title: Ch25h.none.none.0.1 (OSBP control)

value: BMDM


title: Ch25h.none.none.0.3 (OSBP control)

status: Public on Apr 03 2024

type: SRA

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

country: USA

institute: Seattle Children's Research Institute

library_source: transcriptomic

data_processing:
Performed initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Assembly: mm10
Supplementary files format and content: A .tsv file with raw counts for all genes

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: Bone marrow derived macrophages were prepared as described in Gold, E. S. et al. ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation. J. Exp. Med. 209, 807–817 (2012) and Olson, G. S. et al. Type I interferon decreases macrophage energy metabolism during mycobacterial infection. Cell Rep. 35, 109195 (2021)

extract_protocol:
Cells were harvested for total RNA extraction using SV 96 total isolation RNA kit (Promega Z3500).
Illumina TruSeq stranded

treatment_protocol: Cells were treated for 18 hours with either 25-hydroxycholesterol (5 uM), itraconazole (1 uM), or OSW-1 (0.3 uM) and then stimulated with lipopolysaccharide (10 ng/mL).

tag: cell type

tag: genotype

tag: mouse

tag: treatment

tag: stimulus

tag: stimtime


title: Morula HFD-1

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

country: Germany

institute: Helmholtz Zentrum München

description: Morula rna-seq LFD rep 4

data_processing:
Read mapping and differential expression analysis was performed using the A.I.R (Artificial Intelligence RNA-Seq) software from Sequentia Biotech.
GRCm38
tab-delimited text files include count values for each sample

molecule: total RNA

source_name: Morula

extract_protocol:
Total RNA was prepared from Morula, Sperm and Round spermatids using the RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA purity, integrity and quality was examined by Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
Transcript Libraries were constructed using the Nextera Library Prep Kit (Illumina) according to the manufacturer’s instructions and sequenced on an Illumina HiSeq 2500.

value: Morula

value: C57BL/6 wildtype

value: High Fat Diet


title: C-39

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 5

data_processing:
The small RNA sequencing data analysis was performed with the XICRA pipeline and XICRA.stats, the R companion package (Sanchez Herrero, Pluvinet, Luna de Haro and Sumoy, 2021). See additional details in https://xicra.readthedocs.io/en/latest/ or https://github.com/HCGB-IGTP/XICRA.
We checked raw data quality before and after trimming the reads to discard sequencing adapters using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and cutadapt (Martín, 2011), respectively.
For the mapping and the biotype feature assignment of all reads we used STAR mapping software (Dobin et al., 2013) and featureCounts (Liao et al., 2014) using as a reference GRCh38
For miRNA identification, we used miraligner (within the SeqBuster software, which can resolve canonical and other isomiR variants (Pantano et al., 2010) and a miRBase (Kozomara et al., 2019) (v22) as the reference database. Then, using miRTop, we formatted results into standardized files and generated expression count matrices.
The analysis of differential expression of small RNA we employed XICRA.stats, running DESeq2 (Love et al., 2014, Zhu et al., 2019) and other packages under the R software environment.
Assembly: hg38 (Ensembl release 78, Homo_sapiens.GRCh38.dna.primary_assembly), and mature miRBase v22
Supplementary files format and content: Supplementary excel file includes DESeq2 normalized read counts for miRNAs

organism: Homo sapiens

source_name: blood

growth_protocol: This cross-sectional study included plasma samples from 40 hospitalized patients with acute SARS-CoV-2 from the KING observational study at the Hospital Universitari Germans Trias i Pujol (Badalona, Spain), which aimed to characterize virological and immunological features of SARS-CoV-2 infection (49). The study was approved by the Hospital Universitari Germans Trias i Pujol Ethics Committee Board (reference PI-20-122). Participants were enrolled after a positive test for SARS-CoV-2 infection (either a virological test performed by RT-qPCR analysis of nasopharyngeal swabs in routine clinical screenings or a serological test performed by in-house ELISA of plasma samples). Plasma samples from a previously described (14) cohort of 21 healthy, uninfected volunteers were also analyzed as a control group. Patient and healthy donor samples were obtained with written informed consent, as required by the Ethics Committee Board. Blood was collected by venipuncture in EDTA vacutainer tubes (BD Bioscience). Plasma was obtained by centrifugation of blood at 1200 g for 10 min and stored at –80 °C until use.

extract_protocol:
Total RNA was extracted with a miRCURY Isolation kit- Biofluids (Exiqon) following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.. Tests of the robustness of the plasma RNA isolation procedure and the detection of hemolysis were performed with the Exiqon serum qPCR panel with all samples entering the experiment having deltaCq (miR‐ 23a‐miR‐451)<5.
Small RNA sequencing libraries were prepared according to the TruSeq Small RNA Sample Preparation Guide (Illumina) using as input all the RNA extracted from 200 ul pf plasma and 15 cycles of PCR amplification. Prior to pooling and size selection, individual library yields and molarities were determined, based on an integration of the 135–160-bp size range, with the DNA 1000 Kit on a Bioanalyzer 2100 (Agilent Technologies). Libraries exhibited visible size patterns and yields according to specifications (with major peaks expected around 142 bp for miRNAs and 152 for piwiRNAs). All libraries were indexed on the basis of barcoded adapter ligation. Libraries were combined to form independent pools. Next, an automated pooled library size selection was carried out. Each individual pool was size selected for products between 115 and 165 bp with the Pippin Prep automated gel system and 3% agarose dye-free gel cassettes with internal standards (Sage Science). Library pools were cleaned and concentrated by performing column centrifugation, prior to and after size selection, with the QIAquick PCR purification kit (Qiagen). Size-selected library pool quality was reassessed with the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). The final concentration was derived with qPCR, performed with the KAPA library quantification Kit for Illumina (Kapa Biosystems) on a 7900-HT PCR system (Applied Biosystems, Thermo Fisher). For each of the two pools, sequencing was performed on three independent HiSeq-2500 lanes (Illumina). Sequencing was performed on cBot and HiSeq-2500 instruments (Illumina), with the HiSeq single-read cluster generation, version 4, designed for the cBot-HiSeq, and the HiSeq sequencing-by-synthesis 50-cycle kit, according to manufacturer protocols. Per-sample raw data files were generated in fastq format with bcl2fastq conversion software (Illumina). A quality control step to select samples with minimal signs of hemolysis was also performed. None of the miRNA sequences that were DE between cases and controls overlapped with miRNA sequences that originated in platelets or erythrocytes.

tag: tissue

value: blood

tag: biofluid

value: plasma

tag: disease state

value: COVID 19 with acute infection

tag: gender

value: Male

tag: oxygen flow

value: No oxygen

tag: age

tag: hemolysis score


title: U2OS cells, B2M site 1 gDNA

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

library_source: genomic

data_processing:
library strategy: BreakTag
NGSpipe2go Breaktag pipeline (https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/master/pipelines/breaktag)
Reads without breaktag adaptor were filtered out
Reads with breaktag adaptor were mapped using BWA v0.7.15 with “bwa mem” on genome assembly hg38 and filtered out reads with mapping quality below 60
Deduplication of mapped reads based on unique molecular identifiers (UMIs)
Mapped read ends are summed up and reported in BED format
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: Breaktag signal as a proxy of double strand breaks counts, a a standard 6-columns BED containing the “chromosome | start | end | name | breaktag_signal | strand”

molecule: genomic DNA

source_name: derived from sarcoma of the tibia

extract_protocol:
gDNA was extracted with DNeasy® Blood & Tissue kit
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O.  Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip

value: derived from sarcoma of the tibia

tag: cell line

value: sarcoma of the tibia

value: WT

value: digested with B2M site 1 sgRNA


title: Morula LFD-1

description: Morula rna-seq HFD rep 1

value: Low Fat Diet


title: B6.prOsw_0.3.LPS.18.3

value: LPS


title: Control #3

city: Ames

first: Minhong

middle: Neenah

last: Huang

state: Iowa

address: 1800 Christensen Dr

department: Deparment of Biomedical Sciences

institute: Iowa State University

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Mouse brain tissue

growth_protocol: All mice used for this study were bred and maintained under a 12-h light cycle in a climate-controlled mouse facility (22±1°C) with food and water available ad libitum.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: None of them were treated.

tag: sample type

value: Littermate control brain cells


title: C-38

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 4


title: U2OS cells, AAVS1 site 12 gDNA

value: digested with AAVS1 site 12 sgRNA


title: B6.prOsw_0.3.LPS.18.2

value: BMDM


title: HSC, 5FU-1, d6, rep3

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

country: Japan

institute: National Center for Global Health and Medicine

description: HSCs from mice at day 6 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 3

data_processing:
Single reads with 75bp long were sequenced. Following raw fastq files were obtained, TopHat (version 2.0.13; with default parameters) was used for mapping to the reference genome (UCSC/mm10) with annotation data from iGenomes (Illumina). Then, gene expression levels were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters)
Assembly: mm10
Supplementary files format and content: Raw count data with a tab-delimited text

source_name: Bone marrow

extract_protocol:
Total RNA was isolated with RNeasy Micro Kit (QIAGEN) according to the manufacturer's instruction.
cDNA was synthesized and amplified using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Inc., Shiga, Japan). RNA-seq libraries were prepared using the Nextera XT Kit (Illumina, San Diego, CA, USA).

treatment_protocol: PBS or 5-FU (150 mg/kg) was administered i.p. at day 1, and 3000-3500 HSCs were isolated at day 6 and day 21 (5-FU group) or day 6 alone (PBS group). Fresh old HSCs were collected separately.

value: Bone marrow

value: Hematopoietic stem cells

value: Wild type


title: Morula LFD-3

description: Morula rna-seq LFD rep 3

value: Morula

value: C57BL/6 wildtype


title: B6.prOsw_0.3.LPS.18.1


title: HSC, 5FU-1, d6, rep2

description: HSCs from mice at day 6 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 2


title: C-37

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 3

value: blood

value: plasma

value: COVID 19 with acute infection

value: Female


title: U2OS cells, AAVS1 site 10 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with AAVS1 site 10 sgRNA


title: B6.prItra_1.LPS.18.3

value: itraconazole


title: U2OS cells, AAVS1 site 11 gDNA

value: WT

value: digested with AAVS1 site 11 sgRNA


title: C-36

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 23

value: Male

value: Low Flow


title: C-35

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 22


title: B6.prItra_1.LPS.18.2

value: BMDM

value: LPS


title: HSC, 5FU-1, d6, rep1

description: HSCs from mice at day 6 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 1

value: Bone marrow

value: Hematopoietic stem cells

value: Wild type


title: HSC, PBS-1, d6, rep2

description: HSCs from mice at day 6 after the 1st round of PBS treatment as a control, replicate 2

value: PBS


city: China

first: Hongjie

last: Wu

state: Jiangsu

address: Xianlin Road

country: China

institute: Nanjing University of Chinese Medicine

description:
H929 wildtype cells treated with 4μM FHND004
H_WT_004

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple Myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype


description:
H929 wildtype cells treated with 4μM FHND008
H_WT_008


title: C-34

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 21

value: blood

value: plasma

value: COVID 19 with acute infection


title: B6.pr25HC_5.LPS.18.3


title: C-33

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 20


title: U2OS cells, AAVS1 site 1 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with AAVS1 site 1 sgRNA


title: H929 wildtype cells

description:
H929 wildtype cells with no treatment
H_WT_ZY

value: No treatment


title: HSC, old, fresh, rep3

description: Fresh HSCs from a 2yo mouse, replicate 3

value: Fresh


title: B6.pr25HC_5.LPS.18.2


description:
ARP1 wildtype cells treated with 4μM FHND008
A_WT_008


title: C-32

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 19

value: Male


title: C-31

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 18

value: Low Flow


title: B6.pr25HC_5.LPS.18.1

value: BMDM


title: HSC, old, fresh, rep2

description: Fresh HSCs from a 2yo mouse, replicate 2


title: C-30

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 17


title: HSC, old, fresh, rep1

description: Fresh HSCs from a 2yo mouse, replicate 1


title: ARP1 wildtype cells

description:
ARP1 wildtype cells with no treatment
A_WT_YYX


title: B6.none.LPS.18.3

value: LPS


title: HSC, PBS-1, d6, rep3

description: HSCs from mice at day 6 after the 1st round of PBS treatment as a control, replicate 3

value: Bone marrow


title: B6.prItra_1.LPS.18.1

value: itraconazole


title: C-29

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 16


title: 12M, CO, multiome, RNA-seq

city: New York

first: James

last: Nicholson

address: 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices for downstream preprocessing and analysis using the Seurat v4.0 R package
For quality control, cells with fewer than 750 genes detected or greater than 10% mitochondrial gene expression were removed
Raw Multiome sequencing data were converted to fastq format and subsequently aligned to the GRCh38 genome using “cellranger-arc mkfastq” and “cellranger-arc count” (10X Genomics, v2.0.0).
Assembly: GRCh38
Supplementary files format and content: Cellranger cell x feature output matrices

molecule: nuclear RNA

source_name: 12M, CO

growth_protocol: Cerebral Organoids and GSCs lines were generated and maintained as  previosuly described (Linklous et al. 2019, Cell Reports)

extract_protocol:
COs were dissociated into single-cell suspensions using the Papain Dissociation System following manufacturers instructions (Worthington Biochemical, LK003150). 2D cultures were dissociated following standard passaging protocols using Trypsin. Cells were filtered through a 40um strainer and resuspended on ice-cold PBS/2%BSA. For GLICO samples, GFP-positive/DAPInegative spGSCs were sorted by FACS (Becton-Dickinson Aria II) and collected on PBS/2%BSA for Single-cell ATAC-/ RNA-sequencing. For PDX samples, bulk tumor was dissected and dissocated as above.
Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237)

value: Cerebral Organoid

tag: patient line

tag: glioma model

tag: time


title: B6.none.LPS.18.2

tag: cell type

tag: genotype


title: HSC, 5FU-3, d21, rep3

description: HSCs from mice at day 21 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 3

value: Hematopoietic stem cells

value: Wild type

tag: treatment


title: HSC, 5FU-3, d21, rep2

description: HSCs from mice at day 21 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 2


title: HSC, PBS-1, d6, rep1

description: HSCs from mice at day 6 after the 1st round of PBS treatment as a control, replicate 1

value: PBS


title: C-28

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 15

value: blood

value: plasma


title: C-27

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 14

value: COVID 19 with acute infection


title: B6.prOsw_0.3.none.0.3

tag: mouse

tag: stimulus


title: B6.none.LPS.18.1

tag: stimtime


title: C-26

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 13

tag: tissue

tag: biofluid

value: Female


title: 5M, CO, mulitome, RNA-seq

source_name: 5M, CO


title: HSC, PBS-3, d6, rep3

description: HSCs from mice at day 6 after the 3rd round of PBS ip as a control, replicate 3


title: 12M, CO, multiome, ATAC-seq


description:
ARP1 wildtype cells treated with 4μM FHND004
A_WT_004

value: wildtype


title: B6.prOsw_0.3.none.0.1


title: HSC, PBS-3, d6, rep2

description: HSCs from mice at day 6 after the 3rd round of PBS ip as a control, replicate 2


title: C-25

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 11

tag: disease state

tag: gender

value: High Flow


title: B6.prOsw_0.3.none.0.2


title: 8M, CO, multiome, ATAC-seq

source_name: 8M, CO


title: B6.prItra_1.none.0.3


title: HSC, PBS-3, d6, rep1

description: HSCs from mice at day 6 after the 3rd round of PBS ip as a control, replicate 1


title: 5M, CO, mulitome, ATAC-seq


title: C-22

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 8

tag: oxygen flow

tag: age


title: HSC, 5FU-3, d6, rep3

description: HSCs from mice at day 6 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 3


title: 8M, CO, multiome, RNA-seq


title: C-23

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 9

tag: hemolysis score


title: B6.prItra_1.none.0.1


title: 24M, CO, 2

source_name: 24M, CO


title: 24M, CO, 1


title: B6.pr25HC_5.none.0.3


title: HSC, 5FU-3, d21, rep1

description: HSCs from mice at day 21 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 1


title: HSC, 5FU-3, d6, rep2

description: HSCs from mice at day 6 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 2


title: B6.prItra_1.none.0.2


title: C-21

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 7


title: HSC, 5FU-3, d6, rep1

description: HSCs from mice at day 6 after the 3rd round of 5-FU treatment (150 mg/kg ip), replicate 1


title: 18M, CO, 2

source_name: 18M, CO


title: C-20

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 6


title: B6.pr25HC_5.none.0.2


title: C-24

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 10


title: C-19

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 2

value: No oxygen


title: HSC, 5FU-1, d21, rep3

description: HSCs from mice at day 21 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 3


title: B6.pr25HC_5.none.0.1


title: B6.none.none.0.3 (OSBP control)


title: C-18

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 1


title: HSC, 5FU-1, d21, rep1

description: HSCs from mice at day 21 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 1


title: 12M, CO, 1


title: 12M, CO, 2


title: HSC, 5FU-1, d21, rep2

description: HSCs from mice at day 21 after the 1st round of 5-FU treatment (150 mg/kg ip), replicate 2


title: SUB07650_S1

city: Segrate

first: Roberta

last: Alfieri

state: MI

address: Via Fratelli Cervi 93

department: ITB

country: Italy

institute: CNR

description: multiplexed sample

library_source: transcriptomic single cell

data_processing:
Preliminary analysis using the InDrops pipeline from BradhamLab using default parameters.
Filtering, Normalization, Scaling using the R package Seurat.
Identification of clusters using the Louvain algorithm privded by the R package Seurat.
Identification of differentially expressed genes using the Seurat function FindAllMarkers with default parameters.
Assembly: GRCm38
Supplementary files format and content: Count matrix

source_name: Lung

extract_protocol:
Gentle MACS Tumor Dissociation Kit #130-096-730
V3 libraries with Nextera style indexing

value: Lung

value: multiplexed sample


title: C-17

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 12

value: Male

value: Low Flow


title: B6.none.none.0.2 (OSBP control)

value: BMDM


title: B6.none.none.0.1 (OSBP control)


title: SUB07778_S1

description: multiplexed sample


title: C-15

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 10


title: C-16

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 11


title: 8M, CO, 1


title: 8M, CO, 2


title: sodium butyrate_3

city: Hangzhou

first: Bin

last: Yang

email: rayyangbin@163.com, binyang@zju.edu.cn

state: Zhejiang

address: No. 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
Quality control was performed on the raw data by removing reads containing adapters or poly-N, as well as low-quality reads using CASAVA (version 1.8, Illumina).
The clean data was mapped to the sheep genome using HISAT2
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: comma-delimited csv file includes raw counts for each Sample

organism: Ovis aries

source_name: rumen epithelium

growth_protocol: Cells were cultured in DMEM containing 2% FBS, 50 U/ml penicillin, 50 μg/ml streptomycin, and 1% mixed additive (including 25 ng/ml epidermal growth factor, 100 ng/ml hydrocortisone, 10 μg/ml insulin, 5 μg/ml transferrin, 87 ng/ml cholera toxin, and 1.3 × 10–2 ng/ml triiodothyronine), and incubated at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted from RE cells using a total RNA extraction kit (Aidllab, Beijing, China) following the instructions.
A total of 3 μg of RNA per sample was used to generate a cDNA library using the NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s instructions.

treatment_protocol: Control group was cultured under normal condition. Sodium butyrate group was treated with 1 μM sodium butyrate for 24 h.

value: rumen epithelium

tag: cell line

value: primiary cell

value: rumen epithelial cells

value: WT


title: SUB09248_S1

description: multiplexed sample


title: C-14

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 9


title: C-12

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 7


title: sodium butyrate_2

value: treated with 1 μM sodium butyrate for 24 h


title: SUB07649_S1

description: multiplexed sample


title: SUB07014_S1

description: multiplexed sample


title: 18M, CO, 1

value: Cerebral Organoid

tag: patient line


title: 4M, CO, 2

source_name: 4M, CO

tag: glioma model


title: C-13

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 8

value: blood

value: plasma


title: 2M, CO, 2

source_name: 2M, CO

tag: time


title: control_3 (sodium butyrate )

tag: cell type

value: no treatment


title: 4M, CO, 1


title: control_2 (sodium butyrate )

tag: genotype


title: C-10

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 5

value: COVID 19 with acute infection

value: Female


title: 1M, CO, 2

source_name: 1M, CO


title: C-11

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 6


title: 2M, CO, 1


title: control_1 (sodium butyrate )

tag: treatment


title: B6.none.none.pB

data_processing:
Duplicate reads were removed and, using the start and end locations of the pairs to define fragment lengths, only reads with lengths < 500 nucleotides were retained.
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome (NCBI GRCm38 mm10) using GSNAP with splice detection disabled.
Broad peaks were called using called MACS2 (2.1.0)
Assembly: mm10
Supplementary files format and content: bigWig and broadPeak

source_name: BMDM

extract_protocol:
Immunoprecipitation (IP) for acetyl-H4 was performed  using a rabbit polyclonal antibody (Millipore catalog number 06-866) as described in Gilchrist, M. et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173–178 (2006).
Libraries were prepared from immunoprecipitated DNA using the KAPA Hyper Prep kit (KR0961-v3.15)

tag: mouse

value: B


title: 1M, CO, 1


title: verteporfin_3

data_processing:
Quality control was performed on the raw data by removing reads containing adapters or poly-N, as well as low-quality reads using CASAVA (version 1.8, Illumina).
The clean data was mapped to the sheep genome using HISAT2
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample

treatment_protocol: Control group was cultured under normal condition. GA-017 group was treated with 10 μM GA-017 for 24 h. Verteporfin group was treated with 5 μM verteporfin for 24 h.

value: treated with 5 μM verteporfin for 24 h


title: C-09

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 4


title: sodium butyrate_1


title: HEL_CARM1Y149F/Y334F_input

city: Miami

first: Jun

last: Sun

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Base calling using Illumina BCL2fastq v2.19.0.316
Trimmed fastq files with cutadapt v.1.18  -a AGATCGGAAGAGCACACGTC -A AGATCGGAAGAGCGTCGTGT -m 30
Aligned to the hg19 genome assembly using bowtie2 2.2.6 with the default parameters.
Assembly: hg19
Supplementary files format and content: bw file was generated by deeptools 3.1.1 that was normalized to CPM.

source_name: HEL_CARM1Y149F/Y334F cells

growth_protocol: HEL cells were grown in RPMI 1640 media with 10% fetal bovine serum.

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min at RT. Sonicated nuclear lysates were used in immunoprecipitation with a target antibody.
Libraries were prepared using ThruPLEX DNA-Seq Kit (Takara, #112219).

treatment_protocol: CARM1 alleles in HEL cells were replaced with CARM1 mutant alleles for CARM1 Y149F, Y334F, or Y149F/Y334F, respectively.

value: HEL

value: Acute myeloid leukemia cell line

tag: genotype/variation

tag: chip antibody


title: verteporfin_2

tag: tissue


title: B6.none.none.pA

value: A

tag: stimulus

tag: stimtime


title: HEL_CARM1Y334F_input

source_name: HEL_CARM1Y334F cells


title: C-08

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 3

source_name: blood

tag: biofluid

tag: disease state

tag: gender

value: Low Flow


title: verteporfin_1

value: rumen epithelium


title: GA-017_3

value: primiary cell

value: treated with 10 μM GA-017 for 24 h


title: B6.none.PAM3.pA

value: BMDM


title: HEL-WT_input

source_name: HEL cells


title: C-07

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 2

tag: oxygen flow

tag: age

tag: hemolysis score


title: B6.25HC.none.pB


title: B6.none.PAM3.pB


title: C-06

description: SARS-COV2 infected, hospitalized, assisted with respirator, low oxygen flow, replicate 1


title: CARM1-Y149/Y334F_RUNX1_ChIPSeq rep2

tag: cell line


title: HEL_CARM1Y149F_input

source_name: HEL_CARM1Y149F cells


title: B6.25HC.PAM3.pA


title: GA-017_1

value: rumen epithelial cells

value: WT


title: B6.25HC.PAM3.pB


title: C-05

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 5

value: blood

value: Male

value: High Flow


title: GA-017_2


title: B6.25HC.none.pA


title: C-04

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 4

value: plasma

value: COVID 19 with acute infection


title: C-03

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 3


title: control_3

value: no treatment


title: B6.Ly6Gneg_Ly6CLow

data_processing:
Performed initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 25 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Assembly: mm10
Supplementary files format and content: A .tsv file with raw counts for all genes

source_name: Splenic macrophages

extract_protocol:
RNA was prepared from sorted cells using TRIzol reagent.
KAPA RNA HyperPrep kit

treatment_protocol: Mice were infected iv.with 1e5 Listeria monocytogenes. At day 3 post-infection, ~100,000 resident splenic macrophages (CD11b+, Ly6G-, Ly6clow) were isolated by flow cytometery.

value: Splenic macrophages

tag: infection

value: Listeria monocytogenes


title: Ch25h.Ly6Gneg_Ly6CLow

tag: cell type


title: CARM1-Y334F_RUNX1_ChIPSeq rep2

value: HEL

value: Acute myeloid leukemia cell line


title: C-02

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 2

value: Female


title: Ch25h.none.PAM3.18.3

treatment_protocol: Cells were left untrated or treated for 18 hours with 25-hydroxycholesterol (5 uM) and then stimulated with Pam3CSK4  (300 ng/mL).

tag: genotype


title: control_2

value: rumen epithelium

tag: treatment


title: CARM1-Y334F_RUNX1_ChIPSeq rep1


title: C-01

description: SARS-COV2 infected, hospitalized, assisted with respirator, high oxygen flow, replicate 1


title: Ch25h.none.PAM3.18.2

tag: mouse


title: control_1

value: primiary cell


title: CARM1-Y149F_RUNX1_ChIPSeq rep2

tag: genotype/variation


title: D6_2i_50uM_R3

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

data_processing:
Fastq files with 86 nt reads were quality-checked with FastQC (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and aligned to the mouse genome (GRCm38/mm10) with STAR (Dobin et al., 2013)
Differentially expressed genes (DEGs) were obtained using DESeq2 v1.32.0 and an adjusted p-value<0.05 as threshold.
Assembly: GRCm38/mm10
Supplementary files format and content: TSV

source_name: Embyonic stem cells

growth_protocol: R1 129 murine male embryonic stem cells (129/Sv background; CNIO Mouse Genome Editing Unit) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) with Ultraglutamine 1 and 4.5 g/L glucose (Lonza) complemented with 15 % FBS (Sigma), 50 U/mL penicillin - 50 mg/mL streptomycin (Invitrogen), Minimum Essential Medium Non-Essential Aminoacids (MEM NEA; Invitrogen), 100 μM 2-mercaptoethanol (Invitrogen) and 103 U/mL ESGRO mLIF medium supplement (Millipore) on 0.1 % gelatin-coated plates and incubated at 37 ºC. Culture medium was changed every day and cells were split every 2 days. Cells were tested monthly for mycoplasma contamination

extract_protocol:
Total RNA was extracted with NZY Total RNA Isolation kit (NZYtech #MB13402) and were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen #191)
Library generation was initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contained Illumina-compatible sequences. Libraries were completed by PCR and sequenced in Illumina NextSeq 550 according to manufacturer's protocols

treatment_protocol: Primed mESCs (day 0) were treated with 2i or 2i + 25/50 uM MRE11i for 6 days.

value: Embyonic stem cells

value: mESCs

value: 2i + 50uM MRE11i


title: S28_HIP_S15

city: Winston-Salem

first: Kip

middle: D

last: Zimmerman

state: NC

address: Medical Center Blvd

institute: Wake Forest School of Medicine

data_processing:
FASTQC
STAR alignment
Feature Counts
DESeq2
Assembly: Mmul_10
Supplementary files format and content: Normalized read counts

organism: Macaca mulatta

source_name: Hippocampus

extract_protocol:
All-Prep DNA/RNA/miRNA Universal kit
TruSeq stranded mRNA library prep Kit

value: Hippocampus

tag: Sex

value: male


title: D6_2i_50uM_R2

tag: tissue


title: CARM1-Y149F_RUNX1_ChIPSeq rep1

tag: chip antibody


title: CARM1-Y149/Y334F_RUNX1_ChIPSeq rep1


title: S27_HIP_S11


title: Ch25h.none.none.0.2 (25-hydroxycholesterol control)

value: BMDM

tag: stimulus

tag: stimtime


title: D6_2i_25uM_R3

value: 2i + 25uM MRE11i


title: Ch25h.none.none.0.3 (25-hydroxycholesterol control)


title: Ch25h.none.PAM3.18.1


title: D6_2i_50uM_R1


title: S26_HIP_S4


title: S29_HIP_S4


title: CARM1-Y149/Y334F_RUNX1R319me2a_ChIPSeq rep2

value: RUNX1 R319me2a


title: S25_HIP_S8


title: B6.none.PAM3.18.3


title: CARM1-WT_RUNX1_ChIPSeq rep2


title: D6_2i_25uM_R1


title: S24_HIP_S3


title: Ch25h.none.none.0.1 (25-hydroxycholesterol control)


title: B6.none.PAM3.18.2


title: CARM1-Y334F_RUNX1R319me2a_ChIPSeq rep2


title: S23_HIP_S11


title: CARM1-Y334F_RUNX1R319me2a_ChIPSeq rep1


title: CARM1-WT_RUNX1_ChIPSeq rep1


title: B6.none.PAM3.18.1


title: D6_2i_R2


title: B6.none.none.0.3 (25-hydroxycholesterol control)


title: D6_2i_25uM_R2


title: B6.none.none.0.2 (25-hydroxycholesterol control)


title: S22_HIP_S13


title: CARM1-Y149F_RUNX1R319me2a_ChIPSeq rep1


title: CARM1-Y149F_RUNX1R319me2a_ChIPSeq rep2


title: S20_HIP_S6


title: S21_HIP_S1


title: D6_2i_R1


title: CARM1-WT_RUNX1R319me2a_ChIPSeq rep2


title: CARM1-Y149/Y334F_RUNX1R319me2a_ChIPSeq rep1


title: D0_Primed_R2


title: B6.none.none.0.1 (25-hydroxycholesterol control)


title: S17_HIP_S11


title: B6.25HC.PAM3.18.3


title: D0_Primed_R3


title: S16_HIP_S7


title: D0_Primed_R1


title: Paeruginosa ∆ PA14_17650 Rep3

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

description:
P. aeruginosa ∆PA14_17650 chemically defined media replicate 3
PA14_17650_processed.csv

data_processing:
Raw fastqs were mapped using bowtie2 2.5.1
samtools 1.17 was used to extract tRNA reads containing the 3'CCA
Rsamtools 2.12.0 was used to perform pileup analysis of BAM files
Assembly: Custom transcriptomes for P. Aeruginosa
Supplementary files format and content: Count files containing counts of individual tRNA transcripts
Supplementary files format and content: CSVs containing read depth, reference base, calculated misincorporation scores, and calculated termination scores for each group of replicates at each position at each tRNA of the sample species

organism: Pseudomonas aeruginosa PA14

source_name: bacterial cell

extract_protocol:
RNA isolation with Trizol reagent, precipitation with GlycoBlue
Sequencing libraries were prepared from inputs and captured s4u-containing RNA. 3’ end adaptors (Table 6) were ligated 100 ng of RNA in an overnight reaction at 16C (250 nM adaptor, 1x T4 RNA ligase buffer, 1 ml of T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (M0437M), 50 mM DTT (Sigma 43816-10mL), 6 ml of 50% PEG 8000 (NEB B1004A), 40 units of Ribolock RNase inhibitor EO0382). All samples were then gel purified on a denaturing 10% polyacrylamide gel (National Diagnostics, EC-829). Gels were cut between 60 to 200 nt and purified via crush and soak overnight tumble at 4C (crush gel through needle punched bottom of 500 ml tubes into 1.7 mL Eppendorf tubes, soak in 10 mM Tris pH 7.5 (15567-027), 500 mM NaCl (AM9759), 1 mM EDTA (AM9261), 0.1% SDS (351-032-101). Gel buffer mix is then transferred to SpinX columns (CLS8162-96EA) to remove remaining gel. Three volumes of 100% ethanol are added to the RNA-containing buffer for precipitation. The purified RNA was then reverse transcribed using TGIRT and uniquely barcoded RT primers per sample. RT included the RNA Plus 1 ml of TGIRT enzyme (TGIRT50 from InGex), 1x buffer (20 mM Tris HCl pH 7.5 (15567-027), 5 mM MgCl2 (AM9530G), 450 mM NaCl (AM9759), 1 ml 100 mM DTT (18091050), and 1 ml of 3 mM RT primer, in a 19 ml reaction (Table 6). This mix was incubated for 30 min at room temperature, followed by the addition of 1 ml of 25 mM dNTPs (N0446S), and incubation for 1 hour at 60C. cDNAs were then released from the RT TGIRT complex by treating with 1 ml of 5M NaOH, incubating at 95C for 3 min, and followed by neutralization of cooled sample with 1 ml of 5M HCl. cDNAs were then pooled in groups, such as inputs or captured samples, and cleaned using the Zymo DNA Clean and Concentrator kit (D4014). Individually barcoded and cleaned pools of samples were then gel purified to remove excess primer, following the same protocol as above, except that eluted cDNA was cleaned through Zymo DNA Clean and Concentrator kit (D4014). Eluted pools were then subjected to circularization using a CircLigase-II kit (CL9021K) (cDNA, 0.75 ml MnCl2, 0.75 ml circligase-II, 1.5 ml buffer in a 15 ml reaction). After circularization cDNA was cleaned mixing with 30 ml of Ampure XP beads (A63881) and 75 ml of isopropanol, incubated 10 min RT, applied to magnet, washing two times 30 seconds each with freshly made 80% EtOH. Beads with cDNA were air dried for 5 min and cDNA was then eluted from beads in 14 ml of H2O. Directly following clean up, cDNA was amplified with a first set of oligos in a PCR reaction on a qPCR machine to detect amplification in real time to capture linear amplification (0.75 ml of 20 mM P3tall and P6tall oligo mix, 15 ml of 2x NEB Next (M0541L), 14 ml cDNA, and 0.25 ml 25x diluted Sybr green (S7563) in a 30 ml reaction). PCR parameters were 98° C for 40 seconds, cycling of 98° C for 20 seconds, 65° C for 30 seconds, 72° C for 45 seconds, and a final extension at 72° C for 5 minutes. Number of cycles was determined by real time amplification. Samples were then cleaned again using Ampure XP beads (A63881) (54 ml of beads, 4 ml of isopropanol, and eluted in 10 ml of H2O). Eluted cDNA was amplified for three more cycles using a second set of oligos, P3 and P6 solexa primers for Illumina sequencing in a NEB Next master mix reaction. Following the second PCR, samples were cleaned one last time on the Ampure XP beads (36 ml of beads, 2.7 ml of isopropanol, and eluted in 12 ml of H2O). Final libraries were analyzed by DNA high sensitivity tape station.

value: bacterial cell


title: HEL-Y149F/Y334F-G12-3

first: Hidehiro

last: Itonaga

address: 1501 NW 10th Ave

department: Department of Biochemistry and Molecular Biology

institute: Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami

data_processing:
FASTQ data were processed with cutadapt v1.15 (--nextseq-trim=20 -m 18) to remove low quality reads.
Gene level counts were estimated using RSEM v1.3.0 and STAR v2.6.0c alignment to the human hg19 transcriptome (GENCODE V19 annotation).
RUVseq v1.12.0 was sed adjusted gene counts by removing unwanted variance using exogenous ERCC spike-in RNA.
DESeq2 version 1.18.1 and R (version 3.4.1) were used for sample normalization and differential expression analysis with a q value < 0.25 and an FC > 2.0 (Wald test).

source_name: erytroleukemia cell

extract_protocol:
RNA was extracted using Direct-zol RNA Microprep (ZYMO RESEARCH, R2061) and cDNA synthesized by qScript cDNA Super-Mix (Quanta bio, #95048-100), according to the manufacturer’s instructions.
RNA-seq library prep was carried out using the Illumina TruSeq Total Total Stranded kit (RS-122-2201) with Ribo-Zero rRNA reduction following the manufacturer’s protocol without modification.

value: HEL cells

value: Untreated

value: Y149F/Y334F double mutation (G12 clone)


title: B6.25HC.PAM3.18.1

data_processing:
Performed initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Assembly: mm10
Supplementary files format and content: A .tsv file with raw counts for all genes

extract_protocol:
Cells were harvested for total RNA extraction using SV 96 total isolation RNA kit (Promega Z3500).
Illumina TruSeq stranded


title: CARM1-WT_RUNX1R319me2a_ChIPSeq rep1

value: HEL


title: HEL-Y149F/Y334F-G12-2


title: S44_HIP_S89


title: S15_HIP_S6


title: B6.25HC.none.0.3


title: Paeruginosa ∆ PA14_17650 Rep1

description:
P. aeruginosa ∆PA14_17650 chemically defined media replicate 1
PA14_17650_processed.csv


title: B6.25HC.none.0.2


title: HEL-Y149F/Y334F-D2-3

value: Y149F/Y334F double mutation (D2 clone)


title: HEL-Y149F/Y334F-G12-1


title: Paeruginosa tRNA Rep3

description:
P. aeruginosa PA14 chemically defined media replicate 3
PA14_WT_processed.csv


title: HEL-Y149F/Y334F-D2-2


title: S14_HIP_S5


title: S13_HIP_S12


title: B6.25HC.none.0.1


title: Ecoli LB06 Capture Rep2

description: WT_Ecoli_OD06LB_MTSEA-Capture_collated_processed.csv

data_processing:
Raw fastqs were mapped using bowtie2 2.5.1
samtools 1.17 was used to extract tRNA reads containing the 3'CCA
Assembly: Custom transcriptomes for E. Coli and P. Aeruginosa
Supplementary files format and content: Mapped and subsetted BAM files containing mature tRNA reads

organism: Escherichia coli BW25113

extract_protocol:
RNA isolation with Trizol reagent, precipitation with GlycoBlue
Sequencing libraries were prepared from inputs and captured s4u-containing RNA. 3’ end adaptors (Table 6) were ligated 100 ng of RNA in an overnight reaction at 16C (250 nM adaptor, 1x T4 RNA ligase buffer, 1 ml of T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (M0437M), 50 mM DTT (Sigma 43816-10mL), 6 ml of 50% PEG 8000 (NEB B1004A), 40 units of Ribolock RNase inhibitor EO0382). All samples were then gel purified on a denaturing 10% polyacrylamide gel (National Diagnostics, EC-829). Gels were cut between 60 to 200 nt and purified via crush and soak overnight tumble at 4C (crush gel through needle punched bottom of 500 ml tubes into 1.7 mL Eppendorf tubes, soak in 10 mM Tris pH 7.5 (15567-027), 500 mM NaCl (AM9759), 1 mM EDTA (AM9261), 0.1% SDS (351-032-101). Gel buffer mix is then transferred to SpinX columns (CLS8162-96EA) to remove remaining gel. Three volumes of 100% ethanol are added to the RNA-containing buffer for precipitation.

value: WT

tag: media condition

value: LB OD 0.6

tag: fraction

value: captured s4u-containing RNA


title: B6.25HC.PAM3.18.2


title: Ecoli LB06 Capture Rep3


title: HEL-Y149F/Y334F-D2-1


title: S12_HIP_S6


title: S11_HIP_S18


title: IgG-3.IgG

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

description: co-immunoprecipitated RNA

data_processing:
Briefly, Paired-end reads were harvested and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome by STAR software.
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Binding sites on RNAs (peaks) were identified by MACS software. Differentially binding sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.GO and Pathway enrichment analysis were performed by the differentially binding mRNA coding genes.
Assembly: mm39
Supplementary files format and content: Microsoft Office excel files include peak enrichment information for each Sample

growth_protocol: CT26.WT cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% antibiotics, at 37 °C in 5% CO2.

extract_protocol:
lnput and co-IP RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Mouse colon cancer

value: co-immunoprecipitated RNA by IgG


title: Paeruginosa tRNA Rep1

description:
P. aeruginosa PA14 chemically defined media replicate 1
PA14_WT_processed.csv


title: S45_HIP_S14


title: IgG-2.IgG

description: co-immunoprecipitated RNA


title: S10_HIP_S7


title: HEL-Y334F-H8-2

value: Y334F single mutation (H8 clone)


title: HEL-Y334F-H8-1


title: Ecoli LB06 Input Rep3

description: WT_Ecoli_OD06LB_Input_collated_processed.csv

value: Input


title: Paeruginosa ∆ PA14_17650 Rep2

description:
P. aeruginosa ∆PA14_17650 chemically defined media replicate 2
PA14_17650_processed.csv


title: HEL-Y334F-H8-3


title: IgG-1.IgG

description: co-immunoprecipitated RNA


title: Paeruginosa tRNA Rep2

description:
P. aeruginosa PA14 chemically defined media replicate 2
PA14_WT_processed.csv


title: Ecoli LB06 Input Rep2


title: HEL-Y334F-H14-3

value: Y334F single mutation (H14 clone)


title: S7_HIP_S2

value: Hippocampus

value: male


title: Ecoli LB06 Input Rep1


title: HuR-3.IP

description: co-immunoprecipitated RNA

value: co-immunoprecipitated RNA by endogenous HuR


title: HEL-Y334F-H14-2


title: S6_HIP_S6


title: HuR-1.Input

description: input total RNA

value: no


title: S5_HIP_S3


title: Ecoli LB06 Capture Rep1

value: bacterial cell


title: HuR-1.IP

description: co-immunoprecipitated RNA


title: HEL-Y334F-H14-1

value: HEL cells

value: Untreated


title: Ecoli Spent0 Capture Rep1

description: WT_Ecoli_CDM_MTSEA-Capture_collated_processed.csv

value: chemically defined media


title: S3_HIP_S11


title: S4_HIP_S19


title: HuR-2.IP

description: co-immunoprecipitated RNA


title: Ecoli Spent0 Input Rep3

description: WT_Ecoli_CDM_Input_collated_processed.csv


title: HEL-Y149F-K3-2

value: Y149F single mutation (K3 clone)


title: HEL-Y149F-K3-3


title: S8_HIP_S16


title: Ecoli Spent0 Input Rep2

value: WT


title: HEL-Y149F-G19-3

value: Y149F single mutation (G19 clone)


title: S2_HIP_S8


title: D6_2i_R3

value: Embyonic stem cells

value: mESCs


title: Ecoli Spent0 Capture Rep3

value: captured s4u-containing RNA


title: HEL-Y149F-K3-1


title: S1_HIP_S6


title: NUBIA2

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

institute: Guangxi University

data_processing:
Transcripts were mapped to the corresponding reference genome (https://www.ncbi.nlm.nih.gov/genome/10731?genome_assembly_id=281266) using the10X Genomics Cell Ranger pipeline (version 5.0.0). The read count matrices for each sample were generated by Cell Ranger count. Then count data were imported into the Seurat R package and quality control of each library was performed to remove outlier cells and genes. Assuming a Gaussian distribution of the UMI/gene number per cell, we applied a criterion to filter the limit of the UMI/gene number beyond the mean ± two-fold standard deviations. After visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells in which > 20% of the counts belonged to mitochondrial genes. And genes were retained if they were expressed in at least 5 cells. For cells captured in sequencing, in order to avoid the bias brought by doublets, we set the threshold to 10% and detected the doublet cells according to the method recommended by Scrublet software.
Assembly: Capra_hircus_premrna
Supplementary files format and content: tab-delimited text files include  matrix/genes/barcodes for each Sample …
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Capra hircus

source_name: ovary

extract_protocol:
The experiment population consisted of a polytocous group (n=7, litter size≥ 3) ——Nubian goat and a monotocous group (n=7, litter size=1) ——Du’an goat based on three lambing records. The animals were maintained at Standardized sheep breeding farm. Without any other extra exogenous hormones that may induce superovulation in goat, all goats treated with controlled internal drug releasing (CIDR, progesterone 300 mg) for 17days to achieve synchronous estrus. Ovarian tissue samples from 2 Nubian goats (about 3 years old) and 2 Du’an goat (about 3 years old) were collected and processed for snRNA-seq analysis. Single cells were suspended in calcium- and magnesium-free PBS containing 0.04%weight/volume BSA.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manfacturer's protocol.

tag: breed

value: Nubian

tag: tag

value: ovary


title: Ecoli ∆ThiI Input Rep3

description: ThiI_Ecoli_OD06LB_Input_collated_processed.csv

value: deltaThiI

value: LB OD 0.6

value: Input


title: HEL-Y149F-G19-1


title: NUBIA1


title: Ecoli ∆ThiI Input Rep2


title: HEL-WT3

value: Wild-type


title: HEL-WT2


title: DUAN1

value: Du'an


title: Mel_dsx_neurons

city: Philadelphia

first: Justin

last: Walsh

state: PA

address: 3740 Hamilton Walk

institute: University of Pennsylvania

description:
10X Genomics
Global_Trimmed_MelYak.Rds
TN1OnlyMelYak.Rds

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software v7.1.0
Assembly: GCA_000001215.4
Assembly: GCA_016746365.2
Supplementary files format and content: tab-separated value files, matrix files, and Rds files

organism: Drosophila melanogaster

source_name: neurons

extract_protocol:
The central nervous system of approximately 100 doublesex-GAL4 x UAS-nls::tdTomato flies were dissected in ice cold Schneider's medium and digested in a solution containing Liberase DH for 45 mins. The tissue was washed with Schneider's medium and broken apart via pipetting before FACS sorting out the tdTomato+ cells.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10X Genomics)

value: neurons

value: male

tag: age

value: 4-8 day old adults


title: HEL-WT1

tag: cell line

value: HEL cells

value: Untreated


title: HEL-Y149F-G19-2


title: stomach_Trim28_heavy_tumor_rep1

status: Public on Apr 02 2024

city: Grand Rapids

first: Luca

last: Fagnocchi

address: 333 Bostwick AVE NE

institute: VAI

data_processing:
All reads from fastq files were quality controlled, trimmed from adapters, mapped, and counted on featured by using the mRNA-seq pipeline of snakePipes (v2.7.3)
Mapping was performed with STAR on the GRCm38/mm10 mouse genome.
Reads were counted on features with featureCounts and the obtained matrices of raw counts were used as input for DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: raw_counts_matrix.tsv comprise the output of featureCounts

source_name: stomach

growth_protocol: Ear punch biopsies were collected at 10 days and placed in 20 µl reaction mix composed of genomic DNA lysis buffer (100 mM Tris-HCl pH 8.5, 5 mM EDTA, 0.2% SDS, 100 mM NaCl) supplemented with 20 mg proteinase K (Thermo Scientific, EO0491).

extract_protocol:
Quick-DNA/RNA Microprep Plus Kit (Zymo)
Libraries were prepared by the Van Andel Genomics Core from 142 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect -rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent TapeStation 4200 (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA). Individually indexed libraries were pooled and 2x100 bp sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 50M raw paired-reads per transcriptome. Base calling was performed by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq2 v2.20.

treatment_protocol: Digestion was carried out overnight in a Thermocycler under the following conditions: 55C for 16 hours, 95C for 10 minutes, 4C hold (lid at 105C). After lysis, the lysate was diluted by adding 160 µl of nuclease-free water (Invitrogen, AM9938) to the same tube (180 µl final volume).

value: stomach

tag: status tissue

value: tumor

tag: phenotype

value: heavy

tag: age sacrifice


title: stomach_Trim28_heavy_tumor_rep2

tag: genotype


title: seminal_vesicle_Trim28_light_tumor_rep3

value: light


title: Ecoli Spent0 Input Rep1

tag: cell type

value: bacterial cell

value: WT

value: chemically defined media


title: seminal_vesicle_Trim28_light_tumor_rep2


title: stomach_Trim28_heavy_normal_rep2

value: normal


title: stomach_Trim28_heavy_normal_rep1


title: seminal_vesicle_Trim28_light_normal_rep3


title: seminal_vesicle_Trim28_light_normal_rep1


title: Ecoli ∆ThiI Input Rep1

value: deltaThiI

value: LB OD 0.6


title: DUAN2

value: ovary


title: seminal_vesicle_Trim28_heavy_tumor_rep2


title: seminal_vesicle_Trim28_heavy_normal_rep3


title: seminal_vesicle_Trim28_light_normal_rep2


title: seminal_vesicle_Trim28_heavy_tumor_rep1


title: seminal_vesicle_Trim28_heavy_normal_rep2


title: seminal_vesicle_Trim28_heavy_normal_rep1


title: Saline, Rep3

type: genomic

city: Charlottesville

first: Joshua

last: Danoff

state: VA

address: 485 McCormick Road

institute: University of Virginia

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina HorvathMammalianMethylChip40 BeadChip using standard Illumina protocol

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

data_processing: Data were checked for quality control measures and normalized by SeSaMe method in R statistical software

label: Cy3, Cy5

organism: Microtus ochrogaster

source_name: Nucleus accumbens

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen AllPrep

value: Male

value: Postnatal day 20


title: prostate_Trim28_light_tumor_rep2

source_name: prostate

value: prostate

value: male


title: prostate_Trim28_light_tumor_rep1


title: seminal_vesicle_Trim28_light_tumor_rep1


title: Saline, Rep4


title: prostate_Trim28_light_normal_rep2


title: prostate_Trim28_light_normal_rep1


title: prostate_Trim28_heavy_normal_rep2


title: prostate_Trim28_light_normal_rep3


title: prostate_Trim28_heavy_tumor_rep2


title: prostate_Trim28_heavy_normal_rep1


title: Ecoli Spent0 Capture Rep2

value: captured s4u-containing RNA


title: Saline, Rep2


title: prostate_Trim28_heavy_tumor_rep1


title: Oxytocin, Rep4


title: lungs_Trim28_light_tumor_rep1

source_name: lungs

value: lungs


title: lungs_Trim28_light_normal_rep1


title: Oxytocin, Rep2


title: intestine_Trim28_light_tumor_rep2

source_name: intestine

value: intestine


title: intestine_Trim28_light_tumor_rep1

value: tumor


title: lungs_Trim28_heavy_tumor_rep1

value: heavy


title: lungs_Trim28_heavy_normal_rep2


title: lungs_Trim28_heavy_normal_rep1


title: prostate_Trim28_light_tumor_rep3

value: light


title: intestine_Trim28_light_normal_rep1


title: intestine_Trim28_heavy_tumor_rep1


title: intestine_Trim28_heavy_normal_rep2


title: lungs_Trim28_heavy_tumor_rep2


title: intestine_Trim28_heavy_normal_rep3


title: intestine_Trim28_heavy_tumor_rep2


title: intestine_Trim28_heavy_normal_rep1


title: Oxytocin, Rep3


title: day10eaclip_WT_rep4

source_name: ear

value: ear

tag: developmental stage

value: day 10


title: day10eaclip_Trim28_rep10

tag: Sex


title: day10eaclip_Trim28_rep7

tag: tissue


title: day10eaclip_WT_rep5

value: WT


title: day10eaclip_Trim28_rep9


title: day10eaclip_Trim28_rep6


title: day10eaclip_Trim28_rep8


title: day10eaclip_Trim28_rep4


title: intestine_Trim28_heavy_tumor_rep3


title: day10eaclip_Trim28_rep5


title: day10eaclip_WT_rep1


title: intestine_Trim28_light_normal_rep2

value: normal


title: day10eaclip_Trim28_rep2


title: Tet3OE_T_M1

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For RNA-seq, Ladaptors were trimmed using trim galore (v0.6.7) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.9a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.00001 -f BAMPE --keep-dup all.
For WGBS, bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.0% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -adaMR 0.25 -ada_trim -polyX 50 -minReadLen 100 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
For hmeDIP, cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.0001 -f BAMPE --keep-dup all.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10

source_name: Neuroectoderm cells

growth_protocol: ESCs were cultured on gelatin in serum/LIF for 24 hours. LIF was removed and 1uM retinoic acid (RA) was added for 72 hours to generate NE cells, which were harvested for subsequent high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA was extracted from NE cells using Qiagen RNeasy Mini kit. For WGBS, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit. For hmeDIP, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). HmeDIP libraries were prepared by NEBNext HiFi 2x PCR Master mix. CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.

value: Neuroectoderm cells

tag: strain

value: V6.5 Male mixed 129/C57BL/6

value: Tet3 mutant


title: Tet3OE_T_K1

value: Tet3 knockout


title: day10eaclip_Trim28_rep1


title: Tet3OE_T_W1

value: Tet3 wildtype


title: Saline, Rep1

value: Male

value: Postnatal day 20


title: Tet3OE_EV_M1


title: Dnmt1OE_D_K2


title: Oxytocin, Rep1


title: Dnmt1OE_D_K1


title: Tet3OE_EV_W1


title: day10eaclip_WT_rep3

value: male


title: Dnmt1OE_D_M1


title: day10eaclip_Trim28_rep3


title: Dnmt1OE_EV_K2


title: Dnmt1OE_EV_K1


title: Dnmt1OE_D_W1


title: Dnmt1OE_EV_M2


title: Dnmt1OE_EV_W2


title: CD8mIL2+aPD1_D4_FB_1

city: South San Francisco

first: Manu

last: Kumar

state: California

address: 650 Gateway Blvd Suite 100

institute: Asher Biotherapeutics

description:
F-D4_matrix.mtx.gz
F-D4_features.tsv.gz
F-D4_barcodes.tsv.gz

data_processing:
Fastq files were processed using the Cell Ranger (v7.1.0) multi pipeline with the default parameters. Gene expression libraries were aligned to the mouse transcriptome (mm10-2020-A) and TCR sequences were aligned to the VDJ reference dataset (GRCm38-alts-ensembl-5.0.0).
Assembly: mm10
Supplementary files format and content: Standard Cellranger v7.1.0 output
Library strategy: scRNA-seq,TCR-seq, feature barcoding, and barcode enabled antigen mapping

source_name: tumor

extract_protocol:
Total CD8+ T cells were enriched using a CD8+ T cell positive selection kit (Miltenyi). Tumors from individual mice were labeled with one of the following antibodies before pooling in order to identify cells from individual tumors in downstream analysis: 1) TCRb (TotalSeq™-C0120 anti-mouse TCR β chain antibody, Cat# 109259, BioLegend), 2) CD90.2 (TotalSeq™-C0075 anti-mouse CD90.2 (Thy1.2) antibody, Cat#, 105353, BioLegend), and 3) CD45 (TotalSeq™-C0096 anti-mouse CD45 antibody, Cat# 103169, BioLegend).
Samples were submitted to the Genome Institute at Washington University in St. Louis to generate 10x libraries using 10x 5'v2 Single Cell RNAseq, V(D)J enrichment, feature barcoding, and Barcode Enabled Antigen Mapping kits.

treatment_protocol: T3 tumor-bearing mice were treated on day twelve post-tumor transplant.

value: CD8+ T cell

tag: treatment

value: paired-end

value: CD8-mIL2 + anti-PD1

tag: time


title: naIL2+aPD1_D4_FB_1

description:
D-D4_matrix.mtx.gz
D-D4_features.tsv.gz
D-D4_barcodes.tsv.gz

value: tumor

value: CTRL-not-a-mIL2 + anti-PD1


title: Dnmt1OE_EV_M1


title: CD8mIL2_D4_FB

description:
E-D4_matrix.mtx.gz
E-D4_features.tsv.gz
E-D4_barcodes.tsv.gz


title: Veh_D4_FB

description:
A-D4_matrix.mtx.gz
A-D4_features.tsv.gz
A-D4_barcodes.tsv.gz

value: Vehicle


title: Dnmt1OE_D_W2


title: CD8mIL2+aPD1_D4_FB_2


title: naIL2+aPD1_D4_FB_2


title: Tet3OE_EV_K1


title: CD8mIL2_D2_FB_2

description:
E-D2_matrix.mtx.gz
E-D2_features.tsv.gz
E-D2_barcodes.tsv.gz


title: CD8mIL2+aPD1_D2_FB

description:
F-D2_matrix.mtx.gz
F-D2_features.tsv.gz
F-D2_barcodes.tsv.gz


title: Dnmt1OE_EV_W1


title: day10eaclip_WT_rep2

value: ear

value: day 10


title: naIL2_D4_FB

description:
C-D4_matrix.mtx.gz
C-D4_features.tsv.gz
C-D4_barcodes.tsv.gz


title: naIL2_D2_FB

description:
C-D2_matrix.mtx.gz
C-D2_features.tsv.gz
C-D2_barcodes.tsv.gz


title: CD8mIL2+aPD1_D4_BEAM_1


title: Veh_D2_FB

description:
A-D2_matrix.mtx.gz
A-D2_features.tsv.gz
A-D2_barcodes.tsv.gz


title: naIL2+aPD1_D2_FB

description:
D-D2_matrix.mtx.gz
D-D2_features.tsv.gz
D-D2_barcodes.tsv.gz


title: aPD1_D2_FB

description:
B-D2_matrix.mtx.gz
B-D2_features.tsv.gz
B-D2_barcodes.tsv.gz


title: CD8mIL2_D2_FB_1


title: naIL2+aPD1_D4_BEAM_2


title: naIL2_D4_BEAM


title: naIL2+aPD1_D4_BEAM_1


title: CD8mIL2_D4_BEAM_1


title: CD8mIL2+aPD1_D2_BEAM


title: aPD1_D4_BEAM


title: CD8mIL2_D2_BEAM_2


title: naIL2_D2_BEAM_2


title: naIL2+aPD1_D2_BEAM_2


title: CD8mIL2_D2_BEAM_1


title: Veh_D2_BEAM_2


title: naIL2+aPD1_D2_BEAM_1


title: aPD1_D4_FB

description:
B-D4_matrix.mtx.gz
B-D4_features.tsv.gz
B-D4_barcodes.tsv.gz


title: CD8mIL2+aPD1_D4_TCR


title: Veh_D2_BEAM_1


title: CD8mIL2_D4_TCR


title: aPD1_D2_BEAM


title: CD8mIL2+aPD1_D4_BEAM_2


title: Dnmt1OE_D_M2


title: naIL2_D4_TCR


title: aPD1_D4_TCR


title: CD8mIL2_D4_BEAM_2


title: Veh_D4_TCR


title: Veh_D4_BEAM


title: CD8mIL2+aPD1_D2_TCR


title: naIL2+aPD1_D2_TCR


title: CD8mIL2_D2_TCR


title: naIL2_D2_TCR


title: aPD1_D2_TCR


title: Veh_D2_TCR


title: CD8mIL2+aPD1_D4_GEX


title: CD8mIL2_D4_GEX


title: naIL2_D2_BEAM_1


title: Veh_D4_GEX


title: naIL2+aPD1_D4_GEX


title: CD8mIL2_D2_GEX


title: aPD1_D4_GEX


title: naIL2+aPD1_D4_TCR


title: naIL2+aPD1_D2_GEX


title: naIL2_D2_GEX


title: CD8mIL2+aPD1_D2_GEX


title: naIL2_D4_GEX


title: aPD1_D2_GEX


title: budding organoid (BO) cultured intestinal progenitor cells derived from adult intestine, replicate 1

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
Base-calling was performed with bcl2fastq program (v2.20).
The sequence reads were aligned to the mouse reference genome assembly (Ensemble GRCm38) using bowtie2 (v2.3.1).
Unique molecular identifier (UMI) count was calculated from raw read count data that were estimated from aligned data by using HTSeq (v0.6.0) as descrived in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include UMI count values of all samples

source_name: small intestine

growth_protocol: Hepatocytes were isolated from 10 week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979) and carefully separated from non-parenchymal cells and residual blood cells by repeated centrifugation. Isolated hepatocytes were cultuerd in the standard medium (Suzuki et al., 2000; Suzuki et al., 2002; Suzuki et al., 2008) with EGF (20 ng/mL). Cultured hepatocytes dedifferentiate into expandable progenitor-like cells. These dedifferentiated hepatocytes, termed dediHeps, can be maintaied in monolayer culture under the same culture condition. dediHeps can re-differentiate into mature hepatocytes by forming aggregates in each well of ultra-low attachment 96-well plates coated with poly 2-hydroxyethyl methacrylate and maintained in the medium used in a previous study (Yamamoto et al., 2018). In organoid culture, 3 × 104 dediHeps, adult intestinal crypts obtained from 10 weeks-old mice and fetal intestinal cells obtained from E13.5 mouse embryos were embedded in Matrigel (BD Biosciences, San Jose, CA) and cultured in the medium used in a previous study (Miura and Suzuki, 2017).

extract_protocol:
Total RNA was prepared from hepatocytes, dediHeps, dediHep aggregates, dediHep-derived organoids, FIPC-derived organoids, ISC-derived organoids, and CLiPs using an ISOGEN II (Nippon gene, Tokyo, Japan) or RNeasy mini kit (QIAGEN, Venlo, Netherlands), according to the manufacturer’s instructions.
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".

value: small intestine

value: intestinal stem cell

value: WT

value: in vitro organoid culture condition


title: budding organoid (BO) cultured intestinal progenitor cells derived from adult intestine, replicate 3


title: spherical organoid (SO) cultured intestinal progenitor cells derived from fetal intestine, replicate 2

source_name: fetal intestine

value: fetal intestine

value: intestinal progenitor cell


title: spherical organoid (SO) cultured intestinal progenitor cells derived from fetal intestine, replicate 1


title: spherical organoid (SO) cultured intestinal progenitor cells derived from fetal intestine, replicate 3


title: budding organoid (BO) cultured intestinal progenitor cells derived from adult intestine, replicate 4


title: budding organoid (BO) cultured intestinal progenitor cells derived from adult intestine, replicate 2


title: monolayer cultured CLiP cells, replicate 3

source_name: liver

value: liver

value: Hepatocyte

value: in vitro monolayer culture condition


title: Veh_D2_GEX

value: CD8+ T cell


title: budding organoid (BO) cultured dediHeps tranfected with Cdx2, replicate 1


title: monolayer cultured CLiP cells, replicate 1


title: monolayer cultured CLiP cells, replicate 2


title: spherical organoid (SO) cultured dediHeps, replicate 3


title: budding organoid (BO) cultured dediHeps tranfected with Cdx2, replicate 2


title: spherical organoid (SO) cultured dediHeps, replicate 1


title: spherical organoid (SO) cultured dediHeps, replicate 2


title: aggregation cultured dediHeps, replicate 2

value: in vitro aggregation culture condition


title: budding organoid (BO) cultured dediHeps tranfected with Cdx2, replicate 3


title: aggregation cultured dediHeps, replicate 1


title: monolayer cultured dediHeps, replicate 2


title: monolayer cultured dediHeps, replicate 5


title: monolayer cultured dediHeps, replicate 4


title: aggregation cultured dediHeps, replicate 3


title: monolayer cultured dediHeps, replicate 3


title: monolayer cultured dediHeps, replicate 1


title: monolayer cultured hepatocytes for 7 days with verteporfin, replicate 2


title: monolayer cultured hepatocytes for 7 days with DMSO (control), replicate 1


title: monolayer cultured hepatocytes for 14 days, replicate 1


title: monolayer cultured hepatocytes for 14 days, replicate 3


title: monolayer cultured hepatocytes for 14 days, replicate 2


title: monolayer cultured hepatocytes for 7 days with verteporfin, replicate 1


title: monolayer cultured hepatocytes for 7 days, replicate 2


title: monolayer cultured hepatocytes for 7 days with DMSO (control), replicate 2


title: monolayer cultured hepatocytes for 7 days, replicate 1


title: monolayer cultured hepatocytes for 4 days, replicate 3


title: monolayer cultured hepatocytes for 4 days, replicate 2


title: monolayer cultured hepatocytes for 4 days, replicate 1


title: monolayer cultured hepatocytes for 2 days, replicate 2


title: monolayer cultured hepatocytes for 1 day, replicate 2


title: monolayer cultured hepatocytes for 1 day, replicate 1


title: monolayer cultured hepatocytes for 2 days, replicate 3


title: monolayer cultured hepatocytes for 3 hs, replicate 3


title: monolayer cultured hepatocytes for 3 hs, replicate 1


title: freshly isolated hepatocytes, replicate 1

value: freshly isolated from tissue


title: NSG control Replicate 3

city: Minneapolis

first: Sarah

last: Crist

state: Minnesota

address: 2231 6th St SE

institute: University of Minnesota

description:
NSG_PBS_19174
NSG_PBS_19174

data_processing:
Reads were trimmed using Trimmomatic (v0.33) and quality control on raw reads was performed with FastQC(v0.11.9) (mean quality score 36) was assessed.
STAR(v2.7.3a) was used to align to human (hg38) and mouse (mm10) reference genomes.
Subtraction of mouse sequences was performed using XenofilteR(v1.6).
Aligned reads were counted for gene associations against the UCSC genes data base with HTSeq(v0.11.0).
Differentially expressed genes were identified using edgeR (v3.42.4, negative binomial)
Assembly: mm10 and hg38
Supplementary files format and content: Comma separated value text files of raw counts for each sample (.CSV) - there is one file for counts mapped to human genome and one file for counts mapped to mouse genome
Supplementary files format and content: Raw sequencing data for each sample (.FASTQ)

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated from iPAX7 in vitro-differentiated myotubes and homogenized tibialis anterior muscles using TRIzol (Invitrogen) and the PureLink RNA mini kit (Invitrogen, #12183025) with on-column DNaseI treatment following the manufacturer’s recommendations.
500 ng of total RNA was used to for generate unique dual-indexed (UDI) TruSeq stranded mRNA libraries.

treatment_protocol: 6–8-week-old male NSG and NSG-mdx4Cv mice were used for these experiments. One day before intramuscular cell transplantation, target muscles (tibialis anterior) were pre-injured with cardiotoxin (15 μl of 10 μM stock).  Myogenic progenitors were injected at 1.65×106 (resuspended in 15 μl of PBS) using a 26 g Hamilton syringe. As control, contralateral legs were injected with the same volume of PBS. Two months after transplantation muscles were collected for RNA isolation.

value: Skeletal muscle

value: CTX + PBS


title: NSG control Replicate 1

description:
NSG_PBS_19172
NSG_PBS_19172


title: monolayer cultured hepatocytes for 3 hs, replicate 2


title: NSG-mdx control Replicate 2

description:
MDX_PBS_19351
MDX_PBS_19351

value: DMD


title: freshly isolated hepatocytes, replicate 3


title: monolayer cultured hepatocytes for 2 days, replicate 1


title: monolayer cultured hepatocytes for 7 days, replicate 3


title: Tet3_knockout_RNAseq_rep1

data_processing:
For RNA-seq RNA was extracted using Qiagen RNeasy Mini kid (74104). Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.7) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.9a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.00001 -f BAMPE --keep-dup all.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.0% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -adaMR 0.25 -ada_trim -polyX 50 -minReadLen 100 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
For RNA-seq, RNA was extracted from NE cells using Qiagen RNeasy Mini kit. For WGBS, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.
RNA-seq, WGBS, CUT&Tag

treatment_protocol: For CUT&Tag, NE cells were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex.

value: Neuroectoderm cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet3 knockout


title: Tet3_mutant_RNAseq_rep3

value: Tet3 mutant


title: Tet3_mutant_RNAseq_rep2


title: Tet3_wildtype_RNAseq_rep2

value: Tet3 wildtype


title: Tet3_wildtype_RNAseq_rep1


title: Tet3_mutant_RNAseq_rep1


title: TSA Zygote EU+ RNA rep2

city: Kofu

first: Mizuki

last: Sakamoto

institute: University of Yamanashi

data_processing:
For LET-seq and RNA-seq data, paired-end reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore! with a ‘--clip_R2 3’ option. After the reads were aligned, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts (version 1.6.5) and GENCODE annotation of the mm10 mouse genome (vM25) was used to analyze transcription levels with options ‘-p -O --fraction’. bigWig files were generated by deeptools bamCoverage with options '-bs 25 --normalizeUsing RPKM -ignore chrX chrM chrY --smoothLength 75'. The expression of each annotated gene was quantified by calculating TPM (transcripts per million) using R.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with options  ‘-X 700 --dovetail’ after removing adaptor sequences and low-quality reads by Trim Galore!. bigWig files were generated by bamCoverage from deepTools with parameters ‘-bs 50 --normalizeUsing RPKM --smoothLength 500’. MACS2 was used to call peaks with options ‘-q 0.05 -f BAMPE’.
Assembly: mm10
Supplementary files format and content: bigWig, tab-delimited text files indicating TPM values (for RNA-seq)
Library strategy: LET-seq

growth_protocol: Early embryos were cultured in KSOM. Male mouse embryonic stem cells were cultured with the medium consists of GMEM containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates.

extract_protocol:
For LET-seq and RNA-seq, total RNA from whole-cell lysate was used.  For CUT&RUN, chromatin was digested by protein A- potein G-MNase.
LET-seq protocol was used. For total RNA-seq, SMART-seq stranded kit (TAKARA) was used. For CUT&RUN library preparation, NEBnext Ultra II DNA Library Prep Kit (NEB) was used.

treatment_protocol: For LET-seq with inhibitors, zygotes were cultured in KSOM containing DMSO, 10 μM A-485 or 100 nM TSA from 18 to 24 hphCG, and then cultured in KSOM medium containing the same inhibitor and 1 mM EU from 24 to 27 hphCG. For RNA-seq of mESC samples, plasmids were transfected into mESCs using Lipofectamine 2000.  For RNA-seq of SCNT embryos, MII oocytes were enucleated, and the nuclei of cumulus cells were placed into ooplasm. SCNT embryos were then injected with 10 ng/µl of Obox3 or EGFP mRNA. For CUT&RUN, mESCs were collected at 24 hours after the transfection of pPB-CAG-3xFLAG-Obox3-2A-Puro or pPB-CAG-2A-puro control plasmid.

value: Zygote

value: wild-type


title: Tet3_wildtype_RNAseq_rep3


title: TSA Zygote EU+ RNA rep1


title: A-485 Zygote EU+ RNA rep2


title: A-485 Zygote EU+ RNA rep1


title: DMSO Zygote EU+ RNA rep1


title: DMSO Zygote EU+ RNA rep2


title: Blastocyst unlabeled RNA rep2

value: Blastocyst


title: Blastocyst unlabeled RNA rep1


title: Morulal unlabeled RNA rep2

value: Morula


title: NSG-mdx control Replicate 3

description:
MDX_PBS_19353
MDX_PBS_19353


title: Morula unlabeled RNA rep1


title: 8-cell unlabeled RNA rep1


title: 8-cell unlabeled RNA rep2


title: 4-cell unlabeled RNA rep1


title: 4-cell unlabeled RNA rep2


title: NSG-mdx control Replicate 1

description:
MDX_PBS_19350
MDX_PBS_19350


title: Tet3_knockout_RNAseq_rep2


title: Aphidicolin late 2-cell unlabeled RNA rep1

value: Late 2-cell


title: Late 2-cell unlabeled RNA rep3


title: Aphidicolin late 2-cell unlabeled RNA rep2


title: freshly isolated hepatocytes, replicate 2

value: liver

value: Hepatocyte

value: WT


title: Late 2-cell unlabeled RNA rep2


title: Late 2-cell unlabeled RNA rep1


title: Early 2-cell unlabeled RNA rep2

value: Early 2-cell


title: Early 2-cell unlabeled RNA rep3


title: monolayer cultured hepatocytes for 1 day, replicate 3

value: in vitro monolayer culture condition


title: Early 2-cell unlabeled RNA rep1


title: Zygote unlabeled RNA rep2


title: Blastocyst EU+ RNA rep2


title: Zygote unlabeled RNA rep1


title: Blastocyst EU+ RNA rep1


title: Zygote unlabeled RNA rep3


title: Morulal EU+ RNA rep2


title: Morula EU+ RNA rep1


title: 8-cell EU+ RNA rep2


title: 4-cell EU+ RNA rep2


title: Aphidicolin late 2-cell EU+ RNA rep2


title: 8-cell EU+ RNA rep1


title: Aphidicolin late 2-cell EU+ RNA rep1


title: Late 2-cell EU+ RNA rep3


title: Zygote EU+ RNA rep3


title: Zygote EU+ RNA rep2


title: Late 2-cell EU+ RNA rep1


title: Early 2-cell EU+ RNA rep2


title: Late 2-cell EU+ RNA rep2


title: Early 2-cell EU+ RNA rep3


title: Early 2-cell EU+ RNA rep1


title: Zygote EU+ RNA rep1


title: MII oocyte total RNA rep1

data_processing:
For LET-seq and RNA-seq data, paired-end reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore! with a ‘--clip_R2 3’ option. After the reads were aligned, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts (version 1.6.5) and GENCODE annotation of the mm10 mouse genome (vM25) was used to analyze transcription levels with options ‘-p -O --fraction’. bigWig files were generated by deeptools bamCoverage with options '-bs 25 --normalizeUsing RPKM -ignore chrX chrM chrY --smoothLength 75'. The expression of each annotated gene was quantified by calculating TPM (transcripts per million) using R.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with options  ‘-X 700 --dovetail’ after removing adaptor sequences and low-quality reads by Trim Galore!. bigWig files were generated by bamCoverage from deepTools with parameters ‘-bs 50 --normalizeUsing RPKM --smoothLength 500’. MACS2 was used to call peaks with options ‘-q 0.05 -f BAMPE’.
Assembly: mm10
Supplementary files format and content: bigWig, tab-delimited text files indicating TPM values (for RNA-seq)

value: Oocyte


title: heart biopsy: 3221

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: heart biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: heart biopsy

tag: lowlvef (yes, no)

value: no


title: MII oocyte total RNA rep2


title: heart biopsy: 2553


title: PR8 influenza control

city: Columbus

first: Amy

last: Lovett-Racke

state: Ohio

address: 460 W. 12TH AVE

department: Microbial Infection & Immunity

institute: Ohio State Wexner Medical Center

data_processing:
Binary Base call (BCL) files were converted into FASTQ files through Cell Ranger software (10x Genomics Cell Ranger 6.1.2).
Cell Ranger trimmed adapters and primer sequences, mapped reads to the mm10 reference genome, and quantified expression levels.
Assembly: mm10
Supplementary files format and content: Barcodes, features, matrix

source_name: Spleen

extract_protocol:
Splenic B cells were isolated from wild-type B10.PL mice using negative magnetic bead isolation
Library was prepared by GeneWiz Azenta Life Sciences

value: Spleen

value: B cells

value: PR8 influenza


title: PBS control

value: PBS


title: heart biopsy: 2551


title: MHV68, replicate 1


title: heart biopsy: 2550


title: heart biopsy: 2547


title: NSG control Replicate 2

description:
NSG_PBS_19173
NSG_PBS_19173

value: Skeletal muscle

value: CTX + PBS


title: heart biopsy: 2548


title: heart biopsy: 2546


title: heart biopsy: 2545


title: heart biopsy: 2543


title: heart biopsy: 2544


title: heart biopsy: 2542


title: heart biopsy: 2540

value: yes


title: heart biopsy: 2537


title: heart biopsy: 2538


title: heart biopsy: 2536


title: heart biopsy: 2534


title: heart biopsy: 2539


title: MHV68, replicate 2

value: wild-type


title: heart biopsy: 2533


title: heart biopsy: 2531


title: heart biopsy: 2552


title: heart biopsy: 2530


title: heart biopsy: 2527


title: heart biopsy: 2521


title: heart biopsy: 2529


title: heart biopsy: 2528


title: heart biopsy: 2549


title: heart biopsy: 2532


title: heart biopsy: 2520


title: heart biopsy: 2513


title: heart biopsy: 2517


title: heart biopsy: 2523


title: heart biopsy: 2494


title: heart biopsy: 2493


title: heart biopsy: 2541


title: heart biopsy: 2495


title: heart biopsy: 2535


title: heart biopsy: 2503


title: heart biopsy: 2490


title: heart biopsy: 2481


title: heart biopsy: 2485


title: heart biopsy: 2482


title: heart biopsy: 2480


title: heart biopsy: 2479


title: heart biopsy: 2477


title: heart biopsy: 2478


title: heart biopsy: 2474


title: heart biopsy: 2473


title: heart biopsy: 2475


title: heart biopsy: 2470


title: heart biopsy: 2472


title: heart biopsy: 2468


title: heart biopsy: 2511


title: heart biopsy: 2471


title: heart biopsy: 2489


title: heart biopsy: 2467


title: heart biopsy: 2512


title: heart biopsy: 2466


title: heart biopsy: 2464


title: heart biopsy: 2463


title: heart biopsy: 2462


title: heart biopsy: 2476


title: heart biopsy: 2460


title: heart biopsy: 2456


title: heart biopsy: 2458


title: heart biopsy: 2452


title: heart biopsy: 2457


title: heart biopsy: 2469


title: heart biopsy: 2454


title: heart biopsy: 2449


title: heart biopsy: 2448


title: heart biopsy: 2445


title: heart biopsy: 2447


title: heart biopsy: 2450


title: heart biopsy: 2465


title: heart biopsy: 2442


title: heart biopsy: 2453


title: heart biopsy: 2441


title: heart biopsy: 2444


title: heart biopsy: 2434


title: heart biopsy: 2443


title: heart biopsy: 2461


title: heart biopsy: 2432


title: heart biopsy: 2440


title: heart biopsy: 2431


title: heart biopsy: 2455


title: heart biopsy: 2430


title: heart biopsy: 2429


title: 4-cell EU+ RNA rep1


title: heart biopsy: 2451


title: heart biopsy: 2428


title: heart biopsy: 2446


title: heart biopsy: 2423


title: heart biopsy: 2425


title: heart biopsy: 2424


title: heart biopsy: 2427


title: heart biopsy: 2439


title: heart biopsy: 2422


title: heart biopsy: 2421


title: heart biopsy: 2419


title: heart biopsy: 2420


title: heart biopsy: 2417


title: heart biopsy: 2418


title: heart biopsy: 2426


title: heart biopsy: 2416


title: heart biopsy: 2415


title: heart biopsy: 2410


title: heart biopsy: 2414


title: heart biopsy: 2459


title: heart biopsy: 2409


title: heart biopsy: 2412


title: heart biopsy: 2413


title: heart biopsy: 2411


title: heart biopsy: 2408


title: heart biopsy: 2406


title: heart biopsy: 2405


title: heart biopsy: 2407


title: heart biopsy: 2404


title: heart biopsy: 2402


title: heart biopsy: 2403


title: heart biopsy: 2401


title: heart biopsy: 2398


title: heart biopsy: 2433


title: heart biopsy: 2397


title: heart biopsy: 2394


title: heart biopsy: 2395


title: heart biopsy: 2396


title: heart biopsy: 2391


title: heart biopsy: 2390


title: heart biopsy: 2389


title: heart biopsy: 2388


title: heart biopsy: 2386


title: heart biopsy: 2385


title: heart biopsy: 2384


title: heart biopsy: 2381


title: heart biopsy: 2380


title: heart biopsy: 2387


title: heart biopsy: 2382


title: heart biopsy: 2377


title: heart biopsy: 2383


title: heart biopsy: 2378


title: heart biopsy: 2372


title: heart biopsy: 2379


title: heart biopsy: 2369


title: heart biopsy: 2370


title: heart biopsy: 2371


title: heart biopsy: 2368


title: heart biopsy: 2367


title: heart biopsy: 2366


title: heart biopsy: 2365


title: heart biopsy: 2400


title: heart biopsy: 2364


title: heart biopsy: 2363


title: heart biopsy: 2362


title: heart biopsy: 2360


title: heart biopsy: 2356


title: heart biopsy: 2355


title: heart biopsy: 2352


title: heart biopsy: 2348


title: heart biopsy: 2347


title: heart biopsy: 2350


title: heart biopsy: 2346


title: heart biopsy: 2345


title: heart biopsy: 2344


title: heart biopsy: 2349


title: heart biopsy: 2351


title: heart biopsy: 2342


title: heart biopsy: 2338


title: heart biopsy: 2333


title: heart biopsy: 2330


title: heart biopsy: 2322


title: heart biopsy: 2321


title: heart biopsy: 2343


title: heart biopsy: 2324


title: heart biopsy: 2359


title: heart biopsy: 2319


title: heart biopsy: 2320


title: heart biopsy: 2318


title: heart biopsy: 2358


title: heart biopsy: 2357


title: heart biopsy: 2361


title: heart biopsy: 2317


title: heart biopsy: 2313


title: heart biopsy: 2312


title: heart biopsy: 2311


title: heart biopsy: 2339


title: heart biopsy: 2309


title: heart biopsy: 2310


title: heart biopsy: 2305


title: heart biopsy: 2306


title: heart biopsy: 2334


title: heart biopsy: 2307


title: heart biopsy: 2308


title: heart biopsy: 2299


title: heart biopsy: 2298


title: heart biopsy: 2304


title: heart biopsy: 2294


title: heart biopsy: 2327


title: heart biopsy: 2297


title: heart biopsy: 2290


title: heart biopsy: 2292


title: heart biopsy: 2293


title: heart biopsy: 2291


title: heart biopsy: 2283


title: heart biopsy: 2288


title: heart biopsy: 2286


title: heart biopsy: 2282


title: heart biopsy: 2285


title: heart biopsy: 2289


title: heart biopsy: 2271


title: heart biopsy: 2284


title: heart biopsy: 2267


title: heart biopsy: 2265


title: heart biopsy: 2258


title: heart biopsy: 2255


title: heart biopsy: 2243


title: heart biopsy: 2257


title: heart biopsy: 2269


title: heart biopsy: 2212


title: heart biopsy: 2215


title: heart biopsy: 2143


title: heart biopsy: 2144


title: heart biopsy: 2137


title: heart biopsy: 2140


title: heart biopsy: 2951


title: heart biopsy: 2136


title: heart biopsy: 2247


title: heart biopsy: 2135


title: heart biopsy: 2197


title: heart biopsy: 2134


title: heart biopsy: 2022


title: heart biopsy: 2222


title: heart biopsy: 1585


title: heart biopsy: 1586


title: heart biopsy: 1589


title: heart biopsy: 1587


title: heart biopsy: 1584


title: heart biopsy: 1588