title: AMO1 P19 OE

city: Boston

first: TENGTENG

last: YU

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
The sequencing libraries were clustered on a single lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequencing adapters and low-quality bases were trimmed using Trimmomatic 0.38
MACS2 2.1.2 was used for peak calling to identify open chromatin regions. Valid peaks from each group or condition were then merged and peaks called in at least 66% of samples were kept for downstream analyses
Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
Assembly: hg38
Supplementary files format and content: peaks.xls

source_name: Blood

growth_protocol: AMO1 cells  were grown in RPMI-1640 (Invitrogen,Carlsbad, CA) with 10% fetal bovine serum (Hyclone, Logan, UT), 2 mM/L L-glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (Invitrogen).

extract_protocol:
Live cell samples were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

treatment_protocol: They were transfected with PCDH-empty vector and vector with PHF19 plasmids separately

value: Blood

value: Multiple Myeloma

value: PHF19 overexpression

value: PHF19 plasmids transfection


title: AMO1 ctrl

status: Public on Jan 31 2023

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: empty vector transfection


title: 80dpi split-seq library 3

city: London

first: Athanasios

last: Dimitriadis

address: 33 Cleveland Street

country: United Kingdom

institute: MRC Prion Unit at UCL

description: SPLiT-seq

library_source: transcriptomic single cell

data_processing:
The fastq files were aligned to the mouse genome using STAR aligner. The resulting sam files were converted to a binary format and were processed by the SPLiT-seq bioinformatics open-source tools (https://github.com/yjzhang/split-seq-pipeline) to generate a count matrix. Transcriptome GRCm39 (mm39) was used for aligning the mouse data. The count matrix generated was used as an input for the subsequent analyses.
Assembly: mm39
Supplementary files format and content: comma-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Brain frontal lobe

extract_protocol:
Flash-frozen mouse brain was left to partially thaw. The olfactory bulb removed, and a small slice of the frontal cortex was cut and transferred to a glass 2 mL dounce tissue homogenizer on ice. All following steps were carried out on ice and using ice-cold solutions. All centrifugation steps were performed at 500 g for 5 minutes at 4oC using a pre-chilled centrifuge, unless otherwise specified. 2 mL of Nuclei EZ prep was added, and tissue was homogenised using 20 strokes of the loose and 20 strokes of the tight pestle. The suspension was transferred to a 15 mL tube and 2 mL of Nuclei EZ prep was added. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, 4 mL of Nuclei EZ prep was added, and the pellet was resuspended using a P1000 pipette. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, and the pellet was resuspended in 4 mL Nuclei Suspension Buffer (NSB; 1x PBS, 0.01% BSA (Cambridge Bioscience; 227-10210) and 0.1% NxGen RNAse inhibitor (Lucigen; 30281-2)). The suspension was centrifuged, the supernatant discarded, and the pellet resuspended in 1 mL NSB. The suspension was filtered through a 35 um filter (Fisher Scientific; 10585801), and stored on ice. For nuclei fixation, 3 mL of 1.33% formalin solution were added to the 1 mL of nuclei suspension. The suspension was incubated on ice for 10 minutes. 169 uL of 5% Triton-X was added to the fixed nuclei, the solution was mixed by pipetting and then incubated on ice for 3 minutes. Nuclei were centrifuged at 500g for 5 minutes at 4oC, supernatant was discarded, and the pellet was resuspended in 500 uL cold NSB. 500 uL of cold 100 mM Tris and 20 uL of 5% Triton-X were added. Nuclei were centrifuged again under the same conditions; supernatant was discarded, and the pellet was resuspended in 400 uL of cold 0.5X PBS. Nuclei were filtered through a 35 um filter, counted using a Neubauer-Improved haemocytometer, and diluted to a final concentration of 2000 nuclei/uL using cold 0.5x PBS supplemented with 0.2 units/uL SUPERase In RNAse inhibitor. The nuclei were stored frozen at -80oC until library preparation.
Sequencing libraries from the mouse brain samples were prepared using the SPLiT-seq protocol (version 3) (Rosenberg et al. 2018). A summary of the methodology and optimisations is given below.
For the reverse transcription, 4 uL the first 24 wells of Stock plate 1 were transferred to a new PCR plate on ice. 8 uL of RT mix (per reaction: 4 uL Maxima 5x RT buffer, 0.124 uL NxGen RNAse inhibitor, 0.25 uL SUPERase In, 1 uL 10 mM Takara dNTPs, 2 uL Maxima H minus enzyme, 0.625 uL H2O) was added to each well and then 8 uL of fixed nuclei suspension. The plate was placed in a thermocycler and PCR was carried out as per protocol instructions. All wells were then pooled together, Triton-X was added to a final concentration of 0.1% and suspension was centrifuged for 3 minutes at 500g. The supernatant was discarded, and nuclei were resuspended in 2 mL 1x NEBuffer 3.1 (New England Biolabs; B7203S) + 20uL NxGen RNase Inhibitor.
For ligation round 1, the ligation mix (1337.5 uL water, 500 uL 10x T4 ligase buffer (included with ligase enzyme), 100 uL T4 DNA Ligase (New England Biolabs; M0202L), 100 uL BSA 10 mg/mL, 12.5 SUPERase In, 40 uL NxGen RNAse inhibitor) was added to the nuclei suspension and into a basin. 40 uL of the suspension were pipetted in each well of the Ligation round 1 barcode plate and the plate was incubated in a plate shaker at 37oC for 30 minutes and 300 rpm rotation. Then 10 uL of the Ligation Round 1 blocking solution (316.8 uL 100 uM BC_0216, 300 uL 10x Ligase buffer, 583.2 uL water) were added to each well and the plate was incubated again under the same conditions.
For ligation round 2, the nuclei suspensions were pooled in a 15 mL Falcon and passed through a 40 um strainer to another Falcon. 100 uL T4 DNA ligase was added and the mix was transferred to a basin. 50 uL of the mix was added to each well of the Ligation Round 2 barcode plate. The plate was incubated as previously. Then 20 uL of the Ligation Round 2 blocking solution (369 uL 100 uM BC_0066, 800 uL 0.5 M EDTA, 2031 uL water) was added to each well. The wells were pooled in a 15 mL Falcon and passed through a 40 um strainer into another Falcon.
70 uL 10% Triton-X was added to the mix and nuclei were centrifuged for 5 minutes at 1000g. The supernatant was aspirated, and nuclei were washed with 4 mL wash buffer (4 mL 1x PBS, 40 uL 10% Triton-X, 10 uL SUPERase In) and centrifuged again under the same conditions. Supernatant was aspirated and nuclei were resuspended in 100 uL 1x PBS + 2 uL SUPERase In. Nuclei were counted using a Neubauer-Improved haemocytometer and a desired number of them was aliquoted in each 1.5 mL Eppendorf tube. PBS was used to fill each tube up to 50 uL. Each tube is referred to as a “sublibrary”.
For nuclei lysis, 50 uL 2x lysis buffer (final concentrations: 20 mM Tris pH 8, 400 mM NaCl, 100 mM EDTA pH 8, 4.4% SDS (Thermo Fisher Scientific; AM9822)) were added to each tube followed by 10 uL 20 mg/mL Proteinase K. The mix was incubated at 55oC for 2 hours with shaking at 300 rpm. Lysates were frozen at -80oC and processed the following day.
5 uL 100 uM AEBSF (Abcam; ab141403) was used to stop proteinase reaction. Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific; 65002) were washed and used to bind the barcoded transcripts as per protocol. Beads were resuspended in 200 uL Template Switch mix (88 uL water, 44 uL 5x Maxima buffer, 44 uL 20% Ficoll PM-400, 22 uL 10 mM Takara dNTPs, 5.5 uL NxGen RNAse inhibitor, 5.5 uL 100 μM Template Switch Oligo, 11 uL Maxima H minus enzyme) and incubated at a rotating incubator at room temperature for 30 minutes and at 42oC for 1.5 hours.
The sample was then washed, resuspended in PCR mix (121 uL 2x Kapa Hifi Master Mix, 9.68 uL 10 uM BC_0108, 9.68 uL 10 uM BC_0062, water up to 242 uL) and split equally in 4 different wells of a PCR plate. The following PCR programme was then used: 3 min at 95oC, then 20 s at 98oC, 45 s at 65oC, 3 min at 72oC for a total of 5 cycles, and then hold at 4oC. Reactions were combined in a single tube, cleaned with 0.6x AMPure XP beads as per manufacturer’s instructions, eluted in 20 uL water, mixed with 180 uL of the same PCR mix and split in 4 wells (50 uL per well). 2.5 uL EvaGreen (Biotium; #31000) was added to each well and amplification continued in a QuantStudio 7 Flex qPCR machine (Thermo Fisher Scientific) until signal plateaued out of exponential amplification using the following programme: 3 min at 95oC, then 20 s at 98oC, 20 s at 67oC, 3 min at 72oC until signal plateaus out of exponential amplification, then 5 min at 72oC, hold at 4oC. Reactions were combined in a single tube, cleaned with 0.6x AMPure XP beads as per manufacturer’s instructions, eluted in 10 uL water and analysed at TapeStation 2200 using a gDNA tape.
600 pg of each sample was used for tagmentation using the Nextera XT sample prep kit using custom primers one of BC_0076-BC_0083 and BC_0118, according to manufacturer’s instructions. Resulting libraries were analysed on a TapeStation 2200 using a high sensitivity D1000 tape or a high sensitivity D5000 tape.

value: Brain frontal lobe

tag: days post_inoculation

tag: Sex

value: Female

tag: strain

value: FVB/NHan Hsd


title: 8327_PB2IC

city: Pamplona

first: Cristina

last: Perez

address: Av. Pio XII 55

country: Spain

institute: Cima Universidad de Navarra

description: SureSelectXT

data_processing:
Sample demultiplexing, alignment to the reference genome and single-cell gene count was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1 (https://www.10xgenomics.com/). Expression matrixes were analyzed with the R package seurat 4.0 (https://satijalab.org/seurat/) and cells were filtered according to < 10% mitochondrial expression and at least 200 (but less than 2500) mRNA counts per cell. Once scaled and normalized, a genelist including the most variable genes was obtained by the FindVariableFeatures function. After removing genes belonging to the immunoglobulin families (which could work as a confounding factor during clustering), the genelist was used to derive the principal component analysis (PCA) vectors for each sample. The first 100 PCA were used to align samples (batch removal) using the R package harmony. The new harmonized coordinates were used to develop UMAPs (dimensionality reduction). The shared nearest neighbor (SNN) algorithm based on 50 batch-corrected dimensions was used for clustering the cells into homogeneous groups that were manually identified according to the expression of canonical genes (see Supplemental Information) obtained from curated gene-sets. A sequential subclustering strategy (which consists basically in repeating the same steps as before on a specific subpopulation) to focus on clonotypic T cells was performed. Reconstruction of T cell trajectories was performed by ordering single cells in “pseudotime” according to their RNA expression through Monocle 2 R package. This package accurately resolves biological processes (ordering cells) by learning an explicit principal graph from the single cell genomics data through Reverse Graph Embedding algorithm.
Assembly: mm10
Supplementary files format and content: BM_T_mice.rds

source_name: bone marrow

extract_protocol:
scRNA-seq + scTCR-seq were performed in 13 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1), 3 MM (BIcɣ1), 3 MGUS (MIC) and 2 MM (MIC) bearing mice. Cells were FACS sorted (a mix of 0.8x10^5 T cells + 0.8x10^5 NK cells + 0.25x10^5 monocytes + 0.15x10^5 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
WES was performed in 71 BM samples isolated from GFP+ CD138+B220− PCs (purity, >99%), including 62 samples from the MM stage, 3 samples of pooled PCs from nine mice at the MGUS stage (3 mice with similar genotype were included on each pooled sample), and 6 samples from MM-derived cell lines. As MM reference controls, 5TGM1 and 12598Vk*Myc cell lines were also characterized.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Of note, according to TCR-seq protocol from manufacturer, we further sequenced (after specific amplification) CDR3 sequences from each CD3+ T cells.
scRNA-seq, scTCR-seq, WES

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells


title: IFNAMO1 P19 OE


title: 8799_CMAFB2IKC

description: SureSelectXT

value: MafBIc


title: IFNAMO1 ctrl


title: 8273

description: SureSelectXT


title: 8991_MIC

description: SureSelectXT

value: MIc


title: WT rep1

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

library_source: transcriptomic

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with  normalized counts for each sample and each gene, includes gene annotations
Supplementary_files_format_and_content: csv file with raw counts for each sample and each gene

molecule: polyA RNA

source_name: lung

extract_protocol:
TRIzol RNA extraction from lung tissue.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

value: lung

tag: infection

tag: time

value: 2 day post infection


title: 779450

city: Birmingham

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

department: Pediatrics

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using bcl2fastq v2.18.12
Raw sequence files were trimmed using Trim Galore (version 0.6.0) using parameters --paired --trim1 --trim-n
Trimmed sequence files were aligned using STAR (version 2.7.4a) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from alignment files using HTSeq-count (version 0.11.1) using parameters -m union -r pos - t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used for normalization and pairwsie differential expression following the authors vignette
Assembly: Gencode GRCh38 p7 Release 25
Supplementary files format and content: tab-delimited txt file containing Ensembl ID #s for each gene in each sample

source_name: Whole Blood

extract_protocol:
RNA was isolated using the PAXgene whole blood RNA kit (Qiagen Inc).
Poly-adenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 beads. Libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina Inc). Each library was pair-end sequenced  by using the TruSeq SBS Kit v4-HS (Illumina, Inc.), on a Illumina platform
Poly(A) RNA selection RNA-Seq

value: Whole Blood

value: Male

value: Case


title: 40dpi split-seq library 3

description: SPLiT-seq


title: 8332_PB2IC

description: SureSelectXT


title: 6538_B2IC

description: SureSelectXT

value: BIc


title: 56393


title: 20dpi split-seq library 2

description: SPLiT-seq


title: 40dpi split-seq library 2

description: SPLiT-seq


title: 20dpi split-seq library 3

description: SPLiT-seq


title: 775079

value: Control


title: 74123


title: 40dpi split-seq library 1

description: SPLiT-seq


title: 6172_PB2IC

description: SureSelectXT


title: 5764

description: SureSelectXT


title: 5937_B2IC

description: SureSelectXT


title: 775580


title: 20dpi split-seq library 1

description: SPLiT-seq


title: 776913


title: 5749_B2IC

description: SureSelectXT


title: 776390


title: 63088


title: 5719

description: SureSelectXT


title: 716585


title: 5TGM1

description: SureSelectXT


title: 5283_PB2IC

description: SureSelectXT


title: 8120_CMAFB2IC

description: SureSelectXT


title: CXN ciRS-7 KO5 OGD

city: Kuopio

first: Flavia

last: Scoyni

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Sequences have been aligned and quantified to the mouse genome of reference mm10 using the nf-core workflow (1.1.0 version of "smrnaseq" applied without clipping and the three prime adapter "AGATCGGAAGAGCACACGTCT").
Count data were prepared following the workflow defined by Law et al. We filtered out lowly expressed molecules in any condition using the function "filterByExpr" to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for batch effect due to different timings in biological replicates preparation by performing a principal component analysis and unsupervised consensus clustering with Cola. We adjusted the variance between the samples as before (10.1038/npp.2017.164) through winsorization.
Assembly: mm10
Supplementary files format and content: filtered and normalized log cpm count

source_name: cortices

growth_protocol: Cortical neurons isolated from E15 murine cortices grown for 7 days in Neurobasal (Gibco 21103049), B27 Supplement (Gibco, 17504044), 0.2 mM L-glutamine (Lonza, BE17-605E), 0.01 mg/ml Penicillin/Streptomycin (Gibco, 15140122)

extract_protocol:
RNA extraction was performed with TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions. RNA samples were treated with TURBO DNA-free™ Kit (Ambion) following the manufacture’s instruction before library preparation.
RNA libraries for miRNA-seq were prepared using NEBNext® Small RNA Library Prep Set for Illumina (New England Biolabs (UK) Ltd) size selected using pippin prep method following manufacturer's protocols.

treatment_protocol:
Media was changed to Normoxic (in cortical neurons growth media with Neurobasal changed to Gibco A2477501 supplemented with D-Glucose 25mM and Sodium Pyruvate 0.2mM) or OGD (Cortical Neurons Media with Neurobasal changed to Gibco A2477501). Normoxic cells were then put back in the incubator, OGD cells were incubated in hypoxic chamber 37 °C, 5%CO2, 1%O2 for 12h.
Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)

value: cortices

value: Primary cortical neurons

tag: age

value: ciRS-7 KO

value: Oxygen and glucose deprivation

value: Day 7 differentiation, 12h treatment


title: 751480


title: CXN ciRS-7 KO4 OGD


title: CXN ciRS-7 KO3 OGD


title: 774565


title: 776171

value: Female


title: 5263_B2IC

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells


title: 5170_B2IKC

description: SureSelectXT

value: tumor plasma cells

value: KrasBIc


title: CXN ciRS-7 KO2 OGD


title: 763534


title: 774771


title: 763174


title: 5064

description: SureSelectXT


title: 5080

description: SureSelectXT


title: 4098_B2IC

description: SureSelectXT


title: 74476


title: CXN ciRS-7 KO1 OGD


title: CXN ciRS-7 KO3 N

treatment_protocol:
Media was changed to Normoxic (in cortical neurons growth media with Neurobasal changed to Gibco A2477501 supplemented with D-Glucose 25mM and Sodium Pyruvate 0.2mM) or OGD (Cortical Neurons Media with Neurobasal changed to Gibco A2477501). Normoxic cells were then put back in the incubator, OGD cells were incubated in hypoxic chamber 37 °C, 5%CO2, 1%O2 for 12h.
Normoxia (5%CO2, 37C, Glucose +)

value: Normoxia


title: 767465


title: 3672_MMSETB2IC

description: SureSelectXT

value: MmsetBIc


title: 772270

value: Whole Blood


title: 3874_MMSETB2IC

description: SureSelectXT


title: CXN ciRS-7 KO2 N


title: 3410_MMSETB2IC

description: SureSelectXT


title: 79614


title: 3180_MMSETB2IC

description: SureSelectXT


title: 773560


title: CXN ciRS-7 KO5 N


title: 3197_CD1B2IC

description: SureSelectXT


title: 750698


title: KID90, gd T cells, biol rep 3

city: San Francisco

first: Marcel

last: Arias Badia

address: 513 Parnassus Ave

institute: UCSF

data_processing:
The bulk RNA was used in the Demuxlet pipeline to perform SNP-based doublet removal and demultiplexing of pooled scRNA samples. ( https://github.com/statgen/demuxlet ) In short, the fastqs were first concatenated to create one aggregate file for each patient. FastQC and trim-galore were used to trim low quality ends and adapaters from the fastqs. A (STAR) index was created and aligned to the hg38 human genome build. BAMs were sorted and indexed using samtools. SNPs were called using GATK. VCFs were merged and filtered (using GATK). Finally the merged VCF was used by Demuxlet to generate a mapping used to demultiplex (and remove doublets from) scRNA data generated using the same tumor samples. (Tab-delimited matrices reporting complete abundance metrics were not generated.)
Assembly: hg38
Supplementary files format and content: Variant Call Format (VCF) file with single-nucleotide polymorphism (SNP) data for each patient in our dataset. SNP data from a 7th patient whose scRNAseq data was not analyzed in our study has been redacted.

source_name: Renal cell carcinoma

extract_protocol:
Surgical specimens were obtained fresh from the operating field, and dissected in surgical pathology, where tumors were isolated, minced, and transported at room temperature immersed in L15 media with 15 mM HEPES and 600 mg/mL glucose. Resected tumor kidney tissues were further minced using surgical scissors in GentleMACs C Tubes (Miltenyi Biotec) containing RPMI-1640 media with 0.1 mg/mL of Liberase TL and 0.2 mg/mL of DNAse I. Samples were then simultaneously mechanically and enzymatically digested for 1 hour at 37C using a GentleMACS dissociator (Miltenyi Biotec), according to the manufacturer TDK-1 tumor protocol. The digestion reaction was quenched with FACS-buffer (PBS buffer supplemented with 2% heat-inactivated FCS and 2 mM EDTA) and filtered through a 100 μm cell strainer. Samples were resuspended in a 155 mM NH4Cl solution to lyse all erythrocytes and washed in FACS-buffer. Finally, the samples were either frozen for storage or resuspended for flow cytometry staining or RNAseq.
RNA libraries for RNA-seq were prepared according the Smart-seq2 protocol. ( https://www.nature.com/articles/nprot.2014.006 )

value: Renal cell carcinoma

value: Live gd T cells


title: CXN WT4 OGD

value: WT


title: CXN WT5 OGD


title: KID90, gd T cells, biol rep 2


title: CXN ciRS-7 KO4 N


title: KID90, gd T cells, biol rep 1


title: 700704

value: Control


title: CXN WT3 OGD

value: cortices


title: 748196

value: Case


title: CXN WT2 OGD

value: Primary cortical neurons


title: 4 months old young WT natural Treg [PN0185_S14_Young]

city: Belfast

first: Denise

last: Fitzgerald

address: 97 Lisburn Rd

institute: QUB

data_processing:
Data quality checked with FasQC and quality trimming performed with CutAdapt
Trimmed data was mapped on GRCm38/ mm10 mouse genome using STAR aligner (v2.7.0a)
Read count extraction was performed using feature Counts tool *v.2.00) and the red counts matrix analysed using DESeq2 (v1.38.1)
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: Spleen and Lymph Nodes

growth_protocol: Freshly isolated, no growth protocol

extract_protocol:
Cells were lysed in Trizol and then RNA harvested with RNAeasy micro kit (Qiagen) upon trizol chloroform separation step.
Libraries were constructed using the kapa Hyper preparation with riboerase kit.

treatment_protocol: Freshly isolated, no treatment

value: Spleen and Lymph Nodes

value: Natural Tregs

value: 4 months old young


title: 4 months old young WT natural Treg [PN0185_S6_Young]


title: CXN ciRS-7 KO1 N

value: ciRS-7 KO

value: Day 7 differentiation, 12h treatment


title: 771956

value: Male


title: KID90, CD8 T cells, biol rep 1

value: Live CD8 T cells


title: 735331


title: 4 months old young WT natural Treg [PN0185_S5_Young]


title: CXN WT1 OGD

value: Oxygen and glucose deprivation


title: 3173_CD1B2IC

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells


title: 113725

value: Whole Blood

value: Female


title: CXN WT5 N

value: WT

value: Normoxia


title: 768906

value: Case


title: 4 months old young WT natural Treg [PN0185_S4_Young]


title: KID90, CD8 T cells, biol rep 2

value: Renal cell carcinoma


title: KID21, gd T cells, biol rep 3

value: Live gd T cells


title: 18 months old aged WT natural Treg [PN0185_S12_Aged]

value: Spleen and Lymph Nodes

value: Natural Tregs

value: 18 months old aged


title: KID21, gd T cells, biol rep 2


title: 767001


title: 22 months old aged WT natural Treg [PN0185_S11_Aged]

value: 22 months old aged


title: KID21, gd T cells, biol rep 1


title: CXN WT4 N

value: cortices

value: Primary cortical neurons

value: Day 7 differentiation, 12h treatment


title: CXN WT3 N


title: 753223


title: CXN WT2 N


title: 716814


title: CXN WT1 N


title: 16 months old aged WT natural Treg [PN0185_S10_Aged]

value: 16 months old aged


title: KID90, CD4 T cells, biol rep 1

value: Live CD4 T cells


title: 105181


title: 22 months old aged WT natural Treg [PN0185_S9_Aged]


title: KID21, CD8 T cells, biol rep 2

value: Live CD8 T cells


title: 765904

value: Whole Blood


title: KID21, CD8 T cells, biol rep 1


title: 22 months old aged WT natural Treg [PN0185_S8_Aged]


title: KID90, CD4 T cells, biol rep 2


title: 22 months old aged WT natural Treg [PN0185_S13_Aged]


title: KID21, CD4 T cells, biol rep 2


title: 747736

value: Female

value: Control


title: 765414

value: Male


title: KID19, gd T cells, biol rep 3


title: KID21, CD4 T cells, biol rep 1


title: KID19, gd T cells, biol rep 2


title: 762936

value: Case


title: 763792


title: KID19, gd T cells, biol rep 1

value: Renal cell carcinoma


title: 601410


title: LymphNode_sick_mouse_7_CIA

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

country: Sweden

institute: Linköping University

data_processing:
The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software.
Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCh38 (April 2017, Ensembl) using STAR software. Only cells with > 10,000 reads per cell was extracted. Note: none of the cells from Liver or Kidney passed these quality controls, and are thus excluded from further analysis.
Quality control, where cells with less than 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out.
The UMI count data was knn-smoothed, using a k = 12, as described by Wagner et al (doi: https://doi.org/10.1101/217737).
Assembly: mm9
Supplementary files format and content: comma-separated UMI counts expression matrix for pilot study (knn smoothed, >10,000 reads, > 200 genes, > 400 transcrits, & < 20% mitochondrial genes per cell)

source_name: LymphNode

extract_protocol:
All disected organ samples were cryopreserved in 10% DMSO and 90% FBS until further analysis. For sequencing, the samples were quickly thawed in a 37 ºC water bath with continuous agitation, then transferred into 15 mL centrifuge tube with 1 mL pre-warmed thaw solution (90% Hibernate-A and 10% FBS) and incubated at room temperature for 1 minute. Then 2 mL, 5 mL and 5 mL thaw solution were added into the centrifuge tube, separated by a 1-minute incubation. Next, the samples were centrifuged at 350 × g for 5 minutes. Lastly, the samples were resuspended with 1 mL Hibernate-A, after which the supernatant was removed and incubated until next step.   Samples from spleen were squeezed to pass through 70 µm strainer to collect cells in a 50 mL centrifuge tube. After being centrifuged at 350g for 5 minutes, cells were resuspended with 5mL red blood cell lysis buffer for 5 minutes. Lysis reaction was quenched by adding medium (90% RPMI-1640 with 10% FBS). Cells were centrifuged at 350 × g for 5 minutes and washed thrice to remove the lysis buffer. Single cells suspensions were prepared by RPMI-1640 at a density of 1 × 105 cells/mL. Samples from joint, muscle, lung, and skin were quickly transferred into 75mm dishes with 1mL DMEM after thawing, and then minced into ~1mm pieces with scissors. Next, pieces of organ samples were transferred into 15 mL centrifuge tube with 5 mL of DMEM and treated with enzymes (joint: 1.5 mg/mL Collagenase Ⅳ / DnaseⅠ; lung: 1.8 mg/mL Collagenase Ⅳ / DnaseⅠ; muscle: 2 mg/mL Collagenase Ⅱ / DnaseⅠ; skin: 2.6 mg/mL Collagenase Ⅰ/ DnaseⅠ) for 120 minutes. After dissociation, another 5 mL DMEM with 10% FBS was added into the 15mL centrifuge tubes. Then dissociated cells were centrifuged at 350 × g for 5 minutes after passing through 70 µM strainer, after which the cells were washed thrice with PBS. Single cells were re-suspended into RPMI-1640 at a density of 1 × 105 cells/mL for cell loading. All scRNA-seq experiments were then performed using the Seq-Well technique (Gierahn et al., 2017). Briefly, single cell suspensions were counted and co-loaded with barcoded and functionalized oligo-dT beads (Chemgenes, USA; cat. no. MACOSKO-2011-10) on microwell arrays. For each sample, 20,000 live cells were loaded per array, and libraries from three samples were pooled together for sequencing, resulting in a coverage of 6,6 reads per base. The microwell arrays were then covered with previously plasma treated polycarbonate membranes, and the membranes were allowed to seal to the bead and cell co-loaded microwell arrays at 37°C for 30 minutes. Next, cell lysis and hybridization were performed, followed by bead removal, reverse transcription, and whole transcriptome amplification. Libraries were prepared for each sample using the Nextera XT DNA Library Preparation Kit (Illumina, USA; cat. no. FC-131-1096) according to manufacturer’s instructions.
Libraries were prepared from GRCm38 (June 2017, Ensembl) using STAR software.

treatment_protocol: Organ samples were taken from male DBA1/J 6 CIA and 4 healthy mice. The CIA mice were immunized with 100 µg (50µL) bovine collagen II (BC-II, Chondrex, USA) emulsified with 50µL Complete Freund’s Adjuvant (CFA) (Sigma-Aldrich, USA) in 1:1 ratio, via intradermal injection near the base of the tail. A booster immunization was administered on day 20 with 100 µg of BC-II emulsion (prepared with 1:1 incomplete Freund’s adjuvant (IFA)) and injected at the base of the tail. The severity of arthritic limbs was scored on 0-4 scale, 0: Normal, 1: Swelling and redness in one digit, 2: Swelling and redness in more than one digits or swelling and redness in one digit, wrist joint and ankle, 3: Swelling and redness present in paw and digits, 4: maximum inflammation of limb involving all joints and digits.

value: LymphNode

tag: mouse id

tag: disease state

value: Sick

tag: arthritis score

value: male


title: KID19, CD8 T cells, biol rep 2


title: 56119


title: LymphNode_healthy_mouse_7_CIA

value: Healthy


title: KID19, CD4 T cells, biol rep 2


title: KID19, CD4 T cells, biol rep 1


title: DHRS4-AS1-BESST-KO replicate 4

city: Shenzhen

first: Shikuan

last: Zhang

state: Guangdong

address: Tsinghua Shenzhen International Graduate School, University Town of Shenzhen, Nanshan District

department: iBHE

country: China

institute: Tsinghua

data_processing:
The transcriptome sequencing and analysis were conducted by LC-Bio Technology CO., Ltd. (Hangzhou, China).
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
The average insert size for the final cDNA library was 300±50 bp.
StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM = [total_exon_fragments/mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Excel file include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Culture in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal bovine serum in humidified incubator at 37°C with 5% carbon dioxide

extract_protocol:
RNA was harvested using Trizol reagent.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: knockout target sequence by CRISPR-Cas9

value: immortalized human pancreatic duct epithelial cells

value: ko by strategy of BESST


title: KID19, CD8 T cells, biol rep 1


title: DHRS4-AS1-BESST-KO replicate 3


title: Joint_sick_mouse_1_CIA

source_name: Joint

value: Joint


title: Thymus_healthy_mouse_6_CIA

source_name: Thymus

value: Thymus


title: Blood_healthy_mouse_7_CIA

value: Blood


title: DHRS4-AS1-BESST-KO replicate 2


title: LymphNode_healthy_mouse_6_CIA


title: KID18, gd T cells, biol rep 3

value: Live gd T cells


title: DHRS4-AS1-BESST-KO replicate 1


title: KID18, gd T cells, biol rep 2


title: Blood_healthy_mouse_6_CIA


title: DHRS4-AS1-PE-KO replicate 4

value: ko by strategy of promoter-exon1


title: DHRS4-AS1-PE-KO replicate 3


title: KID18, gd T cells, biol rep 1


title: DHRS4-AS1-PE-KO replicate 2


title: KID18, CD8 T cells, biol rep 2

value: Live CD8 T cells


title: Blood_healthy_mouse_4_CIA


title: KID18, CD8 T cells, biol rep 1


title: LymphNode_sick_mouse_7_2CIA


title: DHRS4-AS1-PE-KO replicate 1


title: KID18, CD4 T cells, biol rep 2

value: Live CD4 T cells


title: WT replicate 4

value: wild type


title: KID18, CD4 T cells, biol rep 1


title: WT replicate 3


title: KID06, gd T cells, biol rep 3


title: WT replicate 2


title: KID06, gd T cells, biol rep 2


title: Blood_sick_mouse_7_2CIA


title: WT replicate 1


title: Blood_sick_mouse_6_2CIA


title: LymphNode_sick_mouse_1_2CIA


title: Thymus_sick_mouse_1_2CIA


title: LymphNode_healthy_mouse_4_CIA


title: KID06, gd T cells, biol rep 1


title: LymphNode_sick_mouse_2_2CIA


title: Joint_sick_mouse_1_2CIA (2)


title: Blood_sick_mouse_2_2CIA


title: KID06, CD8 T cells, biol rep 1


title: KID06, CD4 T cells, biol rep 2


title: KID06, CD8 T cells, biol rep 2


title: LymphNode_healthy_mouse_4_2CIA


title: Blood_healthy_mouse_4_2CIA


title: LymphNode_healthy_mouse_3_2CIA


title: KID04, gd T cells, biol rep 3


title: Blood_healthy_mouse_3_2CIA


title: KID06, CD4 T cells, biol rep 1


title: Spleen_healthy_mouse_6_CIA (2)

source_name: Spleen

value: Spleen


title: KID04, gd T cells, biol rep 1


title: DM2

city: hangzhou

first: heyangzi

last: li

state: zhejiang

address: ZheJiang Unisversity yuhang tang road

department: basic medical school

institute: ZhejiangUniversity

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome （Ensembl v101）
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Assembly: GrCM38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: myocardium

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.

value: myocardium

value: STZ injection

value: WT


title: KID04, CD8 T cells, biol rep 1

value: Renal cell carcinoma


title: Ctrl3

value: pbs injection

value: male


title: DM3


title: DM1


title: KID04, CD4 T cells, biol rep 2


title: Skin_healthy_mouse_6_CIA (2)

source_name: Skin

value: Skin

value: Healthy


title: Muscle_healthy_mouse_6_CIA (2)

source_name: Muscle

value: Muscle


title: KID04, CD4 T cells, biol rep 1


title: Lung_healthy_mouse_6_CIA (2)

source_name: Lung

value: Lung


title: KID04, CD8 T cells, biol rep 2


title: Ctrl2


title: Skin_sick_mouse_1_2CIA (2)

value: Sick


title: Muscle_sick_mouse_1_2CIA (2)


title: Spleen_sick_mouse_1_2CIA (2)


title: Spleen_sick_mouse_8_CIA

data_processing:
The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software.
Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCh38 (April 2017, Ensembl) using STAR software. Only cells with > 10,000 reads per cell was extracted. Note: none of the cells from Liver or Kidney passed these quality controls, and are thus excluded from further analysis.
Quality control, where cells with less than 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out.
Assembly: mm9
Supplementary files format and content: tab-separated UMI raw counts expression matrix (>10,000 reads per cell)
Supplementary files format and content: comma separated file containing cell type identifications of those cells passing the quality control (>400 transcripts, >200 genes, and <20% mitochondrial genes per cell). The column ''CellType" contains the cell type identification from mapping the cells towards a reference, including some still unidentified cell types. The column "CellType_markers" contains the final cell type identificatiuon, after verification of previously identified cell types, and further identification  of the unidentified clusters based on marker genes. Additionally, the file contains information of the source of the cells, such as healthy/sick disease group and from which tissue/organ the cells are derived.


title: Skin_sick_mouse_8_CIA


title: KID04, gd T cells, biol rep 2

value: Live gd T cells


title: Ctrl1


title: Lung_sick_mouse_1_2CIA (2)


title: WFF_In

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
exomePeak R package (version 2.16.0) was used for the m6A peak identification
The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
GO enrichment analysis was implemented by the GOseq R package.
Assembly: mouse reference genome(GRCm38/mm10)
Supplementary files format and content: Processed data files; excel; WFF_peaks; WBKO_peaks

source_name: islet

growth_protocol: Wtapflox/flox and Wtap-βKO mice were fed with normal chow for 7 weeks.

extract_protocol:
Islets were isolated from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany).  A total of 2 μg RNAs were pooled from ten Wtapflox/flox mice and nineteen Wtap-βKO mice, respectively.
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

value: islet

tag: chip antibody

value: Wtapflox/flox


title: tMCAo 1dpi ciRS-7 KO6 PI

data_processing:
Sequences have been aligned and quantified to the mouse genome of reference mm10 with the Cdr1as annotation of "chrX:61183248|61186174|.|+" using the nf-core workflow (3.0 version of "rnaseq"), while circular sequences using 1.1 CIRIquant set to Read 1 matching the sense strand.
Count data were prepared following the workflow defined by Law et al. We filtered out lowly expressed molecules in any condition using the function "filterByExpr" to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for batch effect due to different timings in biological replicates preparation by performing a principal component analysis and unsupervised consensus clustering with Cola.
mm10

source_name: Cortex

growth_protocol: Animals were housed with same sex siblings, in controlled temperature, humidity and light (12 hours light/dark cycle) conditions. Animals had access to ad libitum food. Before the beginning of the animal study mice were divided in single cages. Mice were randomized and all the participants were blinded to the genotype

extract_protocol:
RNA extraction was performed with TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions. RNA samples were treated with TURBO DNA-free™ Kit (Ambion) following the manufacture’s instruction before library preparation.
RNA libraries for RNA-seq were prepared using CORALL total RNA-Seq Library Prep Kit (Lexogen GmbH) after ribosomal RNA depletion of 600ng of RNA with RiboCop rRNA Depletion Kit V1.2 (Lexogen GmbH)

treatment_protocol: Transient middle cerebral artery occlusion (tMCAo) was performed in 3-4 months old male. After one hour of occlusion, the monofilament was withdrawn allowing blood reperfusion.

value: Cortex

value: ciRS-7 KO6

value: transient middle cerebral artery occlusion ischemic stroke surgery

value: occlusion 1h reperfusion 1day


title: WFF_3

data_processing:
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing N  base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2  (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate .  padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly  differential expression.
Assembly: mouse reference genome(GRCm38/mm10)
Supplementary files format and content: Processed data files; excel; fpkm of each gene

extract_protocol:
Islets were isolated from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. One islet sample was combined from three mice. Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to  degrade the RNA. Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends  via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA  fragments, Adaptor with hairpin loop structure were ligated to prepare for  hybridization. In order to select cDNA fragments of preferentially 370~420 bp in  length, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the  effective concentration and the target amount of data off the machine, then being  sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is  generated. The basic principle of sequencing is to synthesize and sequence at the same  time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase  and splice primers were added to the sequenced flowcell and amplified. When the  sequence cluster extends the complementary chain, each dNTP labeled by  fluorescence can release the corresponding fluorescence. The sequencer captures the  fluorescence signal and converts the optical signal into the sequencing peak by  computer software, so as to obtain the sequence information of the fragment to be  tested.


title: Joint_healthy_mouse_3_2CIA (2)

value: Joint


title: tMCAo 1dpi ciRS-7 KO4 PI

value: ciRS-7 KO4


title: tMCAo 1dpi ciRS-7 KO5 PI

value: ciRS-7 KO5


title: WFF_IP

value: m6A antibody (Merk Millipore)


title: WbKO_2

value: Wtap-{beta}KO


title: WFF_1


title: WFF_2


title: MPTP_IRISIN_rep3

city: Shanghai

first: Xi

address: No.1239 Siping Road

institute: Tongji University

data_processing:
A cDNA library constructed by technology from the pooled RNA from midbrain samples of mouse was sequenced run with Illumina sequence platform. 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.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs were selected with |log2foldchange| ≥ 1 and p value < 0.05 by R package
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample and each gene

source_name: midbrain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: midbrain

value: male

value: Irisin delayed-treatmnt (200ug/kg/d, 5days, intraperitoneal injection) after MPTP treatment (30mg/kg/d, 5days,intraperitoneal injection)

value: 6 weeks


title: Skin_sick_mouse_6_CIA

value: Skin

value: Sick


title: WBKO_In

value: islet

value: Wtap-betaKO


title: WbKO_3


title: WBKO_IP


title: tMCAo 1dpi ciRS-7 KO2 PI

value: Cortex

value: ciRS-7 KO2


title: tMCAo 1dpi ciRS-7 KO1 PI

value: ciRS-7 KO1

value: transient middle cerebral artery occlusion ischemic stroke surgery


title: WbKO_1


title: Lung_sick_mouse_6_CIA

value: Lung


title: Lung_sick_mouse_8_CIA


title: Joint_sick_mouse_8_CIA

value: Joint


title: Spleen_sick_mouse_6_CIA

value: Spleen


title: tMCAo 1dpi ciRS-7 KO3 CL

value: ciRS-7 KO3

value: occlusion 1h reperfusion 1day


title: Muscle_sick_mouse_8_CIA

value: Muscle


title: MPTP_IRISIN_rep2

value: midbrain

value: male


title: Muscle_sick_mouse_5_CIA


title: Patient-3

city: Bern

first: Aref

last: Hosseini

address: Inselspital, INO-F

country: Swaziland

institute: university of Bern

data_processing:
The quality of the RNA-seq data was assessed using fastqc v. 0.11.9.
The reads were mapped to the reference genome using HISAT2 v. 2.2.1
FeatureCounts v. 2.0.1 was used to count the number of reads overlapping with each gene as specified in the genome annotation (Homo_sapiens.GRCh38.94)
Subsequent data analysis was performed in R v. 4.1.0. The Bioconductor package DESeq2 v. 1.32.0 was used to analyze differentially expressed genes with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count reads for each gene for each sample

extract_protocol:
Total RNA was isolated from formalin-fixed, paraffin-embedded (FFPE) lung tissues of seven patients and three non-covid infected individuals using the Maxwell® RSC RNA FFPE Kit in Maxwell® RSC Instrument (Promega, Dübendorf, Switzerland).  The quantity and quality of the extracted RNA was assessed using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Q10211) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (Agilent, DNF-471), respectively.
Ribosomal RNA was depleted from 100 ng of total RNA samples using a RiboCop for Human/Mouse/Rat (HMR) V2 kit (Lexogen,144) according to the vendors guidelines. Thereafter, sequencing libraries were produced using a Swift RNA Library Kit (Swift Biosciences, 10009985) in combination Swift Unique Dual Indexing Primers (Swift Biosciences, 10009912) and according to a technical note developed by Swift Biosciences entitled "The Swift RNA Library Kit Optimizes RNA-Seq Data Quality and Costs for FFPE RNA".

tag: tissue preparation


title: tMCAo 1dpi ciRS-7 KO2 CL


title: Patient-7


title: Patient-2


title: MPTP_IRISIN_rep1

value: Irisin delayed-treatmnt (200ug/kg/d, 5days, intraperitoneal injection) after MPTP treatment (30mg/kg/d, 5days,intraperitoneal injection)

value: 6 weeks


title: Muscle_sick_mouse_6_CIA

value: Sick


title: tMCAo 1dpi ciRS-7 KO3 PI


title: MPTP_rep3

value: MPTP treatment (30mg/kg/d, 5days,intraperitoneal injection)  before ddH2O treatment (5days, intraperitoneal injection)


title: tMCAo 1dpi ciRS-7 KO6 CL

value: ciRS-7 KO6


title: Patient-5


title: Skin_sick_mouse_5_CIA

value: Skin


title: MPTP_rep1


title: Joint_sick_mouse_6_CIA


title: IRISIN_rep1

value: ddH2O treatment (5days, intraperitoneal injection) before Irisin treatment (200ug/kg/d, 5days, intraperitoneal injection)


title: Spleen_sick_mouse_5_CIA


title: Patient-6


title: tMCAo 1dpi ciRS-7 KO5 CL

value: Cortex

value: ciRS-7 KO5


title: MPTP_rep2


title: IRISIN_rep2


title: CONTROL_rep2

value: ddH2O treatment (10days,intraperitoneal injection)


title: IRISIN_rep3


title: Patient-4

value: Lung


title: tMCAo 1dpi ciRS-7 KO4 CL

value: ciRS-7 KO4

value: transient middle cerebral artery occlusion ischemic stroke surgery


title: Joint_sick_mouse_5_CIA

value: Joint


title: Muscle_healthy_mouse_7_CIA

value: Muscle

value: Healthy


title: Spleen_healthy_mouse_7_CIA

value: Spleen

value: male


title: Lung_sick_mouse_5_CIA


title: tMCAo 1dpi ciRS-7 KO1 CL

value: ciRS-7 KO1

value: occlusion 1h reperfusion 1day


title: tMCAo 1dpi WT5 PI


title: tMCAo 1dpi WT3 PI


title: Joint_healthy_mouse_7_CIA


title: Irisin_MPTP_M_rep2

value: midbrain

value: Irisin pre-treatmnt (200ug/kg/d, 5days, intraperitoneal injection) before MPTP treatment (30mg/kg/d, 5days, intraperitoneal injection)

value: 6 weeks


title: Control-3

value: normal


title: CONTROL_rep1


title: Skin_healthy_mouse_7_CIA

value: Skin


title: CONTROL_rep3


title: tMCAo 1dpi WT6 PI

value: Cortex


title: Irisin_MPTP_M_rep3


title: Control-2


title: Control-1


title: tMCAo 1dpi WT1 PI


title: Spleen_healthy_mouse_6_CIA


title: tMCAo 1dpi WT6 CL


title: Irisin_MPTP_M_rep1


title: hepatocarcinoma tissue, replicate 60 [LR21K17DX194]

first: Qi

last: Feng

address: 180 Fenglin Street, Xuhui District

institute: Zhongshan Hospital

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.
Genome_build: 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: liver

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

tag: disease

value: liver cancer

value: hepatocarcinoma tissue

tag: Stage

value: StageII

tag: grade

value: I-II


title: Lung_healthy_mouse_7_CIA

tag: tissue

value: Lung


title: Patient-1


title: tMCAo 1dpi WT4 PI

tag: genotype

value: transient middle cerebral artery occlusion ischemic stroke surgery


title: hepatocarcinoma tissue, replicate 59 [LR21K17DX193]

value: StageIII

value: III-IV


title: hepatocarcinoma tissue, replicate 58 [LR21K17DX192]

value: male


title: Skin_healthy_mouse_6_CIA

value: Healthy


title: MPTP_M_rep3

tag: treatment

value: ddH2O treatment (5days, intraperitoneal injection) before MPTP treatment (30mg/kg/d, 5days,intraperitoneal injection)


title: tMCAo 1dpi WT2 PI

value: occlusion 1h reperfusion 1day


title: tMCAo 1dpi WT5 CL


title: MPTP_M_rep2

value: midbrain


title: tMCAo 1dpi WT3 CL


title: hepatocarcinoma tissue, replicate 56 [LR21K17DX190]


title: hepatocarcinoma tissue, replicate 55 [LR21K17DX189]

value: female


title: MPTP_M_rep1

value: 6 weeks


title: Skin_healthy_mouse_4_CIA

value: Skin


title: Spleen_healthy_mouse_4_CIA

value: Spleen


title: Control_M_rep2

value: ddH2O treatment (10days,intraperitoneal injection)


title: tMCAo 1dpi WT1 CL

value: Cortex


title: hepatocarcinoma tissue, replicate 53 [LR21K17DX187]

value: liver cancer

value: hepatocarcinoma tissue


title: hepatocarcinoma tissue, replicate 54 [LR21K17DX188]


title: Muscle_healthy_mouse_4_CIA

value: Muscle


title: Lung_healthy_mouse_6_CIA

value: Lung


title: Lung_healthy_mouse_4_CIA


title: hepatocarcinoma tissue, replicate 51 [LR21K17DX185]

value: StageIII


title: tMCAo 1dpi WT2 CL

value: transient middle cerebral artery occlusion ischemic stroke surgery


title: hepatocarcinoma tissue, replicate 57 [LR21K17DX191]

value: III-IV

value: male


title: Control_M_rep1


title: tMCAo 1dpi WT4 CL


title: Muscle_healthy_mouse_6_CIA

value: Healthy


title: Spleen_sick_mouse_3_2CIA

value: Sick


title: Skin_sick_mouse_3_2CIA


title: hepatocarcinoma tissue, replicate 50 [LR21K17DX184]


title: Joint_healthy_mouse_4_CIA

value: Joint


title: Muscle_sick_mouse_3_2CIA


title: Control_M_rep3

value: midbrain


title: hepatocarcinoma tissue, replicate 47 [LR21K17DX181]


title: hepatocarcinoma tissue, replicate 52 [LR21K17DX186]


title: Lung_sick_mouse_3_2CIA


title: hepatocarcinoma tissue, replicate 46 [LR21K17DX180]

value: female


title: hepatocarcinoma tissue, replicate 48 [LR21K17DX182]


title: Joint_sick_mouse_3_2CIA


title: hepatocarcinoma tissue, replicate 45 [LR21K17DX179]

value: StageII

value: I-II


title: Spleen_sick_mouse_2_2CIA

value: Spleen


title: hepatocarcinoma tissue, replicate 49 [LR21K17DX183]


title: Muscle_sick_mouse_2_2CIA


title: hepatocarcinoma tissue, replicate 43 [LR21K17DX177]


title: hepatocarcinoma tissue, replicate 42 [LR21K17DX176]


title: hepatocarcinoma tissue, replicate 44 [LR21K17DX178]


title: Spleen_sick_mouse_1_2CIA


title: Lung_sick_mouse_2_2CIA


title: Skin_sick_mouse_2_2CIA

value: Skin


title: hepatocarcinoma tissue, replicate 40 [LR21K17DX174]

value: liver cancer

value: StageIV


title: Muscle_sick_mouse_1_2CIA

value: Muscle


title: hepatocarcinoma tissue, replicate 38 [LR21K17DX172]

value: hepatocarcinoma tissue


title: Lung_sick_mouse_1_2CIA

value: Lung


title: hepatocarcinoma tissue, replicate 36 [LR21J8DX50]

value: StageIII


title: Joint_sick_mouse_1_2CIA


title: hepatocarcinoma tissue, replicate 37 [LR21K17DX171]

value: StageI


title: hepatocarcinoma tissue, replicate 35 [LR21J8DX49]

value: male


title: hepatocarcinoma tissue, replicate 34 [LR21J8DX48]


title: Spleen_healthy_mouse_3_2CIA

value: Healthy


title: Muscle_healthy_mouse_3_2CIA


title: Skin_healthy_mouse_3_2CIA


title: hepatocarcinoma tissue, replicate 32 [LR21J8DX46]


title: Lung_healthy_mouse_3_2CIA


title: hepatocarcinoma tissue, replicate 33 [LR21J8DX47]

value: III-IV


title: hepatocarcinoma tissue, replicate 39 [LR21K17DX173]


title: Skin_sick_mouse_1_2CIA

value: Sick


title: Joint_healthy_mouse_3_2CIA

value: Joint


title: heart, Ctrl

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38Ensembl92
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: heart

growth_protocol: C57BL/6 mice were purchased from experimental animal center of ZheJiang University.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Male mice (22-25g)  were intraperitoneal injection at a dose of 150mg/kg STZ

value: heart

value: wild type

value: untreated

value: control


title: hepatocarcinoma tissue, replicate 30 [LR21K17DX99]

value: StageII

value: I-II


title: RNA-Seq CXN ciRS-7 KO5 OGD

data_processing:
Sequences have been aligned and quantified to the mouse genome of reference mm10 with the Cdr1as annotation of "chrX:61183248|61186174|.|+" using the nf-core workflow (3.0 version of "rnaseq"), while circular sequences using 1.1 CIRIquant set to Read 1 matching the sense strand.
Count data were prepared following the workflow defined by Law et al. We filtered out lowly expressed molecules in any condition using the function "filterByExpr" to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for batch effect due to different timings in biological replicates preparation by performing a principal component analysis and unsupervised consensus clustering with Cola.
We identified a batch effect due to different timings in biological replicates preparation influencing the grouping of the normoxic and OGD samples in the dataset ciRS-7 KO/WT cortical neurons. We corrected the batch effect of this dataset using the negative binomial regression from Combat. We adjusted the variance between the samples as before (10.1038/npp.2017.164) through winsorization.
Assembly: mm10

source_name: Primary neurons

extract_protocol:
RNA extraction was performed with TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions. RNA samples were treated with TURBO DNA-free™ Kit (Ambion) following the manufacture’s instruction before library preparation.
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio USA, Inc.)  following manufacturer's protocols.

treatment_protocol: Media was changed to Normoxic (in cortical neurons growth media with Neurobasal changed to Gibco A2477501 supplemented with D-Glucose 25mM and Sodium Pyruvate 0.2mM) or OGD (Cortical Neurons Media with Neurobasal changed to Gibco A2477501). Normoxic cells were then put back in the incubator, OGD cells were incubated in hypoxic chamber 37 °C, 5%CO2, 1%O2 for 12h.

tag: cell line

value: Primary neurons

tag: cell type

value: Cortical neurons E15

value: ciRS-7 KO5

value: Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)

value: Day 7 differentiation, 12h treatment

tag: batch


title: hepatocarcinoma tissue, replicate 28 [LR21K17DX97]

value: liver cancer

value: hepatocarcinoma tissue

value: StageI

tag: Sex


title: RNA-Seq CXN ciRS-7 KO3 OGD

tag: strain

value: ciRS-7 KO3

tag: time


title: hepatocarcinoma tissue, replicate 29 [LR21K17DX98]

value: StageIII

value: III-IV

value: female

tag: age


title: A491d

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

data_processing:
a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5)
Obtained fastq files were then aligned using STAR algorithm (version 2.7.1a) on the GRCm38 reference from Ensembl, release 96.
quality control of the alignment realized with Picard tools (version 2.8.1)
Reads count using RSEM (v1.3.1) with the Aligned to Transcriptome bam files
statistical analyses on the read counts were performed with theDESeq2 package version 1.26.0
Assembly: GRCm 38 release 96
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovary

extract_protocol:
Ovaries were dissected and RNA extracted with classic Trizol protocol.
TruSeq mRNA stranded Illumina

value: ovary

value: mutant

value: FOXL2 WT/C134W

tag: disease state

value: Mutant mice hyperplasia


title: hepatocarcinoma tissue, replicate 41 [LR21K17DX175]

value: I-II


title: FOX14-2


title: hepatocarcinoma tissue, replicate 27 [LR21K17DX96]

value: male


title: FOX18

value: WT

value: FOXL2 WT/WT

value: WT mice


title: A800

value: Mutant mice granulosa cell tumor


title: heart, DM

description: 10X Genomics

value: heart

value: wild type

value: STZ-induced

value: diabetes


title: hepatocarcinoma tissue, replicate 26 [LR21K17DX95]

value: liver cancer

value: hepatocarcinoma tissue

value: StageII


title: A491i

value: ovary


title: RNA-Seq CXN ciRS-7 KO4 OGD

value: Primary neurons

value: Cortical neurons E15

value: ciRS-7 KO4

value: Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)

value: Day 7 differentiation, 12h treatment


title: FOX6-1

value: mutant

value: FOXL2 WT/C134W

value: Mutant mice hyperplasia


title: FOX8

value: Mutant mice granulosa cell tumor


title: RNA-Seq CXN ciRS-7 KO2 OGD

value: ciRS-7 KO2


title: hepatocarcinoma tissue, replicate 25 [LR21K17DX94]

value: StageIII

value: III-IV

value: female


title: RNA-Seq CXN ciRS-7 KO1 OGD

value: ciRS-7 KO1


title: hepatocarcinoma tissue, replicate 24 [LR21K17DX93]

value: liver cancer

value: hepatocarcinoma tissue

value: I-II

value: male


title: hepatocarcinoma tissue, replicate 23 [LR21K17DX92]

value: StageII


title: RNA-Seq CXN ciRS-7 KO4 N

value: Primary neurons

value: Cortical neurons E15

value: ciRS-7 KO4

value: Normoxia (5%CO2, 37C, Glucose +)


title: hepatocarcinoma tissue, replicate 31 [LR21J8DX45]

value: StageI


title: RNA-Seq CXN ciRS-7 KO3 N

value: ciRS-7 KO3

value: Day 7 differentiation, 12h treatment


title: FOX17

value: ovary

value: WT

value: FOXL2 WT/WT

value: WT mice


title: RNA-Seq CXN WT5 OGD

value: Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)


title: hepatocarcinoma tissue, replicate 19 [LR21K17DX88]

value: liver cancer

value: StageIII

value: III-IV

value: female


title: B7 Ifnar +/-

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.0.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

organism: Mus

source_name: Lin-Kit+ cells

extract_protocol: 10x Genomics Chromium single cell preparation 3' ver3.1

value: P14 (14 days old)


title: RNA-Seq CXN WT4 OGD

value: Primary neurons


title: B6 Ifnar -/-

source_name: Lin-Sca1+Kit+ cells

value: P0 (newborn)


title: hepatocarcinoma tissue, replicate 21 [LR21K17DX90]

value: hepatocarcinoma tissue

value: StageII

value: I-II

value: male


title: hepatocarcinoma tissue, replicate 22 [LR21K17DX91]

value: StageI


title: RNA-Seq CXN ciRS-7 KO1 N

value: Cortical neurons E15

value: ciRS-7 KO1

value: Normoxia (5%CO2, 37C, Glucose +)

value: Day 7 differentiation, 12h treatment


title: FOX16

value: ovary

value: WT

value: FOXL2 WT/WT

value: WT mice


title: RNA-Seq CXN ciRS-7 KO2 N

value: ciRS-7 KO2


title: RNA-Seq CXN WT3 OGD

value: Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)


title: B9 Ifnar +/-

value: P14 (14 days old)


title: hepatocarcinoma tissue, replicate 20 [LR21K17DX89]

value: liver cancer


title: RNA-Seq CXN WT2 OGD

value: Primary neurons


title: hepatocarcinoma tissue, replicate 15 [LR21K17DX84]

value: hepatocarcinoma tissue

value: female


title: RNA-Seq CXN ciRS-7 KO5 N

value: ciRS-7 KO5


title: B10 Ifnar -/-


title: hepatocarcinoma tissue, replicate 14 [LR21K17DX83]

value: StageI

value: I-II

value: male


title: hepatocarcinoma tissue, replicate 12 [LR21K17DX81]


title: B5 Ifnar +/-

value: P0 (newborn)


title: L_sat_2WR

city: Norwich

first: Martin

last: Vickers

state: Norfolk

address: Colney Ln

institute: John Innes Centre

description: part of transcriptome drough response experiment

data_processing:
FastQC
Kontaminant pipeline (removing contaminants using sortmerna v2.0)
Trimmed sequence reads (trim_galore v 0.4.1)
read mapping using Kallisto
Assembly: Rbp1.0 grasspea assembly that is published with manuscript
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Lathyrus sativus

source_name: whole root

extract_protocol:
Rneasy Plant Mini Kit Qiagen
TruSeq RNA

value: whole root

value: NIAB field, well-watered

value: 3 months after planting


title: RNA-Seq CXN WT3 N

value: Cortical neurons E15

value: Normoxia (5%CO2, 37C, Glucose +)

value: Day 7 differentiation, 12h treatment


title: hepatocarcinoma tissue, replicate 18 [LR21K17DX87]


title: B8 Ifnar -/-


title: hepatocarcinoma tissue, replicate 11 [LR21K17DX80]

value: StageII


title: MAHA_3ws

source_name: whole shoot

value: whole shoot

value: Mahateora


title: B4 Ifnar -/-


title: hepatocarcinoma tissue, replicate 16 [LR21K17DX85]

value: liver cancer


title: Robust Male [Pool 19]

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

institute: Biodonostia Research institute

data_processing:
QC by FASTQC
mapped by STAR v 2.5.4b or BWA v0.7.17-1
circRNA prediction by Circexplorer2 v 2.3.3 and CIRI2 v2.0.5
DE by DESeq2 v 1.28.1

source_name: Leukocytes from blood

extract_protocol:
miRNeasy Mini Kit Quiagen
Therefore, a total of 20 pools were analyzed (10 robust and 10 frail). Library preparation and Next Generation Sequencing was performed at CD Genomics (Shirley, New York, NY, USA). The concentration and quality of the RNA samples was again measured using Bioanalyzer 2100 instrument (Agilent) before library preparation. After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina) and followed by purification and fragmentation steps. To construct the sequencing libraries, a strand-specific cDNA synthesis was performed, the 3’ ends were adenylated and adaptors were ligated. The resulting libraries were subjected to a quality control and normalization process

value: Leukocytes from blood

value: Robust


title: MAHA_2DS

value: NIAB field, simulated drought


title: hepatocarcinoma tissue, replicate 8 [LR21K17DX77]

value: hepatocarcinoma tissue

value: StageIII

value: III-IV

value: female


title: Control, rep 2, scRNA-seq

city: Omaha

first: Yichao

last: Zhou

state: NE

department: Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description: Seq-well

data_processing:
The demultiplexing, barcoded processing, alignment and digital gene expression extracting were made using the DropSeq pipeline (v2.0.0) (Macosko., et al. Cell (2015). https://github.com/broadinstitute/Drop-seq/blob/v2.4.0/doc/Drop-seq_Alignment_Cookbook.pdf)
For digital gene expression (DGE), a plot  ofcumulative distribution of reads was generated to determine the cells to extract from BAM. We selected 15,000 cells to generate DEG files.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files for each sample after doing quality control. And Tab-separated values files and matrix files and metadata files for integrated (by Seurat) files of CTRL with PHZ_Day3 for both replicates and CTRL with  PHZ_Day1,3,7 for replicate1.

source_name: Spleen cells

extract_protocol:
Spleen cells were isolated and resuspended in spleen isolation media (PBS containing 2% FBS, glucose, EDTA). Kit-positive cells were subsequently isolated by positive selection using biotin-conjugated Anti-mouse CD117(Kit) (clone 2B8) antibody followed by incubation with MojoSort streptavidin conjugated magnetic nanobeads. The sorted cells were resuspended with spleen isolation media and transferred to IMDM meida with 1%FBS before loading into the array.
Library was performed according to the Seq-well protocol from Gierahn, et al. (2017, Nat Method). Briefly, beads binding with cells were removed and resuspended with reverse transcription master mix to make single strand cDNA. Then the samples were treated with Exonuclease I and doing PCR using dN-SMRT oligo to do the Whole Transcriptome Amplification. After purification with SPRI beads and quality checking by BioAnalyzer, cDNA Tagmentation was done by Nextera XT kit. And the library was constructed by adding paired-end adapter of P5 and N7 sequences and a sample index were added. Each sample was purified and quality checked before sequencing.

value: Spleen cells

value: Primary cell

value: Kit+ sorted cells

value: WildType

value: Female


title: PHZ_Day3, rep 2, scRNA-seq

description: Seq-well

value: subcutaneously injection of phenylhydrazine, 100 mg/kg, 3 days


title: RNA-Seq CXN WT1 OGD

value: Primary neurons

value: Cortical neurons E15

value: Oxygen and glucose deprivation (5%CO2, 37C, Glucose -, 1% O2)

value: Day 7 differentiation, 12h treatment


title: hepatocarcinoma tissue, replicate 13 [LR21K17DX82]

value: liver cancer

value: StageI

value: I-II

value: male


title: RNA-Seq CXN WT4 N

value: Normoxia (5%CO2, 37C, Glucose +)


title: hepatocarcinoma tissue, replicate 17 [LR21K17DX86]

value: hepatocarcinoma tissue

value: StageII


title: RNA-Seq CXN WT2 N


title: RNA-Seq CXN WT1 N


title: hepatocarcinoma tissue, replicate 5 [LR21K17DX74]

value: female


title: Robust frail [Pool 15]

value: Leukocytes from blood

value: Robust


title: Control, rep 1, scRNA-seq

description: Seq-well

value: Spleen cells

value: Primary cell

value: Kit+ sorted cells

value: WildType


title: RNA-Seq CXN WT5 N

value: Primary neurons

value: Cortical neurons E15


title: Robust frail [Pool 14]


title: L_sat_1wr

value: whole root

value: NIAB field, well-watered

value: 3 months after planting


title: L_sat_3DS

value: whole shoot

value: NIAB field, simulated drought


title: Robust Male [Pool 16]


title: MAHA_2ws

value: Mahateora


title: MAHA_3DR


title: B3 Ifnar +/-

value: P0 (newborn)


title: hepatocarcinoma tissue, replicate 9 [LR21K17DX78]

value: liver cancer

value: hepatocarcinoma tissue

value: StageI

value: I-II


title: hepatocarcinoma tissue, replicate 10 [LR21K17DX79]

value: male


title: PHZ_Day7, rep 1, scRNA-seq

description: Seq-well

value: Spleen cells

value: Primary cell

value: Female

value: subcutaneously injection of phenylhydrazine, 100 mg/kg, 7 days


title: hepatocarcinoma tissue, replicate 7 [LR21K17DX76]

value: StageII


title: Robust Male [Pool 18]

value: Leukocytes from blood

value: Robust


title: Robust Male [Pool 20]


title: Robust Male [Pool 17]


title: Robust frail [Pool 12]


title: PHZ_Day1, rep 1, scRNA-seq

description: Seq-well

value: Kit+ sorted cells

value: WildType

value: subcutaneously injection of phenylhydrazine, 100 mg/kg , 1 day


title: hepatocarcinoma tissue, replicate 4 [LR21K17DX73]


title: MAHA_3WR

value: whole root

value: Mahateora

value: NIAB field, well-watered

value: 3 months after planting


title: hepatocarcinoma tissue, replicate 6 [LR21K17DX75]

value: liver cancer

value: hepatocarcinoma tissue


title: hepatocarcinoma tissue, replicate 3 [LR21K17DX72]

value: StageI

value: I-II

value: male


title: MAHA_1ws

value: whole shoot


title: PHZ_Day3, rep 1, scRNA-seq

description: Seq-well

value: Spleen cells

value: Primary cell

value: Female

value: subcutaneously injection of phenylhydrazine, 100 mg/kg, 3 days


title: BALB mice, stress 3

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.38 tool.
Trimmed reads are mapped to reference genome (GrCM38/mm10) with HISAT2, splice-aware aligner
The aligned reads were subjected to downstream analyses using StringTie and iDEP.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count for each Sample

source_name: Brain (anterior cingulate cortex)

extract_protocol:
RNA was extracted using Direct-zol RNA kit (Zymo Research). 100 ng of total RNA was used for the construction   of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Ultra low RNA Kit and TruSeq library construction following manufacturer's protocols.  RNA-seq

value: Brain (anterior cingulate cortex)

value: BALB/c

value: social defeat stress


title: Robust frail [Pool 11]

value: Leukocytes from blood

value: Robust


title: BALB mice, non-stress 3

value: Non-stress


title: MAHA_3DS

value: Mahateora

value: NIAB field, simulated drought

value: 3 months after planting


title: MAHA_2WR

value: whole root

value: NIAB field, well-watered


title: MAHA_1wr


title: Robust frail [Pool 13]


title: MAHA_2DR


title: BALB mice, stress 2


title: hepatocarcinoma tissue, replicate 2 [LR21K17DX71]

value: liver cancer

value: hepatocarcinoma tissue

value: StageI

value: I-II

value: male


title: BALB mice, stress 1


title: L_sat_3ws

value: whole shoot


title: Frail Male [Pool 9]

value: Frail


title: hepatocarcinoma tissue, replicate 1 [LR21K17DX70]


title: Frail Male [Pool 8]


title: MAHA_1DR


title: L_sat_1ws


title: L_sat_3WR


title: BALB mice, non-stress 2

value: Brain (anterior cingulate cortex)

value: BALB/c


title: Frail Male [Pool 10]

value: Leukocytes from blood


title: LRIF1LKO rep3

city: Leiden

first: Darina

last: Sikrova

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Centre

data_processing:
Quality assessment of the raw Fastq files was done with FastQC  v0.11.6 and adapters were removed with TrimGalore v0.4.5 with the option "--paired''
Quality-filtered reads were mapped to human reference genome with STAR aligner v2.5.1
Read count table was obtained with HTSeq-count v0.9.1 using the GENCODE V29 annotation with the option “–stranded no”.
The differential expression analysis was done with DESeq2 v1.24.0
Genome_build: GRCh38
Supplementary_files_format_and_content: DEseq2 output in separate excel sheet for each knock-out condition

extract_protocol:
total RNA was isolated with RNeasy Mini Kit from Qiagen, including on-column DNAse digestion step
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used for library preparation
oligo-dT enriched RNA was used for library preperation

value: immortalized myoblasts


title: LRIF1LSKO rep3


title: LRIF1LSKO rep2


title: Frail Male [Pool 6]


title: L_sat_2ws


title: L_sat_2DR


title: Frail Male [Pool 7]


title: L_sat_3DR


title: LSEC-only-3

city: Osaka

first: Hoang

middle: Huu

last: Truong

state: Select a State or Province

address: 1-4-3 Asahi-machi, Abeno-ku, Osaka-City, Osaka, Japan

department: Hepatology

institute: Graduate School of Medicine, Osaka City University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage. Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM(Transcripts Per Kilobase Million).
IIn groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: mm10
Supplementary files format and content: Expression_Profile.mm10.table.xlsx

source_name: Liver

growth_protocol: 5× 10^5 LSECs were cultured in completed LSECs medium in the bottom of 12 wells insert-plate, 1× 10^5 Hepa1-6 cells were cultured in DMEM supplemented with 10% FBS, 1% Penicillin/streptomycin in the 3um-insert.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E.

treatment_protocol: Next day,  removed the medium in both cell types, wash 3 times by DMEM solution, then co-cultured using DMEM supplemented with 2% FBS, 1% penicillin/ streptomycin. After 24 hours, mRNA was extracted.

value: Liver

value: primary LSECs

tag: culture conditions

value: mono-culture


title: LSEC-only-1


title: LSEC-only-2


title: Frail Female [Pool 4]


title: LRIF1LSKO rep1


title: Frail Female [Pool 5]


title: BALB mice, non-stress 1

value: Non-stress


title: LRIF1LKO rep2


title: L_sat_2DS

value: NIAB field, simulated drought

value: 3 months after planting


title: LSEC-H1-6-1

value: primary LSECs, hepatoma cells

value: co-culture


title: LSEC-H1-6-3


title: SMCHD1KO rep3


title: L_sat_1DR

value: whole root


title: Frail Female [Pool 3]


title: LSEC-H1-6-2


title: LRIF1LKO rep1


title: LS007 genomic HiC

description: HiC data used for assembly scaffolding

source_name: juvenile whole leaf

extract_protocol:
cross-linked, Phase Genomics extraction
Phase Genomics proprietary

value: juvenile whole leaf

value: 4 weeks after imbibing


title: H1-6-only-2

value: hepatoma cells


title: SMCHD1KO rep2


title: WT rep3

value: WT


title: LSWT11 early pod RNA [Sample_1348_LIB14298_LDI12360]

description: part of multi-tissue transcriptome, used for read counting

source_name: early pod stages 1&2

extract_protocol:
Sigma Spectrum Plant Total RNA kit
TruSeq RNA

value: early pod stages 1&2

value: 3 months after imbibing


title: P60Tx_Liver

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

description:
Single-cell RNA-Seq
mRNA

data_processing:
To distinguish the human cancer cells from the mouse TME cells, we aligned the sequencing data of each sample to GRCh37 (hg19) and GRCm38 (mm10) reference genomes separately using the Cell Ranger Single-Cell Software Suite (v-2.0.1, 10X Genomics), and estimated the unique molecular identifiers (UMIs) with the default parameters.
We then merged the UMI files of the 4 samples (P5Tx Liver, P5Tx Tumor, P60Tx Liver and P60Tx Tumor) for both human cancer cells and mouse TME cells with an in-house script. Thereafter, we introduced the Seurat (v-3.2.2, PMID: 31178118) R package to remove the low-quality cells following these criteria: human cancer cells expressed < 1000 or > 8000 genes or mitochondrial gene content > 15% of total UMIs; mouse TME cells expressed <200 or >3000 genes or mitochondrial gene content > 10% of total UMIs.
To normalize the data, we divided the UMI count of each gene by the total UMI counts of the cell and scaled the library size to 1,000,000, followed by a natural log plus 1 transformation (“NormalizeData”). Then the normalized data was further scaled so that the mean expression across cells is 0 and the variance is 1 (“ScaleData”). The principle component analysis (PCA) was employed for dimensionality reduction (“RunPCA”). To determine the number of components to choose, we implemented a resampling test inspired by the JackStraw procedure (“JackStraw” and “ScoreJackStraw”) and picked the first 15 principal components which explained sufficient observed variance. Thereafter, to identify the clusters from the reduced dimensional space, we constructed a k-nearest neighborhood (KNN) graph based on the Euclidean distance in PCA space and refined the edge weights among cells based on the shared overlap in local neighborhoods (“FindNeighbors”). We then applied the modularity optimization technique named Louvain algorithm to iteratively group cell together with a resolution parameter of 0.5 (“FindClusters”). Finally, the Uniform Manifold Approximation and Projection (UMAP) was used to visualize the clustering results (“DimPlot”).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: *.tar.gz: Tar archives include Cell Ranger count matrix for single cells in each sample; barcodes.tsv, genes.tsv, matrix.mtx.

organism:
Homo sapiens
Mus musculus

source_name: Liver tissue from model established in postnatal day 60

extract_protocol:
The liver tissue and bulk tumors were minced and then enzymatically digested in advanced DMEM/F-12 (Thermo Fisher Scientific, Waltham, MA), containing 10 U/mL Papain (Worthington, Lakewood, NJ), 1 mmol/L N-acetyl cysteine (Sigma-Aldrich, St. Louis, MO), 12mg/mL DNase I (Sigma-Aldrich). The mixture was incubated at 37°C for about 30 min for the enzymatic digestion. The additional mechanical digestion was performed by gently pipetting up and down. Thereafter, the cell suspensions were passed through a 100-μm strainer and washed twice with 5ml of cold Advance DMEM/F12 and centrifugated at 300g for 5min at 4°C.
The single cells dissociated from liver and tumor tissues were processed by the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) as per the manufacturer’s protocol. Briefly, the single cells were washed once with PBS plus 0.04% BSA and counted with Luna-FL Fluorescence Cell Counter (VitaScientific). Then the cells were added to each lane of the chip and partitioned into Gel Beads in emulsion in the Chromium Controller. The cells were lysed, barcoded and reversely transcribed, followed by amplification, fragmentation, adaptor attachment and indexing. The libraries were sequenced by Novaseq 6000 (Illumina).

treatment_protocol: Around 37.5 thousand HepG2 cells suspended in 1.5 ul of Matrigel were injected to each liver of five-day-old (P5) and sixty-day-old NSG mice.

tag: mouse strain

value: NOD scid gamma mouse

tag: mouse age at model establishment

value: Liver tissue


title: H1-6-only-3

value: Liver


title: SMCHD1KO rep1

value: immortalized myoblasts


title: WT rep2


title: H1-6-LSEC-2

value: hepatoma cells, primary LSECs


title: L_sat_1DS

value: whole shoot


title: LSWT11 late pod RNA [Sample_1348_LIB14299_LDI12361]

source_name: late pod stages 3&4

value: late pod stages 3&4


title: WT rep1


title: Frail Female [Pool 1]

value: Leukocytes from blood

value: Frail


title: H1-6-LSEC-1

value: co-culture


title: P5Tx_Tumor

description:
Single-cell RNA-Seq
mRNA

source_name: Liver bulk tumor from model established in postnatal day 5

value: Liver bulk tumor


title: LSWT11 flower RNA [Sample_1348_LIB11628_LDI11334]

source_name: open flower

value: open flower


title: LSWT11 root RNA [Sample_1348_LIB11627_LDI11333]

source_name: juvenile whole root

value: juvenile whole root

value: 3 weeks after imbibing


title: P60Tx_Tumor

description:
Single-cell RNA-Seq
mRNA

source_name: Liver bulk tumor from model established in postnatal day 60


title: HC_3_m6A_seq

city: hefei

first: Jun

last: Wu

state: Anhui

address: Meishan Road 81

institute: Anhui medical university

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: Version GRCh38.p10
Supplementary_files_format_and_content: txt,tab-delimited text files include RPKM values for each Sample ...

source_name: peripheral blood

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.
Immunoprecipitated m6A RNA fragments for m6A-seq (IP), total RNA for RNA-Seq (Input).

value: peripheral blood

value: peripheral blood mononuclear cell

value: healthy control


title: Frail Female [Pool 2]