title: Liver, Multigenerational WD with fibrosis, rep1

description: Library name: AH01-14

value: Multigenerational WD with fibrosis


status: Public on Jun 18 2025

type: SRA

city: Beijing

first: Yao

last: Lv

state: Beijing

address: No. 7 Science Park Road, Zhongguancun Life Science Park, Changping District,   Beijing 102206, P.R. China

country: China

institute: National Institute of Biological Sciences,Beijing

description:
NCI-H292 cell line, seq2 Aeg-S/L+EGTA2, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_SLEGTA2

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using Fastp (version 0.19.7) to remove adaptors and low-quality reads according to the following criteria: (1) paired reads were discarded if either read contained adapter contamination; (2) paired reads were discarded if more than 10% of bases were uncertain in either read; (3) paired reads were discarded if the proportion of low-quality bases (Phred quality < 5) exceeded 50% in either read.
Filtered reads were then aligned to the mouse reference genome (mm10) or the human reference genome (hg19) using HISAT2 (v2.2.1)
The resulting SAM files were converted to sorted BAM files using Samtools
Gene annotations were based on the GENCODE mouse release M25 and GENCODE human release 19 comprehensive gene annotation files.Rawcounts were extracted with featureCounts (v2.0.2)
Read count normalization and differential gene expression analysis were performed using DESeq2 (v1.36.0) in the R environment (v4.2.2)
Assembly: mm10, hg19
Supplementary files format and content: format:txt, content:raw counts of each sample in the experiment

molecule: total RNA

organism: Homo sapiens

growth_protocol: Mice were bred and maintained in the animal facility under specific pathogen-free conditions.Cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (GEMINI Cat 900-108), 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco), and were maintained in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNAprep Pure Cell/Bacteria Kit (TIANGEN, Cat: DP430)
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocols.

tag: cell line

tag: cell type

value: epithelial cell; Non-small cell lung cancer cell line


title: Neuronal cells after MH treatment 4

city: Guangzhou

first: Huasong

last: Zhang

state: Guangdong

address: 63 Duobao Road, Liwan District, Guangzhou

institute: The Third Affiliated Hospital, Guangzhou Medical University

description: Library name: MH4

data_processing:
Beginning from raw data of double-trim RNA sequencing on mouse samples, we used fastp software1 (https://github.com/OpenGene/fastp) to carry out data-cleaning workflow. Fastp is a tool providing fast all-in-one preprocessing for FastQ files, so all parameters were kept as default to preprocess the raw data, including (but not restricted to) striping adaptors, filtering out low-quality reads, correcting mismatched base pairs and  trimming poly G ends.
After pre-processing, the RNAseq data was delivered to salmon tool (https://salmon.readthedocs.io/en/latest/salmon.html) to generate gene expression matrix. In detail, reads were aligned to GRCm9 (http://asia.ensembl.org/Mus_musculus/Info/Index) gene annotation file downloaded from Ensemble web service.
After filtering off genes that exhibited raw counts of 0 in each sample, raw counts of gene symbol along all mouse samples were generated.
In parallel, we generated another gene expression matrix by the popular STAR tool  (https://github.com/alexdobin/STAR) for one randomly selected sample, and the significant linear co-relationship of all gene expressions respectively calculated by STAR7 and salmon in this sample confirmed the reliability of the gene expression matrix generated by alignment-free method.
Assembly: After pre-processing, the RNAseq data was delivered to salmon tool to generate gene expression matrix. In detail, reads were aligned to GRCm9 (http://asia.ensembl.org/Mus_musculus/Info/Index) gene annotation file downloaded from Ensemble web service.
Supplementary files format and content: “raw_counts.csv” is the comma-seperated matrix of gene raw counts of all the sample mouse. The rows are gene symbols and the columns are sample IDs.
Supplementary files format and content: “FPKM_normalized.csv” is the comma-seperated matrix of gene FPKM-normalized abundance of all the sample mouse. The rows are gene ensembl IDs and the columns are sample IDs.

organism: Mus musculus

source_name: Hippocampal tissue

growth_protocol: C57BL/6J male mice were randomly assigned into six groups, namely the control group (NC), the Sodium phenylbutyrate (SP) group, the Rotenone (ROT) group, the ROT+SP group, the Meclofenoxate-hydrochloride (MH) group, and the ROT+MH group. The mice in the NC group received dimethylsulfoxide (DMSO) (olive oil only); the mice in the SP group were treated with SP (300 mg/kg bw/d; intraperitoneal [i.p.]) for 4 consecutive weeks; the mice in the ROT group were given rotenone (1 μg/g bw/d; i.p.) for 3 consecutive weeks; the mice in the ROT+SP group received SP prophylaxis (300 μg/g bw/d; i.p.) for 1 week followed by ROT (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 consecutive weeks; the mice in the MH group were administered with MH (50  μg/g bw/d; i.p.) for 4 consecutive weeks; the mice in the ROT+MH group received MH prophylaxis (50 μg/g bw/d; i.p.) for 1 week followed by ROT challenge (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 weeks.

extract_protocol:
Total RNA was extracted from tissue or cell samples using a standardized RNA extraction kit, following the manufacturer’s instructions. Briefly, samples were lysed and homogenized in a denaturing buffer to inactivate RNases. RNA was separated from DNA and proteins through phase separation using acid-phenol:chloroform, followed by RNA precipitation with isopropanol. The RNA pellet was washed with 75% ethanol and dissolved in RNase-free water. The quantity and purity of RNA were measured using a NanoDrop spectrophotometer (OD260/280 and OD260/230 ratios), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Only high-quality RNA samples (RIN ≥ 7.0) were used for downstream library construction.
Total RNA was extracted using a standardized protocol and assessed for integrity and concentration with the Agilent 2100 Bioanalyzer. mRNA was enriched either by poly(A) selection with Oligo(dT) magnetic beads or by rRNA depletion. Fragmentation of mRNA was performed in NEB Fragmentation Buffer. First-strand cDNA synthesis was conducted using random hexamer primers and M-MuLV reverse transcriptase, followed by second-strand synthesis with either dNTPs (standard libraries) or dUTP substitution (strand-specific libraries). After end repair, A-tailing, and adapter ligation, size selection (250–300 bp) was carried out using AMPure XP beads. Strand-specific libraries underwent USER enzyme digestion prior to PCR amplification. Libraries were quantified by Qubit 2.0 and qRT-PCR, and insert sizes were assessed using the Agilent 2100 Bioanalyzer. Qualified libraries (effective concentration >2 nM) were pooled and sequenced on an Illumina platform using sequencing-by-synthesis technology. Library preparation was performed using the NEBNext® Ultra™ RNA Library Prep Kit or the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: The mice in the MH group were administered with MH (50  μg/g bw/d; i.p.) for 4 consecutive weeks; the mice in the ROT+MH group received MH prophylaxis (50 μg/g bw/d; i.p.) for 1 week followed by ROT challenge (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 weeks.

tag: tissue

value: Hippocampal tissue

value: Neuronal cells

tag: genotype

value: WT

tag: treatment

value: Neuronal cells after MH treatment 4


title: Liver, NC/NC, rep4

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: AH01-7

data_processing:
Raw read QC was done using FastQC (v0.11.9)
Adapter and quality trimming was done using cutadapt (v3.5)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.9a)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.2)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3)
Assembly: Mus musculus GRCm39 (Ensembl release 104)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: liver

extract_protocol:
RNA was extracted using the Aurum Total RNA Mini Kit (Bio-rad Laboratories)
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: liver

value: NC/NC


title: Neuronal cells after MH treatment 3

description: Library name: MH3

value: Neuronal cells after MH treatment 3


description:
NCI-H292 cell line, seq2 Aeg-S/L+EGTA1, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_SLEGTA1


title: Liver, NC/NC, rep3

description: Library name: AH01-6


title: Neuronal cells after MH treatment 2

description: Library name: MH2

value: Neuronal cells after MH treatment 2


title: Liver, NC/WD, rep1

description: Library name: AH01-5

value: NC/WD


description:
NCI-H292 cell line, seq2 Aeg-S/L+BAPTA-AM1, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_SLBAPTA1


title: Liver, NC/NC, rep2

description: Library name: AH01-3


title: Neuronal cells 3

description: Library name: NC3

value: Neuronal cells 3


title: Neuronal cells after MH treatment 1

description: Library name: MH1

value: Neuronal cells after MH treatment 1


title: NCI-H292 cell line, seq2 Aeg-S/L2, 4h

description:
NCI-H292 cell line, seq2 Aeg-S/L2, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_S+L2


title: Liver, NC/NC, rep1

description: Library name: AH01-1


title: NCI-H292 cell line, seq2 Aeg-S/L1, 4h

description:
NCI-H292 cell line, seq2 Aeg-S/L1, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_S+L1


title: WT_19667_kidney

city: Bellinzona

first: Anna

last: Rinaldi

address: Zorzi

country: Switzerland

institute: EOC

library_source: transcriptomic single cell

data_processing:
The sequencing data were processed using CellRanger (version 5.0.1), with reads aligned to the murine reference genome (mm10-2020-A).
The Cell Ranger cellranger count function output filtered gene–cell expression matrices, removing cell barcodes not represented in cells.
UMI count table utilizing both exonic and intronic reads was generated for downstream analysis.
Assembly: mm10-2020-A
Supplementary files format and content: integrated_batch_20230921_KO.rds includes renal cells of all samples

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Mice were perfused with ice-cold PBS and kidney halves collected for snRNA-seq analysis. Half kidney was cut into small pieces (>25) and transferred into a 2-ml Dounce homogenizer (Sigma, Cat#D8938) loaded with 1 ml of NEZ Lysis Buffer (Sigma, Cat#N3408) with RNase inhibitor (NEB, Cat#M0314) at final concentration of 0.4U/µl) on ice. Samples were then Dounce homogenized on ice with five strokes of the looser pestle every 2 min for 8 min (25 strokes in total). Samples were then slowly Dounce homogenized 25 times with the tighter pestle on ice. The  homogenized sample was filtered through a 40-μm Falcon Nylon Cell Strainer, then the filter was washed with 8 ml of 1% BSA PBS, and the nuclear suspension spun in a precooled (4 °C) centrifuge at 650g for 8 min. Supernatant was removed and the pellet resuspended in 1% BSA PBS (plus RNase inhibitor) and moved to a low-bind Eppendorf tube. Nuclear quality and number were assessed with trypan blue staining. Nuclei were sorted as DAPI positive on a BD Aria into 2% BSA solution with RNA inhibitor.
Barcoded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions

value: kidney

tag: strain

value: PCK1 WT

tag: age

value: At 8 weeks-old

tag: Sex

value: Male

tag: time

value: euthanized at 8 days

value: No treatment


title: Whole placenta, Bulk RNA-seq, 22

city: Cambridge

first: Grace

middle: Jennifer

last: Hattersley

address: Hills Road

country: United Kingdom

institute: University of Cambridge

description: Library name: SLX.64

data_processing:
STAR was used to map reads to the GRCm38 genome
Assembly: mm10
Supplementary files format and content: Raw counts matrix (txt) - individual libraries

source_name: Placenta

extract_protocol:
35-45mg of placental tissue was isolated from 12 control and 12 metformin treated placentas. RNA was extracted using the miRNeasy micro kit (QIAGEN), with DNA contamination removed using the DNAse kit (QIAGEN). Both steps were performed according to the manufacturer’s instructions.
RNA quality and concentration was assessed by nanodrop analysis. RNA integrity (RIN) of > 8 for all samples was confirmed by analysis with the Agilent Bioanalyser 2100 system (Agilent RNA 6000 Nano Kit). 400ng of total RNA was used for library construction (TruSeq Stranded mRNA Library Pre Kit; Illumina). Indexed libraries were normalized, pooled and sequenced on a NovaSeq 6000 (50bp paired-end).

treatment_protocol: Wild-type C57BL/6J mice obtained from Charles River Laboratories were bred in house. Female mice were ad libitum fed a well-established obesogenic diet (no. 824053, Special Dietary Services) (Fernandez-Twinn et al., 2012) supplemented with condensed milk (no. 12029969, Nestlé) from weaning (3 weeks of age). A first pregnancy was commenced at 6 weeks of age, and mating for the second pregnancy was commenced when the mice achieved a body weight of ≥35g (~18 weeks of age). The day of the plug was considered embryonic day 0.5 (E0.5) and fetuses were culled at E18.5. Mice were randomized to receive metformin (0215169-CF, MP Biomedicals) in the condensed milk one week before mating and throughout the subsequent pregnancy to a dose of 300mg/kg/day (equivalent to 1.7g in a 70kg man) (Salomäki et al., 2014).

value: Placenta

value: Wild-type

value: Metformin

tag: batch


title: Whole placenta, Bulk RNA-seq, 23

description: Library name: SLX.65


title: Whole placenta, Bulk RNA-seq, 24

description: Library name: SLX.66


title: Whole placenta, Bulk RNA-seq, 21

description: Library name: SLX.63


title: WT_19666_kidney


description:
NCI-H292 cell line, seq1 aegl KO ALT2, 4h
H292seq1_CKOALT_counts.txt
H292seq1_aeglKO2

value: epithelial cell; Non-small cell lung cancer cell line


title: KO_19664_kidney

value: PCK1 KO


title: Whole placenta, Bulk RNA-seq, 20

description: Library name: SLX.62


description:
NCI-H292 cell line, seq1 aegl KO ALT1, 4h
H292seq1_CKOALT_counts.txt
H292seq1_aeglKO1


title: Whole placenta, Bulk RNA-seq, 19

description: Library name: SLX.61


description:
NCI-H292 cell line, seq2 Aeg-S/L+BAPTA-AM2, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_SLBAPTA2


title: WT_19662_kidney


description:
NCI-H292 cell line, seq1 aegs KO ALT2, 4h
H292seq1_CKOALT_counts.txt
H292seq1_aegsKO2


title: KO_19661_kidney


title: KO_19659_kidney


title: Whole placenta, Bulk RNA-seq, 18

description: Library name: SLX.60


title: rsmF_TOB_replicate3

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

country: France

institute: Institut Pasteur

description:
rnaseqrsmFTOB vs WT TOB.xlsx
rsmFtob3_S72

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: excel or csv files containing number of reads and differencial expression values

organism: Vibrio cholerae

source_name: bacterial culture

growth_protocol: growth in liquid MH up to OD 0,25

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: tobramycin 0,4 µg/ml or ciprofloxacin 0.0005 µg/ml

value: bacterial culture

tag: growth phase

value: exponential phase OD 0.25

value: delta-rsmF

tag: strain background

value: Vibrio cholerae N16961 hapR+

value: TOB 0,4 µg/ml


title: rsmF_TOB_replicate2

description:
rnaseqrsmFTOB vs WT TOB.xlsx
rsmFtob2_S71


title: NCI-H292 cell line, seq1 WT ALT1, 4h

description:
NCI-H292 cell line, seq1 WT ALT1, 4h
H292seq1_CKOALT_counts.txt
H292seq1_WTALT1


title: Whole placenta, Bulk RNA-seq, 15

description: Library name: SLX.57


title: Whole placenta, Bulk RNA-seq, 16

description: Library name: SLX.58


title: NCI-H292 cell line, seq2 DPBS ctrl2, 4h

description:
NCI-H292 cell line, seq2 DPBS ctrl2, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_mock2


title: rsmF_TOB_replicate1

description:
rnaseqrsmFTOB vs WT TOB.xlsx
rsmFtob1_S70


title: NCI-H292 cell line, seq2 DPBS ctrl1, 4h

description:
NCI-H292 cell line, seq2 DPBS ctrl1, 4h
H292seq2_ALTCainhibitor_counts.txt
H292seq2_mock1


title: rsmC_TOB_replicate3

description:
RNAdiff - rsmc.csv
rsmCtob3_S69

value: delta-rsmC


title: NCI-H292 cell line, seq1 DPBS ctrl1, 4h

description:
NCI-H292 cell line, seq1 DPBS ctrl1, 4h
H292seq1_CKOALT_counts.txt
H292seq1_mock1


title: Whole placenta, Bulk RNA-seq, 14

description: Library name: SLX.56


description:
NCI-H1437 cell line, seq4 aegl KO ALT2, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_aeglKO2


title: Whole placenta, Bulk RNA-seq, 13

description: Library name: SLX.55


title: rsmC_TOB_replicate2

description:
RNAdiff - rsmc.csv
rsmCtob2_S68


title: CB cells, efnA5, DNMT1-ChIP, rep 2

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Neuroepigenetics

country: Germany

institute: RWTH Aachen University

library_source: genomic

data_processing:
FASTQ files generated from the ChIP-seq experiment were processed using the nf-core/chipseq pipeline (version 2.0.0) with the mm10 reference genome (Ewels et al., 2020) . Differential peak calling between the samples was performed using THOR with default settings (Allhoff et al., 2016).
Assembly: mm10
Supplementary files format and content: BigWig files containing the ChIP-seq peaks for each replicate as well as the pooled inputs.

molecule: genomic DNA

source_name: Immortalized cerebellar granulle cells

extract_protocol:
Native ChIP-DNMT1 was performed and the DNA was isolated as previously published in Yildiz et al. (2023). https://doi.org/10.1186/s13072-023-00516-4
The sequencing libraries were prepared using the NEBNext® Ultra II DNA Library Prep kit (#E7410S, New England Biolabs, U.S.A.) as per manufacturer's instructions. The input controls were pooled across samples in equimolar proportions. The libraries were amplified via PCR on a T100 Thermal Cycler (Bio-Rad, U.S.A.) with the following conditions: initial denaturation at 98°C for 30 s, 15 cycles of denaturation at 98°C for 10 s and annealing/extension at 65°C for 75 s, followed by a final extension at 65°C for 5 min. To account for the laddering caused by the enzymatic digestion, the libraries were size selected on a 2% (v/v) agarose gel and purified using the QIAquick Gel Extraction Kit (#28704, Qiagen, Germany).

value: Immortalized cerebellar granulle cells


title: CB cells, efnA5, input


title: Whole placenta, Bulk RNA-seq, 11

description: Library name: SLX.53

value: Control


title: Whole placenta, Bulk RNA-seq, 12

description: Library name: SLX.54


title: rsmC_TOB_replicate1

description:
RNAdiff - rsmc.csv
rsmCtob1_S67


title: truA_TOB_replicate3

description:
rnaseqtruATOB vs WT TOB.xlsx
truAtob3_S66

value: delta-truA


description:
NCI-H292 cell line, seq1 aegs KO ALT1, 4h
H292seq1_CKOALT_counts.txt
H292seq1_aegsKO1


description:
NCI-H1437 cell line, seq4 aegl KO ALT1, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_aeglKO1


description:
NCI-H1437 cell line, seq4 aegs KO ALT2, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_aegsKO2


title: Whole placenta, Bulk RNA-seq, 10

description: Library name: SLX.52


title: NCI-H292 cell line, seq1 WT ALT2, 4h

description:
NCI-H292 cell line, seq1 WT ALT2, 4h
H292seq1_CKOALT_counts.txt
H292seq1_WTALT2


title: Whole placenta, Bulk RNA-seq, 17

description: Library name: SLX.59


title: CB cells, ctrl, DNMT1-ChIP, rep 2


title: NCI-H292 cell line, seq1 DPBS ctrl2, 4h

description:
NCI-H292 cell line, seq1 DPBS ctrl2, 4h
H292seq1_CKOALT_counts.txt
H292seq1_mock2


description:
NCI-H1437 cell line, seq4 aegs KO ALT1, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_aegsKO1


title: NCI-H1437 cell line, seq4 WT ALT2, 4h

description:
NCI-H1437 cell line, seq4 WT ALT2, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_WTALT2


title: truA_TOB_replicate1

description:
rnaseqtruATOB vs WT TOB.xlsx
truAtob1_S64


title: CB cells, ctrl, DNMT1-ChIP, rep 1


title: truA_TOB_replicate2

description:
rnaseqtruATOB vs WT TOB.xlsx
truAtob2_S65


title: Whole placenta, Bulk RNA-seq, 9

description: Library name: SLX.51


title: Whole placenta, Bulk RNA-seq, 7

description: Library name: SLX.49


title: CB cells, efnA5, DNMT1-ChIP, rep 1


title: NCI-H1437 cell line, seq4 WT ALT1, 4h

description:
NCI-H1437 cell line, seq4 WT ALT1, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_WTALT1


title: ravvia_TOB_replicate2

description:
RNAdiff - ravviatob.csv
M092tob2_S62

value: delta-ravvia


description:
NCI-H1437 cell line, seq4 DPBS ctrl2, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_mock2


title: ravvia_TOB_replicate3

description:
RNAdiff - ravviatob.csv
M092tob3_S63


title: Whole placenta, Bulk RNA-seq, 8

description: Library name: SLX.50


title: Irradiated Dnmt3a mutant, replicate 3

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
Irradiated Dnmt3a mutant LSK cells
irra.mu_S15

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm10 using Rsubread v2.0.1.
Read counts were summarized using the Rsubread featureCounts function and GENCODE annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent ENSEMBL Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: LSK cells

extract_protocol:
RNA was extracted using the QIAGEN miRNeasy kit with optional on-column Dnase digestion.
Libraries were prepared using the Nextera XT DNA Library prep kit (Illumina) as per manufacturer's instructions.

treatment_protocol: 4-week-old female Dnmt3aR878H/+ or WT control littermates received a single dose of g-irradiation (2Gy) or no irradiation (Baseline). 2 hours after irradiation, bone marrow was harvested and LSK cells were isolated by cell sorting.

value: LSK cells

value: Gamma irradiation


title: CB cells, ctrl, input


title: ravvia_TOB_replicate1

description:
RNAdiff - ravviatob.csv
M092tob1_S61


title: Irradiated wild type, replicate 2

description:
Irradiated WT LSK cells
irra.WT_S14

value: WT


description:
NCI-H1437 cell line, seq4 DPBS ctrl1, 4h
H1437seq4_CKOALT_counts.txt
H1437seq4_mock1


title: Whole placenta, Bulk RNA-seq, 5

description: Library name: SLX.47

value: Placenta

value: Wild-type


description:
NCI-H1437 cell line, seq3 Aeg-S/L+EGTA2, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SLEGTA2

value: epithelial cell; Non-small cell lung cancer cell line


title: dusB_CIP_replicate3

description:
RNAdiff - dusb cip.csv
dusBcip3_S57

value: delta-dusB

value: ciprofloxacin 0.0005 µg/ml


title: dusB_CIP_replicate2

description:
RNAdiff - dusb cip.csv
dusBcip2_S56

value: bacterial culture

value: exponential phase OD 0.25


title: Irradiated Dnmt3a mutant, replicate 2

description:
Irradiated Dnmt3a mutant LSK cells
irra.mu_S13


title: Whole placenta, Bulk RNA-seq, 6

description: Library name: SLX.48


title: Whole placenta, Bulk RNA-seq, 3

description: Library name: SLX.45


title: Irradiated wild type, replicate 1

description:
Irradiated WT LSK cells
irra.WT_S12


description:
NCI-H1437 cell line, seq3 Aeg-S/L+EGTA1, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SLEGTA1


title: Whole placenta, Bulk RNA-seq, 4

description: Library name: SLX.46


title: Irradiated Dnmt3a mutant, replicate 1

description:
Irradiated Dnmt3a mutant LSK cells
irra.mu_S11


title: dusB_CIP_replicate1

description:
RNAdiff - dusb cip.csv
dusBcip1_S55

value: Vibrio cholerae N16961 hapR+


description:
NCI-H1437 cell line, seq3 Aeg-S/L+BAPTA-AM2, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SLBAPTA2


title: Untreated wild type, replicate 4

description:
Untreated WT LSK cells
untr.WT_S9

value: Untreated


title: Whole placenta, Bulk RNA-seq, 2

description: Library name: SLX.44


title: WT_CIP_replicate3

description:
RNAdiff - dusb cip.csv
J085cip3_S54


title: Whole placenta, Bulk RNA-seq, 1

description: Library name: SLX.43


title: Untreated Dnmt3a mutant, replicate 4

description:
Untreated Dnmt3a mutant LSK cells
untr.mu_S8


title: NCI-H1437 cell line, seq3 Aeg-S/L2, 4h

description:
NCI-H1437 cell line, seq3 Aeg-S/L2, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SL2


title: Untreated wild type, replicate 3

description:
Untreated WT LSK cells
untr.WT_S7


title: WT_CIP_replicate2

description:
RNAdiff - dusb cip.csv
J085cip2_S53


title: NCI-H1437 cell line, seq3 Aeg-S/L1, 4h

description:
NCI-H1437 cell line, seq3 Aeg-S/L1, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SL1


description:
NCI-H1437 cell line, seq3 DPBS ctrl2, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_mock2


title: dusB_TOB_replicate3

description:
RNAdiff - dusb tob.csv
dusBtob3_S48

value: TOB 0,4 µg/ml


title: Untreated Dnmt3a mutant, replicate 3

description:
Untreated Dnmt3a mutant LSK cells
untr.mu_S6


title: smallRNA_seq _X2

city: TaiAn

first: min

last: zhang

state: ShanDong

address: 61 Daizong Street

department: College of Animal Science and Technology

institute: ShanDongAgricultural University

description: Library name: Sample 11

data_processing:
Firstly, we processed raw data (raw reads) of fastq format through in-house perl scripts. During this step, we obtained clean data (clean reads) after removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, we calculated Q20, Q30, GC-content and sequence duplication level of the clean data. We performed all the downstream analyses based on clean data with high quality
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sampl
Supplementary files format and content: ecsv files include FPKM/tpm values for each Sample

source_name: granulosa cells in the antral follicles

growth_protocol: The COCs were cultured in either PMS or GMS medium for 18 h or 24 h in microdroplets (20-30 COCs per 100 µl droplet) at 37.5 °C in air containing 5% CO2.

extract_protocol:
We extracted total RNA from CC samples using a TRlzol Reagent kit(Life technologies, California, USA) for mRNA and miRNA sequencing.
: Biomarker Technologies (Beijing, China) carried out the library preparation and sequencing. They used a total amount of 1 µg RNA per sample as input material for the RNA sample preparations. They generated sequencing libraries using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina from Yeasen Biotechnology (Shanghai) Co., Ltd.q: A VAHTSTM Small RNA Library Prep Kit for Illumina (NR801-02, Nanjing Vazyme Biotech Co., Ltd.)

treatment_protocol: The PMS medium was a simplified MEM (s-MEM), and the GMS medium was composed of s-MEM supplemented with 0.05 IU/ml FSH and 5% fetal bovine serum (FBS)(Gibco, Grand Island, New York, USA)

value: granulosa cells in the antral follicles

value: cumulus cells

value: Granulosa cells

value: untreated


description:
NCI-H1437 cell line, seq3 DPBS ctrl1, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_mock1


title: dusB_TOB_replicate2

description:
RNAdiff - dusb tob.csv
dusBtob2_S47


title: Untreated Dnmt3a mutant, replicate 2

description:
Untreated Dnmt3a mutant LSK cells
untr.mu_S4

value: LSK cells


description:
NCI-H1437 cell line, seq2 Aeg-S/L+Tra2, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegSLTra2


title: smallRNA_seq _F3

description: Library name: Sample 9

value: treated with FSH and FBS for 18 hours


title: smallRNA_seq _F2

description: Library name: Sample 8

value: WT


description:
NCI-H1437 cell line, seq3 Aeg-S/L+BAPTA-AM1, 4h
H1437seq3_SLCainhibitor_counts.txt
H1437seq3_SLBAPTA1


title: dusB_TOB_replicate1

description:
RNAdiff - dusb tob.csv
dusBtob1_S46


title: WT_TOB_replicate3

description:
RNAdiff - dusb tob.csv
J085tob3_S45


title: Untreated wild type, replicate 1

description:
Untreated WT LSK cells
untr.WT_S2


title: Neuronal cells after SP treatment 4

description: Library name: SP4

value: Hippocampal tissue

value: Neuronal cells

value: Neuronal cells after SP treatment 4


title: Untreated wild type, replicate 2

description:
Untreated WT LSK cells
untr.WT_S3


title: WT_TOB_replicate2

description:
RNAdiff - dusb tob.csv
J085tob2_S44


description:
NCI-H1437 cell line, seq2 Aeg-S/L+Tra1, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegSLTra1

value: epithelial cell; Non-small cell lung cancer cell line


title: NCI-H1437 cell line, seq2 Aeg-S/L2, 4h

description:
NCI-H1437 cell line, seq2 Aeg-S/L2, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegSL2


title: Untreated Dnmt3a mutant, replicate 1

description:
Untreated Dnmt3a mutant LSK cells
untr.mu_S1


title: smallRNA_seq _X3

description: Library name: Sample 12


title: RNA_seq _X3

description: Library name: Sample 6


title: WT_CIP_replicate1

description:
RNAdiff - dusb cip.csv
J085cip1_S52

value: ciprofloxacin 0.0005 µg/ml


title: NCI-H1437 cell line, seq2 Aeg-S/L1, 4h

description:
NCI-H1437 cell line, seq2 Aeg-S/L1, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegSL1


title: WT_TOB_replicate1

description:
RNAdiff - dusb tob.csv
J085tob1_S43

value: bacterial culture


title: RNA_seq _X2

description: Library name: Sample 5


title: smallRNA_seq _X1

description: Library name: Sample 10


title: third wheat, root sample2

city: Kiel

first: Zheng

last: Zhou

state: Schleswig-Holstein

address: Hermann-Rodewald-Straße, 9

department: Molecular Phytopathology

institute: CAU Kiel

description:
Library name: W3R2
treatment

data_processing:
Raw data (raw reads) of fastq format were processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-endcleanreads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0).
Assembly: wheat reference genome (IWGSC RefSeq v2.1)

organism: Triticum aestivum

source_name: root

growth_protocol: The field experiment was conducted at the Hohenschulen experimental field site (54°19′05″N, 9°58′38″E), which is owned by the Christian-Albrechts-University of Kiel, Germany, in 2021.

extract_protocol:
TRIzol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers,followed by the second strand cDNA synthesis using dUTP for directional library.

treatment_protocol: The soil at the site was pseudogleyic sandy loam (Luvisol), with 21% clay and 35% silt, 44% sand, a pH of 6.7, and organic carbon content of 1.3%, total nitrogen content of 0.15%, and available phosphorous and potassium contents of 9 mg.kg-1 and 15 mg.kg-1, respectively.

value: root

value: third wheat


title: third wheat, root sample3

description:
Library name: W3R4
treatment


title: dusB_MH_replicate3

description:
RNAdiff - dusb mh.csv
dusBMH3_S39

value: exponential phase OD 0.25

value: delta-dusB

value: Vibrio cholerae N16961 hapR+


title: RNA_seq _X1

description: Library name: Sample 4

value: granulosa cells in the antral follicles

value: cumulus cells


title: NCI-H1437 cell line, seq2 Aeg-L2, 4h

description:
NCI-H1437 cell line, seq2 Aeg-L2, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegL2


title: dusB_MH_replicate2

description:
RNAdiff - dusb mh.csv
dusBMH2_S38


title: NCI-H1437 cell line, seq2 Aeg-L1, 4h

description:
NCI-H1437 cell line, seq2 Aeg-L1, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegL1


title: third wheat, root sample1

description:
Library name: W3R1
treatment


title: RNA_seq _F3

description: Library name: Sample 3

value: Granulosa cells


title: smallRNA_seq _F1

description: Library name: Sample 7


title: third wheat, leaf sample2

description:
Library name: W3L2
control

source_name: leaf

value: leaf


title: WT_MH_replicate3

description:
RNAdiff - dusb mh.csv
J085MH3_S36


title: third wheat, leaf sample3

description:
Library name: W3L4
control


title: dusB_MH_replicate1

description:
RNAdiff - dusb mh.csv
dusBMH1_S37


title: RNA_seq _F2

description: Library name: Sample 2

value: treated with FSH and FBS for 18 hours


title: RNA_seq _F1

description: Library name: Sample 1

value: WT


description:
NCI-H1437 cell line, seq2 DPBS ctrl2, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_mock2


title: HPi_40

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

description: Library name: 105831-001-040

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: Liver, right lobe

growth_protocol: Male Ldlr-/-.Leiden mice were group-housed in a temperature-controlled room on a 12h light-dark cycle at 50-60% humidity. Mice had access to food and heat-sterilized tap water ad libitum. Body weight, food intake at the cage level and clinical signs were monitored regularly. After a run-in period on a high fat diet (HFD) containing 24% (w/w) fat from lard (D12451; Research Diets, New Brunswick, NJ, USA), mice were matched into comparable groups based on age, body weight, blood glucose, plasma cholesterol and triglycerides.

extract_protocol:
Next generation sequencing (NGS) was performed in tot-RNA samples extracted from right liver lobe samples. RNA was isolated using the RNA-Bee total-RNA isolation kit (Bio-Connect, Huissen, the Netherlands) and evaluated for quality with the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-50 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: Mice either received no intervention (HFD control), 20 mg/kg/day cenicriviroc (Advanced ChemBlocks, Hayward, CA, USA), 10 mg/kg/day pioglitazone (Sigma Aldrich, Saint Louis, MO, USA) or 10 or 20 mg/kg/day obeticholic acid (OCA; Bio-Connect, Huissen, the Netherlands), all as admixture to the diet or 20 mg/kg/day OCA via daily gavages. Control mice were continuously fed on standard Chow diet (C). During the diet treatments, 12-17 week old mice were first fed the HFD for 15 weeks to induce obesity-associated MASH. Then, at t=0, treatment was started for four weeks, with n=8 mice per group receiving either 20 mg/kg/d cenicriviroc, 10 mg/kg/d pioglitazone, 10 mg/kg/d OCA, 20 mg/kg/d OCA or no treatment (HFD control). Appropriate group sizes were calculated a priori by power analysis (GPower26), using an average standard deviation/sigma of 15%, a minimal effect size of 25% and two-sided test with 95% confidence interval, power of 90% and α of 0.05. After four weeks, mice were sacrificed non-fasted by gradual-fill CO2 asphyxiation, and livers were weighed and collected for transcriptome analysis.

value: Liver, right lobe

value: HPi

tag: treatment description

value: HFD+Pioglitazone


title: WT_MH_replicate2

description:
RNAdiff - dusb mh.csv
J085MH2_S35


title: first wheat, root sample3

description:
Library name: W1R3
treatment

value: first wheat


description:
NCI-H1437 cell line, seq2 DPBS ctrl1, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_mock1

value: epithelial cell; Non-small cell lung cancer cell line


title: NCI-H1437 cell line, seq1 ALT+Tra3, 4h

description:
NCI-H1437 cell line, seq1 ALT+Tra3, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALTTra3


title: WT_MH_replicate1

description:
RNAdiff - dusb mh.csv
J085MH1_S34

value: bacterial culture


title: HPi_39

description: Library name: 105831-001-039


title: EGI-1 cells,Comb2,day3

first: Jianfeng

last: Chen

address: 651East Dongfeng Road

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
adpators were removed by trim_galore
Aliments were performed followed by hisat2 instruction
featureCounts were used for counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: HUCCT1 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.EGI-1 cellls were cultured in DMEM medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
total RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: 1.HUCCT1 cells were plated into 6-well plate 24 h before treatment (vehicle and decitabine 1μM）and harvest cells for RNA extraction at 72h.  2.EGI-1 cells were plated into 6-well plate 24 h before treatment (vehicle, decitabine 0.5μM,talazoparib 200nM or combinational treatment）and harvest cells for RNA extraction at 72h.

value: human cholangiocarcinoma cells

value: decitabine and talazoparib


title: first wheat, root sample2

description:
Library name: W1R2
treatment

value: root


title: HPi_38

description: Library name: 105831-001-038


title: EGI-1 cells,Talb2,day3

value: talazoparib


title: NCI-H1437 cell line, seq2 Aeg-S1, 4h

description:
NCI-H1437 cell line, seq2 Aeg-S1, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegS1


title: NCI-H1437 cell line, seq2 Aeg-S2, 4h

description:
NCI-H1437 cell line, seq2 Aeg-S2, 4h
H1437seq2_SLMEKinhibitor_counts.txt
H1437seq2_AegS2


title: HPi_37

description: Library name: 105831-001-037


title: first wheat, leaf sample3

description:
Library name: W1L3
control


title: NCI-H1437 cell line, seq1 ALT+Tra2, 4h

description:
NCI-H1437 cell line, seq1 ALT+Tra2, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALTTra2


title: HPi_36

description: Library name: 105831-001-036


title: NCI-H1437 cell line, seq1 ALT+Tra1, 4h

description:
NCI-H1437 cell line, seq1 ALT+Tra1, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALTTra1


title: first wheat, leaf sample2

description:
Library name: W1L2
control


title: HPi_35

description: Library name: 105831-001-035


title: first wheat, leaf sample1

description:
Library name: W1L1
control


title: NCI-H1437 cell line, seq1 ALT3, 4h

description:
NCI-H1437 cell line, seq1 ALT3, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALT3


title: EGI-1 cells,Comb1,day3


title: third wheat, leaf sample1

description:
Library name: W3L1
control

value: third wheat


title: HPi_34

description: Library name: 105831-001-034


title: EGI-1 cells,ctrl2,day3

value: DMSO


title: NCI-H1437 cell line, seq1 ALT2, 4h

description:
NCI-H1437 cell line, seq1 ALT2, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALT2


title: EGI-1 cells,Talb1,day3


title: NCI-H1437 cell line, seq1 ALT1, 4h

description:
NCI-H1437 cell line, seq1 ALT1, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_ALT1


title: HPi_33

description: Library name: 105831-001-033


description:
NCI-H1437 cell line, seq1 DPBS ctrl3, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_mock3


title: EGI-1 cells,DAC1,day3

value: decitabine


title: HCe_32

description: Library name: 105831-001-032

value: HCe

value: HFD+Cenicriviroc


title: first wheat, root sample1

description:
Library name: W1R1
treatment


title: WK4-3miR29b-2

city: Memphis

first: Athena

last: Starlard-Davenport

state: TN

address: 71 S Manassas Street

department: Genetics, Genomics and Informatics

country: USA

institute: University of Tennessee Health Science Center

data_processing:
The index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: GRCm38
Supplementary files format and content: :tab-delimited file with mapped read counts for each gene of 36 samples

source_name: peripheral blood

growth_protocol: The humanized Townes SCD transgenic mouse were maintained at the Augusta University, and genotyping was performed with gene-specific primers followed by high-performance liquid chromatography confirmation to confirm sickle cell phenotype.

extract_protocol:
Total RNA was isolated by TRIzol reagent. RNA was depleted of globin mRNA (α-globin and β-globin) using the Ambion GLOBINclear Kit.
RNA libraries for RNA seq were prepared by Novogene using a Library Prep Kit following manufacturer's protocols.

treatment_protocol: Townes mice were treated with 2 or 3 mg/kg Scrambled control or MIR29B at 0, 2 and 4 weeks using a mini-osmotic pump. Peripheral blood was collected and RNA isolated at the different time points

value: peripheral blood

value: Townes sickle cell mice

value: erythrocytes

value: MIR29B overexpression

value: 3mg MIR29B Wk4


title: WK4-3miR29b-3


title: EGI-1 cells,ctrl1,day3

value: WT


title: EGI-1 cells,DAC2,day3


title: HCe_31

description: Library name: 105831-001-031

value: Liver, right lobe


description:
NCI-H1437 cell line, seq1 DPBS ctrl1, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_mock1

value: epithelial cell; Non-small cell lung cancer cell line


title: HUCCT1 cells,DAC2,day3

value: human cholangiocarcinoma cells

value: decitabine 1μM


title: WK4-3Scr-2

value: scrambled (Scr) control

value: 3mg Scr at Wk4


title: HCe_30

description: Library name: 105831-001-030


title: WK4-3Scr-3


title: HUCCT1 cells,ctrl2,day3


title: MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep2

city: San Francisco

first: Xianhua

last: Piao

state: CA

institute: University of California, San Francisco

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the 10X Cell Ranger software v6.0.2
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: human organoids

growth_protocol: MGE organoids and iMG were independent cultured. iMG were transplanted into MGE organoids when organoids are 6-week-old.

extract_protocol:
MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced.
Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library.

value: human organoids

value: MGEo organoids


title: WK4-3Scr-1


title: HUCCT1 cells,DAC1,day3


title: HCe_28

description: Library name: 105831-001-028


title: HCe_29

description: Library name: 105831-001-029


title: HUCCT1 cells,ctrl1,day3

value: DMSO


title: WK4-2miR29b-3

value: 2mg MIR29B Wk4


title: HCe_27

description: Library name: 105831-001-027

value: HCe

value: HFD+Cenicriviroc


description:
NCI-H1437 cell line, seq1 DPBS ctrl2, 4h
H1437seq1_ALTMEKinhibitor_counts.txt
H1437seq1_mock2


title: WK4-2miR29b-2

value: peripheral blood

value: Townes sickle cell mice


title: WK4-3miR29b-1

value: erythrocytes

value: MIR29B overexpression


title: MGEO,-iMG, 6wks organoids,rep1

description: 10x Genomics


title: C42_GH3

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg19 human genome using TopHat2.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg19
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: C4-2 human prostate tumor cell line

growth_protocol: Human PCa C4-2 cells (provided by Dr. Leland WK Chung at Cedars-Sinai Medical Center, Los Angeles, CA) were routinely cultured in T-medium (Life Technologies, Carlsbad, CA) supplemented with 5% fetal bovine serum (FBS; Atlanta Biologicals, Atlanta, GA) and penicillin-streptomycin (Corning, Corning, NY).

extract_protocol:
Total RNA was prepared with the Qiagen RNeasy Kit (Valencia, CA).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: male

value: prostate tumor cell line

value: prostate cancer

value: Cells were treated with GH501 (0.6 mM) for 6 hours.

tag: timepoint

value: 6 hr


title: WK4-2Scr-3

value: scrambled (Scr) control

value: 2mg Scr at Wk4


title: total genomic DNA, polysome-matched, CAG

city: Ithaca

first: Andrew

middle: William

last: Grimson

state: NY

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
A custom python script was used to count barcodes in all libraries. The barcode sequence was extracted from the constant region of reads and each barcode was counted.
Barcode count tables were imported into R, each barcode was linked to its cognate 3′UTR, and normalized for library depth (counts per million, CPM).
Assembly: Not applicable
Supplementary files format and content: A count matrix with barcode counts for 3′UTR is included (utrome_barcode_counts.tsv). The first column is "position," which specifies the 3′UTR and its position (plate and well) within the cloned library, and the second column is "barcode" which specifies the 12 nt barcode for that 3′UTR. The remaining 81 columns correspond to the 81 samples.
Library strategy: Barcode amplicon sequencing

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
For barcode libraries derived from RNA, Trizol was used for extraction. Genomic DNA was extracted using the Qiagen Gentra Puregene Cell DNA Extraction Kit. For polysome libraries, cells were treated with 100 μg/mL cycloheximide and lysed. The lysate was run over a 15 45% (w/v) sucrose gradient to separate polysomes. RNA was extracted from each fraction.
For RNA libraries and RNA extracted from polysome fractions, cDNA was generated using RevertAid Reverse Transcriptase and RT primer 5′CTCCACTTTGTACAAGAAAG. The cDNA was purified and concentrated with the Zymo DNA Clean & Concentrator Kit and all was used as template in PCRI. For DNA libraries, all genomic DNA was used in PCRI. For both assays, three PCR cycles were performed with ExTaq polymerase (primers 5′GTCAACCACCGCGGTCTC and 5′ACGACGCTCTTCCGATCTNNNNNNNNNNcactttgtacaagaaagttgaacg). Reactions were then purified with SPRIselect beads (Beckman Coulter) using a 0.7x one sided size selection protocol and used in PCRII (primers 5′CGTGTGCTCTTCCGATCTcgaccactaccagcagaaca and 5′ACACTCTTTCCCTACACGACGCTCTTCCGATCT), which was then purified with SPRIselect beads using a 0.6x to 1.2x two sided size selection protocol. A portion of this reaction was used for a final (PCRIII) reaction to add Illumina-compatible sequences (index primers from the NEBNext Multiplex Oligos for Illumina Kit). The final libraries were purified and concentrated with SPRIselect beads using a 0.5x to 1x two sided size selection protocol, quantified and submitted for Illumina sequencing.

value: CAG landing pad


title: iMG, GFP-enriched, 6wk organoid, 2wk post iMG transplantation

description: 10x Genomics

value: human organoids

value: induced microglia


title: WK4-2miR29b-1

value: 2mg MIR29B Wk4


title: C42_GH2


title: HCe_25

description: Library name: 105831-001-025

value: Liver, right lobe

value: HCe


title: C42_GH1


title: part2, H_16

description: Library name: 105831-001-016

value: H

value: HFD


title: WK4-2Scr-2

value: peripheral blood

value: Townes sickle cell mice

value: erythrocytes


title: WK4-2Scr-1


title: C42_NT3

value: male

value: prostate tumor cell line

value: Cells were treated with DMSO vehicle for 6 hours.


title: MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep1

description: 10x Genomics

value: MGEo organoids


title: part2, H_15

description: Library name: 105831-001-015


title: C42_NT2

value: prostate cancer

value: 6 hr


title: MGEO,-iMG, 6wks organoids,rep2

description: 10x Genomics


title: part2, H_14

description: Library name: 105831-001-014


title: polysome, fraction 14, CAG

value: CAG landing pad


title: WK2-3miR29b-3

value: MIR29B overexpression

value: 3mg MIR29B Wk2


title: WK2-3miR29b-2


title: C42_NT1


title: polysome, fraction 13, CAG


title: HCe_26

description: Library name: 105831-001-026

value: HFD+Cenicriviroc


title: part2, H_12

description: Library name: 105831-001-012

value: Liver, right lobe


title: polysome, fraction 12, CAG


title: Li_S5_Brain

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

description:
Library name: S5-10X-050922
Li

data_processing:
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10 × Genomics. The Cell Ranger pipeline (10 × Genomics) was used to perform sample demultiplexing and to generate FASTQ files for read 0, read 2, and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, unique molecular identifiers filtering, and single-cell 3’ gene counting were performed using the Cell Ranger suite and Seurat v.3.0.1. The total number of cells across all libraries was 8112 cells. The filtered matrices were processed using the Seurat integration workflow. The SCTransform function was used to normalize counts based on read depth and the 2000 most variable features per sample were identified for integration with corrected counts. Integration anchors between matrices were identified using reciprocal PCA, and genes for integration were ranked by their presence in the matrices. Subsequent dimensionality reduction utilized preprocessed genes and values, while raw and normalized counts were maintained for subsequent testing for differential expression. Dimensionality reduction was performed using PCA, resulting in 25 principal components. An elbow plot confirmed that these 25 principal components contained the major sources of variation in the dataset. These components were then used as input for UMAP dimensionality reduction. For each identified cluster, differentially expressed genes (DEGs) were calculated by comparing gene expression within the cluster to all other clusters. The statistical workflow for differential expression followed Seurat's implementation of the Wilcoxon signed-rank test. DEGs were deemed significant if the Bonferroni-adjusted p-value was less than 0.05 and the natural log fold change was below -0.25 or above 0.25. To investigate the differential regulation of biological pathways in each cluster, DEGs exceeding the significance threshold were exported to Ingenuity Pathway Analysis (IPA) (Qiagen) for a comprehensive core and comparative analysis.
Assembly: Mouse mm10
Supplementary files format and content: matrix.mtx.gz: a gzipped Matrix Market file containing the sparse matrix of gene expression values (cell x gene).
Supplementary files format and content: barcodes.tsv.gz: a gzipped TSV file listing the cell barcodes, corresponding to columns in the matrix.
Supplementary files format and content: features.tsv.gz: a gzipped TSV file listing the gene identifiers and names, corresponding to rows in the matrix.

source_name: Brain

extract_protocol:
Processing and tissue collection were performed as previously described (69), using the Act-Seq method (70) to limit dissociation-induced gene expression. Briefly, the brains of 23-week-old homozygous mutated (Disc1LI/LI) and wild-type (Disc1WT/WT) littermate controls (n = 6 males per group) were pooled and cut into small pieces with a scalpel, then incubated with enzyme mix (30 U/ml DNAse I (Roche), 10 U/ml collagenase type I (Worthington) and 400 U/ml collagenase type IV (Worthington) diluted in 1X Hanks’ buffered salt solution (HBSS, Gibco)), containing 15 μM ActD at 11 °C for 40 min. Every 10 min the solution was cut and resuspended to ensure full dissociation of the tissue. Subsequently, the solution was resuspended, filtered twice over a 100 μm nylon filter, and centrifuged at 400 g for 10 min. The pellet was resuspended in 5 ml 70% standard isotonic Percoll (SIP, GE Healthcare) diluted in 1X HBSS and gently overlaid with 5 ml of 30% SIP, followed by a 5 ml layer of 30% SIP, forming a three-layered density gradient (centrifuged at 650 g, 4°C, 30 min without acceleration/braking). All gradient buffers contained 3 µM ActD. The cell cloud at the 70/30% interphase was collected, centrifuged, and resuspended in staining buffer (2 mM EDTA, 2% FCS in 1X HBSS). Subsequently, cells were incubated with anti-mouse CD16/CD32 (clone 2.4G2), anti-CD45-Pacific Blue (clone 30-F11, BioLegend), and CD11bAF647 (clone M1/70, BioLegend) for 20 min on ice. CD45lowCD11b+ immune cells were sorted into 100% FCS using a BD FACS ARIA II with a sorting nozzle of 85 µm.
Cellular suspensions were loaded on a Chromium Chip B (10 × Genomics, No.1000074), or Chip G (10 × Genomics, No. 2000177) on a GemCode Single Cell Instrument (10 × Genomics) to generate single-cell gel beads-in-emulsion (GEM). GEMs and scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library Kit (v3 and v3.1, 10xGenomics, No. 1000075) and the Chromium i7 Multiplex Kit (10 × Genomics, No. 120262) according to the manufacturer’s instructions.

treatment_protocol: FACS-based microglia isolation

value: Brain

value: Microglia

value: Disc1 locus impairment


title: WK2-3Scr-3

value: peripheral blood

value: scrambled (Scr) control

value: 3mg Scr at Wk 2


title: part2, H_11

description: Library name: 105831-001-011

value: H

value: HFD


title: WK2-3miR29b-1

value: Townes sickle cell mice

value: erythrocytes


title: WK2-3Scr-2


title: polysome, fraction 10, CAG


title: polysome, fraction 11, CAG


title: polysome, fraction 9, CAG


title: KO_4

city: New York

first: Jordan

address: 413 E 69th St

institute: Weill Cornell Medical College

description: ENTREZID, SYMBOL, KO.5, KO.6, KO.7, KO.8, WT.1, WT.2, WT.3, WT.4

data_processing:
The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated matrix

source_name: Large Intestine

extract_protocol:
Large intestine from Stingfl/fl and Stingfl/fl RORγtcre mice were dissected and fat tissues were removed. Intestines were opened longitudinally, extensively cleaned with cold Dulbecco's PBS (Corning) and cut approximately into 0.5-cm sections. Cut tissues were incubated in Hanks' balanced salt solution) containing 5 mM EDTA (Thermo Fisher Scientific), 1 mM dithiothreitol (Sigma-Aldrich) and 2% fetal bovine serum twice at 37 °C for 20 min to dissociate epithelial cells. Tissues were vortexed, transferred to digestion buffer containing collagenase III (1 mg mL-1; Worthington), dispase (0.4 U mL-1; Thermo Fisher Scientific), DNase I (20 μg mL-1 ;Sigma-Aldrich) and 10% FBS in RPMI 1640 (Corning), and incubated in a shaker at 200 rpm for 1 hour at 37°C. Leukocytes were enriched by 40/80% Percoll gradient (GE Healthcare).
Library construction was performed by epigenomics core at Weill Cornell Medicine.

value: Large Intestine

value: CCR6+ ILC3s

value: Sting fl/fl ROR-gamma-tcre


title: part2, H_10

description: Library name: 105831-001-010


title: polysome, fraction 15, CAG

value: CAG landing pad


title: KO_3


title: part2, H_09

description: Library name: 105831-001-009


title: polysome, fraction 8, CAG


title: KO_2


title: WK2-2miR29b-3

value: MIR29B overexpression

value: 2mg MIR29B Wk2


title: WK2-3Scr-1


title: KO_1


title: polysome, fraction 7, CAG


title: part2, H_13

description: Library name: 105831-001-013

value: Liver, right lobe


title: part2, C_07

description: Library name: 105831-001-007

value: C

value: Chow


title: part2, C_06

description: Library name: 105831-001-006


title: WT_4

value: Sting fl/fl


title: WK2-2miR29b-2

value: peripheral blood


title: polysome, fraction 6, CAG


title: WT_S4_Brain

description:
Library name: S4-10X-050922
WT

value: Brain

value: Microglia

value: Wildtype


title: WK2-2miR29b-1


title: polysome, fraction 5, CAG


title: WK2-2Scr-3

value: scrambled (Scr) control

value: 2mg Scr at Wk2


title: part2, C_05

description: Library name: 105831-001-005


title: WT_3


title: WK2-2Scr-2

value: Townes sickle cell mice

value: erythrocytes


title: part2, C_04

description: Library name: 105831-001-004


title: polysome, fraction 4, CAG


title: WT_2

value: Large Intestine

value: CCR6+ ILC3s


title: polysome, fraction 3, CAG

value: CAG landing pad


title: WT_1


title: part2, C_08

description: Library name: 105831-001-008


title: polysome, fraction 2, CAG


title: WK2-2Scr-1


title: part2, C_03

description: Library name: 105831-001-003


title: HA in control wt cells

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.1.2 with the following parameters --no-unal -m 1 --seedlen 40 --best --strata --chunkmbs 1024 --sam --tryhard.
Wig and BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.11.0 with default parameters except for “-norm 2e7 -fragLength 200”.
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: bigwig

source_name: ES cells

extract_protocol:
Cells were fixed with 0,4 % PFA for sonicated chromatin and with 1% PFA for MNase digested chromatin. Cells were sonicated on E220 Focused-ultrasonicator (Covaris) either MNase digested according protocol described in (Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells. T. Yamakawa , K. Itakura. J Vis Exp. 2019 May 10:(147). doi: 10.3791/59375). Precipitated chromatin was de cross-linked and DNA was purified with phenol-chloroform.
ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 0.1 to 7 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (10 + 4 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: ES cells

value: no treatment


title: WK0-3miR29b-3

value: MIR29B overexpression

value: 3mg MIR29B Wk0


title: part2, C_02

description: Library name: 105831-001-002

value: Liver, right lobe

value: C

value: Chow


title: part2, C_01

description: Library name: 105831-001-001


title: HA in 3XHA-Taf13 expressing cells


title: polysome, fraction 1, CAG


title: I-R9

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

institute: The Second Hospital of Dalian Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.4)software
The transcript abundances for each sample was estimated with StringTie（1.2.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Assembly: mm10
Supplementary files format and content: The xls format file contains the FPKM value of gene in every sample

source_name: small intestine

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment;2)Random primed first strand cDNA synthesis;3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: small intestine

value: ischemia/reperfusion


title: polysome, cytoplasmic fraction, CAG


title: total genomic DNA, polysome-matched, PGK

value: PGK landing pad


title: O20g_32

description: Library name: 104930-001-032R

value: OCA 20 mg/kg/day via gavage


title: WK0-3Scr-3

value: peripheral blood

value: scrambled (Scr) control

value: 3mg Scr at Wk 0


title: O20g_31

description: Library name: 104930-001-031R


title: WK0-3miR29b-1

value: Townes sickle cell mice

value: erythrocytes


title: I-R7


title: polysome, fraction 15, PGK


title: I-R6


title: O20g_30

description: Library name: 104930-001-030R


title: WK0-3Scr-2


title: O20g_29

description: Library name: 104930-001-029R


title: polysome, fraction 14, PGK


title: sham5

value: sham


title: WK0-3Scr-1


title: WK0-3miR29b-2


title: sham1


title: WK0-2miR29b-2

value: 2mg MIR29B Wk0


title: polysome, fraction 13, PGK


title: WK0-2miR29b-3


title: polysome, fraction 12, PGK


title: O20g_28

description: Library name: 104930-001-028R


title: sham3


title: WK0-2miR29b-1


title: Rv- bystander macrophages 4 + T. S12. rep 4 [Rv_T4_bM_S12]

city: St. Louis

first: Jennifer

middle: A

last: Philips

state: Missouri

address: 660 S Euclid Avenue

department: Department of Medicine

institute: Washington University in St.louis

data_processing:
convert fastq files to unaligned .bam files (Samtools:FastqToSam)
adapter trimming (Trimmomatic)
genome indexing and read mapping (HiSat2)
genewise read counts (featureCounts)
Assembly: GRCm38.97
Supplementary files format and content: genomic features read count matrix (tab delimited)

source_name: Bone marrow (BM)

growth_protocol: BMDMs were cultured at a density of 1 million/ml

extract_protocol:
After 24 hrs, infected BMDMs, unifected BMDMs, T cells were sorted by flow cytometry using antibodies specific for surface markers on macrophages and T cells. RNA was extracted from sorted cells using miRNAeasy Micro Kit
RNA-Seq by PolyA selection

treatment_protocol: BMDMs were infected with mCherry-Mtb (H37Rv) at an MOI of 1. After 3 hrs, Nur77-GFP P25TCR-Tg CD4 T cells were added to the macrophages at a ratio of 1:1 and co-cultured for 24 hrs

value: Bone marrow (BM)

value: BM derived macrophages

tag: group

value: T

tag: status

value: bM

value: Infected + T cells


title: polysome, fraction 11, PGK


title: polysome, fraction 10, PGK


title: O20g_25

description: Library name: 104930-001-025R

value: Liver, right lobe


title: O20g_26

description: Library name: 104930-001-026R


title: Rv- infected macrophages 4 + T S8. rep 4 [Rv_T4_iM_S8]

value: iM


title: WK0-2Scr-3

value: 2mg Scr at Wk0


title: O10d_24

description: Library name: 104930-001-024R

value: OCA 10 mg/kg/day via diet


title: Rv- infected macrophages  3 + T. S7 rep 3 [Rv_T3_iM_S7]


title: polysome, fraction 9, PGK

value: PGK landing pad


title: polysome, fraction 8, PGK


title: Rv- bystander macrophages 3 + T. S11. rep 3 [Rv_T3_bM_S11]


title: O10d_23

description: Library name: 104930-001-023R


title: WK0-2Scr-2

value: peripheral blood


title: WK0-2Scr-1

value: scrambled (Scr) control


title: O10d_22

description: Library name: 104930-001-022R


title: Rv- infected macrophages  2 + T. S6. rep 2 [Rv_T2_iM_S6]


title: polysome, fraction 7, PGK


title: O20g_27

description: Library name: 104930-001-027R

value: OCA 20 mg/kg/day via gavage


title: Rv- bystander macrophages 2 + T. S10. rep 2 [Rv_T2_bM_S10]


title: polysome, fraction 5, PGK


title: O10d_21

description: Library name: 104930-001-021R


title: TetOff, total RNA, rep1

description: Library name: p83_totalRNA_rep1

data_processing:
A custom python script was used to count barcodes in all libraries. The barcode sequence was extracted from the constant region of reads and each barcode was counted.
Supplementary files format and content: A count matrix with barcode counts for 3′UTR is included (utrome_barcode_counts.tsv). The first column is "position," which specifies the 3′UTR and its position (plate and well) within the cloned library, and the second column is "barcode" which specifies the 12 nt barcode for that 3′UTR. The remaining columns correspond to all barcode library samples.

treatment_protocol: 2 ug/ml doxycycline was used for treatment following timepoint collection

value: Tet-Off landing pad


title: Rv- infected macrophages  1 + T. S5. rep 1 [Rv_T1_iM_S5]


title: O10d_20

description: Library name: 104930-001-020R


title: polysome, fraction 4, PGK


title: Rv- bystander macrophages 1 + T. S9. rep1 [Rv_T1_bM_S9]


title: TetOff, total genomic DNA, rep2

description: Library name: p83_DNA_rep2


title: Rv- infected macrophages 4 no T. S24. rep 4 [Rv_NT4_iM_S24]

value: NT

value: Infected no T cells


title: polysome, fraction 3, PGK


title: O10d_19

description: Library name: 104930-001-019R


title: O10d_18

description: Library name: 104930-001-018R


title: TetOff, total genomic DNA, rep1

description: Library name: p83_DNA_rep1


title: polysome, fraction 2, PGK


title: O10d_17

description: Library name: 104930-001-017R


title: polysome, fraction 1, PGK


title: Rv- infected macrophages  2 no T. S22. rep 2 [Rv_NT2_iM_S22]


title: H_16

description: Library name: 104930-001-016R

value: H

value: HFD


title: TetOff, dox 8 hour timepoint, rep2

description: Library name: p83_T08_rep2

value: dox 8 hour timepoint


title: TetOff, dox 8 hour timepoint, rep1

description: Library name: p83_T08_rep1


title: Rv- infected macrophages  3 no T. S23. rep 3 [Rv_NT3_iM_S23]

value: Bone marrow (BM)

value: BM derived macrophages


title: polysome, cytoplasmic fraction, PGK


title: Rv- bystander macrophages 2 no T. S26. rep 2 [Rv_NT2_bM_S26]

value: bM


title: TetOff, dox 4 hour timepoint, rep2

description: Library name: p83_T04_rep2

value: dox 4 hour timepoint


title: H_15

description: Library name: 104930-001-015R

value: Liver, right lobe


title: Large HEK Torin

first: Marko

last: Jovanovic

state: New York

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

description: Library name: Sample 3

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8
RPM (ATCAGCACTTA) sequence was trimmed using Cutadapt v3.4 from both 5’ and 3’ read ends
The barcodes of trimmed reads were identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline)
RNA read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to the human (hg38) genome using STAR aligner. Only reads that mapped uniquely to the genome were kept for further analysis.
Clusters of barcodes were filtered for repeat UMIs, out-of-order barcodes, and PCR duplicates
Reads from the remaining clusters were split into bam files based on user defined cutoffs for the minimum number of oligos per bead, the maximum number of oligos per bead, and the proportion of oligos with the same ID
Bigwig files were generated from individual antibody DNA alignment files using deeptools v3.5.5
Assembly: hg38
Supplementary files format and content: Bigwig

extract_protocol:
For each experiment, 10 million cells were lysed in 1 mL RIPA buffer (50mM HEPES pH 7.4, 100mM NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS) supplemented with 20 μL Protease Inhibitor Cocktail (Sigma, #P8340-5mL), 10 μL of Turbo DNase (Invitrogen, #AM2238), 1X Manganese/Calcium mix (2.5 mM MnCl2, 0.5 mM CaCl2), and 5 μL of RiboLock RNase Inhibitor (Thermo Fisher, #EO0382)). Samples were incubated on ice for 10 minutes to allow lysis to proceed. After lysis, cells were sonicated at 3-4 W of power for 3 minutes (pulses 0.7 s on, 3.3 s off) using the Branson sonicator and then incubated at 37°C for 10 minutes to allow for DNase digestion. DNase reaction was quenched with addition of 0.25 M EDTA/EGTA mix for a final concentration of 10 mM EDTA/EGTA. RNase If (NEB, #M0243L) was then added at a 1:500 dilution and samples were incubated at 37°C for 10 minutes to allow partial fragmentation of RNA to obtain RNAs of approximately ~300-400 bp in length. RNase reaction was quenched with addition of 500 μL ice cold RIPA buffer supplemented with 20 μL Protease Inhibitor Cocktail and 5 μL of RiboLock RNase Inhibitor, followed by incubation on ice for 3 minutes. Lysates were then cleared by centrifugation at 15000 x g at 4°C for 2 minutes. The supernatant was transferred to new tubes and diluted in additional RIPA buffer such that the final volume corresponded to 1 mL lysate for every 100 μL of Protein G beads used. Lysate was then combined with the labeled antibody-bead pool and 1 M biotin was added to a final concentration of 10 mM as to quench any disassociated streptavidin-coupled oligos. Beads were left rotating overnight at 4°C on a HulaMixer. Following immunoprecipitation, beads were washed twice with RIPA buffer, twice with high salt wash buffer (50 mM HEPES pH 7.4, 1 M NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS), and twice with Tween buffer (50 mM HEPES pH 7.4, 0.1% Tween-20).
After split-and-pool barcoding, beads were aliquoted into 5% aliquots for library preparation and sequencing. RNA in each aliquot was degraded by incubating with RNase H (NEB, #M0297L) and RNase cocktail (Invitrogen, #AM2286) at 37°C for 20 minutes. 3’ ends of the resulting cDNA were ligated to attach dsDNA oligos containing library amplification sequences using a “splint” ligation as previously described (Quinodoz et al 2021)31. The “splint” ligation reaction was performed with 1X Instant Sticky End Master Mix (NEB #M0370) at 24°C for 1 hour with shaking at 1400 rpm on a ThermoMixer. Barcoded cDNA and biotinylated oligo tags were then eluted from beads by boiling in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsarcosine, 2.5 mM TCEP) for 6 minutes at 91°C, with shaking at 1350 rpm. Biotinylated oligo tags were first captured by diluting the eluant in 1X oligo binding buffer (0.5X PBST, 5 mM Tris pH 8.0, 0.5 mM EDTA, 1M NaCl) and subsequently binding to MyOne Streptavidin C1 Dynabeads (Invitrogen, #65001) at room temperature for 30 minutes. Beads were placed on a magnet and the supernatant, containing cDNA, was moved to a separate tube. Biotinylated oligo tags were amplified on-bead using 2X Q5 Hot-Start Mastermix (NEB #M0494) with primers that add the indexed full Illumina adaptor sequences.

value: Human embryonic kidney cells


title: CAG, RNA-seq, rep3

data_processing:
Illumina pipeline software was used for base calling.
Raw reads were trimmed with cutadapt (version 4.6) with parameters -q 20 --poly-a --minimum length=10  -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Reads mapping to PhiX or ribosomal DNA were removed using bowtie2 (version 2.5.1) with parameters --fast-local --dovetail --un-conc.
Reads were mapped to the human genome (hg19) with hisat2 (version 2.2.1) using default parameters.
Exonic reads were counted for each gene using Gencode (v19) annotations and featureCounts (version 2.0.3) with parameters -s 2 -p --countReadPairs -F SAF.
Assembly: hg19
Supplementary files format and content: The featureCounts output, a matrix with gene counts for all six samples, is provided (rnaseq_gene_counts.tsv).

extract_protocol:
Cells were scraped from 70% confluent 10 cm plates in ice-cold PBS, pelleted, and Trizol was added. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared for each sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation, by the RNA Sequencing Core and the Transcriptional Regulation and Expression Facility at Cornell University.

value: CAG landing pad


title: polysome, fraction 6, PGK

value: PGK landing pad


title: TetOff, total RNA, rep2

description: Library name: p83_totalRNA_rep2


title: Rv- infected macrophages  1 no T. S21. rep1 [Rv_NT1_iM_S21]

value: iM


title: PGK, RNA-seq, rep3


title: TetOff, dox 4 hour timepoint, rep1

description: Library name: p83_T04_rep1


title: H_14

description: Library name: 104930-001-014R


title: H_13

description: Library name: 104930-001-013R


title: Rv- bystander macrophages 1 no T. S25. rep1 [Rv_NT1_bM_S25]


title: Control (Uninfected) macs+T. S2. rep 2 [Mo_CON_2_S2]

value: T

value: Uninfected


title: TetOff, dox 3 hour timepoint, rep1

description: Library name: p83_T03_rep1

value: Tet-Off landing pad

value: dox 3 hour timepoint


title: control (Uninfected) macs+T. rep 1 [Mo_CON_1_S1]


title: H_12

description: Library name: 104930-001-012R


title: H_11

description: Library name: 104930-001-011R


title: PGK, RNA-seq, rep2


title: CAG, RNA-seq, rep1


title: 12VHPC-FED

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description:
Library name: S12
10x Genomics 3' gene expression v3.1

data_processing:
Samples were demultixpled, aligned, and counted using CellRanger v8.0.1.
Assembly: Mmul10
Supplementary files format and content: Tab separated value files and matrix files

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Fresh frozen tissue samples were homogenized and used to generate nuclei suspensions as detailed in accompanying manuscripts.
Libraries were constructed using the manufacturer protocol for the 10x Genomics dual index 3' gene expression assay v3.1

value: brain

value: Fed


title: H_10

description: Library name: 104930-001-010R

value: H

value: HFD


title: H_09

description: Library name: 104930-001-009R


title: 11VHPC-FAST

description:
Library name: S11
10x Genomics 3' gene expression v3.1

value: Fast


title: TetOff, dox 20 hour timepoint, rep2

description: Library name: p83_T20_rep2

value: dox 20 hour timepoint


title: TetOff, dox 20 hour timepoint, rep1

description: Library name: p83_T20_rep1


title: 10VHPC-FED

description:
Library name: S10
10x Genomics 3' gene expression v3.1


title: C_08

description: Library name: 104930-001-008R

value: C

value: Chow


title: 9VHPC-FAST

description:
Library name: S9
10x Genomics 3' gene expression v3.1


title: NK_DMSO_rep2 (ATAC-seq)

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

institute: CNRS

data_processing:
Libraries were sequenced using an Illumina Novaseq 6000 sequencer as paired-end 50 base reads.
Image analysis and base calling were performed using NovaSeq Control Software, Real‑Time Analysis 3 (RTA) and bcl2fastq.
Reads were processed using nf-core/atacseq (ATAC-seq peak-calling and QC analysis pipeline; doi: 10.5281/zenodo.2634132) with default settings except MACS2 "--narrow_peak" mode detection.
Assembly: hg38/GRCh38p12
Supplementary files format and content: bigWig

source_name: blood

growth_protocol: PBMCs were purified from either buffy coat of healthy blood donors using density-based centrifugation method (Histopaque 1077- H8889 Sigma-Aldrich). Myeloid cells were purified from PMBCs using CD33+ microbeads (Miltenyi Biotech 130-045-501) according to manufacturer guidelines. The flow through, depleted from CD33+ cells, was then processed using negative selection NK cells isolation Kit (Miltenyi Biotech 130-092-657). Purified NK cells were cultured in RPMI medium + 10% fetal calf serum.

extract_protocol:
100,000 NK cells were washed once with ice cold PBS and lysed with cold lysis buffer (containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 (Sigma-I8896)). After lysis, Nuclei were harvested by centrifugation and DNA was digested with Tagment DNA Enzyme 1 (Illumina, 15027865) for 30 min at 37°C. Tagmented DNA fragments were purified using Monarch PCR and DNA Cleanup Kit (T1030L).
Tagmented DNA fragments were amplified for 11 cycles by PCR using Q5 High Fidelity DNA Polymerase (NEBNext Ultra II Q5 - M0544) and Ad1 and Ad2 primers. (The quality, size and concentration of cDNA libraries were checked using the High Sensitivity NGS kit Fragment Analyzer and qPCR (ROCHE Light Cycler 480).I am not sure)
PE50

treatment_protocol: Purified NK cells were treated with TAK-981 (100 nM) for 6 h.

value: blood

value: natural killer

value: DMSO


title: C_07

description: Library name: 104930-001-007R

value: Liver, right lobe


title: TetOff, dox 1 hour timepoint, rep2

description: Library name: p83_T01_rep2

value: dox 1 hour timepoint


title: C_06

description: Library name: 104930-001-006R


title: TetOff, dox 1 hour timepoint, rep1

description: Library name: p83_T01_rep1


title: TetOff, dox 3 hour timepoint, rep2

description: Library name: p83_T03_rep2


title: NK_DMSO_rep1 (ATAC-seq)


title: TetOff, dox 2 hour timepoint, rep2

description: Library name: p83_T02_rep2

value: dox 2 hour timepoint


title: CAG, RNA-seq, rep2

value: CAG landing pad


title: NK_TAK981_rep1 (ATAC-seq)


title: 8VHPC-FED

description:
Library name: S8
10x Genomics 3' gene expression v3.1


title: TetOff, dox 2 hour timepoint, rep1

description: Library name: p83_T02_rep1

value: Tet-Off landing pad


title: C_05

description: Library name: 104930-001-005R


title: hypoxia/reoxygenation H-R3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: The xls format file contains the FPKM value of gene in every sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).

value: intestinal epithelial cells

value: WT

value: hypoxia/reoxygenation


title: C_04

description: Library name: 104930-001-004R

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).


title: TetOff, dox 0 hour timepoint, rep2

description: Library name: p83_T00_rep2

value: dox 0 hour timepoint


title: PGK, RNA-seq, rep1

value: PGK landing pad


title: TetOff, dox 0 hour timepoint, rep1

description: Library name: p83_T00_rep1


title: NK_TAK981_rep2 (ATAC-seq)


title: 6VHPC-FED

description:
Library name: S6
10x Genomics 3' gene expression v3.1

value: brain

value: Fed


title: Huvecs_irradiated_3

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

description: Library name: PU01015

data_processing:
FASTQ files were generated with bcl2fastq (v2.19.1.403, Illumina).
Adapter trimming and quality filtering, including poly(A) tail removal and exclusion of reads containing ambiguous bases (N), were conducted using cutadapt (v1.15). Each sample initially yielded approximately 8 million reads; to ensure uniform sequencing depth across samples, all datasets were downsampled to 5 million reads.
Reads were aligned to the human reference genome GRCh38  with Gencode v29 annotations  using the STAR aligner (v2.6.1a).
Assembly: Reference genome GRCh38 with Gencode v29 annotations
Supplementary files format and content: raw_gene_counts_GeneSymbols_GeneTypes.tsv: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner; Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)

source_name: Umbilical Cord

growth_protocol: HUVECs were grown on gelatin pre-coated cell culture dishes in M199-based medium supplemented with 20% FBS, 0.4% endothelial cell growth supplement with heparin (ECGS/H), 2 mM L-glutamine, 0.1% penicillin, 0.1% streptomycin and 0.25 μg/mL fungizone in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using the PeqGOLD Total RNA kit (VWR) and stored at -80°C
Sequencing libraries were prepared from total RNA at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq FWD protocol (Lexogen). The optimal number of PCR amplification cycles was determined by quantitative PCR, according to the manufacturer's instructions. Library quality control was performed using the Agilent Bioanalyzer 2100 with the High Sensitivity DNA Kit to confirm the expected insert size. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (Invitrogen). Pooled libraries were sequenced on an Illumina NextSeq500 system in 1×75 bp single-end mode.

treatment_protocol: Replicative senescent HUVECs were generated by continuos passaging for more than 35 times in a 1:3 ratio. Irradiation-induced premature senescent HUVECs were created by exposure to 10 Gy of ionizing irradiation and subsequent 10 day recovery period. Control HUVECs were cells of early passage.

value: Umbilical Cord

value: HUVEC

value: Endothelial Cells

tag: Stage

value: senescent

value: irradiated


title: hypoxia/reoxygenation H-R2

tag: cell line


title: hypoxia/reoxygenation H-R1

tag: cell type


title: 5VHPC-FAST

description:
Library name: S5
10x Genomics 3' gene expression v3.1

tag: tissue

value: Fast


title: C_03

description: Library name: 104930-001-003R

extract_protocol:
Next generation sequencing (NGS) was performed in tot-RNA samples extracted from right liver lobe samples. RNA was isolated using the RNA-Bee total-RNA isolation kit (Bio-Connect, Huissen, the Netherlands) and evaluated for quality with the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-50 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

value: Liver, right lobe

value: C

value: Chow


title: C_02

description: Library name: 104930-001-002R


title: Huvecs_irradiated_2

description: Library name: PU01014

tag: genotype


title: control3

tag: treatment

value: control


title: 3VHPC-FAST

description:
Library name: S3
10x Genomics 3' gene expression v3.1


title: 4VHPC-FED

description:
Library name: S4
10x Genomics 3' gene expression v3.1


title: C_01

description: Library name: 104930-001-001R


title: Huvecs_irradiated_1

description: Library name: PU01013


title: control2

value: intestinal epithelial cells


title: 2VHPC-FED

description:
Library name: S2
10x Genomics 3' gene expression v3.1


title: Mouse single-cell RNA sequencing Samples 3

city: St Louis

first: Sumanth

last: Prabhu

state: MO

address: 1 Brookings Dr

department: Department of Cardiology

institute: Washington University in St Louis

description:
Library name: Lane3_12Cycles
10X Genomics

data_processing:
Cellswere processed by the Washington University McDonnell Genome Institute (MGI) for scRNAseq using the 10X genomics 16-plex format (10X Genomics CDG000527 Rev E). Cell barcoding on the 10X Chromium X, library construction, amplification and sequencing were performed, and scRNAseq FASTQ files obtained from the MGI were processed using 10X genomics cell ranger pipeline for sequence quality, demultiplexing, and alignment. Processed FASTQ files were exported as H5 files.
Assembly: Reads were aligned to a Mus musculus reference genome using the Cell Ranger pipeline.
Supplementary files format and content: Barcodes.tsv is processed data file that has the required barcode or cell identifier information in tsv format lane-wise.
Supplementary files format and content: Features.tsv contains the genes' information or rows of the expression matrix in tsv format, lane-wise.
Supplementary files format and content: Matrix.mtx contains gene expression matrix in mtx format. It represents number of reads detected for genes, lane-wise.

source_name: Peripheral blood

extract_protocol:
Mouse peripheral blood underwent erythrocyte lysis and leukocytes were centrifuged and collected immediately. Cells were stained with 2 μL DAPI  (564907, BD Pharmingen) and 2 μL Draq5 (62251, Thermo Scientific) for 5 min. Cells were diluted to 4 mL for sorting (FACSMelody, BD Biosciences), and viability was verified by ethidium  homodimer (EtHD) staining (E1169, Thermo Fisher Scientific). Cells were processed for scRNAseq using the 10X fixed sample preparation kit (1000414, 10X Genomics). Cells were  pelleted and resuspended in 1 mL fixation buffer and maintained at 4oC for 24 h. Cells were then collected at 850g at 5 min at RT and resuspended in 1 mL chilled quenching buffer. Cell concentration was determined by EtHD staining (Countess, Thermo Fisher Scientific) and then stored at -80 oC after addition of 100 μL enhancer and glycerol (10% final concentration). Cells  were processed by the Washington University McDonnell Genome Institute (MGI) for scRNAseq using the 10X genomics 16-plex format (10X Genomics CDG000527 Rev E). Cell barcoding on the 10X Chromium X, library construction, amplification and sequencing were performed, and scRNAseq FASTQ files obtained from the MGI were processed using 10X genomics cell ranger. pipeline for sequence quality, demultiplexing, and alignment. Processed FASTQ files were exported as H5 files.
10X Genomics platform was used, 16-plex kit, on a Chromium X, following standard droplet-based scRNA-seq library preparation

value: Peripheral blood

value: 10 week

value: Leuckocytes

value: Male

value: untreated


title: Huvecs_senescent_3

description: Library name: PU01009

value: WT


title: control1


title: 7VHPC-FAST

description:
Library name: S7
10x Genomics 3' gene expression v3.1

value: brain


title: Mouse single-cell RNA sequencing Samples 2

description:
Library name: Lane2_12Cycles
10X Genomics

value: 9 week


title: 1VHPC-FAST

description:
Library name: S1
10x Genomics 3' gene expression v3.1


title: Huvecs_senescent_2

description: Library name: PU01008

value: Umbilical Cord

value: HUVEC

value: Endothelial Cells


title: 15_CTX_Rotenone_B5

city: London

first: Maria

last: Tsalenchuk

address: Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road

institute: King's College London

data_processing:
Initial screening for sample anomalies was performed with FastQC (version 0.11.9). Adapter sequences were trimmed using Trim Galore! (version 0.6.7). For RNA-seq, FASTQ files were aligned, and transcripts were quantified using Salmon (version V1.10.0).
Assembly: Rn7
Supplementary files format and content: quant.sf files

source_name: cortex

extract_protocol:
Samples were homogenised in 1 mL of Trizol reagent (Thermofisher Scientific, Waltham, MA) and total RNA was extracted using the Life Technologies min-RNA purification kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were constructed using the 3’QuantSeq kit (Lexogen) with the following modifications. To enable the removal of PCR duplications, a custom oligo-dT primer was designed using a 12-bp unique molecular identifier.

treatment_protocol: Male Lewis rats aged 8-10 months received either rotenone at a dose of 2.8 mg/kg or a vehicle solution (Miglyol) administered intraperitoneally once daily for 21 days.24 hours after the final rotenone injection, rats were perfused using a saline-buffered solution. The cortex and SN were microdissected and immediately placed on dry ice

value: cortex

value: Rotenone


title: Mouse single-cell RNA sequencing Samples 1

description:
Library name: Lane1_12Cycles
10X Genomics

value: 8 week


title: H-R s-T3

description: H-R s-T3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: The xls format file contains the FPKM value of gene in every sample

value: TMEM2 knockdown

value: hypoxia/reoxygenation


title: Huvecs_control_3

description: Library name: PU01003

value: control


title: d2 replicated, bmem, tbx21pos, mdln, d30, adt

city: Birmingham

first: Frances

last: Lund

state: AL

address: 1720 2nd Ave. South

department: Microbiology

institute: University of Alabama at Birmingham

description:
Library name: d2_mdlnpos_adt
10X genomics, s12

library_source: other

data_processing:
GEX and ADT libraries were processed using Cellranger Count (v4.0.0) for matrix construction
VDJ libraries were processed using Cellranger (v4.0.0) and filtered_contig_fasta files were submitted to IMGT HighVQuest for VDJ call refinement.
processed data were imported into seurat and then merged
GEX were demultiplexed with Seurat(v4.3.0) HTODemux()
Assembly: mm10 + gene encoding ZsGreen
Supplementary files format and content: tab separated values and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: lymph nodes

extract_protocol:
Memory B cells from lymph nodes of D30 influenza-infected mice were stained with NP tetramers, fluorophore-labeled Abs, and Abs conjugated with TotalSeq C oligomer hashtags and other protein targets. NP+ and Npneg Bmem cells (CD4negCD8negLIVE/DEADnegCD19+IgDnegGL-7negPNAnegCD138negCD93negCD38+NP-PE-OligonegNP-APCneg) cells were sort-purified.
Chromium Single Cell 5’ Library and Gel Bead Kit (Next GEM 5’ Kit v 2) as well as the Single Cell 5’ Feature Barcode Library Kit (10XGenomics) and mouse BCR amplification Library Kit (10XGenomics)

value: lymph nodes

value: memory B cell

value: D30 post influenza infection


title: H-R s-T2

description: H-R s-T2

value: intestinal epithelial cells


title: 13_CTX_Rotenone_B1


title: Huvecs_senescent_1

description: Library name: PU01007

value: senescent


title: d2 replicated, bmem, tbx21pos, mdln, d30, vdj

description:
Library name: d2_mdlnpos_vdj
10X genomics, s4

data_processing:
GEX and ADT libraries were processed using Cellranger Count (v4.0.0) for matrix construction
VDJ libraries were processed using Cellranger (v4.0.0) and filtered_contig_fasta files were submitted to IMGT HighVQuest for VDJ call refinement.
processed data were imported into seurat and then merged
GEX were demultiplexed with Seurat(v4.3.0) HTODemux()
Assembly: mm10 + gene encoding ZsGreen
Supplementary files format and content: tab separated values and matrix files


title: H-R3

value: WT


title: H-R s-T1

description: H-R s-T1


title: H-R2


title: d2 replicated, bmem, tbx21pos, mdln, d30, gex

description:
Library name: d2_mdlnpos_gex
10X genomics, s8


title: 14_CTX_Rotenone_B3


title: 5_CTX_Vehicle_A9

value: PBS