title: N4

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat4


title: H3

status: Public on Aug 11 2022

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through Partek GS ANOVA statistic and ToppCluster.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat3

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo (Madison, WI) and were acclimated to our animal facility for 7 days. The use of animals was approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee and conformed to the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. Two or four pregnant rats were used for each experiment, according to the study design. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity.

tag: strain

value: Sprague-Dawley

tag: tissue

value: Lung

tag: age

value: 10 days old


title: N6

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat6


title: H2

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat2


title: H1

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat1


title: N3

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat3


title: N2

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat2


title: 1mo_organoid iPSC 2242 #1 14741X3

type: SRA

city: Salt Lake City

first: Yueqi

last: Wang

state: Utah

address: 20 South 2030 East

institute: University of Utah

library_source: transcriptomic

data_processing:
Reads were processed using the 10X Genomics Cell Ranger 2.0 pipeline and aligned to the human GRCh38 reference assembly (Ensembl v84)
Gene-barcode matrices were constructed for each sample by counting unique molecular identifiers (UMIs).
The four individual samples of the 1-month-old organoids were then aggregated into a single gene-barcode matrix using the Cell Ranger aggr command line function.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files containing the UMI count matrix

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Cortical organoids were dissociated into single cell suspension. Single cells were isolated and lysed using the 10X Genomics Chromium platform.
Reverse transcription and library construction were performed using the 10X Chromium Single Cell 3' Reagent Kit

value: telencephalic organoid

tag: cell line


title: N1

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat1


title: SSF

city: Beijing

first: Lei

last: Zhao

state: Beijing

address: Gongti Nanlu No.8

country: China

institute: Beijing Chaoyang Hospital

data_processing:
Solexa pipline v1.8 software was used in image analysis and base calling.
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
The abundance of tRF & tiRNA and miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). The tRFs & tiRNAs and miRNAs differentially expressed are screened based on the count value with R package edgeR.
Assembly: GRCh37
Supplementary files format and content: excel files included the counts of reads and CPM values of tsRNAs in each samples

source_name: epicardial adipose tissue

extract_protocol:
Total RAN was extracted from frozen EAT with QIAGEN miRNAeasy Mini Kit (Qiagen, Hilden, Germany) followed by instructions of the manufacturer.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

value: epicardial adipose tissue

tag: subject status

value: patient with sinus rhythm

tag: disease state

value: Control


title: WT control 3

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing:
Sequencing data of mice heads were aligned and mapped to the mouse genome GRCm38.p6 using Genetiles server
Image analysis and base calling were done by the Illumina HCS version 1.15.1. At least 15 million reads were obtained that could be mapped to the mouse genome version GRCm38.
DESeq is used to normalise the reads using a DESeq scaling factor, computed as the median of the ratio, for each gene, of its read count over the geometric mean across samples. Then variance and average of the measurement compared to the control is expressed as a P value, by calculating the dispersion per gene using DESeq.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include normalized read values per million for each Sample

organism: Mus musculus

source_name: head

growth_protocol: Mice were kept on a standard-chow diet with ad libitum access to food and water.

extract_protocol:
Frozen ob/ob and C57BL/6 mouse heads (n=4) were thawed in 30 ml of TRIzol Reagent (Life Technologies) and manually crushed in a mortar
Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made: In the adapter ligation step 1 μl instead of 2.5 μl adaptor was used; In the library size selection step, the library fragments were isolated using a double Ampure XP purification with a 0.7x beads to library ratio.

treatment_protocol: No treatment

tag: Sex

value: male

value: head

tag: genotype

value: WT

tag: time

value: week 14


title: 1mo_organoid H9 #2 14741X2


title: 1mo_organoid H9 #1 14741X1


title: WT control 1


title: QP

value: patient with persistent non-valvular AF

value: Atrial fibrillation


title: v2.1.4.p

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

description: nuclear RNA

data_processing:
Alignment: The raw sequencing reads were aligned to a marmoset genome assembly, ASM275486v1 (GCA_002754865.1). To build a reference package suitable for analyzing both unspliced pre-mRNA and mature mRNA in the nuclei, as well as to include sequences of mito-chondrial genome, marmoset DNA sequence (FASTA) and annotation (GTF) files were acquired from the Ensembl release-95 and modified as follows. The complete mitochondrial sequence (NC_025586.1, GenBank) and its annotation (Wang et al., 2016) were manually added to the FASTA and GTF files. Next, a pre-mRNA GTF was made by replacing “transcript” with “exon” as the feature-type entry in the original GTF before making a reference package with CellRanger software (v3.0.2, 10x Genomics). This custom-built reference package was then used in CellRanger (version 3.1.0, 10x Genomics) to align sequencing reads for all samples. The option to estimate cell number automatically was used for most of the samples, unless otherwise speci-fied (see Table S1 for details). A filtered cell barcode-to-gene feature matrix was generated from the software and used for downstream analysis (Figure S2A).
Preprocessing & general quality control: The matrix was loaded to create an object in Seurat v3 (Butler et al., 2018; Stuart et al., 2019). Cells with <200 genes, >5000 genes, or >5% of counts mapped to mitochondrial genome were excluded. Genes observed in <5 cells were excluded. The filtered raw count matrix was then log normalized (ln(counts*100,000+1)) within each cell and scaled to account for differences in sequencing depth with Seurat. Next, DoubletFinder (McGinnis et al., 2019) was used to esti-mate and remove putative doublets to mitigate technical confounding artifacts in droplet-based sequencing data analysis. The top 3000 variable genes calculated by Seurat were used in linear dimension reduction (principal components analysis, PCA), and the top 30 PCA were used for clustering at low resolution (parameter = 0.4) to define crude cell types. These unsupervised clusters were used to provide a quick cluster annotation for homotypic doublet probability model-ing in DoubletFinder. Doublet rate was estimated by fitting a linear equation over a multiplet rate table provided by 10x Genomics. The rate = (0.0008*cell.number + 0.0527)/100) was used to calculate a Poisson distribution with and without homotypic doublet proportion to generate low confidence (DF.found.1) and high confidence (DF.found.2) doublet annotation. Unless otherwise specified, pN = 0.25, pK = 0.005 and automatic doublet removal based on DF.found.2 annotation were used, as the first line of screening. In parallel, SoupX (Young and Behjati, 2020) was used for ambient RNA background correction. Taken from the output of the 10x pipeline (raw_feature_bc_matrix), the ambient RNA from empty droplets that contained <10 unique mo-lecular identifiers (UMI) were profiled, and the “soup” contamination fraction was calculated for each cluster. Given that the nuclear transcriptome was profiled, genes that mapped to the mito-chondrial genome could be considered as ambient input. Therefore, the top mitochondrial genes (species with >1000 accumulated counts across profiled empty droplets) were used to estimate the global contamination fraction and adjust the raw count matrix. Next, the cell barcode that passed the DoubletFinder was used as an index to subset the SoupX-corrected matrix to gener-ate a new matrix as our downstream input (Figure S2A). For individual samples, a Seurat object was created, and the index labels (IL01_uniqueID, IL02_species, IL03_source, IL04_sex, IL05_ageDays, IL06_tissue.1, IL06_tissue.2, IL06_tissue.3, IL07_location, IL08_condition, IL09_illumina, IL10_chemistry, IL11_batch, IL12_LMinDays, IL13_LMaxDays, IL14_dataset, IL15_annotation) were added to the metadata as cell attributes. For each sample, 90% of nuclei were randomly selected, then all 42 samples were merged together for downstream comparison. The remaining 10% of the nuclei were set aside for classification assessment and validation.
Level 1 quality control & clustering: To divide nuclei into classes and facilitate artifact identification, nuclei were first classified using a set of parameters that does not highlight granular detail. In this round of clustering, only 50 PC for Harmony were computed to perform linear correction over IL01_uniqueID, as the el-bow plot from the preliminary analysis showing the standard deviation stopped visually decreas-ing after top 50 PC. The top 5 Harmony-corrected embeddings (H5) were used for Seurat to learn the UMAP and find cell classes at a low resolution (0.2). Canonical cell-type markers (PTPRC for immune cells, PDGFRA for OPC, MAG for oligodendrocytes, GFAP and SLC1A2 for astrocytes, LEPR and CEMIP for vasculature and meningeal cells, and CNTN5 and NRG1 for neurons) annotated 6 of the classes unambiguously. One cluster in the middle of the H5 UMAP had mixed expression of canonical markers, which suggested artifact. The “low quality” cell bar-codes that were found from the H50 condition (defined above) were overlaid on the H5 UMAP, which exclusively highlighted the putative artifact cluster. These nuclei were removed from fur-ther analysis, although the original UMAP embeddings were maintained for plotting purposes (Figure 1 and S3).
Level2 quality control & clustering: Nuclei that passed Level 1 QC were divided into 5 partitions (MIC, OPC, OLI, VAS/AST, NEU) based on the H5 UMAP result. The astrocytes and vasculature/meningeal cells were pooled into a single class prior to subclustering to facilitate artifact identification. Shared features in this class of cells were potentially explainable by their close association at CNS barriers (blood–CSF interface, blood–brain interface, and the CSF–brain interface). For each class, log-normalization and scaling were repeated from the divided raw count matrix, the top 3000 variable genes were used for 50 PC computation, Harmony correction over IL01_uniqueID, UMAP learn-ing, and clustering, as described above. The clustering resolution was iteratively increased from low to high (0–1.2), and clustering stability was tracked with clustree (v0.4.3) (Zappia and Oshlack, 2018). Aided by the branch visualization provided by the clustree, a tentative resolution that was relatively stable was selected, then differentially expressed gene (DEG) analysis on the clusters found with this parameter set was performed. The expression pattern of the top-expressed genes for each cluster within and across classes were checked, and artifacts clus-ters were manually imputed. Doublets tended to form small distinct clusters on UMAP that branched early in the clustering tree analysis with low splitting resolution, had mixed canonical marker-gene expression, and had similar expression patterns to cells in other partitions; thus, these doublets could be easily spotted and removed. For putative doublets within each class, additional rounds of DEG analysis were performed as necessary. Each time nuclei were re-moved, basic normalization, scaling, Harmony, and UMAP learning were repeated. To control for over-splitting, for clusters that appeared to be a single pile in the 2D UMAP space but were anno-tated into >1 cluster, additional rounds of DEG analysis were performed to see if binary markers could be found to label them. In addition, clustering was projected onto a 3D UMAP space to en-sure effects were not masked due to overcrowding in 2D. This strategy also helped to further elucidate cluster associations, aid decision-making with respect to groups of clusters that should be tested further, and spot potential gradient changes among clusters. If unique and or binary patterns could not be found in the current splitting resolution after these steps were performed, a step lower in resolution on the clustering tree was examined, and the analysis process was re-peated. The following compound naming convention to la

organism: Callithrix jacchus

extract_protocol:
Tissue dissection: On the day of tissue harvest, marmosets were deeply anesthetized with 5% isoflurane until all visible signs of breathing were no longer detected. Animals were transcardially perfused with ice-cold artificial cerebrospinal fluid (aCSF) for 5 min with a pump. Brains were removed from the skull and submerged into ice-cold aCSF, and after removal of meninges within the solu-tion, were positioned in a custom-designed brain holder within 10 min post-perfusion. The brain was sectioned at 3 mm into 12–13 slabs in one step with a homemade blade-separator set in the solution. Each brain slab was transferred into a 6-well plate, submerged into RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen) with a homemade brain trap, and stored at 4°C overnight. The following day, brain slabs were positioned in 25 x 20 x 5 mm molds (Tis-sue-Tek® Cryomold®, 4557, Sakura Finetek) on ice to facilitate target sampling. Slabs were matched to MRI for each animal, and tissue annotation for gray (Liu et al., 2018a) and white matter (Liu et al., 2020) was informed by marmoset 3D MRI atlases V1 and V2. A cylinder of tissue 2 mm in diameter and 3 mm in height for each region (Figure 1B and S1) was collected with a tissue punch (EMS-core sampling tool, 69039-20, EMS). There were 5 white matter sam-ples from temporal and parietal lobes that did not exactly match in the two animals, however they were paired in lobes of the brain and showed no significant differences in later analysis (Figure 1B, SS05, SS06, and SS08). The cylinders were ejected into PCR tubes filled with 100 µL of RNAlater and stored at −80°C. Single-nucleus dissociation: Nuclei preparation was carried out as described (Matson et al., 2018), with minor modifi-cations. Briefly, on the day of dissociation, tissue samples were thawed on ice, removed from solution, dabbed with Kimwipes to remove residual RNAlater, and placed in a 1 mL douncer tube (Dounce Tissue Grinder, 357538, Wheaton). Each tissue was homogenized in 500 μL of lysis buffer containing 0.1% Triton-X100 in low sucrose buffer (0.32 M sucrose, 10 mM HEPES, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, and 1 mM DTT in ddH2O, pH8) with loose pestle 25 times and tight pestle 10 times. The homogenate was filtered through a 40-μm mesh (Falcon® 40 µm Cell Strainer, 352340, Corning) to a 50-mL Falcon tube on ice. An additional 5 mL of low sucrose buffer was used to rinse the douncer tube and cell strainer. The filtered homogenate was further mixed with a handheld homogenizer (VWR® 200 Homogenizer) at a speed of ~1000 rpm to brake nuclei clumps for 5 sec. After homogenization, a serological pipet filled with 12 mL of high sucrose buffer (1 M sucrose, 10 mM HEPES, 3 mM MgAc, and 1 mM DTT in ddH2O, pH8) was placed underneath the lysate and disconnected from the pipettor, and the buffer was released from the serological pipette by gravity and set on ice. When most of high sucrose buffer was re-leased to form a density layer underneath the homogenate, the serological pipet was retrieved along the wall of the Falcon tube gently, without disturbing the low-high sucrose interface. The Falcon tube was capped and placed in a swing bucket to be centrifuged at 3,200 rcf for 30 min at 4°C. At the end of spin, the supernatant was decanted quickly without tabbing, and 1 mL of re-suspension buffer (0.02% BSA in 1X PBS, pH7.4) was added to the Falcon tube. Slow pipetting was employed to resuspend nuclei along the Falcon tube wall below the 5-mL mark to preserve nuclei integrity. Specifically, nuclei were rinsed off the wall in courses of 2 sec per trituration for 20 times total per tube. The Falcon tube was then capped and spun at 3,200 rcf for 10 min at 4°C. At the end of spin, the supernatant was removed by gently tabbing the tube until no visible liquid drop was left behind, and 200 μL of resuspension buffer was added to each sample to collect the nuclei. The nuclei suspension was filtered through a 35-μm mesh (Cell Strainer Snap Cap, 352235, Corning) twice and counted on a hemocytometer by trypan blue staining. During count-ing, the size and quantity of myelin and other debris were visually inspected under the scope, and the suspension was filtered 1–3 more times through the 35-μm mesh if necessary. Only round and dark-blue stained nuclei were considered of good quality and included in the final count.
10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v2 and v3

value: F

value: GM

value: Telencephalon

value: fCTX

value: NaiveCtrl


title: LSQ


title: v2.1.3.p

description: nuclear RNA

value: M


title: KE23

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

country: Spain

institute: CRG

data_processing:
Illumina adapters were trimmed using /software/tgraf/TrimGalore/trim_galore with default parameters
Reads were aligned using STAR (outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -sjdbOverhang 100 –outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
Bigwig files were generated using bamcoverage (--binSize 1 --normalizeUsing RPGC --extendReads 141)
Gene expression was quantified using STAR (--quantMode GeneCounts)
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Assembly: mm10
Supplementary files format and content: bw

source_name: 8-cells stage embryo

growth_protocol:
Bcell_WT_Rep1, Bcell_WT_Rep2,Bcell_KO_Rep1,Bcell_KO_Rep2: freshly isolated B cells were infected with C/EBPα-ER-hCD4 retrovirus and hCD4 positive cells were plated at 500 cells/cm2 in gelatinized 12-well plates onto wild type inactivated MEF feeders in 20%-FBS( 10270-106, GIBCO) RPMI medium (12633012, GIBCO) with 10 ng/mL IL-7(217-17, Preprotech)
Pulse_WT_Rep1,Pulse_WT_Rep2,Pulse_KO_Rep1, Pulse_KO_Rep2: freshly isolated B cells were infected with C/EBPα-ER-hCD4 retrovirus and hCD4 positive cells were plated at 500 cells/cm2 in gelatinized 12-well plates onto wild type inactivated MEF feeders in 20%-FBS( 10270-106, GIBCO) RPMI medium (12633012, GIBCO) with 10 ng/mL IL-7(217-17, Preprotech) and the transcription factor was shuttled into the nucleus by the addition of 100 nM β-estradiol for 18 hours
Day4_WT_Rep1, Day4_WT_Rep2, Day4_KO_Rep1, Day4_KO_Rep2,Day6_WT_Rep1, Day6_WT_Rep2, Day6_KO_Rep1, Day6_KO_Rep2: After β-estradiol washout, the cultures were switched to N2B27 medium (50% DMEM-F12 (12634010, GIBCO), 50% Neurobasal (21103049, GIBCO), 100X N2 supplement (17502048, GIBCO) and 50X B27 supplement (17504044, GIBCO)) and addition of 10 ng/ml IL-4 (217-14, Preprotech, 10ng/mL IL-7 and 2 ng/mL IL-15 (210-15, Preprotech). The final culture medium also contained 100X MEM Non-Essential Amino Acid solution (11140068, GIBCO), 1 mM sodium pyruvate (11360070, GIBCO), 100 U/mL Penicillin- 100 ng/mL Streptomycin, 2 mM L-Glutamine and 0.1 mM 2-Mercaptoethanol. The OSKM expression was activated by the addition of 2 μg/mL of doxycycline (D9891, Sigma).
KB01 to KB25: Zygotes were collected from the ampulla and cumulus cells removed by incubation with 300 µg/mL hyaluronidase (H4272, Sigma) in M2 medium (M7167, Sigma). After washing the embryos in a few drops of KSOM medium (MR-106-D, Millipore), they were cultured in KSOM microdrops under mineral oil (NO-400K, Nidacon) in an incubator with 5% CO2 at 37°C for 4 days until reaching the blastocysts stage (KB samples).
KE01 to KE25: Zygotes were collected from the ampulla and cumulus cells removed by incubation with 300 µg/mL hyaluronidase (H4272, Sigma) in M2 medium (M7167, Sigma). After washing the embryos in a few drops of KSOM medium (MR-106-D, Millipore), they were cultured in KSOM microdrops under mineral oil (NO-400K, Nidacon) in an incubator with 5% CO2 at 37°C for 2 days until reaching the 8-16 cell morula stage (KE samples).

extract_protocol:
B cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from B cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
Pulsed cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from Pulsed cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
Day 4 and Day 6 cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from Day 4 and Day 6 cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
For blastocysts, RNA was extracted and retro-transcribed into cDNA using a SMART-Seq v4 Ultra Low Input RNA kit (634894, Takara). RNA concentration and quality was determined as above. Libraries for RNA-sequencing were prepared as previously described (Picelli et al., 2014).
For morulas, RNA was extracted and retro-transcribed into cDNA using a SMART-Seq v4 Ultra Low Input RNA kit (634894, Takara). RNA concentration and quality was determined as above. Libraries for RNA-sequencing were prepared as previously described (Picelli et al., 2014).
For RNA-sequencing, libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (Illumina) followed by single-end sequencing (50 bp) on an HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

treatment_protocol:
B cell infection with C/EBPα-ER-hCD4 retrovirus as described in (Di Stefano et al., 2014).
C/EBPa induction (shuttling into cell nuclei) upon 18h pulse of β-estradiol
OSKM induction with doxycycline

tag: cell type

value: 8-cells stage embryo


title: KE25


title: KE22


title: v2.1.1

description: nuclear RNA

value: other

value: SpinalCord

value: cSC


title: LJ

value: epicardial adipose tissue

value: patient with sinus rhythm

value: Control


title: KE17


title: KE19


title: v2.1.2.fo

description: nuclear RNA


title: KE21


title: BYP


title: KE18


title: KE20


title: AGZ


title: SHY


title: KE16


title: WT control 2

value: male

value: head

value: WT


title: ICOS_2

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

data_processing:
Reads were mapped to the Homo Sapiens hg19 reference assembly using TopHat v2.0.10
Gene counts were computed using htseq-count and the GENCODE v24 gene annotation.
Genome_build: human GRCh37 / hg19
Supplementary_files_format_and_content: all.data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples.

source_name: PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from buffy coats provided by the local Blood Transfusion Service. Naïve CD4+ T cells from PBMC were purified with the EasySep™ Human naïve CD4+ T cells Negative Selection Kit.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen), following manufacturer instructions
Libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: 100.000 Naïve CD4+ T cells were plated on round-bottom 96-well plates; cells were stimulated with anti-CD3 mAb (OKT3, 10 ug/ml)+ B7h-Fc (5 ug/ml) or anti-CD3 mAb (OKT3, 10 ug/ml)+ B7.1-Fc (5 ug/ml)

value: Naive CD4+ T cells

tag: treatment

value: ICOS


title: KE15


title: LX2 cells, siSHMT2_2

city: nanjing

first: Gao

last: yanjie

state: Jiangsu

address: 163 Xianlin Road, Qixia District

department: School of life science

institute: Nanjing University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean
reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: LX2 cells were maintained in DMEM supplemented with 2% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA were extracted using Trizol regent
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LX2 cells were transfect with siNC and siSHMT2 for 36 h.

value: liver

value: Non parenchymal cell

value: SHMT2 knockdown

value: siSHMT2 transfected


title: LX2 cells, siSHMT2_3


title: ICOS_1


title: KE14


title: KE13


title: LX2 cells, siSHMT2_1


title: JIH5_IgG ChIP-Seq

city: Memphis

first: Xujie

state: TN

address: 246 Danny Thomas Place, MS 313

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Paired-end reads of 100bp were mapped human genome hg19(GRCh37-lite)by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by fastp(version 0.20.0, paired-end mode, parameters “--trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 --detect_adapter_for_pe”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2)
Peaks were called by MACS2 (version 2.1.1.20160309 , “--extsize 200 --nomodel --keep-dup all”)
hg38

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using ACTIVE MOTIF ChIP-seq kit
Libraries were made using NEB ultra II DNA library protocol

value: ALL cell line

tag: antibody


title: KE12

value: 8-cells stage embryo


title: CD28_3


title: KE11


title: LX2 cells, siNC_2

value: siNC transfected


title: KE08


title: KE09


title: KE10


title: KE07


title: CD3_2


title: LX2 cells, siNC_1


title: KE24


title: KE02


title: KE03


title: KE05


title: CD3_1


title: dermal fibroblasts, black male, vehicle, TBS, biol rep 1

city: Providence

first: Calvin

last: Leung

state: RI

address: 70 Ship Street

department: MCB

institute: Brown University

data_processing:
TBS: Reads were aligned to the hg19 genome and methylation calls were performed using Bismark using default settings.
Assembly: hg19
Supplementary files format and content: Excel file includes TBS methylation values.

source_name: normal dermal tissue

extract_protocol:
DNA was extracted using the GenFind V3 DNA extraction and purification kit (Beckman Coulter).
TBS libraries were generated using the Collibri PCR-free DNA Library Prep Kit (ThermoFisher Scientific).
Targeted bisulfite sequencing (TBS)

value: normal dermal tissue

value: primary dermal fibroblasts

tag: race

value: black

value: vehicle


title: dermal fibroblasts, black male, cortisol, TBS, biol rep 1

value: cortisol


title: KE01


title: dermal fibroblasts, black female, cortisol, TBS, biol rep 1

value: female


title: KB25

source_name: blastocyst stage embryo

value: blastocyst stage embryo


title: KE06


title: KB24


title: Reference cells (IQDD22 reporter), plus inh, high light - rep3

city: La Jolla

first: Carl

last: Procko

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2)
Reads were aligned to Arabidopsis TAIR10 using TopHat version 2.0.9 (strand-specific).
Gene counts were determined using HTSeq 0.6.1 (intersection-strict) and edgeR for determining differential gene expression (paired experimental design where appropriate).
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Text files of gene counts determined by HTSeq.

organism: Arabidopsis thaliana

source_name: Leaf protoplasts

growth_protocol: Plants were grown for 17 d on 0.5X LS 0.7% agar under constant white light (50 uE.m-2.s-1).

extract_protocol:
RNA was extracted using TRIzol LS and digested with TURBO DNase.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Libraries were then quantified, pooled and sequenced at single-end 50 base-pair reads using the Illumina HiSeq 2500 platform. Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).

treatment_protocol: Protoplasts from first true leaves or roots were generated (with or without transcription inhibitors) and sorted based on fluorescent properties. For high light treatments, plants were treated for 2 h with 300 uE.m-2.s-1 immediately prior to protoplasting.

value: Leaf protoplasts

value: Reference cell

value: plus transcription inhibitors, high light

tag: pairing

value: L


title: KE04


title: KB23


title: CD28_2

value: Naive CD4+ T cells


title: LX2 cells, siNC_3

value: liver

value: Non parenchymal cell

value: WT


title: Palisade cells (IQD22 reporter), plus inh, high light - rep3

value: Palisade cell


title: CD28_1


title: dermal fibroblasts, black female, vehicle, TBS, biol rep 1


title: KB22


title: Palisade cells (IQD22 reporter), plus inh, high light - rep2

value: K


title: KB20


title: dermal fibroblasts, white male, cortisol, TBS, biol rep 1

value: normal dermal tissue

value: male

value: white


title: Reference cells (IQDD22 reporter), plus inh, high light - rep2


title: KB19


title: dermal fibroblasts, white male, vehicle, TBS, biol rep 1

value: primary dermal fibroblasts

value: vehicle


title: Reference cells (IQDD22 reporter), plus inh, high light - rep1

value: J


title: dermal fibroblasts, white female, cortisol, TBS, biol rep 1

value: female

value: cortisol


title: Reference cells (IQDD22 reporter), plus inh - rep3

value: Leaf protoplasts

value: Reference cell

value: plus transcription inhibitors, low light

value: I


title: Palisade cells (IQD22 reporter), plus inh, high light - rep1

value: plus transcription inhibitors, high light


title: IMR90 cells, cortisol, TBS, biol rep 6

source_name: normal lung tissue

value: normal lung tissue


title: KB18

value: blastocyst stage embryo


title: KB17


title: dermal fibroblasts, white female, vehicle, TBS, biol rep 1


title: KB16


title: KB14


title: KB15


title: KB13


title: KB12


title: IMR90 cells, cortisol, TBS, biol rep 5


title: KB11


title: KB21


title: Palisade cells (IQD22 reporter), plus inh - rep3

value: Palisade cell


title: KB10


title: Reference cells (IQDD22 reporter), plus inh - rep2

value: H


title: IMR90 cells, cortisol, TBS, biol rep 4


title: KB09


title: IMR90 cells, cortisol, TBS, biol rep 3


title: KB07


title: Palisade cells (IQD22 reporter), plus inh - rep2


title: KB08


title: KB06


title: Reference cells (IQDD22 reporter), plus inh - rep1

value: G


title: KB05


title: KB04


title: KB03


title: KB02


title: IMR90 cells, cortisol, TBS, biol rep 1


title: Total root protoplasts 3

source_name: Root protoplasts

value: Root protoplasts

value: no transcription inhibitors, low light


title: KB01


title: IMR90 cells, vehicle, TBS, biol rep 6


title: Day6_KO_Rep2

value: Primary B cells

value: Il6 K.O.

tag: time point


title: Total root protoplasts 2


title: IMR90 cells, vehicle, TBS, biol rep 5

value: vehicle


title: Day4_KO_Rep2


title: Day4_KO_Rep1


title: IMR90 cells, vehicle, TBS, biol rep 4


title: Pulse_KO_Rep2

value: Pulse


title: Palisade cells (JR11-2), no inh - rep3

value: F


title: Pulse_KO_Rep1


title: IMR90 cells, vehicle, TBS, biol rep 3


title: Bcell_KO_Rep2


title: IMR90 cells, cortisol, TBS, biol rep 2

value: cortisol


title: Day6_WT_Rep2

value: wildtype


title: Reference cells (JR11-2), no inh - rep3

value: Leaf protoplasts

value: Reference cell


title: IMR90 cells, vehicle, TBS, biol rep 2


title: Palisade cells (IQD22 reporter), plus inh - rep1

value: plus transcription inhibitors, low light


title: Palisade cells (JR11-2), no inh - rep2

value: E


title: IMR90 cells, vehicle, TBS, biol rep 1

value: normal lung tissue


title: Day4_WT_Rep2


title: Day4_WT_Rep1


title: Reference cells (JR11-2), no inh - rep2


title: Day6_KO_Rep1


title: Pulse_WT_Rep2


title: Total root protoplasts 1


title: IMR90 cells, cortisol and relacorilant, RNA, biol rep 6

data_processing:
Reads were aligned to the human reference genome hg38 using STAR v2.7.3a using default settings.
Gene counts were generated from STAR-aligned files using HTSeq v0.13.5 using default settings.
Differentially expressed genes were identified using DESeq2 v1.32.0 using default settings.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes normalized abundance measurements.  Excel file includes treatment groups compared to cortisol treatment.

extract_protocol:
RNA was harvested using the RNeasy Micro Kit (QIAGEN). DNA was extracted using the GenFind V3 DNA extraction and purification kit (Beckman Coulter).
RNA-seq libraries were prepared at Novogene Co., Ltd. (https://en.novogene.com/).

value: cortisol and relacorilant


title: Bcell_WT_Rep2


title: IMR90 cells, cortisol and relacorilant, RNA, biol rep 5


title: Pulse_WT_Rep1


title: Reference cells (JR11-2), no inh - rep1

value: D


title: Bcell_WT_Rep1


title: TSCs_C2_0

data_processing:
Reads were aligned using STAR (outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -sjdbOverhang 100 –outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
Bigwig files were generated using bamcoverage (--binSize 1 --normalizeUsing RPGC --extendReads 141)
Gene expression was quantified using STAR (--quantMode GeneCounts)
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Assembly: mm10
Supplementary files format and content: BigWig

source_name: trophoblast stem cell

growth_protocol:
ESCs: Embryonic stem cells (E14TG2) were cultured on gelatinized plates in 15% ES-FBS (16141079, Life Technologies) Knockout-medium (10829018, GIBCO) containing 1000 U/ml leukemia inhibitory factor (LIF) (ESG1106, Merck Millipore). The final culture medium also contained 100 U/mL Penicillin- 100 ng/mL Streptomycin (15140122, GIBCO), 2 mM L-Glutamine (25030081, GIBCO), 0.1 mM 2-Mercaptoethanol (31350010, Invitrogen)., 100X MEM Non-Essential Amino Acid solution (11140068, GIBCO) and 1 mM sodium pyruvate (11360070, GIBCO). ESCs were detached with accutase (A1110501, GIBCO).
Trophoblast stem cell lines (TSCs) were originally established in Janet Rossant’s laboratory and kindly provided by Dr. Manuel Irimia (CRG). They were cultured in feeder-free conditions as previously described (Kubaczka, C. et al., 2014). Briefly, TSCs were grown in 20%-FBS (10270-106, GIBCO) RPMI medium (12633012, GIBCO)  mixed with conditioned medium in a 3:7 proportion. To obtain feeder-conditioned medium, mitomycin-C inactivated MEFs were cultured in the presence of 20%-FBS RPMI, the supernatants collected from day 3 to 9 of culture and cleared through 0.45 µm filters (SLHV033RB, Millex). The final culture medium also contained 100 U/mL Penicillin- 100 ng/mL Streptomycin, 2 mM L-Glutamine, 0.1 mM 2-Mercaptoethanol, 100X MEM Non-Essential Amino Acid solution and 1 mM sodium pyruvate. TSCs were detached by trypsinization (25300096, GIBCO).

extract_protocol:
RNA was extracted from ESCs with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
For RNA-sequencing, libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (Illumina) followed by single-end sequencing (50 bp) on an HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

treatment_protocol: For C/EBPa expression, cells were infected with inducible C/EBPa-ERT2-dTomato lentiviral vector and single cell clones were expanded after FACS-sorting. For C/EBPa induction, cells were treated with 1 μM 4-hydroxytamoxifen (4-OHT) (H7904, Sigma) that shuttle the factor into the cell nucleus.

value: trophoblast stem cell


title: IMR90 cells, cortisol and relacorilant, RNA, biol rep 4


title: TSCs_C1_0


title: IMR90 cells, cortisol and relacorilant, RNA, biol rep 3


title: Reference cells (IQDD22 reporter), no inh - rep3

value: C


title: Day6_WT_Rep1


title: ESCs_C2_72

source_name: embryonic stem cell

value: embryonic stem cell


title: Palisade cells (IQD22 reporter), no inh - rep3

value: Palisade cell

value: no transcription inhibitors, low light


title: ESCs_C2_48


title: IMR90 cells, cortisol and relacorilant, RNA, biol rep 2


title: ESCs_C2_12


title: ESCs_C2_24


title: IMR90 cells, cortisol and relacorilant, RNA biol rep 1


title: Reference cells (IQDD22 reporter), no inh - rep2

value: B


title: Palisade cells (JR11-2), no inh - rep1


title: ESCs_C1_72


title: IMR90 cells, relacorilant, RNA, biol rep 6

value: relacorilant


title: ESCs_C1_48


title: ESCs_C1_24


title: ESCs_C1_12


title: Palisade cells (IQD22 reporter), no inh - rep1

value: A


title: Reference cells (IQDD22 reporter), no inh - rep1


title: ESCs_C1_0


title: IMR90 cells, relacorilant, RNA, biol rep 5


title: IMR90 cells, relacorilant, RNA, biol rep 4


title: Day 45 RNA-seq KO 3

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

description: processed data file: LFC_D45.csv, geneCounts.csv

data_processing:
Illumina NextSeq Control Software v2.2.0.4 for base calling
RNA-seq: Reads aligned to GRCm38/mm10; Gencode vM24 using STAR v2.7.3a with default settings
RNA-seq: Transcript abundance measured using Salmon v1.4.0 in alignment mode with seqBias and gcBias settings
RNA-seq: Differential gene expression determined using DESeq2
scRNA-seq: Cellranger v5.0.0 used to demultiplex and convert to fastq
scRNA-seq: barcode detection, read mapping, quality filtering and transcript counting performed with Alevin (Salmon v1.4.0). Processing steps are documented in "scRNAseq_commands.txt"
Genome_build: GRCm38/mm10; Gencode vM24
Supplementary_files_format_and_content: csv file showing KO vs WT differential gene expression metrics for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: csv file showing gene counts for each gene in each sample for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: matrix file for gene counts per cell for scRNA-seq. Output of Salmon Alevin.

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse beta cells with S2 cell spike-in

extract_protocol:
RNA-seq: FACS-enriched beta cells were pooled with a 10% spike-in of S2 cells. RNA was isolated using Trizol.
RNA libraries were prepared from 400ng of total RNA per sample using poly-A capture beads and NEBNext directional RNA-seq library prep kit for Illumina (E7760). scRNA-seq libraries were prepared using Chromium Single Cell 3’ protocol with Reagent Kit v3.1 (10X Genomics)

value: PdxCreER mTmG

value: Mouse beta cells with S2 cell spike-in

tag: genotype/variation


title: Day 45 RNA-seq KO 2


title: Day 45 RNA-seq KO 1


title: 6W rep2 RNA-seq

city: Blacksburg

first: Zachary

last: Johnson

state: VA

address: 1015 Life Science Cir

department: FLSI

institute: Virginia Tech

description: 6W rep2 RNA-seq RNA-seq

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Assembly: mm10
Supplementary files format and content: tab-delimited transcript abundance counts for all RNAseq samples
Supplementary files format and content: tab-delimited files containing methylation calling information for each called methylated site

source_name: Whole brain tissue

extract_protocol: Total RNA is extracted using TRIzol reagent combined with RNeasy min kit (QIAGEN) with DNase I on-column digestion. To enrich poly(A)-containing mRNAs, two rounds of poly(A) selection are performed using oligo(dT) beads (ThermoFisher) following the manufacturer’s instructions.

value: Whole brain tissue


title: 6W rep1 RNA-seq

description: 6W rep1 RNA-seq RNA-seq


title: IMR90 cells, relacorilant, RNA, biol rep 2


title: ESCs_C2_0


title: Palisade cells (IQD22 reporter), no inh - rep2

value: Leaf protoplasts


title: IMR90 cells, relacorilant, RNA, biol rep 3


title: Day 45 RNA-seq WT 1

value: CTRL


title: Day 15 RNA-seq KO 3

description: processed data file: LFC_D15.csv, geneCounts.csv


title: P17 rep1 RNA-seq

description: P17 rep1 RNA-seq RNA-seq


title: P17 rep2 RNA-seq

description: P17 rep2 RNA-seq RNA-seq


title: Day 15 RNA-seq KO 2


title: Day 15 RNA-seq KO 1


title: IMR90 cells, cortisol, RNA, biol rep 6

value: cortisol


title: IMR90 cells, cortisol, RNA, biol rep 5

value: normal lung tissue


title: IMR90 cells, cortisol, RNA, biol rep 4


title: Day 15 RNA-seq WT 1


title: P0 rep1 RNA-seq

description: P0 rep1 RNA-seq RNA-seq


title: Day 15 RNA-seq WT 3


title: Day 45 H3K27me3 ChIP-seq KO 2

data_processing:
Illumina NextSeq Control Software v2.2.0.4 for base calling
Reads aligned to GRCm38/mm10 using  Bowtie2 v2.3.4.1 with options ‘--very-sensitive --no-unal --no-discordant’
Multi-mapped reads, reads with mapping quality MAPQ < 20, and suspected PCR-duplicates were discarded using Samtools
bw files were generated using BEDtools, adjusted using the Drosphila read fraction, and bedGraphToBigWig
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwigs showing genome enrichment scores, adjusted by drosophila cell spike-in read fraction

extract_protocol:
FACS-enriched beta cells were pooled with a 50% spike-in of drosophila S2 cells. Chromatin was fragmented with MNase and histone-DNA complexes were extracted using antibodies
ChIP libraries were prepared using NEBNext II Ultra DNA library prep kit for Illumina (E7645)

tag: chip antibody


title: Day 45 RNA-seq WT 3

tag: strain


title: IMR90 cells, cortisol, RNA, biol rep 3

tag: tissue


title: Day 45 RNA-seq WT 2


title: IMR90 cells, relacorilant, RNA, biol rep 1


title: Neuron rep2 RNA-seq

description: Neuron rep2 RNA-seq RNA-seq

source_name: Cortical neuron culture

value: Cortical neuron culture


title: Neuron rep1 RNA-seq

description: Neuron rep1 RNA-seq RNA-seq


title: Day 45 H3K27me3 ChIP-seq WT 2


title: Day 45 H3K27me3 ChIP-seq KO 1


title: Day 45 H3K27me3 ChIP-seq WT 1


title: IMR90 cells, cortisol, RNA, biol rep 2


title: IMR90 cells, cortisol, RNA, biol rep 1


title: P0 rep2 RNA-seq

description: P0 rep2 RNA-seq RNA-seq


title: Day 45 H3K27ac ChIP-seq KO 2


title: Final-biol_rep_1

city: Wuhan

first: Haoran

last: Yang

address: Shizishan Street No.1, Hongshan Distric

institute: Huazhong Agricultural University

data_processing:
The obtained raw reads were subsequently undergone a series of quality control processes including the removal of reads containing adaptor contamination as well as those containing more than 5% of the unknown bases (N) for downstream analysis.
Reads with accepted quality were then mapped to the reference genome and reference genes with HISAT (2.0.1-beta) and Bowtie2 (2.2.5) software, respectively.
RSEM software was used to calculate the expression value of each gene, which was presented with Fragments Per Kilobase Million (FPKM) value.
Based on the comparison scheme, differently expressed genes were identified by DESeq2 algorithm.
Assembly: Assembly: GCA_002173515.1
Supplementary files format and content: tab-delimited text files include FPKM values as well as log2 (Fold Change) value for the corresponding samples.

organism: Komagataeibacter europaeus

extract_protocol:
RNA was extracted with RNAprotect Bactera Reagent (Qiagen) according to manufacturer's instructions.
cDNA library was constructed with Illumina TruSeq Stranded Kit

value: bacterial cells

value: fermentation final stage (acidity 11.7percent)


title: Final-biol_rep_2


title: NSC rep1 RNA-seq

description: NSC rep1 RNA-seq RNA-seq

source_name: Neural stem cells

value: Neural stem cells


title: NSC rep2 RNA-seq

description: NSC rep2 RNA-seq RNA-seq


title: IMR90 cells, vehicle, RNA, biol rep 6

value: vehicle


title: Day 45 H3K27ac ChIP-seq KO 1


title: Day 15 RNA-seq WT 2


title: Mid-biol_rep_2

value: fermentation mid stage (acidity 10.5percent)


title: Mid-biol_rep_1


title: IMR90 cells, vehicle, RNA, biol rep 5


title: 6W rep1 RNA Bisulfite-seq

description: 6W rep1 RNA Bisulfite-seq RNA Bisulfite-seq

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Assembly: mm10
Supplementary files format and content: tab-delimited transcript abundance counts for all RNAseq samples
Supplementary files format and content: tab-delimited files containing methylation calling information for each called methylated site
Library strategy: RNA bisulfite-seq

extract_protocol:
Total RNA is extracted using TRIzol reagent combined with RNeasy min kit (QIAGEN) with DNase I on-column digestion. To enrich poly(A)-containing mRNAs, two rounds of poly(A) selection are performed using oligo(dT) beads (ThermoFisher) following the manufacturer’s instructions.
RNA bisulfite conversion was performed as described previously with minor modifications. Briefly, poly(A) RNA was first mixed with spiked-in Xef1 unmethylated RNA at a ratio of 0.5%. The spiked-in unmethylated mRNA was transcribed from the pTRI-Xef plasmid supplied by the MEGAscript™ T7 Transcription Kit (Invitorgen), which encodes 1.85 kb Xenopus elongation factor 1α mRNA according to the manufacturer’s manual. Briefly, the linearized pTRI-Xef plasmid was in vitro transcribed in a reaction with MEGAscript T7 RNA polymerase (Ambion) at 37 °C for 4 h, followed by DNase treatment at 37 °C for 15min to remove DNA template and then purified by RNeasy Mini Kit (QIAGEN).  RNA bisulfite conversion was performed with an initial denaturation at 95°C for 1min, followed by three cycles of 70°C for 10min and 64°C for 45min using the EZ RNA methylation Kit (Zymo Research). The bisulfite converted RNA was subjected to stranded RNA-seq library construction procedure using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).


title: 6W rep2 RNA Bisulfite-seq

description: 6W rep2 RNA Bisulfite-seq RNA Bisulfite-seq


title: Day 45 H3K27ac ChIP-seq WT 2


title: Day 45 H3K27ac ChIP-seq WT 1


title: Initial (CK) -biol_rep_2

description:
K8_1-VSK10_5.xls
K8_1-VSK11_7

value: fermentation initial stage (acidity 8.1percent)


title: IMR90 cells, vehicle, RNA, biol rep 4


title: P17 rep2 RNA Bisulfite-seq

description: P17 rep2 RNA Bisulfite-seq RNA Bisulfite-seq


title: Initial (CK) -biol_rep_1

description:
K8_1-VSK10_5.xls
K8_1-VSK11_7


title: Day 45 H3K4me1 ChIP-seq KO 2


title: P17 rep1 RNA Bisulfite-seq

description: P17 rep1 RNA Bisulfite-seq RNA Bisulfite-seq


title: IMR90 cells, vehicle, RNA, biol rep 3


title: IMR90 cells, vehicle, RNA, biol rep 2


title: Day 45 H3K4me1 ChIP-seq WT 2


title: P0 rep1 RNA Bisulfite-seq

description: P0 rep1 RNA Bisulfite-seq RNA Bisulfite-seq


title: P0 rep2 RNA Bisulfite-seq

description: P0 rep2 RNA Bisulfite-seq RNA Bisulfite-seq


title: leaf_scRNA-seq

first: Travis

middle: Andrew

last: Lee

description: Single-cell sequencing of mature leaf protoplasts, processed by 10X Genomics 3' Gene Expression, v3

data_processing:
Raw sequencing reads were demultiplexed demultiplexed and aligned to the TAIR10 genome, Araport 11 201606 transcriptome using CellRanger v3.1.0
Low quality cells were filtered by low UMI and low number of genes detected using Seurat v3.0
Doublets were identified and removed from the filtered subset of cells using DoubletDecon v1.1.4
The filtered dataset was normalized and scaled using Seurat v3.0
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: matrix.mtx.gz: mtx cell-by-gene file of cells following filtering by CellRanger
Supplementary_files_format_and_content: Final_doublets_groups_IQD22.txt: txt file of doublet cells identified by DoubletDecon
Supplementary_files_format_and_content: Seurat_dedoublet.rds: Seurat rds object of SCTransformed and normalized data using Seurat v3.0

extract_protocol: 10X Genomics 3' Gene Expression v3

tag: cultivar

value: constant light (50 uE.m-2.s-1)


title: Neuron rep2 RNA Bisulfite-seq

description: Neuron rep2 RNA Bisulfite-seq RNA Bisulfite-seq


title: Treat-2

city: Shanghai

first: Tony

last: Xu

address: 69 Yuanfeng Road, Baoshan District

institute: Shanghai Drug Farm Biotechnology Co.

data_processing:
Sequence reads were mapped to mouse genome GRCm38.p6 by HISAT and the read count of each gene was used as the quantification for downstream analysis
Assembly: mm9
Supplementary files format and content: tab-delimited text files include gene expression and counts for each Sample

source_name: Liver

growth_protocol: Male C57B6/J mice were bred in a specific-pathogen-free facility under a 12 hour light 12 hour dark cycle. At 4-5 weeks age, mice were inoculated with AAV-HBV through i.v. injection and maintained for another 28 days until compound treatment.

extract_protocol:
Four hours after oral administration, liver tissue was dissected, homogenized directly in TriZOL reagent at 4 ℃, and total RNA was extracted following manufacturer's manual.
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added for end-repair. cDNA fragments were amplified by PCR, and products were purified by Ampure XP Beads (Beckman Coulter, Pasadena, CA), then dissolved in Tris buffer. The double stranded PCR products were heated, denatured and circularized by the splint oligo sequence to get the final single strand circle DNA (ssCir DNA) library. The final library was amplified with phi29 to make DNA nanoball (DNB) and DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform.

treatment_protocol: Vehicle (saline) or 10 μg/kg b.w. DF-006 were injected into mice through oral gavage in a volume of 10 ml/kg b.w.

value: male

value: Liver

tag: model

value: 28 days after 1011vg/mouse AAV-HBV inoculation


title: Treat-1


title: Treat-3


title: Day 45 H3K4me3 ChIP-seq KO 2

value: PdxCreER mTmG

value: Mouse beta cells with S2 cell spike-in


title: Control-3

value: Vehicle


title: lepb-/- 3

description: 150 nucleotides

data_processing:
Sequencing data of zebrafish larvae were aligned and mapped to the zebrafish genome GRCz11 using Salmon v1.2.1, and differential gene expression was analyzed using DESeq2 v1.21.1.
Gene Ontology (GO) term enrichment and KEGG pathway analysis were performed in DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: tab-delimited text files include normalized read values per million for each Sample

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from lepb+/+ and lepb-/- groups (n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: lepb mutation

value: whole embryos

value: 5 days post fertilization

value: lepb-/-


title: Neuron rep1 RNA Bisulfite-seq

description: Neuron rep1 RNA Bisulfite-seq RNA Bisulfite-seq

value: Cortical neuron culture


title: Day 45 H3K4me3 ChIP-seq KO 1


title: NSC rep2 RNA Bisulfite-seq

description: NSC rep2 RNA Bisulfite-seq RNA Bisulfite-seq


title: Day 45 H3K4me1 ChIP-seq KO 1


title: Day 45 H3K4me3 ChIP-seq WT 2

value: CTRL


title: lepb-/- 1

description: 150 nucleotides


title: Control-1


title: lepb+/+ 3

description: 150 nucleotides

value: wild type

value: lepb+/+


title: Day 45 H3K4me3 ChIP-seq WT 1


title: Day 45 H3K4me1 ChIP-seq WT 1


title: NSC rep1 RNA Bisulfite-seq

description: NSC rep1 RNA Bisulfite-seq RNA Bisulfite-seq

value: Neural stem cells


title: IMR90 cells, vehicle, RNA, biol rep 1

value: normal lung tissue

tag: cell line

value: vehicle


title: P7_L1L2AKO_adipocyte_rep 3

first: Hongyu

last: Shen

address: Wang Kezhen Building, No.5 Yiheyuan Road

institute: Peking University

data_processing:
Sub-pixel Registration used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using HISAT2 (v2.1.0)
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated by StringTie (v1.3.5)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Adipocytes were isolated from four pooled male P7 L1L2-FF or L1L2-AKO mice. Inguinal scWAT were minced carefully with scissors for 3-5 min and digested with 4 mg/ml Collagenase Type I (in 4 mL PBS containing 1% BSA) at 37°C with agitation at 170 rpm for 12-15 min. The digested cell suspension was quenched in 4 mL PBS containing 1% BSA, followed by free floating for 5 min. After removing infranatant with a syringe and needle, floated cells were filtered using a 300 μm strainer and washed with 3 mL PBS containing 1% BSA. Floated adipocytes were collected by centrifugation at 30 × g for 5 min and lysed with Trizol reagent for total RNA extraction.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

value: adipocyte

value: subcutaneous white adipose tissue

tag: developmental stage

value: male


title: lepb+/+ 2

description: 150 nucleotides


title: lepb+/+ 1

description: 150 nucleotides


title: lepb-/- 2

description: 150 nucleotides


title: Control-2

tag: Sex

value: Liver

value: 28 days after 1011vg/mouse AAV-HBV inoculation


title: RY1384

data_processing:
RNA-seq fastq reads were mapped to mm10 genome using STAR. Reads mapped to genes were counted using HTSeq and normalized using vst function from the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

source_name: bone marrow

extract_protocol:
Bone marrow was isolated from dissected tibiae and femur from mice. B220 positive B cells were harvested by flow cytometry sorting.
Total RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.

value: bone marrow

tag: genotype

value: willdype

value: B220 B cells


title: RY1388

value: Arid5b overexpression


title: RY1390


title: P7_L1L2FF_adipocyte_rep 3


title: RY1381

value: wildtype


title: Dapi.pos.100nuc.monkey.techrep1

city: Rehovot

first: Daniella

last: Apelblat

address: Hertzl

department: Neuroscience

country: Israel

institute: Weizmann Institute of Science

description: Dapi+ 100 nuclei monkey technical replicate 1

data_processing:
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Mouse samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the mm10 genome using STAR version 2.5.3a.
Monkey samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the Macaca fascicularis 6.0 genome using STAR version 2.5.3a.
Genome_build: mm10, Macaca fascicularis 6.0
Supplementary_files_format_and_content: .csv files include raw read values for every gene in the sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Macaca fascicularis

source_name: Monkey Visual Cortex

extract_protocol:
Freshly dissected visual cortices were snap frozen in liquid nitrogen and stored at -80C. Nuclei were then extracted,  stained with antibodies and Dapi and FACS-sorted  into 0.2ml low-bind tubes containing 2.03 µl lysis buffer.
Libraries were prepared based on the Smart-Seq2 protocol with small modifications. Briefly, 100 nuclei were collected directly into 2.03 microliter lysis buffer (0.2% Triton X-100 in ddW) supplemented with dNTPs (2mM each), SMART-dT30VN primers (1mM), ERCC (1:1.25x107), and RNAse inhibitor. Reverse transcription was performed directly on isolated nuclei, followed by PCR-amplification (17 cycles). After cleanup with Agencourt Ampure XP beads (Beckman Coulter), the amplified cDNA underwent library generation using Nextera XT (Illumina). Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).

value: cortex


title: P7_L1L2AKO_adipocyte_rep 1


title: Dapi.pos.100nuc.monkey.techrep2

description: Dapi+ 100 nuclei monkey technical replicate 2


title: Neuron N40K (replicate 3)

first: Yingxue

last: Fu

state: Tennessee

address: 262 Danny Thomas Place

description: Construct includes short CaMKII promoter, N40K, a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) and long terminal repeats (LTR).

data_processing:
Basecalls performed using Illumina Casava software.
Fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
BAM files were converted to BED files using bedtools (bamToBed, v2.16.1). Table Browser program (http://genome.ucsc.edu) was used to generate three BED files: (i) RefSeq Genes (Whole Gene), (ii) RefSeq Genes (Exons) and (iii) RefSeq Genes (Introns).
intersectBed (v2.16.1) was used to define the intersections between mapped reads and the three RefSeq BED files.
A splicing deficiency (Sd) score was calculated for each gene as the ratio of length-corrected read counts aligned to introns and exons
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table of Sd scores for every gene and every sample

growth_protocol: Mouse cortical neurons were isolated from mouse embryos (C57BL/6) at E18, and cultured in completed Neurobasal A (Life Technologies) supplemented with B27 complex and GlutaMAX.

extract_protocol:
For neuronal culture, total RNA was extracted by RNAeasy Mini kit (Qiagen). For mouse hippocampus or cortex, total RNA was extracted by RNA-easy Lipid Tissue Kit (Qiagen) as described in the manual, including with DNAse I digestion to remove contaminated DNA.
RNA sequencing libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina), including poly(A) RNA purification. Libraries were then quantified using the Quant-iT PicoGreen dsDNA assay (Thermo Fisher) and MiSeq Reagent Kit Nano v2 (Illumina). One hundred cycle paired-end sequencing (100 bp) was performed on an Illumina HiSeq 2500.

treatment_protocol: At DIV 7, neurons were treated with lentiviral particles of vector control FCK1.3GW or FCK1.3GW-N40K for 3 days.

value: Cortical neuron culture

tag: lentivirus


title: Prox1neg.NeuNpos.100nuc.monkey.techrep2

description: Prox1- NeuN+ 100 nuclei monkey technical replicate 2


title: P7_L1L2FF_adipocyte_rep 2

tag: cell type


title: P7_L1L2FF_adipocyte_rep 1


title: Neuron N40K (replicate 2)


title: P7_L1L2AKO_adipocyte_rep 2


title: Nbmockpoly_4

city: Daejeon

first: Hyo-Jun

address: Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Sequencing adapters were trimmed using the Cutadapt and low quality bases were removed using the DynamicTrim and the LengthSort of the SolexaQA package.
High quality reads were mapped to the reference transcripts using the HISAT2 software.
Normalization was performed using the DESeq library of R software and expression was analyzed using the HTSeq(v.0.11.0).
Functional annotation information was obtained from SGN (https://solgenomics.net)
Assembly: Nicotiana benthamiana reference transcripts v1.0.1 (https://solgenomics.net)
Supplementary files format and content: An excel file containing read counts and differentially expressed genes

organism: Nicotiana benthamiana

source_name: Leaves

growth_protocol: Plants were grown in soil for 5 weeks under long-day conditions at light intensity of 100 mmol m-2 s-1

extract_protocol:
Total RNA and polysome RNA were extracted using Trizol
Library construction was performed according to the protocol of Seeders, an RNA-sequencing company in South Korea

treatment_protocol: Plants were left at 23oC or exposed to 37oC for 1 h.

tag: treatment

value: Left at 23oC for 1 h

value: 5-week-old plants grown in soil

tag: fraction

value: Polysome RNA


title: Prox1neg.NeuNpos.100nuc.monkey.techrep1

description: Prox1- NeuN+ 100 nuclei monkey technical replicate 1


title: Prox1pos.NeuNpos.100nuc.monkey.techrep2

description: Prox1+ NeuN+ 100 nuclei monkey technical replicate 2


title: Neuron N40K (replicate 1)


title: Neuron Control (replicate 3)

description: Construct includes short CaMKII promoter, EGFP, a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) and long terminal repeats (LTR).


title: Nbmockpoly_3


title: Prox1pos.NeuNpos.100nuc.monkey.techrep1

description: Prox1+ NeuN+ 100 nuclei monkey technical replicate 1


title: Neuron Control (replicate 2)


title: Nbmockpoly_2


title: Nbmockinput_7


title: Neuron Control (replicate 1)


title: oQSC, RNA Rep2

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: aging.csv

data_processing:
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown

source_name: In situ fixed old satellite cells

extract_protocol:
RNA was isolated using miRNeasy FFPE Kit (Qiagen).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol and processed for library generation using Tn5-mediated library generation. Sequencing was carried out in 2 × 100 cycle paired-end mode on a DNBSEQ-G400 sequencer (BGI).

treatment_protocol: Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.

value: Skeletal muscle

value: Muscle stem cells

tag: time


title: Nbmockinput_6


title: oQSC, RNA Rep1

description: aging.csv


title: 12 month Tau P301S (replicate 6)

description: Tau P301S littermates by crossing Tau P301S and WT mice

source_name: Cortex

extract_protocol:
Total RNA was extracted by RNAeasy Mini kit (Qiagen). For mouse hippocampus or cortex, total RNA was extracted by RNA-easy Lipid Tissue Kit (Qiagen) as described in the manual, including with DNAse I digestion to remove contaminated DNA.
RNA sequencing libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina), including poly(A) RNA purification. Libraries were then quantified using the Quant-iT PicoGreen dsDNA assay (Thermo Fisher) and MiSeq Reagent Kit Nano v2 (Illumina). One hundred cycle paired-end sequencing (100 bp) was performed on an Illumina HiSeq 2500.

value: Tau P301S

tag: mating

value: Tau P301S +/- x  WT

value: Cortex


title: Nbmockinput_5


title: 28dpi, RNA Rep2

description: regeneration.csv

source_name: 28 days post-injured satellite cells followed by in situ fixation

value: BaCl2 injury


title: 12 month Tau P301S (replicate 5)


title: 28dpi, RNA Rep1

description: regeneration.csv


title: 12 month Tau P301S (replicate 4)


title: Nbheatpoly_7

value: Exposed to 37oC for 1 h


title: 14dpi, RNA Rep2

description: regeneration.csv

source_name: 14 dayspost-injured satellite cells followed by in situ fixation


title: 12 month Tau P301S (replicate 3)


title: Nbheatpoly_6


title: Nbheatpoly_5


title: 12 month Tau P301S (replicate 2)


title: Nbheatinput_4


title: 7dpi, RNA Rep2

description: regeneration.csv

source_name: 7 days post-injured satellite cells followed by in situ fixation


title: Nbheatinput_3


title: 7dpi, RNA Rep1

description: regeneration.csv


title: 60hpi, RNA Rep2

description: activation.csv

source_name: 60 hours post-injured satellite cells followed by in situ fixation


title: 12 month Tau P301S (replicate 1)


title: 14dpi, RNA Rep1

description: regeneration.csv

source_name: 14 days post-injured satellite cells followed by in situ fixation


title: 12 month WT (replicate 3)

description: Wild-type littermates by crossing Tau P301S and WT mice

value: WT


title: Nbheatinput_2


title: 60hpi, RNA Rep1

description: activation.csv


title: v3.9.8

first: Daniel

description: nuclear RNA

data_processing:
Alignment: The raw sequencing reads were aligned to a marmoset genome assembly, ASM275486v1 (GCA_002754865.1). To build a reference package suitable for analyzing both unspliced pre-mRNA and mature mRNA in the nuclei, as well as to include sequences of mito-chondrial genome, marmoset DNA sequence (FASTA) and annotation (GTF) files were acquired from the Ensembl release-95 and modified as follows. The complete mitochondrial sequence (NC_025586.1, GenBank) and its annotation (Wang et al., 2016) were manually added to the FASTA and GTF files. Next, a pre-mRNA GTF was made by replacing “transcript” with “exon” as the feature-type entry in the original GTF before making a reference package with CellRanger software (v3.0.2, 10x Genomics). This custom-built reference package was then used in CellRanger (version 3.1.0, 10x Genomics) to align sequencing reads for all samples. The option to estimate cell number automatically was used for most of the samples, unless otherwise speci-fied (see Table S1 for details). A filtered cell barcode-to-gene feature matrix was generated from the software and used for downstream analysis (Figure S2A).
Preprocessing & general quality control: The matrix was loaded to create an object in Seurat v3 (Butler et al., 2018; Stuart et al., 2019). Cells with <200 genes, >5000 genes, or >5% of counts mapped to mitochondrial genome were excluded. Genes observed in <5 cells were excluded. The filtered raw count matrix was then log normalized (ln(counts*100,000+1)) within each cell and scaled to account for differences in sequencing depth with Seurat. Next, DoubletFinder (McGinnis et al., 2019) was used to esti-mate and remove putative doublets to mitigate technical confounding artifacts in droplet-based sequencing data analysis. The top 3000 variable genes calculated by Seurat were used in linear dimension reduction (principal components analysis, PCA), and the top 30 PCA were used for clustering at low resolution (parameter = 0.4) to define crude cell types. These unsupervised clusters were used to provide a quick cluster annotation for homotypic doublet probability model-ing in DoubletFinder. Doublet rate was estimated by fitting a linear equation over a multiplet rate table provided by 10x Genomics. The rate = (0.0008*cell.number + 0.0527)/100) was used to calculate a Poisson distribution with and without homotypic doublet proportion to generate low confidence (DF.found.1) and high confidence (DF.found.2) doublet annotation. Unless otherwise specified, pN = 0.25, pK = 0.005 and automatic doublet removal based on DF.found.2 annotation were used, as the first line of screening. In parallel, SoupX (Young and Behjati, 2020) was used for ambient RNA background correction. Taken from the output of the 10x pipeline (raw_feature_bc_matrix), the ambient RNA from empty droplets that contained <10 unique mo-lecular identifiers (UMI) were profiled, and the “soup” contamination fraction was calculated for each cluster. Given that the nuclear transcriptome was profiled, genes that mapped to the mito-chondrial genome could be considered as ambient input. Therefore, the top mitochondrial genes (species with >1000 accumulated counts across profiled empty droplets) were used to estimate the global contamination fraction and adjust the raw count matrix. Next, the cell barcode that passed the DoubletFinder was used as an index to subset the SoupX-corrected matrix to gener-ate a new matrix as our downstream input (Figure S2A). For individual samples, a Seurat object was created, and the index labels (IL01_uniqueID, IL02_species, IL03_source, IL04_sex, IL05_ageDays, IL06_tissue.1, IL06_tissue.2, IL06_tissue.3, IL07_location, IL08_condition, IL09_illumina, IL10_chemistry, IL11_batch, IL12_LMinDays, IL13_LMaxDays, IL14_dataset, IL15_annotation) were added to the metadata as cell attributes. For each sample, 90% of nuclei were randomly selected, then all 42 samples were merged together for downstream comparison. The remaining 10% of the nuclei were set aside for classification assessment and validation.
Level 1 quality control & clustering: To divide nuclei into classes and facilitate artifact identification, nuclei were first classified using a set of parameters that does not highlight granular detail. In this round of clustering, only 50 PC for Harmony were computed to perform linear correction over IL01_uniqueID, as the el-bow plot from the preliminary analysis showing the standard deviation stopped visually decreas-ing after top 50 PC. The top 5 Harmony-corrected embeddings (H5) were used for Seurat to learn the UMAP and find cell classes at a low resolution (0.2). Canonical cell-type markers (PTPRC for immune cells, PDGFRA for OPC, MAG for oligodendrocytes, GFAP and SLC1A2 for astrocytes, LEPR and CEMIP for vasculature and meningeal cells, and CNTN5 and NRG1 for neurons) annotated 6 of the classes unambiguously. One cluster in the middle of the H5 UMAP had mixed expression of canonical markers, which suggested artifact. The “low quality” cell bar-codes that were found from the H50 condition (defined above) were overlaid on the H5 UMAP, which exclusively highlighted the putative artifact cluster. These nuclei were removed from fur-ther analysis, although the original UMAP embeddings were maintained for plotting purposes (Figure 1 and S3).
Level2 quality control & clustering: Nuclei that passed Level 1 QC were divided into 5 partitions (MIC, OPC, OLI, VAS/AST, NEU) based on the H5 UMAP result. The astrocytes and vasculature/meningeal cells were pooled into a single class prior to subclustering to facilitate artifact identification. Shared features in this class of cells were potentially explainable by their close association at CNS barriers (blood–CSF interface, blood–brain interface, and the CSF–brain interface). For each class, log-normalization and scaling were repeated from the divided raw count matrix, the top 3000 variable genes were used for 50 PC computation, Harmony correction over IL01_uniqueID, UMAP learn-ing, and clustering, as described above. The clustering resolution was iteratively increased from low to high (0–1.2), and clustering stability was tracked with clustree (v0.4.3) (Zappia and Oshlack, 2018). Aided by the branch visualization provided by the clustree, a tentative resolution that was relatively stable was selected, then differentially expressed gene (DEG) analysis on the clusters found with this parameter set was performed. The expression pattern of the top-expressed genes for each cluster within and across classes were checked, and artifacts clus-ters were manually imputed. Doublets tended to form small distinct clusters on UMAP that branched early in the clustering tree analysis with low splitting resolution, had mixed canonical marker-gene expression, and had similar expression patterns to cells in other partitions; thus, these doublets could be easily spotted and removed. For putative doublets within each class, additional rounds of DEG analysis were performed as necessary. Each time nuclei were re-moved, basic normalization, scaling, Harmony, and UMAP learning were repeated. To control for over-splitting, for clusters that appeared to be a single pile in the 2D UMAP space but were anno-tated into >1 cluster, additional rounds of DEG analysis were performed to see if binary markers could be found to label them. In addition, clustering was projected onto a 3D UMAP space to en-sure effects were not masked due to overcrowding in 2D. This strategy also helped to further elucidate cluster associations, aid decision-making with respect to groups of clusters that should be tested further, and spot potential gradient changes among clusters. If unique and or binary patterns could not be found in the current splitting resolution after these steps were performed, a step lower in resolution on the clustering tree was examined, and the analysis process was re-peated. The following compound naming convention to la

extract_protocol:
Tissue dissection: On the day of tissue harvest, marmosets were deeply anesthetized with 5% isoflurane until all visible signs of breathing were no longer detected. Animals were transcardially perfused with ice-cold artificial cerebrospinal fluid (aCSF) for 5 min with a pump. Brains were removed from the skull and submerged into ice-cold aCSF, and after removal of meninges within the solu-tion, were positioned in a custom-designed brain holder within 10 min post-perfusion. The brain was sectioned at 3 mm into 12–13 slabs in one step with a homemade blade-separator set in the solution. Each brain slab was transferred into a 6-well plate, submerged into RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen) with a homemade brain trap, and stored at 4°C overnight. The following day, brain slabs were positioned in 25 x 20 x 5 mm molds (Tis-sue-Tek® Cryomold®, 4557, Sakura Finetek) on ice to facilitate target sampling. Slabs were matched to MRI for each animal, and tissue annotation for gray (Liu et al., 2018a) and white matter (Liu et al., 2020) was informed by marmoset 3D MRI atlases V1 and V2. A cylinder of tissue 2 mm in diameter and 3 mm in height for each region (Figure 1B and S1) was collected with a tissue punch (EMS-core sampling tool, 69039-20, EMS). There were 5 white matter sam-ples from temporal and parietal lobes that did not exactly match in the two animals, however they were paired in lobes of the brain and showed no significant differences in later analysis (Figure 1B, SS05, SS06, and SS08). The cylinders were ejected into PCR tubes filled with 100 µL of RNAlater and stored at −80°C. Single-nucleus dissociation: Nuclei preparation was carried out as described (Matson et al., 2018), with minor modifi-cations. Briefly, on the day of dissociation, tissue samples were thawed on ice, removed from solution, dabbed with Kimwipes to remove residual RNAlater, and placed in a 1 mL douncer tube (Dounce Tissue Grinder, 357538, Wheaton). Each tissue was homogenized in 500 μL of lysis buffer containing 0.1% Triton-X100 in low sucrose buffer (0.32 M sucrose, 10 mM HEPES, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, and 1 mM DTT in ddH2O, pH8) with loose pestle 25 times and tight pestle 10 times. The homogenate was filtered through a 40-μm mesh (Falcon® 40 µm Cell Strainer, 352340, Corning) to a 50-mL Falcon tube on ice. An additional 5 mL of low sucrose buffer was used to rinse the douncer tube and cell strainer. The filtered homogenate was further mixed with a handheld homogenizer (VWR® 200 Homogenizer) at a speed of ~1000 rpm to brake nuclei clumps for 5 sec. After homogenization, a serological pipet filled with 12 mL of high sucrose buffer (1 M sucrose, 10 mM HEPES, 3 mM MgAc, and 1 mM DTT in ddH2O, pH8) was placed underneath the lysate and disconnected from the pipettor, and the buffer was released from the serological pipette by gravity and set on ice. When most of high sucrose buffer was re-leased to form a density layer underneath the homogenate, the serological pipet was retrieved along the wall of the Falcon tube gently, without disturbing the low-high sucrose interface. The Falcon tube was capped and placed in a swing bucket to be centrifuged at 3,200 rcf for 30 min at 4°C. At the end of spin, the supernatant was decanted quickly without tabbing, and 1 mL of re-suspension buffer (0.02% BSA in 1X PBS, pH7.4) was added to the Falcon tube. Slow pipetting was employed to resuspend nuclei along the Falcon tube wall below the 5-mL mark to preserve nuclei integrity. Specifically, nuclei were rinsed off the wall in courses of 2 sec per trituration for 20 times total per tube. The Falcon tube was then capped and spun at 3,200 rcf for 10 min at 4°C. At the end of spin, the supernatant was removed by gently tabbing the tube until no visible liquid drop was left behind, and 200 μL of resuspension buffer was added to each sample to collect the nuclei. The nuclei suspension was filtered through a 35-μm mesh (Cell Strainer Snap Cap, 352235, Corning) twice and counted on a hemocytometer by trypan blue staining. During count-ing, the size and quantity of myelin and other debris were visually inspected under the scope, and the suspension was filtered 1–3 more times through the 35-μm mesh if necessary. Only round and dark-blue stained nuclei were considered of good quality and included in the final count.
10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v2 and v3

value: F

value: WM

value: Diencephalon

value: OpT

value: NaiveCtrl


title: Bcell_KO_Rep1

first: Gregoire

data_processing:
Illumina adapters were trimmed using /software/tgraf/TrimGalore/trim_galore with default parameters
Reads were aligned using STAR (outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -sjdbOverhang 100 –outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
Bigwig files were generated using bamcoverage (--binSize 1 --normalizeUsing RPGC --extendReads 141)
Gene expression was quantified using STAR (--quantMode GeneCounts)
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
B cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from B cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
Pulsed cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from Pulsed cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
Day 4 and Day 6 cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from Day 4 and Day 6 cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
For blastocysts, RNA was extracted and retro-transcribed into cDNA using a SMART-Seq v4 Ultra Low Input RNA kit (634894, Takara). RNA concentration and quality was determined as above. Libraries for RNA-sequencing were prepared as previously described (Picelli et al., 2014).
For morulas, RNA was extracted and retro-transcribed into cDNA using a SMART-Seq v4 Ultra Low Input RNA kit (634894, Takara). RNA concentration and quality was determined as above. Libraries for RNA-sequencing were prepared as previously described (Picelli et al., 2014).
For RNA-sequencing, libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (Illumina) followed by single-end sequencing (50 bp) on an HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

value: Primary B cells

value: Il6 K.O.


title: 32hpi, RNA Rep2

description: activation.csv

source_name: 32 hours post-injured satellite cells followed by in situ fixation


title: v3.9.3

description: nuclear RNA

value: other

value: SpinalCord

value: cSC


title: 12 month WT (replicate 1)


title: 32hpi, RNA Rep1

description: activation.csv

value: Skeletal muscle

value: Muscle stem cells


title: 12 month WT (replicate 2)

value: Tau P301S +/- x  WT


title: v3.8.2

description: nuclear RNA

value: M

value: Telencephalon

value: tWM


title: 6 month dTg (replicate 3)

description: dTG littermates by crossing N40K-Tg and FAD mice

value: dTG ( N40K,5xFAD)

value: Cortex


title: 6 month dTg (replicate 2)


title: 16hpi, RNA Rep2

description: activation.csv

source_name: 16 hours post-injured satellite cells followed by in situ fixation

value: BaCl2 injury


title: 16hpi, RNA Rep1

description: activation.csv


title: v3.7.2

description: nuclear RNA

value: WM

value: pWM


title: IMR90 cells, cortisol and relacorilant, biol rep 3

type: genomic

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the  Infinium methylation EPIC array according to the standard Illumina protocol.

scan_protocol: Arrays were imaged using the BeadArray Reader.

data_processing: Based on standard quality control procedures, the following probes were removed: (i) previously identified cross-reactive and polymorphic probes; (ii) CpG probes with less than 3 beads or with a detection p-value over 1% in at least 1% of the samples assayed; (iii) CpG probes mapping to the Y chromosome; and (iv) probes containing SNPs with a minor allele frequency > 1% located within 10 bases of the CpG. Raw signal intensities were normalized with subset quantile normalization available in the minfi package.

label: Cy5 and Cy3

source_name: normal lung tissue

label_protocol: Labeling was performed according to the standard Illumina protocol.

extract_protocol: DNA was extracted using the GenFind V3 DNA extraction and purification kit (Beckman Coulter).

value: normal lung tissue

value: cortisol and relacorilant


title: IMR90 cells, cortisol and relacorilant, biol rep 4


title: IMR90 cells, cortisol and relacorilant, biol rep 2


title: IMR90 cells, cortisol and relacorilant, biol rep 5


title: 6 month dTg (replicate 1)


title: IMR90 cells, cortisol and relacorilant, biol rep 1


title: IMR90 cells, relacorilant, biol rep 5

value: relacorilant


title: IMR90 cells, relacorilant, biol rep 3


title: 8hpi, RNA Rep2

description: activation.csv

source_name: 8 hours post-injured satellite cells followed by in situ fixation


title: IMR90 cells, relacorilant, biol rep 6


title: v3.6.6

description: nuclear RNA

value: F

value: pCC

value: NaiveCtrl


title: 6 month 5xFAD (replicate 3)

description: 5XFAD littermates by crossing N40K-Tg and FAD mice


title: 8hpi, RNA Rep1

description: activation.csv

value: Skeletal muscle


title: IMR90 cells, cortisol and relacorilant, biol rep 6


title: v3.6.2

description: nuclear RNA

value: Diencephalon

value: OpT


title: IMR90 cells, cortisol, biol rep 4

value: cortisol


title: 4hpi, RNA Rep2

description: activation.csv

source_name: 4 hours post-injured satellite cells followed by in situ fixation

value: Muscle stem cells


title: 6 month 5xFAD (replicate 1)


title: 12 month WT (replicate 4)

value: WT

value: Tau P301S +/- x  WT


title: IMR90 cells, cortisol, biol rep 5


title: v3.5.8

description: nuclear RNA

value: M

value: other

value: Metencephalon

value: Pons


title: IMR90 cells, relacorilant, biol rep 2

value: normal lung tissue


title: 6 month N40K (replicate 3)

description: N40K-Tg littermates by crossing N40K-Tg and FAD mice

value: Cortex


title: v3.6.7

description: nuclear RNA

value: WM

value: Telencephalon


title: 2hpi, RNA Rep2

description: activation.csv

source_name: 2 hours post-injured satellite cells followed by in situ fixation

value: BaCl2 injury


title: v3.5.7

description: nuclear RNA

value: F

value: NaiveCtrl


title: 6 month 5xFAD (replicate 2)


title: v3.5.6

description: nuclear RNA

value: Mesencephalon

value: MB


title: IMR90 cells, cortisol, biol rep 3

value: cortisol


title: IMR90 cells, cortisol, biol rep 6


title: 6 month N40K (replicate 2)


title: IMR90 cells, relacorilant, biol rep 4

value: relacorilant


title: 2hpi, RNA Rep1

description: activation.csv

value: Skeletal muscle

value: Muscle stem cells


title: IMR90 cells, vehicle, biol rep 5

value: vehicle


title: v3.5.5

description: nuclear RNA

value: other


title: MMS day4

city: Fukui

first: Risa

last: Yamaoka

address: 3-9-1 Bunkyo

country: Japan

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps

source_name: Rat lens, 1mM MMS, 4days,

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

value: Sprague Dawley

value: lens


title: IMR90 cells, cortisol, biol rep 1

value: normal lung tissue


title: MMS day2

source_name: Rat lens, 1mM MMS, 2days,


title: Bleomycin day2

source_name: Rat lens, 800µg/mL Bleomycin, 2days


title: 1hpi, RNA Rep2

description: activation.csv

source_name: 1 hour post-injured satellite cells followed by in situ fixation


title: v3.5.4

description: nuclear RNA

value: M

value: Metencephalon

value: CE


title: 1hpi, RNA Rep1

description: activation.csv

value: BaCl2 injury


title: UPAT_C

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Robosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b)
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: seedlings

growth_protocol: Seeds were surface-sterilized by treatments with 70% EtOH and 5% hypochloryte-1% SDS, washed and stratified at 4°C for 2 days to obtain homogeneous germination. Seedlings were grown at 23°C on solid half-strength Murashige and Skoog (MS/2) medium (Duchefa), under long day conditions (16h light, 95μE.m-2.sec-1/8h dark).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase (Fermentas) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA

value: seedlings


title: 6 month WT (replicate 3)

description: Wild-type littermates by crossing N40K-Tg and FAD mice

source_name: Cortex

value: WT

value: Cortex


title: v3.5.3

last: Reich

address: 10 Center Drive Bldg 10 Rm 5C103

institute: NIH

description: nuclear RNA

value: F

value: NaiveCtrl


title: Control

source_name: Rat lens, Control


title: UPAT_B


title: 0.5hpi, RNA Rep2

description: activation.csv

source_name: 0.5 hours post-injured satellite cells followed by in situ fixation


title: IMR90 cells, cortisol, biol rep 2

value: cortisol


title: 6 month WT (replicate 1)


title: 0.5hpi, RNA Rep1

description: activation.csv

value: Skeletal muscle


title: IMR90 cells, vehicle, biol rep 3


title: v3.5.1

description: nuclear RNA

value: GM

value: Telencephalon

value: CgG


title: 6 month WT (replicate 2)


title: IMR90 cells, vehicle, biol rep 4

value: vehicle


title: UPAT_A


title: APOLO_C


title: uninjured, RNA Rep2

description: activation.csv

source_name: In situ fixed satellite cells

value: Muscle stem cells


title: 4hpi, RNA Rep1

description: activation.csv


title: APOLO_B


title: v3.4.8

description: nuclear RNA

value: oCTX


title: Bleomycin day6

source_name: Rat lens, 800µg/mL Bleomycin, 6days

value: Sprague Dawley

value: lens


title: oASC, ATAC Rep2

data_processing:
Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters‘PE CROP: 50.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--minins 30 --maxins 2000 --dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 30 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 30 -b’.
Peak calling was performed on each individual replicate from the previous section using Genrich (v0.6, available at https://github.com/jsh58/Genrich) with the following parameters: -j -y -r -e chrM -v -f.
Genome_build: mm10
Supplementary_files_format_and_content: NarrowPeak files with blacklisted peaks removed; BigWig files of ATAC-seq signal along mm10 after downsampling step.

source_name: 2.5days post-injured old satellite cells

extract_protocol:
Isolated satellite cells were lysed using ATAC-seq lysis buffer ( (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Library was constructed based on protocols from Buenrostro et al., (2015) and Chen et al., (2016). Briefly, lysates were tagmented with Tn5 (Vazyme), reverse-crosslinked,  and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library was then sequenced using DNBSEQ-G400 sequencer (BGI).

value: 2.5 dpi


title: v3.4.7

description: nuclear RNA


title: WT_C

value: wild type


title: APOLO_A

value: seedlings


title: IMR90 cells, vehicle, biol rep 2

value: normal lung tissue


title: v3.4.5

description: nuclear RNA

value: pCTX


title: oQSC, ATAC Rep2

source_name: In situ fixed old satellite cells


title: WT_B


title: v3.4.4

description: nuclear RNA

value: M

value: tCTX


title: IMR90 cells, relacorilant, biol rep 1

value: relacorilant


title: v3.4.3

description: nuclear RNA

value: F

value: NaiveCtrl


title: uninjured, RNA Rep1

description: activation.csv

value: Skeletal muscle


title: v3.5.2

description: nuclear RNA

value: GM

value: Telencephalon

value: CgG


title: v3.4.6

description: nuclear RNA


title: 28dpi, ATAC Rep2

source_name: 28 days post-injured satellite cells followed by in situ fixation

value: Muscle stem cells

value: BaCl2 injury


title: IMR90 cells, vehicle, biol rep 1

source_name: normal lung tissue

value: vehicle


title: oQSC, ATAC Rep1