:
Nlrp3-/- replicate 1
Spleen KO1 Ly6G


title: hel2_cga_mono_r1


title: Sample gonad from 14GW female1 (10x genomics)

value: 14 gestational weeks


title: spleen G-MDSCs Nlrp3-/- replicate 2

description:
Nlrp3-/- replicate 2
Spleen KO2 Ly6G


title: Sample gonad from 10GW male2 (10x genomics)

value: 10 gestational weeks


title: Sample adrenal from 13GW male1 (10x genomics)


title: MWTSC_2: male WT sc435 rep2

value: liver


title: spleen G-MDSCs WT replicate 4

description:
WT replicate 4
Spleen WT6 Ly6G


title: wt_cga_mono_r2


title: hel2_cga_mono_r3


title: Sample adrenal from 14GW female1 (10x genomics)


title: Sample adrenal from 10GW male2 (10x genomics)


title: Sample adrenal from 10GW male1 (10x genomics)


title: wt_non_mono_r2

value: minNONOPT


title: MWTSC_1: male WT sc435 rep1

value: male


title: MCypCh_4: male Cyp KO chow rep4

value: chow


title: Sample gonad from 9GW female1 (10x genomics)

value: 9 gestational weeks


title: wt_opt_mono_r2

value: minOPT

value: wild type


title: spleen G-MDSCs WT replicate 2

description:
WT replicate 2
Spleen WT3 Ly6G


title: wt_non_mono_r3


title: Sample gonad from 9GW male1 (10x genomics)

value: fetal gonad tissue


title: spleen G-MDSCs WT replicate 3

description:
WT replicate 3
Spleen WT4 Ly6G

value: B16.F10 bearing wild type mice


title: Sample adrenal from 9GW female1 (10x genomics)


title: MCypCh_2: male Cyp KO chow rep2

value: 12 week adult mouse


title: spleen M-MDSCs Nlrp3-/- replicate 3

description:
Nlrp3-/- replicate 3
Spleen KO3 Ly6C

value: M-MDSCs

value: B16.F10 bearing Nlrp3-/- mice


title: Astro_repl1

first: Jeff

last: Coller

address: 725 N. Wolfe St PCTB 505

data_processing:
Library strategy: RNA-Seq (QuantM-seq)
5′ adapter and 3’ CCA and adapter sequences were removed from reads using cutadapt
Reads were mapped with bowtie2 to a mouse tRNA reference generated from GtRNAdb mm10 high-confidence mature tRNA fasta file
Read count tables for each isodecoder were produced with Rsubread package’s featureCounts function in R
Reads were summed to generate anticodon-level tables, and both raw reads or RPM tables were obtained for tRNAs grouped by isodecoders or anticodons.
Differential tRNA expression analysis was performed with DESeq2 in R using default settings and p value adjustment (Benjamin–Hochberg correction).
Genome_build: mm10
Supplementary_files_format_and_content: Csv files that contain RPM for tRNA genes grouped by isodecoders or anticodons, for the 3 cell types. Csv files that contain the log difference and p-value from the DESeq2 differential analysis between OPCs and OLs.

source_name: Astrocytes

extract_protocol:
RNA was extracted with Trizol, deacylated and annealed to a double-stranded adapter with RNA ligase 2.
Reverse transcription was performed with Superscript IV, RNA hydrolyzed and the cDNA precipitated then PAGE purified. After precipitation, the cDNA was circularized with CircLigase (Epicentre) and amplified with the NEBnext Ultra II Q5 next-generation master mix. Sequencing was performed as single-end reads for 110 cycles on a NextSeq 550 (v2.5)

treatment_protocol: OLs were differentiated from OPCs in OL differentiation media that consisted of DMEM/F12 supplemented with N2 Max, B27, 100ng/mL noggin (R&D, 3344NG050), 100ng/mL IGF-1 (R&D, 291G1200), 10uM cyclic AMP (Sigma, D0260-100MG), 10ng/mL NT3 (R&D, 267N3025) and 40ng/mL T3 (Thyroid hormone, Sigma, T-6397). Astros were differentiated from OPCs in neurobasal media and high glucose DMEM supplemented with sodium pyruvate, glutamax, N2 Max, and N-acetyl-cysteine and with growth factors including 20ng/mL bFGF, 5ng/mL Hb-EGF (R&D, 259-HE-050), 10ng/mL CNTF (R&D, 557-NT-010), and 10ng/mL BMP4 (R&D, 314-BP-050).

value: Astros differentiated from OPCs

value: Differentiated with BMP4

value: tRNA


title: Astro_repl2


title: MCypCh_3: male Cyp KO chow rep3


title: spleen M-MDSCs Nlrp3-/- replicate 2

description:
Nlrp3-/- replicate 2
Spleen KO2 Ly6C


title: MWTSC_3: male WT sc435 rep3


title: OL_repl1

source_name: Oligodendrocytes

value: OLs differentiated from OPCs

value: Differentiated with T3


title: Sample adrenal from 9GW male1 (10x genomics)

value: fetal adrenal tissue


title: MWTCh_4: male WT chow rep4

value: liver


title: Sample gonad from 7GW male1 (10x genomics)

value: 7 gestational weeks

value: male


title: MCypCh_1: male Cyp KO chow rep1

value: chow


title: spleen M-MDSCs WT replicate 3

description:
WT replicate 3
Spleen WT4 Ly6C


title: OL_repl2


title: Sample gonad from 7GW female1 (10x genomics)

value: female


title: OPC_repl2

value: Epiblast stem cells-derived OPCs


title: spleen M-MDSCs Nlrp3-/- replicate 1

description:
Nlrp3-/- replicate 1
Spleen KO1 Ly6C


title: spleen M-MDSCs WT replicate 4

description:
WT replicate 4
Spleen WT6 Ly6C


title: Sample adrenal from 7GW male2 (10x genomics)


title: OPC_repl1


title: OPC_repl3


title: MWTCh_3: male WT chow rep3

value: wild type


title: Sample adrenal from 7GW female1 (10x genomics)


title: spleen M-MDSCs Nlrp3-/- replicate 4

description:
Nlrp3-/- replicate 4
Spleen KO5 Ly6C


title: CY2, Pantr2 Knockout, snRNA-seq

status: Public on Aug 07 2022

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Kallisto-bustools (https://www.kallistobus.tools)
Assembly: mm10
Supplementary files format and content: comma-separated values files and matrix files

molecule: nuclear RNA

source_name: Dorsal Telencephalon

extract_protocol:
Day E15.5 embryonic brains were collected from both wildtype and Pantr2-/- mice. The dorsal telencephalon was dissected, flash frozen in liquid nitrogen, and stored at –80°C until ready for nuclei isolation. Nuclei were isolated using a modified version of the Salty-EZ Lysis Buffer method outlined on protocols.io (https://www.protocols.io/view/protocol-for-nuclei-isolation-from-fresh-and-froze-kqdg36ybzg25/v5). In brief, tissues were lysed in 300μl of ice cold Salty-EZ10 lysis buffer containing 10mM Tris HCL pH 7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.03% Tween-20, 10% EZ-lysis Buffer (Sigma Aldrich), 1mM DTT and 0.2U/μl Protector RNase Inhibitor. The tissue was gently triturated using a P200 wide-bore pipette tip on ice until the tissue was completely in solution. Once homogenized, 700μl of ice cold Slaty-EZ10 buffer was added and each sample was gently mixed using a wide-bore pipette tip. Next, the solution was spun down at 4°C at 500G for 5 minutes to pellet the nuclei in suspension. The supernatant was aspirated off and 500μl of WRB2 buffer containing 10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 1% w/v bovine serum albumin (BSA), 1mM DTT and 0.2U/μl Protector RNase Inhibitor. Nuclei were washed three times in 500μl WRB2 buffer before being used as the input material for 10X Genomics Chromium Single Cell V2 kit following standard protocol included with the kit.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Dorsal Telencephalon

value: Pantr2 knockout


title: CZ4, Wildtype, snRNA-seq

description: 10X Genomics

value: Wildtype


title: spleen M-MDSCs WT replicate 2

description:
WT replicate 2
Spleen WT3 Ly6C

value: M-MDSCs

value: B16.F10 bearing wild type mice


title: MWTCh_1: male WT chow rep1

value: 12 week adult mouse


title: spleen G-MDSCs WT replicate 1

description:
WT replicate 1
Spleen WT2 Ly6G

value: G-MDSCs


title: CY3, Pantr2 Knockout, snRNA-seq

description: 10X Genomics


title: CY4, Pantr2 Knockout, snRNA-seq

description: 10X Genomics


title: CY1, Pantr2 Knockout, snRNA-seq

description: 10X Genomics


title: EPSC-NSC_Fusion_1

city: Seoul

first: Jae Hoon

last: Song

address: 201 Songpa-daero, Songpa-gu

institute: ENCell Co., Ltd.

data_processing:
Adapter trimming was performed with a skewer (v0.2.2) with -L 100 and -e options.
Trimmed reads were mapped to the mm10 UCSC Mus musculus genome using the STAR (v2.7.9a).
Mapped reads were quantified and normalized to FPKM values using the Cuffnorm of the Cufflinks (v2.2.1) toolset.
Assembly: mm10
Supplementary files format and content: genes.fpkm_table.txt: Tab-delimited text file of gene expression table in FPKM value generated with Cuffnorm (v2.2.1).

source_name: tetraploid hybrid cell

growth_protocol: Mouse EPS cell lines established from C57BL/6 strain and mouse neural cell lines are fused by polyethylene-glycol (PEG) mediated method. After fusion, cells are maintained in N2B27 medium supplemented with human LIF, CHIR99021, dimethindene maleate, and minocycline hydrochloride. Cells are cultured on mitomycin-C inactivated C3H mouse embryonic fibroblast.

extract_protocol: Total RNA were extracted from the independent samples, and further purified mRNA containing poly A tail using poly T-attached beads. The library was prepared using purified mRNA using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).

value: tetraploid hybrid cell

tag: differentiation state

value: undifferentiated


title: MWTCh_2: male WT chow rep2


title: CZ1, Wildtype, snRNA-seq

description: 10X Genomics


title: CZ2, Wildtype, snRNA-seq

description: 10X Genomics


title: OG2_ROSA_NSC_1

source_name: neural stem cell

growth_protocol: Mouse NS cell lines were maintained under Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with N2, penicillin-streptomycin-gentamycin, EGF, and FGF2. Cell culture dishes were coated with 0.15% gelatin.

value: neural stem cell


title: EPSC-NSC_Fusion_2


title: EPSC_wt_2

source_name: extended pluripotent stem cell

growth_protocol: Mouse EPS cell lines established from C57BL/6 strain were cultured under the N2B27-LCDM condition, as previous reported (Yang et al., 2017). In shorts, cells are maintained in N2B27 medium supplemented with human LIF, CHIR99021, dimethindene maleate, and minocycline hydrochloride. Cells are cultured on mitomycin-C inactivated C3H mouse embryonic fibroblast.

value: extended pluripotent stem cell


title: EPSC_wt_1


title: OG2_ROSA_NSC_2


title: Sample adrenal from 7GW male1 (10x genomics)

value: 7 gestational weeks

value: fetal adrenal tissue


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 20

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

institute: Charité University Medicine

data_processing:
Adapter and polyA trimming with BBDuk (v38.9; options k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20)
Alignment and read counting with STAR aligner (v2.7.8a; default settings apart from --outFilterMismatchNoverLmax 0.1)
Library size normalization and vsd transformation in R v4.1.0 with DESeq2 v1.32.0
Weighted gene co-expression network analysis with WGCNA R package (v1.70) (soft threshold power = 10)
Assembly: GRCm38 and MT952602 (concatenated)
Supplementary files format and content: Tsv-formatted table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: APOE knock-in mice were intranasally infected with SARS-CoV-2 MA10

extract_protocol:
Lungs were resected on day 4 post infection, homogenized in Trizol using a Miltenyi homogenizer (program RNA_01), and RNA was extracted using Zymo's Direct-zol kit including DNAse digestion.
Lexogen 3' FWD kit

tag: disease state

tag: agent

value: SARS-CoV-2 MA10

value: Lung

tag: timepoint

value: 4 dpi


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 16

value: female


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 15


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 13


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 14


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 22


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 21


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 11


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 17


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 19


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 23


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 09


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 18


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 08


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 12


title: Dissociated lung from APOE knock-in mouse with COVID-19, sample 04