title: scDiff_D276_UTD

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

description: 10x Genomics

data_processing:
scRNA-seq data were demultiplexed, aligned to the human reference (GRCh38) and quantified using Cell Ranger (v6.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: sample_matrix.mtx.gz, sample_barcodes.tsv.gz, sample_features.tsv.gz

source_name: Blood

growth_protocol: HSPCs cells were isolated using CD34 Positive Selection Kit II (StemCell technologies), from mononuclear cells obtained by Ficoll-Paque (GE Healthcare) density gradient centrifugation of bone marrow aspirates obtained from healthy donors (n=3, range=18-22 y/o). All subjects provided written informed consent. Ex-vivo liquid culture differentiation assay was performed as previously described27. To evaluate the effect of supernatants from activated CAR-T cells, 2 mL of spCAR, spUTD or media as control were added to the differentiation process. OP9 cells, media, cytokines, and supernatants were renewed every 2-3 days.

extract_protocol:
scRNA-seq was performed on cells cultured under spCAR and spUTD conditions after 24 days of differentiation using Chromium Single Cell 3′ Reagent Kit (10X Genomics) according to the manufacturer’s instructions.
scRNA-seq was performed on cells cultured under spCAR and spUTD conditions after 24 days of differentiation using Chromium Single Cell 3′ Reagent Kit (10X Genomics) according to the manufacturer’s instructions.

value: Blood


title: 28-month males

status: Public on Oct 29 2024

type: SRA

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

country: USA

institute: City of Hope

library_source: transcriptomic

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v5.0.0
Counting data of reference gene expression levels were generated by cellranger v5.0.0 (automatic identification of chemistry properties)
Assembly: mm10
Supplementary files format and content: Tab separated values; MatrixMarket

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
For each age group, bone marrow (BM) was harvested from 2 to 4 mice of the same age group. BM cell side population (SP) were stained with the PE-conjugated lineage antibody cocktail, the cells were washed twice with PBS-BSA buffer and resuspended in 500µl PBS. SP cells were immediately sorted into 400 µl DMEM containing 0.04%  BSA with an Aria SORP cell sorter, and at least 5000 SP cells were collected for each sample. The cell numbers and viability were confirmed by both automated cell counter and manual counting. The cells viability of all samples we processed were greater than 80%.
About 1000 cells were captured per sample on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacture’s instruction. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit high Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 8 cycles of index i7 and 8 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGEN with a depth of 100K - 135K reads per cell.

tag: tissue

value: bone marrow

tag: treatment

value: 28 month males


title: E14_ES_RA4h_rep2_nChIP.H3K27me3

city: Heidelberg

first: Angelika

last: Feldmann

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center

description:
K27me3_peaks_reduced_all.rds
E14_ra4h_H3K27me3_rmdup_MERGED_downsampled.bam.bw

library_source: genomic

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native ChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools and Sambamba.
For annotation data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of reads in each sample.
Upon assessing sample correlation, for each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
Peaks were called using the macs2 callpeak function from MACS2, with native ChIP input samples as control and non-downsampled native ChIP reads as input and the option --scale-to small and --broad. Following parameters were used: H3K27ac: -q 0.1, --broad-cutoff 0.05 H3K4me1: -q 0.01, --broad-cutoff 0.1, peaks were merged at 1kb, H3K27me3: -q 0.1, --broad-cutoff 0.1. The peaks were called individually for each replicate, following which the peaks from different replicates were merged using the reduce() function from GenomicRanges to generate peak intervals. Depending on the number of replicates in a sample, only those peak intervals were retained that were identified in at least 2/3, 3/4 or 2/2 biological replicates. Final peak sets were obtained by combining these filtered peak intervals called for individual samples using reduce().
For quantitative analysis, fragments overlapping peaks were quantified from non-downsampled bam files using the summarizeOverlaps() function from the R package GenomicFeatures, with the parameters mode=’Union’ and paired=TRUE. The resulting count tables were then processed by DESeq2. Normalized read counts were extracted from the DESeq2 results tables and mean normalized counts across replicates for each sample calculated. Mean FPKM were calculated from these mean normalized counts and log-transformed using a pseudocount of 0.1.
Assembly: mm10
Supplementary files format and content: bigWig files representing genome coverage for merged replicates of normalised ChIP-seq profiles. .rds files contain all final high-confidence peak intervals and their normalized read counts extracted from DESeq2.

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
For native ChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following RA treatment) were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x cOmplete protease inhibitor cocktail (Roche)). Each sample was then incubated with 200 units of MNase (ThermoFisher Scientific) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For a given ChIP, purified nuclease-digested chromatin from 5 × 10^6 ES cells was 10-fold diluted in native ChIP incubation buffer (10mM Tris-HCl pH 7.5, 70mM NaCl, 2mM MgCl2, 0.1% Triton X-100, 2mM EDTA, 5mM Sodium butyrate, 1× cOmplete protease inhibitor cocktail (Roche)) before being pre-cleared for 2h with Protein A Dynabeads (Life Technologies #10001D) blocked with 0.05mg/ml tRNA and 0.2mg/ml BSA. The pre-cleared chromatin was further incubated overnight at 4 °C with the appropriate antibody: anti-H3K27ac (CST, #8173, 5µg), anti-H3K27me3 (Millipore, #07-449, 5µg), anti-H3K4me1 (CST, #5326, 5µg). Antibody-bound chromatin was captured using blocked Dynabeads for 1h at 4 °C and isolated through magnetizing on ice. After four washes with ice-cold native ChIP wash buffer (20mM Tris-HCl pH 7.5, 125mM NaCl, 0.1% Triton X-100, 2mM EDTA) and one wash with ice-cold 1x TE buffer, the ChIP DNA was eluted in fresh elution buffer (1% SDS, 0.1 M NaHCO3) and incubated with shaking at 25 °C for 30min. In parallel, a matched 10% input sample was identically processed. Both ChIP and input DNA were purified using ChIP DNA Clean and Concentrator Kit (Zymo Research # D5205) following manufacturer protocol.
Crosslinked ChIP-seq was performed to profile RNAP2 binding (NTD, Ser2p, Ser5p). Briefly, 5 × 10^7 ES cells were washed with 1× PBS and crosslinked with 1% formaldehyde. After 15 min incubation at RT with rotation, the fixation reaction was quenched with 0.15M glycine solution and washed again with 1x PBS. The pellet was stored at -80°C. For the nuclei isolation and sonication, the pellet was thawed on ice and then resuspended in 10mL LB1-solution (10% glycerol, 50mM HEPES-KOH (pH 7.9), 0.14 M NaCl, 1mM EDTA, 0.5 % NP-40 (IGEPAL), 0,25% Triton X100, 1x cOmplete protease inhibitor cocktail (Roche)) and rotated at 4°C for 10min. After centrifugation (5 min, 1000xg, 4°C), the supernatant was removed and the cells were resuspended in 10 mL LB2 solution (10mM Tris-HCl (pH 8.0), 0.2M NaCl, 1mM EDTA, 0.5mM EGTA, 1x cOmplete protease inhibitor cocktail (Roche)), rotated at 4°C for 5min and centrifuged (5 min, 1000xg, 4°C). The cell pellet was resuspended in 1mL LB3 (10mM Tris-HCl (pH 8.0), 0.1M NaCl, 1mM EDTA, 0.5mM EGTA, 1x cOmplete protease inhibitor cocktail (Roche)) and transferred to a sonication tube containing sonication beads (Diagenode). Sonication was performed using the Bioruptor® Pico sonicator (Diagenode) for 20 cycles, 30 sec on / off. The sonicated cell solution was transferred to 1.5 mL collection tubes and 100 µL of 10% Triton X100 in LB3 was added and mixed by inversion. After centrifugation at 20,000 xg for 10 min at 4°C, the supernatant was aliquoted into dry ice-cooled tubes (150µg chromatin/tube). Sonication was confirmed with a 1.5 % agarose gel. For each ChIP, either 150 µg (NTD polymerase) or 300 µg (Ser2p, Ser5p) chromatin were diluted 10-fold in ChIP dilution buffer (10% Triton X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 0.15M NaCl) and then pre-cleared for 2h with Protein A Dynabeads (Life Technologies #10001D) blocked with 0.05mg/ml tRNA and 0.2mg/ml BSA. Prior to the addition of the antibody, 2% input was taken from the pre-cleared chromatin. The pre-cleared chromatin was further incubated overnight at 4 °C with the appropriate antibody: anti-Rpb1 NTD (CST, #14958, 7.5µg/150µg chromatin), anti-phospho-Rpb1 CTD (Ser2p) (CST, #13499, 6.25µg/150µg chromatin), anti-phospho-Rpb1 CTD (Ser5p) (CST, #13523, 6.25µg/150µg chromatin). Antibody-bound chromatin was captured with blocked Dynabeads for 1h at 4 °C and isolated by magnetisation on ice. Dynabeads were washed with low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl (pH 8.0), 0.15M NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl (pH 8.0), 0.5M NaCl), LiCl buffer (0.25M LiCl, 0.1% NP40, 0.1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl (pH 8.0)) and twice with TE buffer (10mM Tris-HCl (pH 8.0), 0.1mM EDTA). The chromatin-bound beads were eluted with 100µl/150µg chromatin elution buffer (1% SDS, 0.1M NaHCO3) and incubated at 25 °C for 30min with shaking. The input sample was topped up to the same volume as the ChIP sample and 4µL 4M NaCl and 2µL RNaseA (Qiagen #19101, 20mg/mL) were added. Samples were incubated overnight at 65°C with slow shaking. Then 1µL of Proteinase K was added and the samples were incubated at 55°C for 1 hour with slow shaking. Both ChIP and input DNA were purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research # D5205) following manufacturer protocol.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size of all libraries was analysed using either the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent, nChIP) or the TapeStation (xChIP). Library concentration was further determined either by using qPCR with SensiMix SYBR (Bioline, UK)  and KAPA Illumina DNA standards (Roche) for nChIP or by quantification via Qubit for xChIP. Libraries were sequenced as 40-42 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicates or quadruplicates.

treatment_protocol: To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 2-72 hours.

tag: cell line

tag: cell type

value: ESC

tag: chip antibody


title: MS27 macrophages stimulated with IL4

city: Paris

first: violetta

last: zujovic

address: 47 boulevard de l'hôpital

country: France

institute: Paris brain institute

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28 on GENCODE v28 reference transcriptome
Assembly: HG38
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM

organism: Homo sapiens

source_name: blood derived macrophages

growth_protocol: Monocytes were isolated with anti-CD14 microbeads (Miltenyi) and plated in 12-well plates (500 000 cells/well) or in 24-well plates (200 000 cells/well) in RPMI 1640 + 10% FBS and granulocyte macrophage colony-stimulating factor (GM-CSF) (500 U/ml, ImmunoTools).

extract_protocol:
Nucleospin RNA extraction kit (Macherey-Nagel)
Truseq mRNA stranded ILLUMINA with UDI

treatment_protocol: After 72h, media was replaced with fresh media and one of the following: GM-CSF (500 U/ml); IL4 (1000 U/ml, ImmunoTools); or combined IFNγ (200 U/ml, ImmunoTools) and ultra-pure LPS (10 ng/ml, InvivoGen).

value: blood derived macrophages

value: MS patient

value: treated with IL4 for 24hours

tag: batch


title: 3-month males

value: 3 month males


title: scDiff_D276_CAR_BCMA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA


title: MS26 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: Cardiac fibroblasts, MCB-613-10-1, 24 hours [CD324]

city: Houaton

first: Rainer

middle: B

last: Lanz

state: TX

address: One Baylor Plaza

department: Molecular and Cellular biology

institute: Baylor College of Medicine

data_processing:
Raw data handling (raw reads of fastq format) to obtain clean reads included the removal of reads containing adapter, reads containing poly-N and low quality reads using Novogene proprietary Perl scripts. Q20, Q30 and GC content of the clean data samples were calculated.
Paired-end clean reads were aligned to the reference genome (mm39) using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene, then the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of all genes were calculated.
Statistics of sequencing quality and mapping for all samples were: error rate <=0.02, Q Phred value Q20 >97.6, Q30 >93.7, total reads >65 million, proper mapping >88.5%,
Differential expression analysis (vehicle control versus MCB-613-10-1) was performed using the DESeq2Rpackage (1.20.0). P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate; genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm39 Genome Reference Consortium Mouse Build 39
Supplementary files format and content: FPKM expression values, with gene mata data
Supplementary files format and content: DESeq differential expression values, all genes, with gene meta data and fpkm values

source_name: Heart

growth_protocol: Isolated primary cardiac fibroblasts were maintained in DMEM with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2  at 37C

extract_protocol:
RNA was harvested using RNAeasy MiniKit (Qiagen)
Library construction included cDNA end repair, A-tailing, adapter ligation, size selection, amplification, and purification, followed by Qubit fluorometric quantification, real-time PCR for quantification and bioanalyzer analysis for size distribution detection

treatment_protocol: Cells were treated with ETOH vehicle control or 6 uM MCB-613-10-1 for 4 or 24 hours

value: Heart

value: Primary cells

value: Cardiac fibroblast

tag: genotype


title: E14_ES_RA48h_rep2_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra48h_merged.bw


title: Cardiac fibroblasts, MCB-613-10-1, 24 hours [CD224]


title: E14_ES_RA6h_rep2_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra6h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: MS26 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: MS26 macrophages stimulated with IL4


title: E14_ES_RA48h_rep2_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra48h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: MS25 macrophages stimulated with LPS+IFNg


title: Cardiac fibroblasts, MCB-613-10-1, 24 hours [CD124]


title: Cardiac fibroblasts, Vehicle control, 24 hours [CC324]

value: control


title: Cardiac fibroblasts, Vehicle control, 24 hours [CC224]


title: 87

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

data_processing:
FASTQC v0.11.2 was used for quality control. FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads.
Alignment was performed with STAR v2.7.3a. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
TopHat v1.4.1 was used for alignment
SAMTools v0.1.19 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Assembly: GRCm38 release 74
Supplementary files format and content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Adult female mouse dosed every 4 days for 92 days

extract_protocol:
Frozen gonadal white adipose tissue (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions.

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 92 days.

tag: strain

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: percent

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

tag: formula

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: MS25 macrophages stimulated with GMCSF

value: blood derived macrophages

value: MS patient


title: MS25 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: Cardiac fibroblasts, Vehicle control, 24 hours [CC124]

value: Heart

value: Primary cells

value: Cardiac fibroblast

value: control


title: E14_ES_RA2h_rep2_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra2h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw

value: ESC


title: 81

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940


title: MS24 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: E14_ES_RA24h_rep2_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra24h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: 85

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage


title: Cardiac fibroblasts, MCB-613-10-1, 4 hours [CD2]

value: Heart


title: MS24macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: MS patient

value: treated with LPS+IFNg for 24 hours


title: E14_ES_RA2h_rep2_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra2h_merged.bw

value: ESC


title: MS24 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: E14_ES_RA24h_rep2_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra24h_merged.bw


title: MCF-7 breast adenocarcinoma cell line,  array 2

type: RNA

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

description: Gene expression profile

hyb_protocol: Fragmented and labeled target (Sense Strand-cDNA 5.2-5.5 µg) was used for hybridization to the “GeneChip Human Transcriptome Array 2.0” according to the protocol supplied by the manufacturer was used for hybridization step. The hybridization has been performed in an hybridization oven at 45°C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed using the Affymetrix Scanner GCS3000 7G.

data_processing: Data analysis was performed using Affymetrix® Expression Console™ software (v.1.4). Expression level analysis was obtained using the normalization method based on the processing algorithm Robust Multi-array Average (RMA).

label: biotin

source_name: breast adenocarcinoma cell line

label_protocol: Biotinylated fragmented sense strand cDNA were prepared according to the protocol supplied by the Affymetrix for Human Transcriptome Array 2.0 (HTA).

growth_protocol: MCF-7 was cultured in Dulbecco's Medium 4.5 g/dL Glucose w/Glutamax (1X Gibco® Cat No. 12430054), while PC-3 was maintained in DMEM/F12 medium nutrient mixture (1X; GIBCO, Cat. No. 21331). Each medium was supplemented with 10% fetal bovine serum (FBS; Cat. No. 10270-106; Life Technologies, Monza, Italy) and 1% of 1/1penicillin–streptomycin (Cat. No 15140- 122; Life Technologies). The cell cultures were grown in flasks (25 cm2) and incubated at 37°C in a humidified atmosphere with 5% CO2 and 95% air. The culture medium was changed twice a week.

extract_protocol: Total RNA (100 ng) was extracted from frozen tissue and cell cultures using RNeasy Mini Kit (Qiagen, Milan - Italy) according to the manufacturer’s instructions. The concentration and the quality of RNA were determined using a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific, USA).

tag: anatomical site

value: Breast

tag: gender

value: female

tag: patient age

value: 69 years

tag: tumor stage

value: breast adenocarcinoma

tag: growth properties

value: confluent cell cultures


title: PC-3 prostate adenocarcinoma cell line, array 1

description: Gene expression profile

source_name: prostate adenocarcinoma cell line

value: Prostate

value: male

value: 62 years

value: prostatic adenocarcinoma


title: 76

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: milliliter

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: MCF-7 breast adenocarcinoma cell line,  array 1

description: Gene expression profile

value: Breast

value: female

value: 69 years

value: breast adenocarcinoma

value: confluent cell cultures


title: E14_ES_RA4h_rep2_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra4h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw

value: ESC


title: 74

value: Charles Rivers Laboratories

value: Male

value: oral gavage


title: E14_ES_RA0h_rep2_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra0h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: Cardiac fibroblasts, Vehicle control, 4 hours [CC3]

tag: tissue

value: Heart

value: Primary cells

value: Cardiac fibroblast

value: control


title: Cardiac fibroblasts, MCB-613-10-1, 4 hours [CD1]

tag: treatment


title: E14_ES_RA0h_rep2_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra0h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw

tag: cell line


title: E14_ES_RA2h_rep2_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra2h_H3K27me3_rmdup_MERGED_downsampled.bam.bw

tag: cell type


title: MS23 (run2) macrophages stimulated with GMCSF

description: re-sequencing of sample for batch effect correction

value: blood derived macrophages

value: MS patient

value: treated with GMCSF for 24 hours

tag: re-sequencing


title: MS23 (run2) macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours

tag: batch


title: Cardiac fibroblasts, Vehicle control, 4 hours [CC1]

tag: genotype


title: E14_ES_RA0h_rep2_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra0h_merged.bw

tag: chip antibody


title: MS21 macrophages stimulated with LPS+IFNg


title: Cardiac fibroblasts, MCB-613-10-1, 4 hours [CD3]


title: 67

tag: strain

tag: Sex

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: milliliter

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: GC-B cells, KO, replicate3

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 6.1.2
Assembly: mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: tar file with raw_feature_bc_matrix files.
Supplementary files format and content: Plain text file with barcodes used in the analysis

source_name: Spleen

extract_protocol:
Spleens were crushed and filtered with a 70µM mesh strainer. Harvested splenic B-cells were enriched by CD43, Ter119 and CD4 negative selection using MACS LS Columns (Miltenyi Biotec). Single-cell suspensions were stained with antibodies and sorted by flow cytometry.
Libraries were prepared with Chromium Single Cell 5' Reagent Kit v.2 (10x Genomics) following the manufacturer's protocols.

treatment_protocol: B cells from 25 week old HEL-specific BCR expressing B cells from female mice were adoptively transferred into congenic mice and immunized with 2x10^8 HEL3x-SRBC. Splenic GC-B cells from these mice were sorted by flow cytometry after five days.

value: Spleen

value: Primary

value: GC-B cells

value: miR-155 KO

value: 7 days after HEL3x-SRBC immunization

tag: cell subtype


title: E14_ES_RA6h_rep1_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra6h_merged.bw

value: ESC


title: MS21 macrophages stimulated with GMCSF

value: blood derived macrophages

value: MS patient

value: treated with GMCSF for 24 hours


title: E14_ES_RA72h_rep1_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra72h_merged.bw


title: 64

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: formula

value: oral gavage

tag: dose


title: MS23 (run2) macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: 70

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: milliliter

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: MS21 macrophages stimulated with IL4

value: blood derived macrophages


title: E14_ES_RA72h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra72h_H3K27me3_rmdup_MERGED_downsampled.bam.bw

value: ESC


title: 72


title: Cardiac fibroblasts, Vehicle control, 4 hours [CC2]

value: Heart

value: Primary cells

value: Cardiac fibroblast

value: control


title: 58

value: Charles Rivers Laboratories

value: Male

value: day

value: percent


title: WT2_CUTRUN_K27ac

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Paired-end fastq files were trimmed to 25 bp and mapped to the mm10 genome with bowtie2 (options -q -N 1 -X 1000).
Mapped reads were duplicate-filtered reads and with insufficient mapping quality (MAPQ ≥ 10) were removed using samtools. Samples were size class filtered for nucleosome size class (150-500bp).
Indexed, sorted BAMs were converted to bigWig files using deepTools with normalization RPGC (options -bs 10 --normalizeUsing RPGC, --effectiveGenomeSize 2862010578). Heatmaps and metaplots were generated using deeptools.
Peaks were called from CUT&RUN samples using MACS2 with no antibody samples as input. For each target, peaks from all samples were combined to create a consensus peak set.
Assembly: mm10
Supplementary files format and content: bigwigs
Library strategy: CUT&RUN

source_name: Cell line

growth_protocol: ES-E14TG2a (E14) mES cells from male Mus musculus origin (RRID:CVCL9108361) were cultured at 37°C and 5% CO2 in DMEM base medium (Sigma Aldrich) supplemented with 10% FBS(Sigma Aldrich), 1X nonessential amino acids (Corning), 2mM L-glutamine (Corning), β-mercaptoethanol (Acros Organics) and LIF on 10cm plates precoated with 0.2% gelatin. For LIF+2i media, LIF media was further supplemented with 3 µM CHIR99021 GSK inhibitor (p212121), and 1 µM PD0325091 MEK inhibitor (p212121). Cells were passaged every ~48 h using trypsin and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma TC hood cleaning was conducted (LookOut DNA Erase spray, Sigma Aldrich) and cell lines were screened to confirm no mycoplasma presence. While generating clones, cells were grown in media with the addition of 1X penicillin/streptomycin (Corning) to prevent bacterial contamination.

extract_protocol:
100,000 nuclei were isolated from cell populations using a hypotonic buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors) and flash frozen. Nuclei were thawed and bound to lectin-coated concanavalin A magnetic beads (50 µL bead slurry per 100,000 nuclei; Polysciences). Immobilized nuclei were pre-blocked with blocking buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5mM spermidine, 0.1% BSA, 2 mM EDTA, fresh protease inhibitors) and washed in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5mM spermidine, 0.1% BSA, fresh protease inhibitors). Nuclei were incubated in wash buffer containing primary antibody (H3.3, K122ac, K27ac) overnight at 4°C with rotation. Nuclei were incubated in wash buffer containing primary antibody for 1 hour at room temperature with rotation. Next, samples were washed twice with wash buffer and incubated in wash buffer containing recombinant pA-MN (for K122ac, K27ac) or pA/G-MN (for H3.3) for 30 minutes at room temperature with rotation. Controls lacking a primary antibody were subjected to the same conditions but incubated in wash buffer without any primary antibody prior to incubation with pA-MN/pA/G-MN. After incubation, samples were washed twice with was buffer and equilibrated to 0°C in an ice/water bath. MNase cleavage was activated upon addition of 3 mM CaCl2. Digestion was chelated for samples containing primary antibodies K27ac, after 30 mins on the ice water bath, using 20 mM EDTA, 4 mM EGTA, 200 mM NaCl, and 1.5 pg MNase-digested S. cerevisiae mononucleosomes were added as a spike-in control. Genomic fragments were released after an RNase A treatment. Released fragments were separated through centrifugation. Digestion was chelated for samples containing primary antibodies K122ac and H3.3 after 30 mins on the ice water bath, using a low-salt treatment: 10 mM EDTA, 2 mM EGTA, 150 nM NaCl, 5 mM TritonX, and 1.5 pg MNase-digested S. cerevisiae mononucleosomes were added as a spike-in control. Genomic fragments were released after being incubated for 1 hour at 4°C and released fragments were separated from beads. The salt concentration of low-salt treated samples were increased to 500 mM and additional RNase A.
Isolated fragments from all samples were used as input for a library build consisting of end repair and adenylation, adapter ligation, and subsequent purification with AMPure XP beads (Agencourt). Barcoded fragments were then amplified by 15 cycles of high-fidelity PCR and purified using agarose gel extraction. Libraries were pooled and sequenced on an Illumina NextSeq500 to a depth of ~10 million mapped reads.

value: Cell line

value: embryonic stem cells

value: Wildtype


title: 54

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: oral gavage


title: E14_ES_RA6h_rep1_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra6h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw

value: ESC


title: 28-month-old male bone marrow sorted SP cells

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
For each age group, bone marrow (BM) was harvested from 2 to 4 mice of the same age group. BM cell side population (SP) staining with the PE-conjugated lineage antibody cocktail, the cells were washed twice with PBS-BSA buffer and resuspended in 500µl PBS. SP cells were immediately sorted into 400 µl DMEM containing 0.04%  BSA with an Aria SORP cell sorter, and at least 5000 SP cells were collected for each sample. The cell numbers and viability were confirmed by both automated cell counter and manual counting. The cells viability of all samples we processed were greater than 80%.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.  Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

value: bone marrow

value: 28 month males


title: GC-B cells, WT, replicate3

value: Spleen

value: Primary

value: GC-B cells

value: WT

value: 7 days after HEL3x-SRBC immunization


title: MS19 (run2) macrophages stimulated with GMCSF

value: blood derived macrophages

value: MS patient

value: treated with GMCSF for 24 hours


title: 53

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: milliliter

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: GC-B cells, KO, replicate2

value: miR-155 KO


title: GC-B cells, WT, replicate2

value: Spleen


title: E14_ES_RA4h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra4h_H3K27me3_rmdup_MERGED_downsampled.bam.bw

value: ESC


title: 49

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: oral gavage


title: GC-B cells, WT, replicate1

value: Primary

value: GC-B cells

value: WT

value: 7 days after HEL3x-SRBC immunization


title: MS16 (run2) macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: MS patient

value: treated with LPS+IFNg for 24 hours


title: 43

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: milliliter

value: microgram per kilogram


title: GC-B cells, KO, replicate1

value: Spleen

value: miR-155 KO


title: KO168-1

city: PARIS

first: Marion

last: Espeli

address: 1 avenue Claude Vellefaux, Inserm U1160, Institut de Recherche Saint Louis

institute: Inserm U1160

data_processing:
Image analysis and base calling was performed using Illumina Real Time Analysis (3.4.4) with default parameters
STAR was used to obtain the number of reads associated to each gene in the Gencode vM24 annotation (restricted to protein-coding genes, antisense and lincRNAs).
Raw counts for each sample were imported into R statistical software. Extracted count matrix was normalized for library size and coding length of genes to compute FPKM expression levels.
The Bioconductor edgeR package was used to import raw counts into R statistical software, and compute normalized log2 CPM (counts per millions of mapped reads) using the TMM (weighted trimmed mean of M-values) as normalization procedure.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: plasma cell_Sec22b B-KO

growth_protocol: For ex vivo plasma cell generation, 1x106 splenocytes were stimulated with 5µg/mL of lipopolysaccharide (LPS) (InVivoGen) for 2 days in complete culture medium composed of RPMI supplemented with 10% foetal calf serum (Sigma), 0.05mM 2-mercaptoethanol, 100U/mL penicillin-streptomycin, 1mM sodium pyruvate and 0.1mM non-essential amino acids (Gibco).

extract_protocol:
RNA were extracted with “RNeasy plus micro kit” (Qiagen) as recommended. Libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ex vivo generated plasma cells upon 2 days of LPS stimulation

value: Sec22b B-KO


title: KO166-1


title: MS19 (run2) macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: E14_ES_RA4h_rep1_nChIP.H3K27ac

value: ESC


title: 34

value: Harlan Teklad

value: Yes

value: Room temperature

value: sesame oil

value: oral gavage

value: Carbon dioxide euthanasia


title: MS19 (run2) macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: MS patient

value: treated with LPS+IFNg for 24 hours


title: E14_ES_RA6h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra6h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: MS16 (run2) macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: KO145-1


title: MS16 (run2) macrophages stimulated with IL4


title: KO143-1


title: 33

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: milliliter

value: microgram per kilogram


title: E14_ES_RA4h_rep1_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra4h_merged.bw

value: ESC


title: MS15 macrophages stimulated with LPS+IFNg


title: 32

value: Harlan Teklad

value: Yes


title: MS15 macrophages stimulated with GMCSF


title: 24

value: Room temperature

value: sesame oil


title: 42

value: oral gavage

value: Carbon dioxide euthanasia


title: E14_ES_RA2h_rep1_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra2h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw


title: E14_ES_RA48h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra48h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA24h_rep1_nChIP.H3K4me1


title: 23


title: 22


title: MS14 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: MS patient


title: E14_ES_RA2h_rep1_nChIP.H3K27me3


title: E14_ES_RA48h_rep1_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra48h_merged.bw


title: MS15 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: 17

value: Charles Rivers Laboratories


title: WT167-1

source_name: plasma cell_WT

value: ex vivo generated plasma cells upon 2 days of LPS stimulation

value: WT


title: WT142-1


title: E14_ES_RA24h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra24h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: WT141-1


title: E14_ES_RA2h_rep1_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra2h_merged.bw


title: MS14 macrophages stimulated with IL4


title: 12

value: Male

value: day

value: percent


title: G2_470-10xscTCR-seq

city: Shanghai

first: s

middle: y

last: h

state: Shanghai

country: China

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell; contig annotation for every cell

source_name: colorectal carcinoma

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 5’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: Stage

value: S. Chamaejasme treated


title: MS29 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: 2

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: milliliter

value: microgram per kilogram


title: 920-10xscTCR-seq

value: untreated


title: MS12 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: G3_320-10xscTCR-seq

value: S. Chamaejasme plus anti-PD-1 therapy


title: MS14 macrophages stimulated with GMCSF

value: blood derived macrophages

value: MS patient


title: 13

value: Charles Rivers Laboratories

value: Yes

value: Room temperature

value: sesame oil

value: oral gavage

value: Carbon dioxide euthanasia


title: MS13 macrophages stimulated with LPS+IFNg


title: 310-10xscTCR-seq


title: E14_ES_RA0h_rep1_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra0h_H3K27me3_rmdup_MERGED_downsampled.bam.bw

value: ESC


title: G3_210-10xscTCR-seq


title: E14_ES_RA72h_rep1_nChIP.Input

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
K27ac_peaks_InBothReplicates.rds
K27me3_peaks_reduced_all.rds


title: G3_320-10xscRNA-seq


title: MS13 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: MS12 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: E14_ES_RA0h_rep1_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra0h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw


title: WT_9

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
cellranger-6.1.2, CellBender remove-background 0.2.0, scDblFinder_1.6.0
Samples raw base calls demultiplexing, barcoded processing, sequence alignment and gene counting  were made using the Cell Ranger software 6.1.2 function. Raw sequence reads were aligned to the latest mouse reference genome (mm10).
Counts were pre-processed for ambient RNA and doublet removal using CellBender remove-background 0.2.0
Doublet removal was performed using scDblFinder_1.6.0 in the R programing language
Downstream analysis were performed in R.
Assembly: mm10_v3.0.0
Supplementary files format and content: h5 files from CellRanger and CellBender, respectively.

source_name: Kidney

extract_protocol:
As each region was sampled, the tissue was chopped into 1mm x1mm cubes and placed in 0.25mg/ml liberase TH (Roche Diagnostics, Indianapolis, USA) dissociation medium. Following further dissection, the samples were incubated at 37°C for 1 hour at 600rpm. Samples were regularly triturated during the incubation period using a 1ml pipette, after which 10% heat- inactivated FBS RPMI was added to stop the digestion. Centrifugation at 500 g for 5 minutes at room temperature with the removal of the supernatant, was followed by the addition of ACK lysing buffer to remove erythrocytes (Thermo Fisher Scientific, Waltham, USA). Following centrifugation, the resulting cell pellet was incubated with Accumax at 37°C for 3 minutes (Innovative Cell Technologies Inc, San Diego, USA). 10% FBS RPMI was again used to neutralize the Accumax and centrifugation was followed by resuspension of the cell pellet in 0.4% BSA/PBS. The single cell suspension was filtered using a 30um CellTrics filter (Sysmex America Inc, Lincolnshire, USA) with cell viability and concentration determined using trypan blue and the Auto T4 cellometer (Nexcelom Bioscience LLC, Lawrence, USA).
17,500 cells were loaded into the 10x Genomics microfluidic system/onto the 10x Genomics platform to achieve a targeted recovery of 10,000 cells (10x Genomics, Pleasanton, USA).

value: Kidney

tag: region

value: Cortex

tag: model

value: WT (chow)

tag: age (weeks)


title: MS13 macrophages stimulated with IL4

tag: tissue

tag: treatment


title: 4

value: Male

value: day

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: milliliter

value: microgram per kilogram


title: E14_ES_RA72h_rep3_nChIP.Input

tag: cell line

tag: cell type


title: E14_ES_RA6h_rep3_nChIP.Input


title: MS02 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: MS patient

value: treated with LPS+IFNg for 24 hours

tag: batch


title: E14_ES_RA72h_rep2_nChIP.Input


title: WT_8

description: 10x Genomics


title: 1

value: Charles Rivers Laboratories

value: Yes

value: Room temperature

value: sesame oil

value: oral gavage

value: Carbon dioxide euthanasia


title: G2_470-10xscRNA-seq

value: S. Chamaejasme treated


title: E14_ES_RA6h_rep1_nChIP.Input

value: ESC


title: MS02 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: E14_ES_RA4h_rep3_nChIP.Input


title: MS12 macrophages stimulated with GMCSF


title: E14_ES_RA6h_rep2_nChIP.Input


title: 920-10xscRNA-seq

value: untreated


title: E14_ES_RA0h_rep1_nChIP.H3K4me1


title: MS01 macrophages stimulated with LPS+IFNg


title: WT_1

description: 10x Genomics

value: Kidney

value: Cortex

value: WT (chow)


title: WTNB-1

value: ex vivo generated plasma cells upon 2 days of LPS stimulation

tag: genotype

value: WT


title: E14_ES_RA4h_rep1_nChIP.Input

tag: chip antibody


title: WT_2

description: 10x Genomics


title: 310-10xscRNA-seq


title: WT_10

description: 10x Genomics


title: E14_ES_RA4h_rep2_nChIP.Input


title: MBT2

city: NY

first: Emily

last: Birnbaum

state: NY

address: 200 West 93rd Street, 6J

institute: CUNY Graduate Center

description: Male, TgF-344AD transgenic rat, BT-11 chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The reads were mapped by STAR 2.7.9a [1] and read counts per gene were quantified using the rat genome rn6
In Partek Flow [2], read counts were normalized by CPM +1.0E-4
All results of differential gene expression analysis utilized the statistical analysis tool, DESeq2
Assembly: rn6
Supplementary files format and content: Raw-Read-Counts-males.xls=> excel file includes raw counts for each sample
Supplementary files format and content: Normalized-Read-Counts-males.xls =>excel file includes Normalized gene expression

organism: Rattus norvegicus

source_name: Left Hippocampus Brain

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
KAPA mRNA-Seq Hyper Prep Kit to generate strand-specific RNA-seq libraries
RNA-seq-Sequencing was performed on Illumina HiSeq3000 for a SE 1x50 run.

value: Left Hippocampus Brain

value: Male

value: Tg-AD


title: MBT3


title: E14_ES_RA48h_rep1_nChIP.Input


title: E14_ES_RA2h_rep2_nChIP.Input


title: MBT5


title: M5

description: Male, TgF-344AD transgenic rat, rodent chow

value: No Treatment


title: HC24 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: healthy control

value: treated with LPS+IFNg for 24 hours


title: G3_210-10xscRNA-seq

value: S. Chamaejasme plus anti-PD-1 therapy


title: HFD_2

description: 10x Genomics

value: HFD


title: MS01 macrophages stimulated with GMCSF

value: MS patient


title: M4


title: MBT4


title: HFD_10

description: 10x Genomics


title: WT_0

description: 10x Genomics


title: E14_ES_RA48h_rep3_nChIP.Input

value: ESC


title: MS01 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: HFD_7

description: 10x Genomics

value: Kidney


title: E14_ES_RA24h_rep3_nChIP.Input


title: WT_7

description: 10x Genomics

value: Cortex


title: MS02 macrophages stimulated with IL4


title: E14_ES_RA48h_rep2_nChIP.Input


title: HFD_9

description: 10x Genomics


title: E14_ES_RA24h_rep2_nChIP.Input


title: HC24 macrophages stimulated with IL4


title: HC25 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: MBT1


title: HFD_0

description: 10x Genomics


title: HC25 macrophages stimulated with IL4


title: E14_ES_RA24h_rep1_nChIP.Input


title: BTBR_ob_section5

description: 10x Genomics

value: Sagittal

value: BTBR ob/ob


title: HC25 macrophages stimulated with LPS+IFNg


title: E14_ES_RA2h_rep1_nChIP.Input


title: M3

value: Left Hippocampus Brain


title: HFD_8

description: 10x Genomics


title: E14_ES_RA0h_rep2_nChIP.Input


title: HFD_1

description: 10x Genomics


title: HC23 macrophages stimulated with IL4


title: HC24 macrophages stimulated with GMCSF


title: HC22 macrophages stimulated with LPS+IFNg


title: M2

value: Male


title: Con_p3

city: Tianjin

first: chen

last: limei

address: Jin jing road 22

institute: Tianjin Agriculture University

description: normal seawater control group

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Pacbio sequencing + Hi-C analysis
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mactra quadrangularis

source_name: mantle

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: mantle

value: normal control


title: BTBR_ob_section2

description: 10x Genomics


title: M1

value: Tg-AD

value: No Treatment


title: PC-3 prostate adenocarcinoma cell line, array 2

description: Gene expression profile

tag: anatomical site

value: Prostate

tag: gender

value: male

tag: patient age

value: 62 years

tag: tumor stage

value: prostatic adenocarcinoma

tag: growth properties

value: confluent cell cultures


title: HC23 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: healthy control

value: treated with LPS+IFNg for 24 hours


title: adipose tissue, Child 3

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

description: 8 years old, male

data_processing:
Next-generation sequencing (NGS) analysis was performed on the BGISEQ-500 platform by BGI Genomics Inc. (Cambridge, MA, USA), generating ~26.2 million reads per sample. Firstly,we remove the reads mapped to rRNA and get raw data. Sequencing reads were checked to remove low-quality, adaptor-polluted and unknown base reads before downstream analyses. After filtering, the clean reads were mapped to the reference genome using HISAT.
On average, 96.8% of reads were mapped, and the uniformity of the mapping result for each sample suggested that the samples were comparable. We mapped clean reads to reference transcripts using Bowtie2, then calculated the gene expression level for each sample with RSEM.
Sequencing data saturation analysis was used to measure whether the depth of sequencing data was sufficient for bioinformatics analysis. Based on their gene expression levels, we identified differentially-expressed genes (DEGs) between sample groups. We used the DEseq2 algorithm to detect the DEGs.
We map clean reads to reference transcripts using Bowtie2. Reference Genome Version: GCF_000001405.39_GRCh38.p13. Source: NCBI, Homo_sapiens
Based on the gene expression level, we can identify  DEGs (Differentially expression genes) between infant and child samples. We used DEseq2 algorithms to detect the DEGs.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Excel showing DEGs. infant_vs_child DEGs.
Supplementary files format and content: read counts.txt

source_name: adipose tissue

extract_protocol:
Total RNA extraction using TRIZOL extraction reagent. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads.
Library was validated on the Agilent Technologies 2100 bioanalyzer.
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

value: adipose tissue

tag: age

value: adipocytes and stromal cells

value: 8 years old


title: HC22 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: Con_p2

description: normal seawater control group


title: E14_ES_RA0h_rep3_nChIP.Input

value: ESC


title: water control2

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

institute: University of Muenster

description:
Water2
counts_mir_E_EH_raw.tsv

data_processing:
Data pruning also according to Hagemann-Jensen M, et al. doi: 10.1038/s41596-018-0049-y
Alignment with STAR aligner version 2.7.10 using default values but transcriptome coordinates (for Salmon) according to protocol Dobin, A. and Gingeras, T.R. 2015 - section 7. Mapping RNA-seq reads with STAR. Curr. Protoc. Bioinform.51:11.14.1-11.14.19. doi: 10.1002/0471250953.bi1114s51.
Quantification with Salmon version 1.10 according to the manual and program defaults.
Further data handling, differential expression analysis [DESeq2], permutation controls, result visualization etc. with mathematical platform R version 3.6.1 to 4.0.5.
Assembly: Current builds of the Human genome reference GRCh38.p14 from EBI in England, mirBase release 22.1.
Supplementary files format and content: Tab separated table format, columns: miRNA-ID/result parameters/samples and expression counts (microRNAs)

organism: blank sample

source_name: water control

extract_protocol:
RNeasy total RNA Kit (Qiagen, Hilden, Germany)
Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.
Small RNA sequencing, single end reads

value: water control

tag: subject status

value: control


title: adipose tissue, Child 1

description: 11 years old, male

value: 11 years old


title: water control1

description:
Water1
counts_mir_E_EH_raw.tsv


title: BTBR_ob_section4

description: 10x Genomics

value: Kidney

tag: region

value: Sagittal

value: BTBR ob/ob


title: HC23 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: adipose tissue, Infant 3

description: 23 months old, male

value: 23 months old

value: male


title: BTBR_ob_2

description: 10x Genomics

value: Cortex

tag: model


title: E14_ES_RA0h_rep1_nChIP.Input


title: BTBR_ob_5

description: 10x Genomics

tag: age (weeks)


title: adipose tissue, Child 2

description: 8 years old, male

tag: tissue


title: BTBR_ob_1

description: 10x Genomics


title: Acd_p2

description: ocean acidification stress group

value: mantle

tag: treatment

value: acidification stress


title: BTBR_ob_4

description: 10x Genomics


title: P56ATM3

data_processing:
Next-generation sequencing (NGS) analysis was performed on the BGISEQ-500 platform by BGI Genomics Inc. (Cambridge, MA, USA), generating ~26.2 million reads per sample. Firstly,we remove the reads mapped to rRNA and get raw data. Sequencing reads were checked to remove low-quality, adaptor-polluted and unknown base reads before downstream analyses. After filtering, the clean reads were mapped to the reference genome using HISAT.
On average, 96.8% of reads were mapped, and the uniformity of the mapping result for each sample suggested that the samples were comparable. We mapped clean reads to reference transcripts using Bowtie2, then calculated the gene expression level for each sample with RSEM.
Sequencing data saturation analysis was used to measure whether the depth of sequencing data was sufficient for bioinformatics analysis. Based on their gene expression levels, we identified differentially-expressed genes (DEGs) between sample groups. We used the DEseq2 algorithm to detect the DEGs.
Assembly: Based on the gene expression level, we can identify  DEGs (Differentially expression genes) between vehicle and NPFF-treated samples. We used DEseq2 algorithms to detect the DEGs.
Supplementary files format and content: Excel showing DEGs.

source_name: adipose tissue macrophages (ATMs) on postnatal day 56

value: adipose tissue macrophages (ATMs)


title: Con_p1

description: normal seawater control group

value: normal control


title: HC21 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: healthy control

value: treated with LPS+IFNg for 24 hours


title: HC18(run2) macrophages stimulated with LPS+IFNg

description: re-sequencing of sample for batch effect correction

tag: re-sequencing


title: BTBR_ob_3

description: 10x Genomics


title: adipose tissue, Infant 2

description: 4.8 months old, male

value: adipose tissue

value: adipocytes and stromal cells

value: 4.8 months old


title: BTBR_WT_4

description: 10x Genomics

value: Kidney

value: WT


title: Acd_p3

description: ocean acidification stress group


title: P6ATM3

source_name: adipose tissue macrophages (ATMs) on postnatal day 6

tag: cell type


title: HC18(run2) macrophages stimulated with GMCSF

source_name: blood derived macrophages

tag: batch


title: HC21 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: HC22 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: Y1 1

city: Chicago

first: chuangyu

last: wen

state: IL

address: 900E 57th Street

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

data_processing:
STAR
Assembly: mm10
Supplementary files format and content: Text file includes normalized_counts for each sample

source_name: bone marrow-derived dendritic cells

growth_protocol: BMDCs were cultured in Iscove’s modified Dulbecco’s medium containing 10% FBS, 1% Penicillin Streptomycin solution, 1% Sodium Pyruvate, 1% MEM non-essential amino acid, 55 mM β-mercaptoethanol, and 100 ng/ml human FLT3L for 9 days. Fresh media with FLT3L was added into culture on day 5, and BMDCs were obtained on day 9. All cells were maintained in a humidified incubator at 37°C and 5% CO2

extract_protocol:
RNA was extracted by using RNeasy Plus Mini Kit (QIAGEN) according to manufacturer’s instruction
Library was generated via a SMARTer Stranded Total RNA-Seq kit v2 (TaKaRa) according to manufacturer’s instruction

tag: cell line

value: bone marrow-derived dendritic cells

tag: genotype


title: adipose tissue, Infant 1

description: 13 months old, male

value: 13 months old

value: male


title: HC18(run2) macrophages stimulated with IL4


title: Y1 2


title: HC19 macrophages stimulated with LPS+IFNg


title: BTBR_WT_section5

description: 10x Genomics

value: Sagittal


title: BTBR_WT_2

description: 10x Genomics

value: Cortex


title: HC17(run2) macrophages stimulated with LPS+IFNg


title: P56ATM1

value: adipose tissue macrophages (ATMs) on postnatal day 56

value: adipose tissue macrophages (ATMs)


title: BTBR_WT_1

description: 10x Genomics


title: WT 1


title: Sham, biol rep 3

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

data_processing:
SOAPnuke v1.5.2
Remove the reads containing the adaptor, the reads whose N content is greater than 5%, and low-quality reads using SOAPnuke (parameter: -l 15 -q 0.2 -n 0.05).
Trimmed sequence reads were mapped to mRatBN7.2 using HISAT2 v2.0.4 (parameter: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF).
Read count extraction and normalization were performed using HISAT2.
Assembly: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

source_name: Synovium

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, German).
Total RNA was used for the construction of sequencing libraries.
mRNA was isolated using oligo dT beads and fragmented.
Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a secondstrand cDNA with dUTP.
After PCR amplification and DNA nanoball synthesis, the products were sequenced by BGISEQ-500.

value: Synovium

value: Sham surgery


title: P56ATM2


title: BTBR_WT_5

description: 10x Genomics


title: HC19 macrophages stimulated with IL4

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28 on GENCODE v28 reference transcriptome
Assembly: HG38
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM

value: blood derived macrophages

value: healthy control


title: HC17(run2) macrophages stimulated with GMCSF


title: HC21 macrophages stimulated with GMCSF


title: Acd_p1

description: ocean acidification stress group

value: mantle

value: acidification stress


title: Sham, biol rep 2


title: 2018-03-06-ob-C-9

description: 10x Genomics

value: Kidney

value: BTBR ob/ob


title: BTBR_WT_3

description: 10x Genomics

value: WT


title: P6ATM2

value: adipose tissue macrophages (ATMs) on postnatal day 6


title: 2018-03-06-ob-C-8

description: 10x Genomics


title: HC16 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: HC19 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: Y1 3

value: bone marrow-derived dendritic cells


title: BTBR_WT_section3

description: 10x Genomics

value: Sagittal


title: cKO_6h_2

city: Shenzhen

first: Tao

last: Zhou

address: Shenzhen Institutes of Advance Technology, 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan District, Shenzhen

institute: The Brain Cognition and Brain Disease Institute of Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

data_processing:
RNA samples were sent to Beijing Genomics Institute (BGI) for RNA sequencing on the DNBSEQ platform. Detailed sequencing data analysis methods can be found on the website (https://www.yuque.com/yangyulan-ayaeq/oupzan/lg32g6). In brief, the sequencing data was filtered using SOAPnuke (v1.5.6), and subsequent analysis and data mining were performed using the Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). Bowtie2 (v2.3.4.3) was employed to align the clean reads to the gene set, and the expression levels of genes were quantified in TPM (Transcripts Per Million) using RSEM (v1.3.1).
Assembly: Ensembl 105
Supplementary files format and content: Excel Open XML Spreadsheet(.xlsx) file include FPKM values for each Sample

source_name: cultured neural progenitor/stem cells (NPCs)

extract_protocol:
At 7 days after lentivirus infection, cultured NPCs were treated with actinomycin-D (ActD, 5 μg/ml, Sigma SBR00013) to halt new RNA synthesis. At 0, 3, and 6 hours post-treatment, cells were washed once with PBS and collected with Trizol reagent for total RNA extraction. The concentration and purity of total RNA were assessed through agarose gel electrophoresis and the Agilent 2100 Bioanalyzer system to ensure high-quality RNA. Subsequently, the RNA samples were sent to Beijing Genomics Institute (BGI) for RNA sequencing on the DNBSEQ platform, following their established protocols available on their website (https://www.yuque.com/yangyulan-ayaeq/oupzan/gu8ls7).
RNA libraries were prepared  by Beijing Genomics Institute (BGI)  following their established protocols available on their website (https://www.yuque.com/yangyulan-ayaeq/oupzan/gu8ls7).

value: cKO


title: cKO_6h_3

value: cultured neural progenitor/stem cells (NPCs)


title: P6ATM1

value: adipose tissue macrophages (ATMs)


title: 2018-03-06-ob-C-10

description: 10x Genomics

value: Cortex


title: HC16 macrophages stimulated with GMCSF

extract_protocol:
Nucleospin RNA extraction kit (Macherey-Nagel)
Truseq mRNA stranded ILLUMINA with UDI


title: WT 2


title: cKO_6h_1


title: pMx, biol rep 2

source_name: Regenerative tissue

value: Regenerative tissue

value: Partial meniscectomy


title: pMx, biol rep 1


title: cKO_6h_4


title: 2018-03-06-ob-S-10

description: 10x Genomics


title: WT 3


title: 2018-03-06-WT-S-10

description: 10x Genomics


title: Intact, biol rep 3

value: Synovium

value: No surgery


title: HC15 macrophages stimulated with GMCSF

value: blood derived macrophages

value: healthy control


title: cKO_3h_2


title: Sham, biol rep 1

value: Sham surgery


title: HC17(run2) macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: pMx, biol rep 3

value: WT


title: HC16 macrophages stimulated with IL4


title: cKO_3h_1


title: cKO_0h_4


title: cKO_3h_3


title: 2018-03-06-WT-C-9

description: 10x Genomics

value: Kidney


title: cKO_0h_2


title: 2018-03-01-WT-S-7

description: 10x Genomics


title: HC15 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: HC14(run2) macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: 2018-03-01-WT-S-6

description: 10x Genomics

value: Sagittal


title: HC14(run2) macrophages stimulated with IL4


title: 2018-03-06-WT-C-8

description: 10x Genomics


title: HeLaK_ZNF512BKD_N2

city: Giessen

first: Sandra

middle: Brigitte

last: Hake

state: Hessen

address: Heinrich-Buff-Ring 58-62

department: Faculty 08 Biology and Chemistry

institute: Institute for Genetics

data_processing:
Raw sequencing files (FASTQ) were adaptor and quality trimmed using trimGalore
Alignment of the trimmed sequencing reads to the hg19 reference genome (downloaded from Illuminaâs iGenomes) was performed using Hisat2 v.2.2.1 with â-- min-intronlen 30 âmax-intronlen 3000â parameters
Read count per gene tables based on BAM files were generated within R using the summarizeOverlaps function of the GenomicAlignments package
Normalization of read counts and detection of differentially expressed genes was calculated with DESeq2
Assembly: hg19
Supplementary files format and content: raw read counts as csv

source_name: HeLaK

growth_protocol: HeLa Kyoto (HeLaK), U2OS, HCT116 and HEK293 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS; Gibco) and 1% penicillin/streptomycin (370C, 5% CO2) and routinely tested with PCR for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on column DNase digest (RNase-Free DNase Set, QIAGEN) according to the manufacturer’s instructions.
Sequencing library contruction was perfomred at Biomarker (Münster, Germany) by using Hieff NGS™ Ultima Dual-mode mRNA Library Prep Kit. Briefly, purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0 and Agilent 2100 once the RNA samples were received. Only RNA with RIN value greater than 8 was used for library construction. The procedures are described as follow: first, mRNA was isolated by Oligo(dT)-attached magnetic beads, followed by random fragmention in fragmentation buffer. Then first-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Subsequently, purification of cDNA was processed with AMPure XP beads. Later, double-strand cDNA was subjected to end repair, where Adenosine was added to the end and ligated to adapters. Also, AMPure XP beads were applied to select fragments within certain size range. Lastly, cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from the previous step. In order to ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration and assure adequate library concentration.

treatment_protocol: Transfections of cells were performed using FUGENE® HD Transfection Reagent according to the manufacturer’s instructions (Promega). 48 hours after transfection, cells were harvested by trypsinization for diverse assays.

value: HeLaK

value: Human cervical cancer cell

value: ZNF512B knockdown

value: Transfection of ZNF512B-specific siRNAs


title: cKO_0h_1

value: cultured neural progenitor/stem cells (NPCs)

value: cKO


title: Rhesus macaque Engineered Heart Muscle, 28 days,Rep1

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

description:
R191112BEHMRhesus_R1
ED Figure 1C (ii) Rhesus macaque Engineered Heart Muscle (RhEHM)
R191112BEHMRhesus_barcodes.tsv.gz
R191112BEHMRhesus_features.tsv.gz
R191112BEHMRhesus_matrix.mtx.gz

data_processing:
Cellranger-4.0.0 mkfastq was used for adapter trimming and converting the base calls
Cellranger-4.0.0 counts was used to align the reads on the pre-mRNA and create the read count matrices
Assembly: hg38
Supplementary files format and content: count matrices, barcode tables, feature tables

organism: Macaca mulatta

source_name: iPSC-derived cardiomyocytes and stromal cells

growth_protocol: described in methods of related paper

extract_protocol:
described in methods of related paper
described in methods of related paper
10X genomics single-cell seq

treatment_protocol: described in methods of related paper

tag: strain

value: Rhesus iPSC 43110-4

value: After 28 days of RhEHM culture

tag: stimulation

value: no stimulation

tag: fraction


title: Rhesus macaque Engineered Heart Muscle, 28 days,Rep3

description:
R191112BEHMRhesus_R3
ED Figure 1C (ii) Rhesus macaque Engineered Heart Muscle (RhEHM)
R191112BEHMRhesus_barcodes.tsv.gz
R191112BEHMRhesus_features.tsv.gz
R191112BEHMRhesus_matrix.mtx.gz

value: iPSC-derived cardiomyocytes and stromal cells


title: 2018-03-06-WT-C-10

description: 10x Genomics

value: Cortex


title: Intact, biol rep 2

value: Synovium

value: No surgery


title: HC15 macrophages stimulated with IL4

city: Paris

first: violetta

last: zujovic

address: 47 boulevard de l'hôpital

institute: Paris brain institute

value: blood derived macrophages

value: healthy control

value: treated with IL4 for 24hours


title: Intact, biol rep 1

value: WT


title: 2018-03-01-ob-S-7

description: 10x Genomics

value: Kidney

value: Sagittal

value: BTBR ob/ob


title: HC14(run2) macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: Rhesus macaque Engineered Heart Muscle, 28 days,Rep4

description:
R191112BEHMRhesus_R4
ED Figure 1C (ii) Rhesus macaque Engineered Heart Muscle (RhEHM)
R191112BEHMRhesus_barcodes.tsv.gz
R191112BEHMRhesus_features.tsv.gz
R191112BEHMRhesus_matrix.mtx.gz


title: WT_6h_4

value: cultured neural progenitor/stem cells (NPCs)


title: Human iPSC-derived stromal cells, 30 days,Rep3

description:
SakibS200211AGMPstromacells4000nuc_R3
ED Figure 1B (i) Human iPSC-derived stromal cells
SakibS200211AGMPstromacells4000nuc_barcodes.tsv.gz
SakibS200211AGMPstromacells4000nuc_features.tsv.gz
SakibS200211AGMPstromacells4000nuc_matrix.mtx.gz

source_name: induced pluripotent stem cells

value: 30 days after start of differentiation

value: induced pluripotent stem cells


title: 2018-03-01-ob-S-6

description: 10x Genomics


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days,Rep3

description:
Diff305CMCardiomyocytesRhesus_R3
ED Figure 1A (iii) Rhesus macaque iPSC-derived cardiomyocytes (extended selection)
Diff305CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff305CMCardiomyocytesRhesus_features.tsv.gz
Diff305CMCardiomyocytesRhesus_matrix.mtx.gz

value: Rhesus iPSC 43110-4

value: 22 days after start of differentiation

value: extended selection


title: HeLaK_ctrlKD_N1

value: HeLaK

value: Human cervical cancer cell

value: Transfection of scrambled siRNAs


title: Rhesus macaque Engineered Heart Muscle, 28 days,Rep2

description:
R191112BEHMRhesus_R2
ED Figure 1C (ii) Rhesus macaque Engineered Heart Muscle (RhEHM)
R191112BEHMRhesus_barcodes.tsv.gz
R191112BEHMRhesus_features.tsv.gz
R191112BEHMRhesus_matrix.mtx.gz

value: After 28 days of RhEHM culture

value: no stimulation

value: iPSC-derived cardiomyocytes and stromal cells


title: HeLaK_ZNF512B_K423AOE_N3

value: GFP-ZNF512B_K423A overexpression

value: Transfection of GFP-ZNF512B_K423A plasmids


title: cKO_3h_4

value: cKO


title: Human Engineered Heart Muscle, 28 days,Rep3

description:
E200407AP3GMPEHM4000nuc_R3
ED Figure 1C (i) Human Engineered Heart Muscle (hEHM)
SakibE200407AP3GMPEHM4000nuc_barcodes.tsv.gz
SakibE200407AP3GMPEHM4000nuc_features.tsv.gz
SakibE200407AP3GMPEHM4000nuc_matrix.mtx.gz

value: After 28 days of hEHM culture


title: HeLaK_ZNF512BOE_N3

value: GFP-ZNF512B overexpression

value: Transfection of GFP-ZNF512B plasmids


title: Human iPSC-derived stromal cells, 30 days,Rep4

description:
SakibS200211AGMPstromacells4000nuc_R4
ED Figure 1B (i) Human iPSC-derived stromal cells
SakibS200211AGMPstromacells4000nuc_barcodes.tsv.gz
SakibS200211AGMPstromacells4000nuc_features.tsv.gz
SakibS200211AGMPstromacells4000nuc_matrix.mtx.gz

value: 30 days after start of differentiation


title: HeLaK_ZNF512BKD_N1

value: ZNF512B knockdown

value: Transfection of ZNF512B-specific siRNAs


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days,Rep4

description:
Diff305CMCardiomyocytesRhesus_R4
ED Figure 1A (iii) Rhesus macaque iPSC-derived cardiomyocytes (extended selection)
Diff305CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff305CMCardiomyocytesRhesus_features.tsv.gz
Diff305CMCardiomyocytesRhesus_matrix.mtx.gz

value: Rhesus iPSC 43110-4

value: 22 days after start of differentiation

value: induced pluripotent stem cells


title: Human Engineered Heart Muscle, 28 days,Rep1

description:
E200407AP3GMPEHM4000nuc_R1
ED Figure 1C (i) Human Engineered Heart Muscle (hEHM)
SakibE200407AP3GMPEHM4000nuc_barcodes.tsv.gz
SakibE200407AP3GMPEHM4000nuc_features.tsv.gz
SakibE200407AP3GMPEHM4000nuc_matrix.mtx.gz


title: cKO_0h_3

value: cultured neural progenitor/stem cells (NPCs)


title: Human iPSC-derived stromal cells, 30 days,Rep1

description:
SakibS200211AGMPstromacells4000nuc_R1
ED Figure 1B (i) Human iPSC-derived stromal cells
SakibS200211AGMPstromacells4000nuc_barcodes.tsv.gz
SakibS200211AGMPstromacells4000nuc_features.tsv.gz
SakibS200211AGMPstromacells4000nuc_matrix.mtx.gz


title: WT_6h_3

value: WT


title: HeLaK_ctrlKD_N2

value: HeLaK

value: Human cervical cancer cell

value: Transfection of scrambled siRNAs


title: HeLaK_ZNF512BOE_N2


title: Human iPSC-derived stromal cells, 30 days,Rep2

description:
SakibS200211AGMPstromacells4000nuc_R2
ED Figure 1B (i) Human iPSC-derived stromal cells
SakibS200211AGMPstromacells4000nuc_barcodes.tsv.gz
SakibS200211AGMPstromacells4000nuc_features.tsv.gz
SakibS200211AGMPstromacells4000nuc_matrix.mtx.gz

value: no stimulation


title: WT_6h_2


title: HeLaK_ZNF512BOE_N1


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days,Rep2

description:
Diff305CMCardiomyocytesRhesus_R2
ED Figure 1A (iii) Rhesus macaque iPSC-derived cardiomyocytes (extended selection)
Diff305CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff305CMCardiomyocytesRhesus_features.tsv.gz
Diff305CMCardiomyocytesRhesus_matrix.mtx.gz

value: extended selection


title: WT_6h_1


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days,Rep1

description:
Diff305CMCardiomyocytesRhesus_R1
ED Figure 1A (iii) Rhesus macaque iPSC-derived cardiomyocytes (extended selection)
Diff305CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff305CMCardiomyocytesRhesus_features.tsv.gz
Diff305CMCardiomyocytesRhesus_matrix.mtx.gz


title: Human Engineered Heart Muscle, 28 days,Rep4

description:
E200407AP3GMPEHM4000nuc_R4
ED Figure 1C (i) Human Engineered Heart Muscle (hEHM)
SakibE200407AP3GMPEHM4000nuc_barcodes.tsv.gz
SakibE200407AP3GMPEHM4000nuc_features.tsv.gz
SakibE200407AP3GMPEHM4000nuc_matrix.mtx.gz

value: iPSC-derived cardiomyocytes and stromal cells


title: HeLaK_ZNF512B_K423AOE_N2

value: GFP-ZNF512B_K423A overexpression

value: Transfection of GFP-ZNF512B_K423A plasmids


title: WT_3h_4


title: HeLaK_GFPOE_N3

value: GFP overexpression

value: Transfection of GFP plasmids


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days, Rep4

description:
Diff236CMCardiomyocytesRhesus_R4
ED Figure 1A (ii) Rhesus macaque iPSC-derived cardiomyocytes
Diff236CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff236CMCardiomyocytesRhesus_features.tsv.gz
Diff236CMCardiomyocytesRhesus_matrix.mtx.gz


title: Human iPSC-derived cardiomyocytes,22 days,Rep3

description:
SakibC617RSM200317AGMPcardiomyocytes4000nuc_R3
ED Figure 1A (i) Human iPSC-derived cardiomyocytes
SakibC617RSM200317AGMPcardiomyocytes4000nuc_barcodes.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_features.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_matrix.mtx.gz


title: WT_0h_3


title: Human iPSC-derived cardiomyocytes,22 days,Rep1

description:
SakibC617RSM200317AGMPcardiomyocytes4000nuc_R1
ED Figure 1A (i) Human iPSC-derived cardiomyocytes
SakibC617RSM200317AGMPcardiomyocytes4000nuc_barcodes.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_features.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_matrix.mtx.gz


title: Rhesus macaque iPSC-derived stromal cells, 30 days,Rep4

description:
Diff286StCStromacellsRhesus_R4
ED Figure 1B (ii) Rhesus macaque iPSC-derived stromal cells
Diff286StCStromacellsRhesus_barcodes.tsv.gz
Diff286StCStromacellsRhesus_features.tsv.gz
Diff286StCStromacellsRhesus_matrix.mtx.gz

value: 30 days after start of differentiation


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days, Rep2

description:
Diff236CMCardiomyocytesRhesus_R2
ED Figure 1A (ii) Rhesus macaque iPSC-derived cardiomyocytes
Diff236CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff236CMCardiomyocytesRhesus_features.tsv.gz
Diff236CMCardiomyocytesRhesus_matrix.mtx.gz


title: WT_0h_2


title: HeLaK_GFPOE_N1


title: WT_3h_3


title: HeLaK_ZNF512B_K423AOE_N1


title: Human Engineered Heart Muscle, 28 days,Rep2

description:
E200407AP3GMPEHM4000nuc_R2
ED Figure 1C (i) Human Engineered Heart Muscle (hEHM)
SakibE200407AP3GMPEHM4000nuc_barcodes.tsv.gz
SakibE200407AP3GMPEHM4000nuc_features.tsv.gz
SakibE200407AP3GMPEHM4000nuc_matrix.mtx.gz

value: After 28 days of hEHM culture


title: Rhesus macaque iPSC-derived stromal cells, 30 days,Rep2

description:
Diff286StCStromacellsRhesus_R2
ED Figure 1B (ii) Rhesus macaque iPSC-derived stromal cells
Diff286StCStromacellsRhesus_barcodes.tsv.gz
Diff286StCStromacellsRhesus_features.tsv.gz
Diff286StCStromacellsRhesus_matrix.mtx.gz

value: Rhesus iPSC 43110-4


title: WT_3h_2


title: WT_0h_1


title: WT_3h_1


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days, Rep1

description:
Diff236CMCardiomyocytesRhesus_R1
ED Figure 1A (ii) Rhesus macaque iPSC-derived cardiomyocytes
Diff236CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff236CMCardiomyocytesRhesus_features.tsv.gz
Diff236CMCardiomyocytesRhesus_matrix.mtx.gz

value: 22 days after start of differentiation


title: Human iPSC-derived cardiomyocytes,22 days,Rep4

description:
SakibC617RSM200317AGMPcardiomyocytes4000nuc_R4
ED Figure 1A (i) Human iPSC-derived cardiomyocytes
SakibC617RSM200317AGMPcardiomyocytes4000nuc_barcodes.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_features.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_matrix.mtx.gz

value: induced pluripotent stem cells


title: AGS infected with CagA-negative H. pylori (ΔCagA) for 5 hours

status: Public on Oct 28 2024

city: Seoul

first: BYEONGMIN

last: YU

address: Yonsei University college of medicine

country: South Korea

institute: Department of Internal Medicine, Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Stomach

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: Stomach

value: AGS

value: epithelial

value: H.pylori {delta}CagA


title: AGS infected with CagA-positive H. pylori (60190) for 5 hours #1

value: WT

value: H.pylori 60190


title: Rhesus macaque iPSC-derived stromal cells, 30 days,Rep1

description:
Diff286StCStromacellsRhesus_R1
ED Figure 1B (ii) Rhesus macaque iPSC-derived stromal cells
Diff286StCStromacellsRhesus_barcodes.tsv.gz
Diff286StCStromacellsRhesus_features.tsv.gz
Diff286StCStromacellsRhesus_matrix.mtx.gz

value: no stimulation


title: AGS without H. pylori infection ,5hr(Control) #2

value: Control


title: AGS without H. pylori infection ,5hr(Control) #3


title: AGS infected with CagA-negative H. pylori (ΔCagA) for 7 hours


title: NV069

city: New York

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
SMART-Seq v4 Ultra Low Input Nextera XT
v2.adj.2021-08-17.rda

data_processing:
single cell RNA seq were processed with 10x Cell Ranger pipeline and downstream analysis was conducted using Seurat
Bulk RNA seq analysis was conducted in R
Assembly: hg19
Supplementary files format and content: RDS object

source_name: colon

extract_protocol:
human intestinal biopsies were collected in RPMI and processed fresh to ontain single cell suspension. Biopsies underwent two 20 minute rounds of dissociation to remove the epithelial layer (Dissociation media: 10 ml HBSS (free of calcium and magnesium) EDTA (0.5M, pH 8, Invitrogen) and HEPES (1M, Lonza)) was followed by transfer to 10 ml of digestion solution (containing RPMI, FBS (Corning 35-010-CV), 0.005 g of Type IV collagenase (Sigma-Aldrich, cat # C5138-1G) and DNAase I (Sigma Aldrich Fine Chemicals Biosciences cat # 10104159001)) and incubated for 40min at 37°C using gentle agitation (180 rpm). The digested tissue was then further mechanically broken down by aspirating 10-times with a 10ml syringe by sequentially filtering through a 100-µm and a 40-µm cell strainer and washed with RPMI twice to obtain a single cell suspension of the intestinal lamina propria.
For scRNASeq, Gene expression libraries were prepared as per 10x Genomics protocol. For RNA-seq Gene expression libraries were prepared as per SMART-Seq v4 Ultra Low Input Nextera XT or SureSelect XT RNA Direct v6 protocols

value: colon

value: Flow-sorted colonic Plasma Cells


title: Rhesus macaque iPSC-derived stromal cells, 30 days,Rep3

description:
Diff286StCStromacellsRhesus_R3
ED Figure 1B (ii) Rhesus macaque iPSC-derived stromal cells
Diff286StCStromacellsRhesus_barcodes.tsv.gz
Diff286StCStromacellsRhesus_features.tsv.gz
Diff286StCStromacellsRhesus_matrix.mtx.gz


title: HIV047


title: WT_0h_4

value: cultured neural progenitor/stem cells (NPCs)


title: HeLaK_GFPOE_N2

value: HeLaK

value: Human cervical cancer cell

value: GFP overexpression

value: Transfection of GFP plasmids


title: HIV044


title: HIV042

description:
SureSelect XT RNA Direct v6
v2.adj.2021-08-17.rda


title: Human iPSC-derived cardiomyocytes,22 days,Rep2

description:
SakibC617RSM200317AGMPcardiomyocytes4000nuc_R2
ED Figure 1A (i) Human iPSC-derived cardiomyocytes
SakibC617RSM200317AGMPcardiomyocytes4000nuc_barcodes.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_features.tsv.gz
SakibC617RSM200317AGMPcardiomyocytes4000nuc_matrix.mtx.gz

value: 22 days after start of differentiation


title: HIV036


title: Rhesus macaque iPSC-derived cardiomyocytes, 22 days, Rep3

description:
Diff236CMCardiomyocytesRhesus_R3
ED Figure 1A (ii) Rhesus macaque iPSC-derived cardiomyocytes
Diff236CMCardiomyocytesRhesus_barcodes.tsv.gz
Diff236CMCardiomyocytesRhesus_features.tsv.gz
Diff236CMCardiomyocytesRhesus_matrix.mtx.gz

value: Rhesus iPSC 43110-4

value: induced pluripotent stem cells


title: AGS infected with CagA-negative H. pylori (ΔCagA) for 6 hours

value: Stomach

value: AGS


title: AGS infected with CagA-positive H. pylori (60190) for 5 hours #3

value: epithelial


title: NV074


title: AGS infected with CagA-positive H. pylori (60190) for 5 hours #2

value: WT


title: AGS without H. pylori infection ,5hr(Control) #1


title: NV042


title: NV072


title: res1OE mutant 9h biol rep 2

city: Berkeley

first: Louise

middle: N

last: Glass

address: Koshland Hall

department: PMB

institute: UC California

data_processing:
raw reads were trimmed with trimmomatic (V 0.39) and quality control of fragments was done with FastQC (V 0.11.09)
mapping on the chromosomes with HiSat2 (V 2.1.0) and turned into SAM files with samtools (V 1.8)
counts per million were counted with a custom R script and further processed
Assembly: ASM22609v1
Supplementary files format and content: RData file containing the  mapped reads

organism: Thermothelomyces thermophilus

growth_protocol: 10^6 conidia/mL were grown in pre-culture medium for the described periods of time

extract_protocol:
Frozen mycelial samples were mixed with 1 mL TRIzol (Thermo Fisher Scientific) and processed for 1 minute on a beadbeater with 250 mg silica beads (0.5mm Zirconia). Samples were then centrifuged and the supernatant mixed with 200 µL chloroform and centrifuged again. The aqueous phase was mixed with isopropanol and RNA was precipitated, centrifuged, and washed with ethanol. RNA was resuspended in RNase free water and DNaseI (NEB) digested and purified on Monarch®
Kapa Biosystems library prep

treatment_protocol: timecourse

value: fungal

value: {delta}res1 PH2A::res1-V5

value: time course


title: res1OE mutant 9h biol rep 1


title: HIV043

value: colon


title: res1OE mutant 7.5h biol rep 3


title: HIV039

value: Flow-sorted colonic Plasma Cells


title: Het-Ctrl, HPC, biological rep 3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
HPCs isolated from heterozygous (Polgwt/mut.) mice transduced with Ctrl vector
xki049

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom™ S Mouse Array by GeneChip® Hybridization Oven 645 according to the protocols recommended by the manufacturer (Affymetrix, Inc).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix, Inc).

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software (Affymetrix, Inc).

source_name: Het-Ctrl, HPC

label_protocol: DLR-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip® WT PLUS Reagent Kit (Affymetrix), according to manufacturer's instructions.

growth_protocol: Lineage-negative BM cells (HPCs) from WT, Het, and Hom mice were separated by the autoMACS. All sorted HPCs were immediately seeded for 48 h in complete BM media (c-BM media)  till transduction with NMyc or Ctrl vectors.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions

treatment_protocol: Six-well plates were coated with retronectin for 16 h, followed by spin at 3000 rpm, 60 min, 4°C with supernatant containing MSCV-IRES-YFP (Ctrl) or MSCV-NMyc-IRES-YFP (NMyc) secreted from GP+E86 cells. HPCs (0.5 × 106/well) from WT, Het, and Hom mice were then seeded on the plates with either Ctrl or NMyc in c-BM media.

value: HPCs

value: Het (Polgwt/mut.)

value: tranduced with Ctrl vector


title: HIV029


title: WT-Ctrl, HPC, biological rep 3

description:
HPCs isolated from wildtype (Polgwt/wt.) mice transduced with Ctrl vector
xki048

source_name: WT-Ctrl, HPC

value: WT (Polgwt/wt.)


title: WT-Ctrl, HPC, biological rep 2

description:
HPCs isolated from wildtype (Polgwt/wt.) mice transduced with Ctrl vector
xki036


title: HIV028


title: Hom-MNyc, HPC, biological rep 1

description:
HPCs isolated from homozygous (Polgmut/mut) mice transduced with NMyc
xki041

source_name: Hom-MNyc, HPC

value: Hom (Polgmut/mut)

value: tranduced with NMyc


title: Het-Ctrl, HPC, biological rep 1

description:
HPCs isolated from heterozygous (Polgwt/mut.) mice transduced with Ctrl vector
xki025


title: res1OE mutant 6h biol rep 1


title: res1OE mutant 6h biol rep 2


title: ∆res1 mutant 9h biol rep 2


title: Het-MNyc, HPC, biological rep 2

description:
HPCs isolated from heterozygous (Polgwt/mut.) mice transduced with NMyc
xki051

source_name: Het-MNyc, HPC


title: Hom-Ctrl, HPC, biological rep 2

description:
HPCs isolated from homozygous (Polgmut/mut) mice transduced with Ctrl vector_Experimental group 170807_2077 Hom-YFP
xki038

source_name: Hom-Ctrl, HPC


title: ∆res1 mutant 7.5h biol rep 3


title: ∆res1 mutant 6h biol rep 3


title: Het-MNyc, HPC, biological rep 1

description:
HPCs isolated from heterozygous (Polgwt/mut.) mice transduced with NMyc
xki040


title: ∆res1 mutant 7.5h biol rep 1


title: res1OE mutant 7.5h biol rep 2


title: res1OE mutant 7.5h biol rep 1


title: WT-MNyc, HPC, biological rep 1

description:
HPCs isolated from wildtype (Polgwt/wt.) mice transduced with NMyc
xki039

source_name: WT-MNyc, HPC


title: Hom-Ctrl, HPC, biological rep 1

description:
HPCs isolated from homozygous (Polgmut/mut) mice transduced with Ctrl vector
xki026


title: Het-Ctrl, HPC, biological rep 2

description:
HPCs isolated from heterozygous (Polgwt/mut.) mice transduced with Ctrl vector
xki037


title: Hom-MNyc, HPC, biological rep 2

description:
HPCs isolated from homozygous (Polgmut/mut) mice transduced with NMyc
xki052


title: WT-MNyc, HPC, biological rep 2

description:
HPCs isolated from wildtype (Polgwt/wt.) mice transduced with NMyc
xki050


title: res1OE mutant 9h biol rep 3


title: ∆res1 complementation  48h biol rep 3

value: {delta}res1 Pres1::res1-gfp


title: WT 9h biol rep 2


title: ∆res1 complementation  48h biol rep 1


title: WT-Ctrl, HPC, biological rep 1

description:
HPCs isolated from wildtype (Polgwt/wt.) mice transduced with Ctrl vector
xki024


title: ∆res1 mutant 6h biol rep 1


title: WT 9h biol rep 3


title: ∆res1 mutant 48h biol rep 3


title: ∆res1 mutant 9h biol rep 1


title: ∆res1 mutant 48h biol rep 2


title: ∆res1 mutant 7.5h biol rep 2


title: WT 9h biol rep 1


title: ∆res1 mutant 48h biol rep 1


title: WT 48h biol rep 1


title: WT 7.5h biol rep 3


title: WT 48h biol rep 2


title: ∆res1 mutant 9h biol rep 3


title: WT 7.5h biol rep 2


title: WT 7.5h biol rep 1


title: WT 6h biol rep 3


title: WT 6h biol rep 2


title: ∆res1 mutant 6h biol rep 2


title: WT 6h biol rep 1


title: ∆res1 complementation  48h biol rep 2


title: ∆res1 mutant 20h biol rep 2


title: WT 20h biol rep 2


title: ∆res1 complementation  20h biol rep 1


title: complement 16h biol rep 3


title: WT 48h biol rep 3


title: ∆res1 mutant 16h biol rep 2


title: ∆res1 complementation  20h biol rep 2


title: ∆res1 mutant 16h biol rep 3


title: WT 16h biol rep 3


title: ∆res1 complementation  20h biol rep 3


title: ∆res1 complementation 14h biol rep 3


title: WT 20h biol rep 3


title: ∆res1 mutant 20h biol rep 3


title: ∆res1 mutant 14h biol rep 1


title: ∆res1 mutant 20h biol rep 1


title: WT 16h biol rep 2


title: WT 16h biol rep 1


title: ∆res1 mutant 16h biol rep 1


title: WT 20h biol rep 1


title: complement 16h biol rep 1


title: ∆res1 complementation 14h biol rep 1


title: ∆res1 complementation 14h biol rep 2


title: ∆res1 mutant 14h biol rep 3


title: ∆res1 mutant 14h biol rep 2


title: ∆res1 complementation 11.5h biol rep 3


title: WT 14h biol rep 2


title: ∆res1 complementation 11.5h biol rep 2


title: WT 14h biol rep 1


title: ∆res1 complementation 11.5h biol rep 1


title: complement 16h biol rep 2


title: ∆res1 mutant 11.5h biol rep 3


title: ∆res1 mutant 11.5h biol rep 1