title: PRE Exercise [29_pre]

city: Ribeirão Preto

first: Guilherme

middle: Da Silva

last: Rodrigues

address: Avenida Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

description: leucocytes peripheral blood

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip EPIC using standard Illumina protocol

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

data_processing: Champ package for Rstudio was used to process data.

extract_protocol: DNA was extracted from the collected whole blood, the technique adopted was automated by magnetic spheres, using the Maxwell MDx equipment.

tag: bm (kg)

tag: wc (cm)

tag: bmi (kg/m2)

tag: vo2 max


title: Renal Microvascular Endothelial Cells, hypoxia/reoxygenation, HR3

status: Public on May 06 2025

type: SRA

city: Hangzhou

first: Yuxian

last: Kuai

state: Zhejiang

address: No. 88 Jiefang Road, Shangcheng District

country: China

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: sample 3

library_source: transcriptomic

data_processing:
Reads mapping: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Expression analysis: We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM（Fragments Per Kilo bases per Million fragments） / TPM（Transcripts per Million） to standardize the expression.
Differential expression analysis: Then difference expression of genes was analyzed by DESeq2 (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used ComplexHeatmap (v2.16.0) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Enrichment analysis: We mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using ClusterProfiler (v4.6.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value < 0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes.  ClusterProfiler (v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value < 0.05.
GSEA(Gene Set EnrichmentAnalysis): ClusterProfiler (v4.6.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn.
Assembly: GRCh38.p13
Supplementary files format and content: .tar.gz

molecule: total RNA

organism: Homo sapiens

source_name: Renal Microvascular Endothelial Cells

extract_protocol:
RNA extraction and detection Reagent kit: InvitrogenTRIzol reagent Operation steps: 1. Homogenization treatment Take the sample in a 2ml grinding tube and thoroughly grind it using a grinder at 60Hz for 60 seconds. Then take 2-4 samples each time, add 1ml TRIzol reagent to the ground powder and mix immediately (the sample needs to be kept at low temperature before adding TRIzol). After adding all the samples to TRIzol, wet beat at 55Hz for 30 seconds and incubate at room temperature for 5 minutes to facilitate complete separation of nuclear protein bodies in the homogenized sample. Centrifuge at 12000rpm for 5 minutes and take the supernatant (a 1.5ml centrifuge tube can be prepared during centrifugation to hold the supernatant). 2. Phase separation Add 0.2ml chloroform to the supernatant, shake the tube vigorously for 30 seconds, and incubate at room temperature for 2-3 minutes. Centrifuge at 4 ° C and 12000rpm for 15 minutes (during centrifugation, prepare a 1.5ml centrifuge tube and write the sample name and number). The mixture separates into a red lower layer (phenol chloroform phase), an intermediate phase, and an upper colorless aqueous phase. RNA exists in the aqueous phase. 3. RNA precipitation Transfer 400 μ l of aqueous phase to a 1.5ml final tube, add 500 μ l of isopropanol, invert and mix well (about 30 times). Incubate the sample at room temperature for 10 minutes. Centrifuge at 4 ° C and 12000rpm for 10 minutes. 4. RNA washing Discard the supernatant and add 1ml of 75% ethanol to wash the precipitate (try to resuspend the precipitate as much as possible). Centrifuge at 4 ° C and 12000rpm for 5 minutes. 5. Dissolve RNA again At the end of the process, briefly centrifuge and extract ethanol, then add an appropriate amount of RNase free water-soluble sample directly. Do not vacuum centrifuge RNA. It is important not to let the RNA precipitate completely dry, as this will greatly reduce its solubility.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

tag: cell line

value: Renal Microvascular Endothelial Cells

tag: treatment

value: hypoxia/reoxygenation (H/R)


title: Renal Microvascular Endothelial Cells, hypoxia/reoxygenation, HR2

description: Library name: sample 2


title: RA_11_1

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description: Library name: Sample17

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data was analyzed using our previously established workflow. Briefly, raw FASTQ files generated by 10× Genomics were aligned and quantified using Cell Ranger (v4.3.0) against the GRCh38 human reference genome (v6.1.2). The Read10X function of the Seurat package was used to read the output of Cell Ranger. Doublets were identified and removed using the scrublet tool in Python, with an expected doublet rate of 0.1. Next, to facilitate downstream analyses, cells were distinctly labeled using the RenameCells function and integrated into a single aggregate object using the Merge function. To ensure data quality, stringent filtering parameters were applied to weed out any empty oil beads, mortality, and doublet cells, excluding cells with fewer than 200 or more than 4,000 detected genes, or with mitochondrial content exceeding 15%. Global scaling normalization was performed using the ‘LogNormalize’ method with a scaling factor of 10,000 to equalize overall gene expression across cells. The FindVariableFeatures function identified the top 2,000 highly variable genes, which were used for dimensionality reduction via principal component analysis (PCA). The first 30 principal components were selected, and the ScaleData function was applied to regress out undesired sources of variation. Sample batch effect correction was performed using the RunFastMNN function, which is based on a multi-canonical correlation analysis algorithm. For clustering, the FindNeighbors and FindClusters functions with the built-in Louvain method were applied. Clusters were visualized using uniform manifold approximation and projection (UMAP). Cluster-specific marker genes were identified using the non-parametric Wilcoxon rank-sum test with Bonferroni correction (adjusted p-value < 0.05; PCT > 0.25) implemented in the FindAllMarkers function. Cell populations were annotated based on canonical marker genes from published literature. Due to the inherent instability of neutrophils during processing and their predominant origin from a small number of samples, this cell type was excluded from subsequent analyses to mitigate technical bias. The proportion of each cluster was estimated by dividing the count of cells within each cluster by the total cell count in the respective sample. These ratios were statistically compared across treatment groups to assess significant differences in cell composition.
Assembly: GRCh38
Supplementary files format and content: rds file

molecule: polyA RNA

source_name: Synovial fluid

extract_protocol:
The patient’s knee joint synovial fluid was extracted under aseptic conditions. Hyaluronidase (20426ES60, Yeasen) was added to the fresh SF sample obtained at a final concentration of 100 U/ml and incubated at 37°C for 30 min. SF samples from each RA patient were obtained from the same joint longitudinal to avoid potential bias.
The cell suspension was placed into 30 (v3) chemistry-equipped Chromium microfluidic chips, and a 10 × Chromium Controller (10×Genomics) was used to barcode the samples. Next, using components from a Chromium Single Cell 30 v3 reagent kit (10×Genomics), sequencing libraries were created using RNA from the barcoded cells after reverse transcription, in accordance with the manufacturer’s instructions.

tag: tissue

value: Synovial fluid

tag: age

tag: Sex

value: Female

value: Treatment-naïve


title: RA_10_1

description: Library name: Sample15


title: RA_10_2

description: Library name: Sample16

value: Tofacitinib


title: RA_9_2

description: Library name: Sample14

value: Adalimumab


title: POST Exercise [36_post]

type: genomic

description: leucocytes peripheral blood

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina protocol


title: RA_6_2

description: Library name: Sample12


title: PRE Exercise [11_pre]

description: leucocytes peripheral blood


title: RA_4_1

description: Library name: Sample7


title: RA_3_2

description: Library name: Sample6


title: RA_5_2

description: Library name: Sample10


title: RA_5_1

description: Library name: Sample9


title: RA_3_1

description: Library name: Sample5


title: POST Exercise [28_post]

description: leucocytes peripheral blood


title: PRE Exercise [30_pre]

description: leucocytes peripheral blood


title: RA_2_1

description: Library name: Sample3


title: RA_1_2

description: Library name: Sample2


title: RA_2_2

description: Library name: Sample4


title: RA_9_1

description: Library name: Sample13


title: PRE Exercise [20_pre]

description: leucocytes peripheral blood


title: WGBS_LU_RAS_D10

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

description: Library name: Sample4

library_source: genomic

data_processing:
Data Quality Control  First of all, we used FastQC (fastqc_v0.11.8) to perform basic statistics on the  quality of the raw reads. Then, those reads sequences produced by the  Illumina pipleline in FASTQ format were pre-processed through fastp (fastp  0.23.1). The remaining reads that passed all the filtering steps was counted as  clean reads and all subsequent analyses were based on this. Finally, we used  FastQC to perform basic statistics on the quality of the clean data reads.
Reference data preparation before analysis Before the analysis, we prepared the reference data for the species we study, including the reference sequence fasta file, the annotation file in gtf format, the GO annotation file, the description file and the gene region file in bed format. We predicted repeats with RepeatMasker, and CGI track from a genome with cpgIslandExt.
Reads mapping to the reference genome Bismark software (version 0.24.0; Krueger et al., 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700--dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead et al., 2012). Clean reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to- A converted) before being aligned to the similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence and the methylation state of all cytosine positions was inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads. The results of methylation extractor (bismark_methylation_extractor,-- no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-conversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts (mC+umC) and the non-conversion rate (r). Sites with FDR-corrected p-value
Assembly: hg19
Supplementary files format and content: bigwig

source_name: primary fibroblasts cells

growth_protocol: MEM, 10% fetal bovine serum, 1× penicillin/streptomycin. Cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total genomic DNA was extracted from rumen contents using the TIANGEN Magnetic Universal Genomic DNA Kit
After samples DNA testing, positive control DNAs were added into the DNAs, and then they were fragmented into 200-400bp using Covaris S220（Covaris, USA）. Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragments. The library kit (Accel-NGS Methyl-Seq DNA Library Kit(Swift, USA, Catalog #: 30096) adds a low complexity polynucleotide tail with an average length of 8 bases to the 3’ end of each fragment during the addition of the first NGS adapter molecule. If these tails are not trimmed bioinformatically from the sequencing data, it is normal and expected to observe them at the beginning of Read 2 (R2). When read length is close to fragment size, the tail may also be observed toward the end of Read 1 (R1) data. Therebefore, it’s highly recommended to trim 10 bases from the beginning of both R1 and R2 to eliminate any artifactual cytosine methylation introduced as a result of filling in overhangs during end repair steps of conventional dsDNA library preparation and low quality bases due to bisulfite treatment. Subsequently, library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR(1.5 nM). Pair-end sequencing of sample was performed on Illumina platform (Illumina, USA).

treatment_protocol: The cells overexpressing Tet-on RASG12V were continuously induced with doxycycline for 0, 2, 4, 6, 8, and 10 days to induce senescence.  Whole-genome bisulfite sequencing (WGBS) analyses were conducted specifically at 0, 2, 4, and 10 days post-induction.

tag: cell type

value: primary fibroblasts cells

tag: genotype

value: Immortalized cells by hTERT

value: indece senescent D10


title: WGBS_LU_RAS_D4

description: Library name: Sample3

value: indece senescent D4


title: WGBS_LU_RAS_D2

description: Library name: Sample2

value: indece senescent D2


title: PRE Exercise [28_pre]

description: leucocytes peripheral blood


title: RA_1_1

description: Library name: Sample1


title: WGBS_LU_RAS_D0

description: Library name: Sample1

value: indece senescent D0


title: PRE Exercise [16_pre]

description: leucocytes peripheral blood


title: POST Exercise [34_post]

description: leucocytes peripheral blood


title: LU_RAS_D10

description: Library name: Sample6

data_processing:
Data quality control.Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
featureCounts was used to count the reads numbers mapped to each gene
For DESeq2 with biological replicates: Differential expression analysis for two groups was performed using the DESeq2 R package, The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was havested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries. Sequencing libraries were use Fast RNA-seq Lib Prep Kit V2.
RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: The cells overexpressing Tet-on RASG12V were continuously induced with doxycycline for 0, 2, 4, 6, 8, and 10 days to induce senescence. RNA sequencing (RNA-seq) analysis was performed at 0, 2, 4, 6, 8, and 10 days post-induction.


title: PRE Exercise [13_pre]

description: leucocytes peripheral blood


title: POST Exercise [16_post]

description: leucocytes peripheral blood


title: LU_RAS_D8

description: Library name: Sample5

value: indece senescent D8


title: PRE Exercise [34_pre]

description: leucocytes peripheral blood


title: LU_RAS_D4

description: Library name: Sample3


title: LU_RAS_D2

description: Library name: Sample2


title: LU_RAS_D0

description: Library name: Sample1


title: POST Exercise [29_post]

description: leucocytes peripheral blood


title: POST Exercise [1_post]

description: leucocytes peripheral blood


title: PRE Exercise [37_pre]

description: leucocytes peripheral blood


title: POST Exercise [13_post]

description: leucocytes peripheral blood


title: POST Exercise [20_post]

description: leucocytes peripheral blood


title: POST Exercise [37_post]

description: leucocytes peripheral blood


title: RA_6_1

description: Library name: Sample11


title: KUR_T181

city: Suita City

first: Yohei

last: Okuda

state: Osaka

address: Yamadaoka 2-2,

country: Japan

institute: The University of Osaka

description: Library name: 119

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Software : Illumina package bcl2fastq
Assembly: GRCh38
Supplementary files format and content: CSV file includes FPKM value for each sample

source_name: Renal cell carcinoma

extract_protocol:
RNA was extracted from Rneasy plus mini kit (Qiagen) followed by provided protocol.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: Renal cell carcinoma


title: KSR_T190

description: Library name: 118


title: KUR_T188

description: Library name: 120


title: POST Exercise [30_post]

description: leucocytes peripheral blood


title: KR_T185

description: Library name: 117


title: KR_T98

description: Library name: 115


title: KR_T96

description: Library name: 113


title: KR_T97

description: Library name: 114


title: LU_RAS_D6

description: Library name: Sample4

value: indece senescent D6


title: KR_T94

description: Library name: 111


title: KR_T99

description: Library name: 116


title: KR_T91

description: Library name: 108


title: KR_T129

description: Library name: 110


title: KR_T92

description: Library name: 109


title: KR_T89

description: Library name: 107


title: KR_T88

description: Library name: 106


title: KR_T87

description: Library name: 105


title: KR_T95

description: Library name: 112


title: RA_4_2

description: Library name: Sample8


title: POST Exercise [11_post]

description: leucocytes peripheral blood


title: KR_T85

description: Library name: 104


title: PRE Exercise [1_pre]

description: leucocytes peripheral blood


title: KR_T82

description: Library name: 102


title: KR_T83

description: Library name: 103


title: KR_T81

description: Library name: 101


title: KR_T7

description: Library name: 95


title: KR_T80

description: Library name: 100


title: KR_T78

description: Library name: 98


title: KR_T74

description: Library name: 97


title: KR_T79

description: Library name: 99


title: KR_T68

description: Library name: 93


title: KR_T73

description: Library name: 96


title: KR_T67

description: Library name: 92


title: KR_T64

description: Library name: 89


title: KR_T69

description: Library name: 94


title: KR_T66

description: Library name: 91


title: PRE Exercise [36_pre]

description: leucocytes peripheral blood


title: KR_T65

description: Library name: 90


title: KR_T62

description: Library name: 88


title: KR_T60

description: Library name: 86


title: KR_T6

description: Library name: 85


title: KR_T59

description: Library name: 84


title: KR_T58

description: Library name: 83


title: KR_T53

description: Library name: 79


title: KR_T56

description: Library name: 81


title: KR_T57

description: Library name: 82


title: KR_T54

description: Library name: 80


title: KR_T52

description: Library name: 78


title: KR_T51

description: Library name: 77


title: KR_T50

description: Library name: 76


title: KR_T5

description: Library name: 75


title: KR_T48

description: Library name: 73


title: KR_T41

description: Library name: 69


title: KR_T49

description: Library name: 74


title: KR_T39

description: Library name: 66


title: KR_T46

description: Library name: 71


title: KR_T45

description: Library name: 70


title: KR_T4

description: Library name: 67


title: KR_T47

description: Library name: 72


title: KR_T38

description: Library name: 65


title: KR_T32

description: Library name: 61


title: KR_T61

description: Library name: 87


title: KR_T35

description: Library name: 63


title: KR_T146

description: Library name: 62


title: KR_T29

description: Library name: 57


title: KR_T28

description: Library name: 56


title: KR_T27

description: Library name: 55


title: KR_T24

description: Library name: 52


title: KR_T25

description: Library name: 53


title: KR_T26

description: Library name: 54


title: KR_T23

description: Library name: 51


title: KR_T22

description: Library name: 50


title: KR_T128

description: Library name: 49


title: KUR_T189

description: Library name: 121


title: KR_T40

description: Library name: 68


title: KR_T2

description: Library name: 48


title: KR_T36

description: Library name: 64


title: KR_T18

description: Library name: 46


title: KR_T19

description: Library name: 47


title: KR_T17

description: Library name: 44


title: KR_T140

description: Library name: 40


title: KR_T31

description: Library name: 60


title: KR_T30

description: Library name: 59


title: KR_T164

description: Library name: 42


title: KR_T166

description: Library name: 43


title: KR_T138

description: Library name: 38


title: KR_TT136

description: Library name: 36


title: KR_T139

description: Library name: 39


title: KR_T137

description: Library name: 37


title: KR_T3

description: Library name: 58


title: KR_T134

description: Library name: 34


title: KR_T133

description: Library name: 33


title: KR_T131

description: Library name: 31


title: KR_T126

description: Library name: 28


title: KR_T125

description: Library name: 27


title: KR_T130

description: Library name: 30


title: KR_T124

description: Library name: 26


title: KR_T177

description: Library name: 45


title: KR_T122

description: Library name: 24


title: KR_T120

description: Library name: 22


title: KR_T121

description: Library name: 23


title: KR_T15

description: Library name: 41


title: KR_T113

description: Library name: 15


title: KR_T116

description: Library name: 18


title: KR_T118

description: Library name: 20


title: KR_T112

description: Library name: 14


title: KR_T115

description: Library name: 17


title: KR_T135

description: Library name: 35


title: KR_T132

description: Library name: 32


title: KR_T119

description: Library name: 21


title: KR_T117

description: Library name: 19


title: KR_T114

description: Library name: 16


title: KR_T109

description: Library name: 11


title: KR_T111

description: Library name: 13


title: KR_T127

description: Library name: 29


title: KR_T106

description: Library name: 8


title: KR_T107

description: Library name: 9


title: KR_T104

description: Library name: 6


title: KR_T105

description: Library name: 7


title: KR_T102

description: Library name: 4


title: KR_T123

description: Library name: 25


title: KR_T101

description: Library name: 3


title: KR_T141

description: Library name: 1


title: RPE1, AURKB+INCENP, ChIP, R2

city: Sevilla

first: Fernando

last: Monje-Casas

state: Sevilla

address: CABIMER. Avda. Americo Vespucio, 24, P.C.T. Cartuja 93, CIF: Q2818002D

department: CABIMER

country: Spain

institute: CSIC

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
FastQ files from libraries were de-multiplexed and trimmed using Illumina FastQ Generation (version 1.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server.Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) and the April 2006D. melanogastergenome assembly (BDGP R5/dm3) using Bowtie (v.1.2.0) with parameters -m1--best.
PCR duplicates were removed with RmDup (v.12.0.1) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Genome coverage was calculated with ‘Genome Coverage’(v.2.30.0) from bedtools using default parameters but normalizing reads to Relative Counts per million (RCPM).
Assembly: hg38 (Homo sapiens) and dm3 (Drosophila melanogaster)
Supplementary files format and content: Bedgraph files include RPE1 RCPM values for each sample

source_name: hTERT RPE-1

growth_protocol: Dulbecco′s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham medium (Sigma-Aldrich) supplemented with 2 mM L-Glutamine solution (Sigma-Aldrich), 10% tetracycline free fetal bovine serum (Capricorn), 100 U/ml penicillin (Sigma-Aldrich) and 100 μg/ml streptomycin (Sigma-Aldrich). Cells were maintained in a humidified incubator at 37°C and with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temp and reaction was stopped by adding glycine to a final 0.125M concentration. After cells were washed and lysed, chromatin was sonicated with a Bioruptur Plus (Diagenode).
Libraries were prepared using the ThruPLEX DNA-Seq kit (Takara Bio). Adaptors used in the kit include an index (bar code) specific for each sample/library. Samples were normalized and mixed at 1 nM into the same pool. Libraries were amplified using 100 cycles to obtain 50 bp paired-end reads.

treatment_protocol: For tetracycline-inducible expression of genes of interest, cells were treated with 2 μg/ml tetracycline (Sigma-Aldrich) for 32 hours.

value: hTERT RPE-1

value: human retinal pigment epithelial cells

tag: chip antibody

tag: overexpressed gene

value: AURKB+INCENP

value: 2 μg/ml tetracycline, 32h


title: RPE1, INCENP, ChIP, R2

value: INCENP


title: KR_T108

description: Library name: 10


title: RPE1, INCENP, ChIP, R1


title: RPE1, AURKB+INCENP, ChIP, R1


title: RPE1, AURKB, ChIP, R2

value: AURKB


title: KR_T110

description: Library name: 12


title: RPE1, AURKB, ChIP, R1


title: RPE1, CONTROL, ChIP, R2


title: RPE1, AURKB+INCENP, INPUT, R2


title: RPE1, INCENP, INPUT, R2


title: RPE1, AURKB, INPUT, R2


title: RPE1, INCENP, INPUT, R1


title: KR_T103

description: Library name: 5


title: RPE1, CONTROL, ChIP, R1


title: RPE1, AURKB, INPUT, R1


title: RPE1, AURKB+INCENP, INPUT, R1


title: RPE1, CONTROL, INPUT, R1


title: KR_T100

description: Library name: 2


title: Aba_empty-vector_compare-to-relA-samples_RNAseq_t=10min_rep2

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin - Madison

description:
Library name: E10-B4
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 10 min after IPTG induction; replicate 2 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv

data_processing:
Sequencing reads were trimmed using Trimmomatic (version 0.39) (default parameters except for Sliding window of 3:30, Minimum length of 36 bp, leading and trailing both a value of 3) and mapped to the A. baumannii ATCC 17978 genome (GCA_001077675.1) using bwa-mem (version 0.7.17-r1188) using default parameters.
Mapped reads were further processed with Picard-tools (version 2.25.10) (CleanSAM and AddOrReplaceReadGroups) and samtools (version 1.2) (sort and index).
Paired aligned reads were mapped to genes with HTSeq (version 0.6.0) with default parameters and normalized using FPKM.
Assembly: GCA_001077675.1
Supplementary files format and content: csv files containing raw counts for each sample (HTSeq)
Supplementary files format and content: csv files containing FPKM values

organism: Acinetobacter baumannii

source_name: bacteria

growth_protocol: Cells were diluted 1:100 from a saturated overnight into AbRDM + kan to maintain the plasmid and grown up shaking at 37°C. Once reaching mid-log (OD 0.3), 1 mM IPTG was added to induce expression, and cell pellets were collected for RNA purification at timepoints from 0 to 60 min (sigAb) or 0 to 10 min (relA) after addition of IPTG. AbRDM is Teknova EZ RDM media supplemented with succinate instead of glucose.

extract_protocol:
Total RNA was extracted using hot phenol organic extraction. Mid-log cells were added to 1.25 mL stop solution (5% water-saturated phenol in ethanol), spun down at 11,000xg for 5 min at 4°C, and pellets were flash frozen in a dry ice:ethanol bath and stored at -80°C. Cells were lysed with lysozyme and SDS, total RNA was purified with phenol, phenol:chloroform, and chloroform extractions followed by ethanol precipitation, and residual DNA was removed with Turbo DNase I treatment. Ribosomal RNA (rRNA) was depleted from the total RNA samples using an RNase H-based protocol. Briefly, DNA oligos complementary to A. baumannii 23S, 16S, and 5S rRNA were annealed to the total RNA samples, RNase H treatment was performed to cleave the annealed rRNA, and the DNA oligos were removed with Turbo DNase I.
rRNA-depleted samples were prepared for next-generation sequencing using NEBNext Ultra II Directional RNA Library Prep kit (NEB; E7765S) following manufacturer's protocol.

value: bacteria

value: WT 17978 with pJMP3719 (empty vector, kanR)

tag: time point


title: Aba_empty-vector_compare-to-relA-samples_RNAseq_t=0min_rep1

description:
Library name: E0-A1
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 0 min after IPTG induction; replicate 1 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: RPE1, CONTROL, INPUT, R2


title: Aba_relA-overexpression_RNAseq_t=0min_rep1

description:
Library name: R0-A9
overexpression RNA-seq; A. baumannii ATCC 17978 RelA overexpression strain (PabstBR, IPTG inducible); timepoint = 0 min after IPTG induction; replicate 1 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv

value: WT 17978 with pJMP3790 (RelA OE, kanR)


title: Aba_empty-vector_compare-to-relA-samples_RNAseq_t=0min_rep2

description:
Library name: E0-B2
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 0 min after IPTG induction; replicate 2 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: Aba_relA-overexpression_RNAseq_t=0min_rep2

description:
Library name: R0-B10
overexpression RNA-seq; A. baumannii ATCC 17978 RelA overexpression strain (PabstBR, IPTG inducible); timepoint = 0 min after IPTG induction; replicate 2 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: RPE1, AURKB+INCENP, R1

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
FastQ files from libraries were de-multiplexed and trimmed using Illumina FastQ Generation (version 1.0.0) from BaseSpace using default parameters.
Data were analyzed using Galaxy Server (https://usegalaxy.eu). Sequencing reads were aligned to human (Homo sapiens (b38): hg38) reference genome using Hisat2.
Number of reads were estimated with featureCounts. Subsequent differential gene expression (DGE) analyses were carried out using DeSeq2.
Genome coverage (bedgraph files) was performed using bamCoverage.
Transcriptional maps form RNA-seq data were generated with the Wig/BedGraph-to-bigWig tool.
Assembly: hg38 (Homo sapiens)
Supplementary files format and content: sequences aligned to reference genome in bam format and genome coverage calculations in bedgraph format.

extract_protocol:
RNA was extracted using the RNeasy Kit (Qiagen). Libraries were constructed starting from 150 ng of total RNA.
Libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit. Adaptors used in the kit include an index (bar code) specific for each sample/library. Samples were normalized and mixed at 1 nM into the same pool. Libraries were amplified using 200 cycles to obtain 75 bp paired-end reads.


title: Aba_empty-vector_compare-to-relA-samples_RNAseq_t=10min_rep1

description:
Library name: E10-A3
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 10 min after IPTG induction; replicate 1 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: RPE1, INCENP, R2


title: Aba_relA-overexpression_RNAseq_t=10min_rep1

description:
Library name: R10-A11
overexpression RNA-seq; A. baumannii ATCC 17978 RelA overexpression strain (PabstBR, IPTG inducible); timepoint = 10 min after IPTG induction; replicate 1 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: Aba_sigAb-overexpression_RNAseq_t=0min_rep1

description:
Library name: sigAb-OV-23
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 0 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv

value: WT 17978 with pJMP3382 (sigAb OE vector, kanR)


title: RPE1, AURKB, R2


title: Aba_relA-overexpression_RNAseq_t=10min_rep2

description:
Library name: R10-B12
overexpression RNA-seq; A. baumannii ATCC 17978 RelA overexpression strain (PabstBR, IPTG inducible); timepoint = 10 min after IPTG induction; replicate 2 for comparison with relA data
20240315_RelA-OE_FPKM-results.csv
20240315_relA-OE_HTseq-counts.csv


title: RPE1, INCENP, R1


title: Aba_sigAb-overexpression_RNAseq_t=0min_rep2

description:
Library name: sigAb-OV-24
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 0 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: RPE1, AURKB, R1


title: Aba_sigAb-overexpression_RNAseq_t=5min_rep2

description:
Library name: sigAb-OV-22
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 5 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: RPE1, CONTROL, R2


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=0min_rep2

description:
Library name: sigAb-OV-20
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 0 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv

value: WT 17978 with pJMP3380 (empty vector, kanR)


title: Aba_sigAb-overexpression_RNAseq_t=5min_rep1

description:
Library name: sigAb-OV-21
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 5 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: RPE1, CONTROL, R1


title: RPE1, AURKB+INCENP, R2


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=5min_rep2

description:
Library name: sigAb-OV-18
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 5 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=5min_rep1

description:
Library name: sigAb-OV-17
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 5 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: IL15 + IL21 + IL12, rep3, scRNAseq

city: Minneapolis

first: Geoffrey

middle: Thomas

last: Hart

state: MN

address: 689 23rd Ave SE

department: Medicine

institute: University of Minnesota

description: 10X Genomics

data_processing:
Cell demultiplexing and per-cell gene expression was quantified for each sample using the BaseSpace® SureCellTM RNA Single-Cell Analysis Workflow v1.2.0 from Illumina, which uses Isas v1.2.6-000184develop for analysis, STAR v2.5.2b for read alignment to the Homo sapiens UCSC hg38 genome, and SAMtools v 1.3. Data was processed downstream using the Seurat single-cell analysis pipeline v4 in R v 4.1.0 (https://doi.org/10.1038/nbt.4096  ).
QC: Cells with nFeatures > 200 were used for analysis.
Cells from each sample were normalized using the SCTransform method in Seurat.
Samples were integrated using Seurat's Integration method (nPCs=30)  to correct for batch effects from separate captures.
Samples were visualized with UMAP and clustered using SNN (algorithm=Louvain) with top 6 PCs.
Cells were defined as IL10+ or CD3+ if raw  counts of those genes in those cells  ≥ 1.
Differential gene expression testing was performed using the Wilcoxon test in Seurat (min.pct=0.1, logfc.threshold=0, only.pos=FALSE)
Assembly: UCSC hg38
Supplementary files format and content: comma-delimited (CSV) raw counts matrix (cell x gene)

source_name: Flow-sorted NK cells from patient 166, treated with IL-15, IL-21, and IL-12 (All)

growth_protocol: Lonza X-VIVO-15 Serum-free hematopoietic cell medium, with L-Glutamine, gentamicin, and phenol red, and 20% heat inactivated human male AB serum (Peak Serum)

extract_protocol: SureCellTM WTA 3' Library Prep Kit (Illumina, San Diego, CA).

treatment_protocol: IL-15 (20ng/ml) alone or IL-15 (20ng/ml) + IL-21 (50ng/ml) for 6 days. Then on final day add IL-12 (3ng/ml) to IL-15+IL-21 group.

value: PBMC

tag: patient id

value: Natural Killer (NK) Cell

value: Male


title: IL15, rep3, scRNAseq

description: 10X Genomics

source_name: Flow-sorted NK cells from patient 166, treated with IL-15


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=0min_rep1

description:
Library name: sigAb-OV-19
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 0 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: IL15 + IL21 + IL12, rep2, scRNAseq

description: 10X Genomics

source_name: Flow-sorted NK cells from patient 132, treated with IL-15, IL-21, and IL-12 (All)

value: Female


title: Aba_sigAb-overexpression_RNAseq_t=10min_rep2

description:
Library name: sigAb-OV-16
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 10 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: IL15, rep2, scRNAseq

description: 10X Genomics

source_name: Flow-sorted NK cells from patient 132, treated with IL-15


title: IL15 + IL21 + IL12, rep1, scRNAseq

description: 10X Genomics

source_name: Flow-sorted NK cells from patient 124, treated with IL-15, IL-21, and IL-12 (All)


title: IL15, rep1, scRNAseq

description: 10X Genomics

source_name: Flow-sorted NK cells from patient 124, treated with IL-15


title: AcOH_replicate 3-2

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

source_name: HeLa S3

growth_protocol: HeLa S3 cells grown in DMEM with 10% FBS and antibiotics at 37 deg C under 5% CO2

extract_protocol:
Cells were collected in lysis buffer, cleared of debris and lysates were snap frozen with liquid nitrogen and stored at -80 deg C
For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: Cells were treated with Acetate solvent or indicated concentration of GC7 overnight

value: wild type

value: Acetate

value: HeLa S3


title: Aba_sigAb-overexpression_RNAseq_t=10min_rep1

description:
Library name: sigAb-OV-15
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 10 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: Aba_sigAb-overexpression_RNAseq_t=30min_rep2

description:
Library name: sigAb-OV-12
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 30 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: AcOH_replicate 3-1


title: GC7_replicate 3-2

value: 10 µM GC7


title: Aba_sigAb-overexpression_RNAseq_t=30min_rep1

description:
Library name: sigAb-OV-11
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 30 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: AcOH_replicate 2-2


title: AcOH_replicate 2-1


title: Aba_sigAb-overexpression_RNAseq_t=60min_rep1

description:
Library name: sigAb-OV-9
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 60 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: GC7_replicate 2-2


title: Aba_sigAb-overexpression_RNAseq_t=60min_rep2

description:
Library name: sigAb-OV-10
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 60 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: GC7_replicate 3-1


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=10min_rep2

description:
Library name: sigAb-OV-8
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 10 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=10min_rep1

description:
Library name: sigAb-OV-7
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 10 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=20min_rep2

description:
Library name: sigAb-OV-6
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 20 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=20min_rep1

description:
Library name: sigAb-OV-5
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 20 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: GC7_replicate 2-1


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=30min_rep1

description:
Library name: sigAb-OV-3
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 30 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: GC7_replicate 1-1


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=60min_rep2

description:
Library name: sigAb-OV-2
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 60 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: C40_TTchem_DMSO_3

city: Riverside

first: Shiyang

last: He

state: CA

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

institute: UCR

description:
C40_TTchem_DMSO_3
C40_TTchem.raw.count.tsv

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR (v2.7.3a) were used to map the RNA and TTchem sequencing reads to human genome (hg38). Bowtie2 (version 2.4.5) was used to map histone End-seq reads to histone cDNA.
Read counts in each gene (gencode v35) were calculated with featureCounts tools (v2.0.0) from Rsubread package
Non-template tails were analyzed with AppEnD (https://github.com/jw156605/append)
Assembly: UCSC hg38
Supplementary files format and content: tab_delimited raw read count for individual gene in all conditions (RNA-seq and TTchem-seq)
Supplementary files format and content: tab_delimited raw read tail individual histone gene
Library strategy: TTchem-seq

source_name: HEK 293T

growth_protocol: HEK293T  cells were maintained in DMEM supplemented with 10% FBS (Cytiva, SH30910.03) and 100 U/ml Penicillin-Streptomycin (Gibico, 15140122) at 37oC and 5% CO2.

extract_protocol:
Total RNA from aliquots of C40 or N21 cells treated with dTAG or DMSO was extracted using Direct-zol RNA miniprep kit (Zymo Research, R2050) according to the manufacturer’s instructions.
For RNA-seq, total RNA was subjected to one round of enrichment for poly(A)-containing RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490S). N21 RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB E7765S). C40 RNA sequencing libraries were constructed as the Buchbender et. al. 2019.
For TTchem-seq, total RNA was isolated, fragmented, and biotinylated as previous shown (Gregersen et. al. 2020). The biotinylated RNA was enriched using µMACS™ Streptavidin Kit (Miltenyi Biotec, 130-133-282). The enriched RNA was constructed into sequencing library with NEBNext Ultra II Directional RNA Library Prep kit (NEB E7765S).
For histone End-seq, the RNA was ligated to a linker oligonucleotide and reverse-transcribed to cDNA, based on the known 3′ linker sequence. Six rounds of PCR were used to amplify several histone H2A or H3 genes using common, H2A- or H3-specific primers and a linker-specific primer. A second round of PCR was then performed using primers extended by the sequence of Illumina adapters. Histone EnD-seq libraries for each sample were prepared as the protocol introduced by Buchbender et. al. 2019.

treatment_protocol: To induce degron-mediated protein depletion, dTAG-13 (Tocris, 6605) and dTAG-V1 (Tocris, 6914) were dissolved in DMSO and used as a mixture at a final concentration of 500 nM (dTAG-13) and 1000 nM (dTAG-V1) for the indicated periods of time. For Ttchem-seq, C40 cells were treated with dTAG or DMSO and labeled with 1 mM 4SU for 10 min.

value: HEK 293T

value: adenovirus-immortalized human embryonic kidney cells

value: RPP40 degron tag

value: DMSO


title: Aba_sigAb-overexpression_RNAseq_t=20min_rep2

description:
Library name: sigAb-OV-14
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 20 min after IPTG induction; replicate 2
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv

value: bacteria


title: Aba_sigAb-overexpression_RNAseq_t=20min_rep1

description:
Library name: sigAb-OV-13
overexpression RNA-seq; A. baumannii ATCC 17978 SigAb overexpression strain (Ptrc, IPTG inducible); timepoint = 20 min after IPTG induction; replicate 1
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv


title: LU_RAS_KD_D10_WT

description: Library name: Sample8

value: primary fibroblasts cells

value: Immortalized cells by hTERT

value: indece senescent D10,shGATAD2A, shJUN


title: LU_RAS_KD_D10_AA

description: Library name: Sample7


title: C40_TTchem_DMSO_2

description:
C40_TTchem_DMSO_2
C40_TTchem.raw.count.tsv


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=60min_rep1

description:
Library name: sigAb-OV-1
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 60 min after IPTG induction; replicate 1 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv

value: WT 17978 with pJMP3380 (empty vector, kanR)


title: NS_NS_7D_D7

city: Oxford

first: Amélie

middle: M

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

data_processing:
Raw FASTQ files were aligned to the human genome (build GRCh38) and quantified by calling salmon (version 1.10.0) via the txseq pipeline (https://txseq.readthedocs.io/en/latest/index.html).
Salmon counts were imported into R (version 4.3.1) and aggregated at the gene-level using tximeta (version 1.20.3), and drawing from Ensembl version 110 for annotations and transcript to gene conversion.
Tximeta gene-level counts were imported to DESeq2 using DESeq2::DESeqDataSet()
Assembly: GRCh38
Supplementary files format and content: Raw count matrix from DESeq2 object (csv table). Genes with zero count across all samples were excluded.
Supplementary files format and content: Abundance (transcripts per million) count matrix from DESeq2 object (csv table). Genes with zero TPM count across all samples were excluded.

source_name: Peripheral blood monocyte

growth_protocol: Monocytes were plated in 96-well plates at 1 x 105 cells/well in RPMI 1640 (Dutch modified) supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate and 50 µg/mL gentamicin (all reagents from Gibco), and rested for 1h before stimulation

extract_protocol:
Monocytes seeded in 12 well plates (1.09x106 cells.well) were isolated and stimulated as described above and RNA was isolated after stimulation using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions
QC and sequencing of RNA samples were performed by Novogene Europe. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Primary stimulation (PRIME) was performed by addition of stimuli into the serum free medium. For the 7D Protocol, medium was collected after priming for 24 hours, cells were washed in PBS and left to rest in medium supplemented with 10% human serum for 5 days.  After resting, medium was collected before addition of the secondary stimulus (TRIGGER) in medium containing 10% human serum for 4 hours. For the 24 hours protocol, medium was collected after priming for 24 hours, cells were washed in PBS and immediately restimulated by addition of the secondary stimulus (TRIGGER) in medium containing 10% human serum for 2 hours.                                                             Cell stimuli were used at the following concentrations: LPS (100 ng/mL for PRIME, 10 ng/ml for TRIGGER), FBG-C (1 µM), POLY-I:C (10 ug/ml), Tris/Nacl buffer was used as vehicle treatment (VEH), which is the same buffer a used for storage of FBG-C.                                                                                Treatment in the above table (treatment colum) is specified as treatment given as PRIME/TRIGGER.

value: Peripheral blood monocyte

tag: donor

tag: resting time

value: 5 days

value: NS/NS


title: LPS_FBG_7D_D7

value: LPS/FBG


title: C40_TTchem_DMSO_1

description:
C40_TTchem_DMSO_1
C40_TTchem.raw.count.tsv


title: C40_TTchem_3h_3

description:
C40_TTchem_3h_3
C40_TTchem.raw.count.tsv

value: dTAG 3h


title: Aba_sigAb_ChIP_HaloTag1

description: Library name: EB-HT-1

data_processing:
ChIP-seq paired end FASTQ files were filtered to remove low quality bases using Trimmomatic (v0.3) (Sliding window of 3:30, Minimum length of 36 bp, leading and trailing both a value of 3) and aligned to the Acinetobacter baumannii ATCC 17978 genome (GCA_001077675.1) using Bowtie2 (v2.2.2) and default parameters.
Samtools (v1.2) and Picard Tools (v1.98) were used to convert the SAM file to a sorted BAM file. Deeptools (v3.5.1) was used to generate IP vs INPUT ratio files for visualization (binsize of 1 and readCount scaleFactorsMethod).
ChIP-seq peaks were identified with the IP and INPUT BAM files using MACS3 (v3.0.0) with default parameters except for using the “nomodel” option and 128 for the “extsize” and all for the “keep-dup” values.
Assembly: GCA_001077675.1
Supplementary files format and content: bigWig

growth_protocol: Cells were grown shaking at 37°C in 100 mL AbRDM + 70µM IPTG + kanamycin to maintain the plasmid until reaching mid-log (~OD 0.3). AbRDM is Teknova EZ RDM media supplemented with succinate instead of glucose.

extract_protocol:
Cultures were crosslinked with formaldehyde, quenched with glycine, and 50 mL cell pellets were harvested. Pellets were sonicated in a Covaris Misonix sonicator for 16 min (20% duty factor, 75 PIP, 200 cycles per burst, 6°C) to achieve ~100-500 bp fragments and immunoprecipitation of HaloTagged-SigAb protein was performed according to Promega HaloChIP protocol. Before IP, 1/10 of each sample was saved as input control.
Input control and HT-enriched samples were prepared for Illumina sequencing using NEBNext Ultra II Library Prep Kit for Illumina (NEB; E7645S) following manufacturer’s protocol.

value: sigAb-HaloTag


title: VEH_FBG_7D_D7

value: VEH/FBG


title: C40_TTchem_3h_1

description:
C40_TTchem_3h_1
C40_TTchem.raw.count.tsv


title: NS_FBG_7D_D7

value: NS/FBG


title: Aba_sigAb_ChIP_HaloTag3

description: Library name: EB-HT-3


title: AcOH_replicate 1

value: wild type

value: Acetate

value: HeLa S3


title: FBG_PIC_7D_D7

value: FBG/PIC


title: C40_TTchem_24h_3

description:
C40_TTchem_24h_3
C40_TTchem.raw.count.tsv

value: HEK 293T

value: adenovirus-immortalized human embryonic kidney cells

value: RPP40 degron tag

value: dTAG 24h


title: VEH_PIC_7D_D7

value: VEH/PIC


title: C40_TTchem_24h_2

description:
C40_TTchem_24h_2
C40_TTchem.raw.count.tsv


title: LPS_LPS_7D_D7

value: Peripheral blood monocyte

value: LPS/LPS


title: Aba_sigAb_ChIP_input1

description: Library name: EB-IN-1

value: bacteria


title: VEH_LPS_7D_D7

value: 5 days

value: VEH/LPS


title: Aba_sigAb_ChIP_input2

description: Library name: EB-IN-2

value: sigAb-HaloTag


title: NS_NS_7D_D4

value: NS/NS


title: Aba_sigAb_ChIP_HaloTag2

description: Library name: EB-HT-2


title: Aba_empty-vector_compare-to-sigAb-samples_RNAseq_t=30min_rep2

description:
Library name: sigAb-OV-4
overexpression RNA-seq; A. baumannii ATCC 17978 EMPTY VECTOR control strain; timepoint = 30 min after IPTG induction; replicate 2 for comparison with sigAb data
20231228_SigAb-OE_FPKM-results.csv
20231228_SigAb-OE_HTseq-counts.csv

value: WT 17978 with pJMP3380 (empty vector, kanR)


title: FBG_FBG_7D_D7

value: FBG/FBG


title: NS_NS_7D_D3


title: NS_LPS_7D_D7

value: NS/LPS


title: H3_DMSO_3

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR (v2.7.3a) were used to map the RNA and TTchem sequencing reads to human genome (hg38). Bowtie2 (version 2.4.5) was used to map histone End-seq reads to histone cDNA.
Read counts in each gene (gencode v35) were calculated with featureCounts tools (v2.0.0) from Rsubread package
Non-template tails were analyzed with AppEnD (https://github.com/jw156605/append)
Assembly: UCSC hg38
Supplementary files format and content: tab_delimited raw read count for individual gene in all conditions (RNA-seq and TTchem-seq)
Supplementary files format and content: tab_delimited raw read tail individual histone gene
Library strategy: Histone End-seq

value: DMSO


title: GC7_replicate 1-2

value: wild type

value: 10 µM GC7

value: HeLa S3


title: NS_NS_7D_D1


title: H3_DMSO_2

value: HEK 293T

value: adenovirus-immortalized human embryonic kidney cells

value: RPP40 degron tag


title: S26_Lung_PM25

city: Beijing

first: Guoqing

last: Feng

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

description:
Library name: Sample26
batch2_raw.h5ad
batch2_normalized.h5ad

data_processing:
The raw sequencing data were preprocessed and analyzed by the Cell Ranger Single-Cell Software Suite (v. 5.0.1) with default settings. The reads were aligned to the mouse reference genome (mm10). Seurat (version 5.1.0) was utilized for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: Raw count matrix: batch1_raw.h5ad, batch2_raw.h5ad
Supplementary files format and content: Normalized count matrix: batch1_normalized.h5ad, batch2_normalized.h5ad

organism: Mus musculus

source_name: Lung

extract_protocol:
Fresh lung tissue of mice was cleaned with sterile as well as cold PBS, and was placed in a tissue preservation solution for isolation.
Isolated total lung cells were pooled and processed using the Chromium Single Cell 3' Reagent Kits v3 (10x Genomics, Pleasanton, CA, USA). The single-cell libraries was also prepared using the DNBelab C Series Single-Cell Library Prep Set and sequenced on a BGISEQ500 sequencer.

value: Lung

tag: group

tag: strain

tag: batch


title: NS_NS_7D_D2

value: Peripheral blood monocyte


title: LPS_FBG_7D_D4

value: LPS/FBG


title: S25_Lung_PM25

description:
Library name: Sample25
batch2_raw.h5ad
batch2_normalized.h5ad


title: C40_TTchem_24h_1

description:
C40_TTchem_24h_1
C40_TTchem.raw.count.tsv

value: dTAG 24h


title: LPS_FBG_7D_D3

value: 5 days


title: S23_Lung_PM25

description:
Library name: Sample23
batch2_raw.h5ad
batch2_normalized.h5ad


title: FBG_LPS_7D_D7

value: FBG/LPS


title: H3_DMSO_1


title: FBG_FBG_7D_D4


title: LPS_FBG_7D_D1


title: S24_Lung_PM25

description:
Library name: Sample24
batch2_raw.h5ad
batch2_normalized.h5ad


title: H3_3h_3

value: dTAG 3h


title: LPS_FBG_7D_D2


title: FBG_FBG_7D_D3


title: FBG_FBG_7D_D2


title: H3_3h_2


title: S22_Lung_PM25

description:
Library name: Sample22
batch2_raw.h5ad
batch2_normalized.h5ad


title: VEH_FBG_7D_D4

value: VEH/FBG


title: FBG_FBG_7D_D1

value: FBG/FBG


title: H3_3h_1


title: VEH_FBG_7D_D3


title: S21_Lung_PM25

description:
Library name: Sample21
batch2_raw.h5ad
batch2_normalized.h5ad


title: Aba_sigAb_ChIP_input3

description: Library name: EB-IN-3

value: bacteria

value: sigAb-HaloTag


title: VEH_FBG_7D_D1


title: S20_Lung_PM25

description:
Library name: Sample20
batch2_raw.h5ad
batch2_normalized.h5ad


title: FBG_PIC_7D_D4

value: FBG/PIC


title: S19_Lung_PM25

description:
Library name: Sample19
batch2_raw.h5ad
batch2_normalized.h5ad


title: H3_24h_1


title: H3_24h_3


title: VEH_FBG_7D_D2


title: FBG_PIC_7D_D3


title: S18_Lung_Control

description:
Library name: Sample18
batch2_raw.h5ad
batch2_normalized.h5ad

value: Control


title: FBG_PIC_7D_D2


title: FBG_PIC_7D_D1


title: VEH_PIC_7D_D4

value: VEH/PIC


title: H2A_DMSO_4

value: HEK 293T

value: DMSO


title: S17_Lung_Control

description:
Library name: Sample17
batch2_raw.h5ad
batch2_normalized.h5ad


title: VEH_PIC_7D_D1


title: VEH_PIC_7D_D3


title: VEH_PIC_7D_D2


title: H2A_DMSO_3

value: adenovirus-immortalized human embryonic kidney cells

value: RPP40 degron tag


title: NS_FBG_7D_D4

value: Peripheral blood monocyte

value: NS/FBG


title: H2A_DMSO_2


title: NS_FBG_7D_D3


title: S15_Lung_Control

description:
Library name: Sample15
batch2_raw.h5ad
batch2_normalized.h5ad

value: Lung


title: S14_Lung_Control

description:
Library name: Sample14
batch2_raw.h5ad
batch2_normalized.h5ad


title: H3_24h_2

value: dTAG 24h


title: H2A_3h_3


title: NS_FBG_7D_D1

value: 5 days


title: H2A_DMSO_1


title: S13_Lung_Control

description:
Library name: Sample13
batch2_raw.h5ad
batch2_normalized.h5ad


title: FBG_LPS_7D_D3

value: FBG/LPS


title: FBG_LPS_7D_D2


title: NS_FBG_7D_D2


title: S12_Lung_Control

description:
Library name: Sample12
batch2_raw.h5ad
batch2_normalized.h5ad


title: FBG_LPS_7D_D1


title: FBG_LPS_7D_D4


title: H2A_3h_2

value: dTAG 3h


title: S11_Lung_Control

description:
Library name: Sample11
batch2_raw.h5ad
batch2_normalized.h5ad


title: H2A_3h_1


title: LPS_LPS_7D_D3

value: LPS/LPS


title: S16_Lung_Control

description:
Library name: Sample16
batch2_raw.h5ad
batch2_normalized.h5ad


title: LPS_LPS_7D_D4


title: H2A_24h_4


title: LPS_LPS_7D_D2


title: LPS_LPS_7D_D1


title: S10_Lung_PM25

description:
Library name: Sample10
batch2_raw.h5ad
batch2_normalized.h5ad


title: NS_LPS_7D_D4

value: NS/LPS


title: S9_Lung_PM25

description:
Library name: Sample9
batch2_raw.h5ad
batch2_normalized.h5ad


title: NS_LPS_7D_D3


title: H2A_24h_3


title: S8_Lung_PM25

description:
Library name: Sample8
batch2_raw.h5ad
batch2_normalized.h5ad


title: NS_LPS_7D_D2


title: H2A_24h_2


title: H2A_24h_1


title: NS_LPS_7D_D1


title: N21_RNA_DMSO_3

description:
N21_RNA_DMSO_3
N21_RNA.raw.count.tsv

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR (v2.7.3a) were used to map the RNA and TTchem sequencing reads to human genome (hg38). Bowtie2 (version 2.4.5) was used to map histone End-seq reads to histone cDNA.
Read counts in each gene (gencode v35) were calculated with featureCounts tools (v2.0.0) from Rsubread package
Non-template tails were analyzed with AppEnD (https://github.com/jw156605/append)
Assembly: UCSC hg38
Supplementary files format and content: tab_delimited raw read count for individual gene in all conditions (RNA-seq and TTchem-seq)
Supplementary files format and content: tab_delimited raw read tail individual histone gene

value: RPP21 degron tag


title: VEH_LPS_7D_D3

value: VEH/LPS


title: S7_Lung_PM25

description:
Library name: Sample7
batch2_raw.h5ad
batch2_normalized.h5ad


title: VEH_LPS_7D_D4


title: S6_Lung_Control

description:
Library name: Sample6
batch2_raw.h5ad
batch2_normalized.h5ad

value: Control


title: VEH_LPS_7D_D2


title: FBG_LPS_24H_D7

value: 24 hours


title: VEH_LPS_7D_D1


title: N21_RNA_DMSO_2

description:
N21_RNA_DMSO_2
N21_RNA.raw.count.tsv

value: HEK 293T


title: S5_Lung_Control

description:
Library name: Sample5
batch2_raw.h5ad
batch2_normalized.h5ad


title: LPS_LPS_24H_D7


title: NS_LPS_24H_D7


title: N21_RNA_DMSO_1

description:
N21_RNA_DMSO_1
N21_RNA.raw.count.tsv

value: DMSO


title: VEH_LPS_24H_D7


title: S3_Lung_Control

description:
Library name: Sample3
batch2_raw.h5ad
batch2_normalized.h5ad


title: N21_RNA_3h_3

description:
N21_RNA_3h_3
N21_RNA.raw.count.tsv

value: adenovirus-immortalized human embryonic kidney cells


title: S2_Lung_PM25

description:
Library name: Sample2
batch1_raw.h5ad
batch1_normalized.h5ad


title: NS_NS_24H_D4

value: NS/NS


title: N21_RNA_3h_2

description:
N21_RNA_3h_2
N21_RNA.raw.count.tsv


title: NS_NS_24H_D3

value: Peripheral blood monocyte


title: NS_NS_24H_D1


title: N21_RNA_3h_1

description:
N21_RNA_3h_1
N21_RNA.raw.count.tsv


title: NS_NS_24H_D2


title: S1_Lung_Control

description:
Library name: Sample1
batch1_raw.h5ad
batch1_normalized.h5ad


title: N21_RNA_24h_3

description:
N21_RNA_24h_3
N21_RNA.raw.count.tsv


title: FBG_LPS_24H_D4


title: FBG_LPS_24H_D1


title: NS_NS_24H_D7


title: N21_RNA_24h_2

description:
N21_RNA_24h_2
N21_RNA.raw.count.tsv


title: LPS_LPS_24H_D1


title: LPS_LPS_24H_D3


title: FBG_LPS_24H_D2


title: C40_RNA_DMSO_3

description:
C40_RNA_DMSO_3
C40_RNA.raw.count.tsv

value: RPP40 degron tag


title: FBG_LPS_24H_D3


title: S4_Lung_Control

description:
Library name: Sample4
batch2_raw.h5ad
batch2_normalized.h5ad

value: Lung


title: N21_RNA_24h_1

description:
N21_RNA_24h_1
N21_RNA.raw.count.tsv

value: dTAG 24h


title: C40_RNA_DMSO_2

description:
C40_RNA_DMSO_2
C40_RNA.raw.count.tsv


title: NS_LPS_24H_D3


title: NS_LPS_24H_D2


title: NS_LPS_24H_D4


title: VEH_LPS_24H_D4


title: LPS_LPS_24H_D2


title: NS_LPS_24H_D1


title: C40_RNA_3h_3

description:
C40_RNA_3h_3
C40_RNA.raw.count.tsv


title: C40_RNA_DMSO_1

description:
C40_RNA_DMSO_1
C40_RNA.raw.count.tsv


title: LPS_LPS_24H_D4


title: VEH_LPS_24H_D3


title: VEH_LPS_24H_D2


title: C40_RNA_3h_2

description:
C40_RNA_3h_2
C40_RNA.raw.count.tsv


title: VEH_LPS_24H_D1


title: C40_RNA_3h_1

description:
C40_RNA_3h_1
C40_RNA.raw.count.tsv


title: Natural and artificial sequences, DMS treated sample, 5mM Mg, 1mM SAM, replicate 0

city: Paris

first: Pierre

last: HARDOUIN

state: France

address: 4 avenue de l'observatoire

department: CiTCoM

country: France

institute: Faculté de pharmacie UMR 8038

description:
Library name: SAMAP_Lib3_152Natural_248Artificial_DMS_replicate0
dsDNA library, 152 SAM-I aptamer natural sequences and 248 Artificial sequences

library_source: other

data_processing:
The demultiplexing is made using cutadapt. (https://cutadapt.readthedocs.io/en/stable/)
Quality trimming, Paired read merging, Sequence alignment, Mutation identification, Mutation counting, Sequence correction, reactivity profile calculation were made by using Shapemapper 2 (https://github.com/Weeks-UNC/shapemapper2)
Supplementary files format and content: Tab-separated values files

molecule: other

organism: Bacteria

source_name: Eubacteria

extract_protocol: RNAs were in vitro transcribed, modified with SHAPE reagent and reverse transcribed with the Superscript III reverse transcriptase (Invitrogen®) and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs®) as manufacter’s instructions.

value: Eubacteria


title: Natural and artificial sequences, DMS denaturated sample, with Mg, without SAM, replicate 0

description:
Library name: SAMAP_Lib4_152Natural_248Artificial_DMS_replicate0
dsDNA library, 152 SAM-I aptamer natural sequences and 248 Artificial sequences


title: Natural and artificial sequences, Untreated sample, Ethanol, replicate 0

description:
Library name: SAMAP_Lib1_152Natural_248Artificial_DMS_replicate0
dsDNA library, 152 SAM-I aptamer natural sequences and 248 Artificial sequences


title: C40_RNA_24h_2

description:
C40_RNA_24h_2
C40_RNA.raw.count.tsv


title: Plasma cfDNA, Sample E

city: Boston

first: Alec

last: Eames

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Library name: Sample E
SMRT Sequencing

data_processing:
Raw subreads were converted to high-accuracy circular consensus sequences (CCS) using PacBio SMRT Tools (v12.0) ccs tool with the --hifi-kinetics flag enabled to retain kinetic signals for subsequent methylation calling.
Samples were demultiplexed using lima along with each sample's barcode
CpG methylation information was extracted from kinetic signals using primrose.
CCS reads were aligned to the human reference genome (hg19) using pbmm2 align under the CCS preset.
Methylation calls were converted to BED format using pb-CpG-tools v2.3.1 with a minimum coverage of 1 and in pileup mode set to count.
Assembly: hg19
Supplementary files format and content: Processed data are BED files for each sample, containing CpG methylation calls

source_name: Plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted from 7–8 mL of plasma using Qiagen’s QIAamp Circulating Nucleic Acid Kit following the manufacturer’s protocol. DNA concentration and genomic DNA contamination were assessed with the Agilent TapeStation 4150 using the cfDNA ScreenTape Assay. Size selection was performed using Zymo’s Select-a-Size MagBead Kit to enrich for longer fragments.
cfDNA was treated with RNase and concentrated using 3X AMPure Beads. Libraries were prepared using the SMRTbell Template Prep Kit 3.0 (Pacific Biosciences), barcoded, pooled (2–3 samples per pool), and bound to polymerase with the Sequel II Binding Kit 3.2. Libraries were sequenced using SMRT Cell 8M on the PacBio Sequel II system with 30-hour movie times.

value: Plasma

value: Female


title: Natural and artificial sequences, DMS treated sample, 5mM Mg, without SAM, replicate 0

description:
Library name: SAMAP_Lib2_152Natural_248Artificial_DMS_replicate0
dsDNA library, 152 SAM-I aptamer natural sequences and 248 Artificial sequences


title: Combo18-NR-2

type: RNA

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

description: post-treatment

hyb_protocol: cRNA was hybridized to Clariom D Assay human array (Thermofisher), washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Thermo Fisher Expression Console 1.4.1 software, and obtained normalized intensity values.

label: biotin

source_name: Peripheral blood, CD8+ sorted

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit (ThermoFisher) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

value: Blood

value: PBMC CD8+T cells

tag: phenotype

value: NR

value: nivolumab and bezafibrate

tag: time

value: post-treatment


title: Combo18-NR-1

description: pre-treatment

tag: treatment

value: untreated

value: pre-treatment


title: Combo16-R-1

description: pre-treatment

tag: tissue

value: R


title: Combo16-R-2

description: post-treatment


title: Combo17-NR-1

description: pre-treatment


title: Plasma cfDNA, Sample C

description:
Library name: Sample C
SMRT Sequencing

tag: age

value: Male


title: Combo15-NR-2

description: post-treatment


title: Plasma cfDNA, Sample A

description:
Library name: Sample A
SMRT Sequencing

tag: Sex


title: Plasma cfDNA, Sample B

description:
Library name: Sample B
SMRT Sequencing


title: WT2_R1,WT.2,Day12

city: Izmir

first: Mustafa

last: Karabicici

address: Mithatpasa Cad. 58/5 Balcova, Izmir/TURKEY

department: Molecular Biology and Genetic

country: Turkey

institute: Dokuz Eylul University(Izmır Biomedicine and Genome Center)

description: Sample 4

data_processing:
Illumina Stranded mRNA Prep kit standart procedure : 1000000124518 v02 was used for RNA libraries
The GRCh38 human reference genome, also known as hg38, and its associated reference annotation (version 42) in the Gene Transfer Format (GTF) were downloaded from the official website of GENCODE project, which can be accessed at https://www.gencodegenes.org/. To align the raw sequencing reads to the human reference genome, we utilized the R-package Subread aligner (v2.0) (Liao et al., 2019) with the following command: subread-align -t 0 -i {index} -T 16 -r {input 1.fastq.gz} -R {input 2.fastq.gz} -o {output.bam}. Subsequently, we employed the featureCounts function (Liao et al., 2013) from the R package to count the number of reads overlapping with GENCODE-annotated genes. In this step, the following command was executed: featureCounts(files = {infile. bam}, annot.ext = “{infile. gtf}”, is GTF AnnotationFile = T, GTF.featureType = “exon”, GTF.attrType = “gene_id”, countMultiMappingReads = T, isPairedEnd = T).
Fragments per kilobase million (FPKM) values were then computed for each gene across all samples. To enhance the detection sensitivity of differentially expressed gene features, we applied a filter to include genes with mean expression values greater than or equal to one FPKM in both control and B4 (TP53KO) groups.
The filtered count matrices were subsequently employed for the differential expression analysis to identify genes with varying expression levels between the control and B4 groups. This analysis was performed using the EdgeR package (v3.40.2) (Robinson et al., 2009) within the R environment.
Trimmed mean of M-values (TMM) normalization (Robinson & Oshlack, 2010) was applied to the count values, and dispersions were estimated using the estimateDisp function for each comparison. To calculate the false discovery rate (FDR) for each gene, we utilized the exactTest function of edgeR.
Assembly: GRCh38 human reference genome, also known as hg38 version 42s
Supplementary files format and content: Commo-deliminated text file includes raw counts for each Sample
Supplementary files format and content: Commo-deliminated text file includes FPKM for each Sample

source_name: iPSC derived organoids

growth_protocol: WT and TP53KO organoids growth in EM and DM medium. EM medium: AdDMEM F12 (Gibco) which containing 100 ng/mL fibroblast growth factor 10 (FGF10), 25 ng/mL hepatocyte growth factor (HGF), 10 mM nicotinamide, 5 μM A83.01 and 10 μM forskolin 1% B27, 1.25 mM N-acetylcysteine, 10 nM gastrin, 50 ng/mL epidermal growth factor (EGF), 10% R-spo1 CM.  DM medium: AdDMEM/F12 with 1% B27, EGF (50 ng/mL), gastrin (10 nM), HGF (25 ng/mL), FGF19 (100 ng/mL), A8301 (500 nM), DAPT ( 10 μM), BMP7 (25 ng/mL), 25 ng/ml BMP7 and dexamethasone (30 μM)

extract_protocol:
RNA isolated by RNeasy Plus Mini Kit (Cat. No. / ID: 74134). For the sequencing ~1.5 ug total RNA was used for construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit (Illumina, ABD, #20040534).

treatment_protocol: No spesific treatment. Organoids at day12 in DM medium collected for analysis.

tag: source

value: İPSC

tag: cell type

value: iPSC derived organoids

value: WT

value: DM


title: C40_RNA_24h_3

description:
C40_RNA_24h_3
C40_RNA.raw.count.tsv

tag: cell line

value: HEK 293T

value: adenovirus-immortalized human embryonic kidney cells

tag: genotype

value: RPP40 degron tag

value: dTAG 24h


title: Combo14-NR-2

description: post-treatment

value: Blood


title: Combo14-NR-1

description: pre-treatment

value: PBMC CD8+T cells


title: WT1_R1,WT.1,Day12

description: Sample 3


title: Capture 1

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
Library name: G000272_1
All samples, capture 1

data_processing:
All samples were captured over 2 batches.
FastQ files were first prepared using bcl2fastq (v2.19.1) and then passed through cellranger multi (v7.0.0) using the Pool lab scRNA-seq optimized transcriptomic references (Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data. Allan-Hermann Pool, Helen Poldsam, Sisi Chen, Matt Thomson, Yuki Oka bioRxiv 2022.04.26.489449) to generate gene level counts
Droplets containing cells were distinguished from empty droplets using the emptyDrops function from the DropletUtils package (v1.24.0)
The data was then demultiplexed using the demuxmix package (v1.6.0)
Assembly: mm38
Supplementary files format and content: Tab separated files containing barcode, features, and matrix for each capture

source_name: Small intestine

extract_protocol:
Small intestine were digested and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted .
After sorting the samples were labelled with hashtags and TotalSeq-A universal antibody panel (Biolegend protocol) then captured on 2x 3'HT lanes and processed according to the 10X Chromium NextGEM Single Cell 3'-HT protocol

value: Small intestine

tag: cell population

value: CD45+ cells


title: WT_3 [WT_3]

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

description:
WT_3
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx

data_processing:
RNA-Seq : Reads were aligned to the mouse genome (GRCm38) using HISAT2.  Bam files were generated from fastq files using SeqMonk.
Principal component analysis was performed with the 300 most variant genes, using Pcaexplorer.
Differentially expressed genes (DEGs) were determined using DESeq2
Metascape analysis was performed using DEGs
Gene set enrichment analysis was performed by using GSEA software.
Assembly: GRCm38
Supplementary files format and content: Normalised counts were generated from the Bam files.

source_name: ES cells (mESCs)

extract_protocol:
RNA-Seq : RNA was harvested from ES cells using Trizol reagent.
RNA-Seq samples were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina NextSeq2000 sequencer, generating paired-end clusters of 50 bases in length

value: ES cells (mESCs)

value: Wild type


title: WT_2 [WT_2]

description:
WT_2
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: Plasma cfDNA, Sample D

description:
Library name: Sample D
SMRT Sequencing

value: Plasma


title: C40_RNA_24h_1

description:
C40_RNA_24h_1
C40_RNA.raw.count.tsv


title: B4-2,P53KO.2,Day12

description: Sample 2


title: Combo17-NR-2

description: post-treatment

value: NR

value: nivolumab and bezafibrate

value: post-treatment


title: Combo15-NR-1

description: pre-treatment

value: untreated

value: pre-treatment


title: B4-1, P53KO.1,Day12

description: Sample 1

value: İPSC

value: iPSC derived organoids

value: DM


title: Capture 2

description:
Library name: G000272_2
All samples, capture 2


title: E5_2 [KO2_2]

description:
KO2_2
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx

value: Kif2a knockout


title: E5_1 [KO2_1]

description:
KO2_1
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: Combo13-R-2

description: post-treatment

value: R


title: eWAT_3_Fgf13_Ko

city: Iowa city

first: Bhagirath

last: Chaurasia

state: Iowa

address: 431 Newton Road

institute: University of Iowa

description:
Library name: eWAT_Sample 6
eWAT_fpkm_values.csv

data_processing:
Salmon was used for mapping and quantifying the expression of transcripts from RNA-seq data.
FastQC and MultiQC were used to check the quality of RNA sequencing data
Differential gene expression analysis was performed on the raw counts after removing the samples with zero counts using the DESeq2 (version 1.38.3)
Assembly: mm32
Supplementary files format and content: Comma Separated Values (CSV) file for FPKM of each sample

source_name: Epididymal white adipose tissue

extract_protocol:
RNA was extracted from the adipose tissue (epididymal white, subcutaneous and brown adipose) using Qiagen RNAeasy mini kit.
1 ug of RNA was used for constructing sequencing libraries. Sequencing was performed by Illumina HiSeq2000 with 50 cycle single/paired end sequencing

value: Epididymal white adipose tissue

value: Fgf13 KO


title: C5_2 [KO1_2]

description:
KO1_2
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: WT_1 [WT_1]

description:
WT_1
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: C5_1 [KO1_1]

description:
KO1_1
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: eWAT_2_Fgf13_Ko

description:
Library name: eWAT_Sample 5
eWAT_fpkm_values.csv


title: Combo12-R-2

description: post-treatment

value: Blood

value: PBMC CD8+T cells


title: eWAT_1_Fgf13_Ko

description:
Library name: eWAT_Sample 4
eWAT_fpkm_values.csv


title: K-562 Smart-seq3xpress uBAM

city: Grand Rapids

first: Benjamin

middle: K

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description:
Library name: Sample7
Smart-seq3xpress uBAM of K-562

data_processing:
Unmapped Smart-seq3xpress (SS3x) HEK293T and K-562 BAM files were demultiplexed to individual cell FASTQ files by extracting reads assigned to expected cell barcodes in the CB BAM tag (concatenation of i5 and i7 indices, yielding a 20 bp barcode) and appending conserved sequences to delineate internal and 5’ UMI containing reads. Briefly, to reconstruct the expected 4 FASTQs per cell file structure, cell barcodes (CB BAM tag) were added to index 1 and index 2 FASTQ files, and respective read 1 and read 2 reads to separate FASTQ files. If the UB BAM tag (UMI) was populated, the conserved ‘ATTGCGCAATG’ sequence motif was added, then the UMI (UB tag), followed by the ‘GGG’ motif. Internal and 5’ UMI containing reads from SS3x were separated as previously described, using the conserved ‘ATTGCGCAATG’ sequence motif at the start of read 1 to delineate 5’ UMI reads. VASA-seq data were demultiplexed to single cell FASTQ files using provided scripts from https://github.com/hemberg-lab/VASAseq_2022. Scripts for STORM-seq de-multiplexing from GEO/SRA/ENA FASTQs can be found at https://github.com/biobenkj/stormseq_protocols/tree/main/analysis/stormseq_manuscript/demux_storm.
VASA-seq data were pre-processed and trimmed using cutadapt (v4.4) through provided scripts at https://github.com/hemberg-lab/VASAseq_2022. After trimming, the UMI and cell barcode were appended to the 5’ end of the read. Importantly, in the provided concatenator.py, a conversion error occurs when extracting and appending the UMI and cell barcode where a base quality score of 14 (ASCII character ‘/’) is unintentionally converted to a base quality score of 46 (ASCII character ‘O’). As a result, during the addition of the UMI and cell barcode to the 5’ end of the read, these base qualities were reverted to their original value.
All subsampling was performed using seqtk (v1.4-r122) sample on pre-processed/trimmed reads across technologies, setting the random seed to 100, unless specified otherwise.
STORM-seq HEK293T, K-562, and RMG-2 reads were mapped and quantified at the gene and transcript isoform level using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) and kb_python (v0.28.2) with the -x STORM-seq preset. For transcript isoform quantification, kb_python was called with the --tcc option enabled to output transcript compatibility counts (TCC). TCCs were quantified using kallisto quant-tcc to produce transcript isoform level counts. Further, fragment length bias was accounted for in quant-tcc as well as including at least 50 bootstraps for gene/transcript isoform quantification. Per-cell mapping rates were extracted from the log files.
Passage matched (for direct comparison to STORM-seq) K-562 and HEK293T VASA-seq data generated by Single Cell Discoveries were mapped and quantified against Ensembl 101 using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) following the kb_python analysis toolchain, with modifications to support this data type. Briefly, kallisto bus was used with default parameters and 1) -x 0,6,8:0,0,6:0,14,0, 2) --fr-stranded. Next, bus files were sorted (bustools sort), inspected (bustools inspect), and counted (bustools count). For bustools count, default parameters were used with the following modifications, 1) --multimapping, 2) --umi-gene. Next, kallisto quant-tcc was used to quantify transcript abundance with default parameters and 1) -t 8, 2) -l 550, 3) -s 300, 4) -b 50, and 5) --matrix-to-files. The average fragment length and standard deviation parameters were specified based on VASA-seq bioanalyzer traces provided (Supp. Fig. 19). Per-cell mapping rates were extracted from the log files.
HEK293T and K-562 pre-processed SS3x FASTQs were mapped and quantified using a similar strategy as VASA-seq, using kallisto|bustools. Briefly, per-cell 5’ UMI reads and internal reads were extracted as described above, prior to subsampling and mapping/quantification. Next, for gene/transcript quantification, kallisto bus was used with 5’ UMI reads with default parameters and the following modifications, 1) -x 0,0,0,1,0,0:2,0,21:2,24,0,3,0,0, 2) --tag ATTGCGCAATG, 3) --paired, 4) --fr-stranded, and 5) -t 8. Transcript abundance quantification was performed using kallisto quant-tcc with default parameters and the following modifications 1) -b 50 and 2) --matrix-to-files.
Assembly: GRCh38 (Ensembl 101)
Supplementary files format and content: Text file STORM-seq metadata for demultiplexing
Supplementary files format and content: Text files of raw UMI counts with multimappers from kallisto|bustools using Ensembl 101 annotations

growth_protocol: The K-562 cell line was purchased from ATCC (CCL-243). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/Streptomycin (Gibco). HEK293T cells were purchased from the American Type Culture Collection (ATCC; CRL-3216) and cultured in DMEM medium supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin/Streptomycin (Gibco). RMG-2 cells were purchased from the JCRB Cell Bank and Seikiusi XenoTech, LLC. RMG-2 cells were maintained in DMEM/F12, supplemented with 10% FBS and sub-cultured at 1:3-1:5 every 7-9 days. Fresh media was added every 2-3 days between sub-culturing.

extract_protocol:
Single cells were deposited in a 384-well plate using a BD FACSymphony S6 equipped with a 130 um nozzle at 14 psi. Single cells were lysed in their respective lysis buffer (e.g., STORM-seq, VASA-seq, or Smart-seq3xpress). Passage matched K-562 and HEK293T cells were deposited same day for both STORM-seq and VASA-seq.
Libraries were constructed as previously described for Smart-seq3xpress (https://doi.org/10.1038/s41587-022-01311-4) or by Single Cell Discoveries following the VASA-seq protocol (https://www.scdiscoveries.com/services/vasa-seq/; https://doi.org/10.1038/s41587-022-01361-8). For STORM-seq, libraries were constructed following https://doi.org/10.5281/zenodo.15178455.


title: Combo12-R-1

description: pre-treatment


title: Combo13-R-1

description: pre-treatment


title: K-562 Smart-seq3xpress

description:
Library name: Sample6
Smart-seq3xpress re-multiplexed from uBAM of K-562


title: eWAT_3_Control

description:
Library name: eWAT_Sample 3
eWAT_fpkm_values.csv

value: WT


title: eWAT_2_Control

description:
Library name: eWAT_Sample 2
eWAT_fpkm_values.csv


title: A2-CAR Tconv, donor 1130

city: Vancouver

first: Megan

last: Levings

state: BC

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

description: Library name: 30-Tconv

data_processing:
Sequencing data was demultiplexed using llumina's BCL Convert.
The de-multiplexed read sequences were then aligned to the Homo sapiens (hg38 no Alts, with decoys) reference sequence and a custom exogenous IL10 sequence using the DRAGEN RNA pipeline.
Immunoglobulin gene segments, pseudo genes, sex-linked genes (Y-chromosome & Xist), and genes aligned to virally-inserted sequences (CAR, tNGFR, and tCD19) were filtered out as well as genes with < 10 counts across samples.
Differential expression analysis was performed using DESeq2 in R.
Gene annotation was obtained by AnnotationDbi package and visualization with ggplot2, RColorBrewer, pheatmap and EnhancedVolcano.
Assembly: Homo sapiens (hg38 no Alts, with decoys) reference sequence and a custom exogenous IL10 sequence.
Supplementary files format and content: Excel spreadsheet for all 15 samples (mlevings_PD1koIL10ki_total counts.xlsx), raw counts were generated using the counts produced by DRAGEN RNA and were corrected using the tximport function in R.

source_name: Tconv

growth_protocol:
A2-CAR Tregs: (Day 0) Naive Tregs were flow-sorted (CD4+CD25hiCD127loCD45RA+CD45RO-) and stimulated with artificial antigen presenting cells (L cells), anti-CD3, and 1000 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were CRISPR-edited using AAV6-mediated homology directed repair, to generate Cas9 alone controls, PD1KO cells, and PD1KOIL10KI cells (referred to as IL10KI). Cells were restimulated with A2+ L cells, then (Day 12) PD1KO and IL10KI CAR-Tregs were bead-purified by positive selection of a truncated CD19 reporter (tCD19). All CAR-Tregs were rested overnight in low (100 IU/mL) IL-2. (Day 13) CAR-Tregs were stimulated with A2+ beads for 16 hours.
A2-CAR Tconvs: (Day 0) Naive Tconvs were flow-sorted (CD4+CD25loCD127hiCD45RA+CD45RO-) and stimulated with L cells, anti-CD3, and 100 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were restimulated with A2+ L cells. (Day 12) CAR-Tconvs were rested overnight in low (10 IU/mL) IL-2, then (Day 13) were stimulated with A2+ beads for 16 hours.
A2-CAR Tr1s: (Day 0) CD4+ T cells were stimulated with CD3/CD28 beads overnight, then Tr1s were flow-sorted using an IL-10 capture approach and were stimulated with L cells, anti-CD3, and 100 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were restimulated with A2+ L cells. (Day 12) CAR-Tr1s were rested overnight in low (10 IU/mL) IL-2, then (Day 13) were stimulated with A2+ beads for 16 hours.
All cells were cultured in in Immunocult-XF T cell media and 1% penicillin-streptomycin.

extract_protocol:
Cells were lysed 16-hrs post-stimulation using TRIzol® and total RNA was extracted with the PureLink RNA MicroKit (as per manufacturer's guidelines).
RNA integrity was confirmed to be >8.0, then RNA was prepared using the Illumina® Stranded mRNA Prep kit.

value: Tconv

tag: sample group

value: female


title: C5_3 [KO1_3]

description:
KO1_3
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx

value: ES cells (mESCs)


title: A2-CAR Tconv, donor 1151

description: Library name: 51-Tconv

tag: donor

value: male


title: E5_3 [KO2_3]

description:
KO2_3
ProcessedKif2amESCRNASeqDataWTvsKO.xlsx


title: A2-CAR Tr1, donor 1151

description: Library name: 51-Tr1


title: Combo11-R-2

description: post-treatment

value: nivolumab and bezafibrate

value: post-treatment


title: A2-CAR Tconv, donor 3526

description: Library name: 26-Tconv


title: A2-CAR Tr1, donor 3526

description: Library name: 26-Tr1


title: eWAT_1_Control

description:
Library name: eWAT_Sample 1
eWAT_fpkm_values.csv


title: A2-CAR Tr1, donor 1130

description: Library name: 30-Tr1


title: Combo10-R-2

description: post-treatment


title: IL10KI A2-CAR Treg, donor 1151

description: Library name: 51-A20

source_name: Treg

value: Treg

value: IL10KI A2-CAR


title: bat_2_Fgf13_Ko

description: Library name: BAT_Sample 5

source_name: Brown adipose tissue

value: Brown adipose tissue


title: IL10KI A2-CAR Treg, donor 1130

description: Library name: 30-A20


title: PD1KO A2-CAR Treg, donor 1151

description: Library name: 51-A21

value: PD1KO A2-CAR


title: bat_1_Fgf13_Ko

description: Library name: BAT_Sample 4


title: bat_3_Control

description: Library name: BAT_Sample 3


title: PD1KO A2-CAR Treg, donor 1130

description: Library name: 30-A21


title: PD1KO A2-CAR Treg, donor 3526

description: Library name: 26-A21


title: Cas9 A2-CAR Treg, donor 3526

description: Library name: 26-Cas9

value: Cas9 A2-CAR


title: bat_2_Control

description: Library name: BAT_Sample 2


title: Cas9 A2-CAR Treg, donor 1130

description: Library name: 30-Cas9


title: bat_1_Control

description: Library name: BAT_Sample 1


title: Combo10-R-1

description: pre-treatment

value: R

value: untreated

value: pre-treatment


title: Combo9-NR-1

description: pre-treatment

value: Blood

value: NR


title: sWAT_3_Fgf13_Ko

description: Library name: sWAT_Sample 6

source_name: Subcutaneous white adipose tissue

value: Subcutaneous white adipose tissue

value: Fgf13 KO


title: Combo9-NR-2

description: post-treatment

value: PBMC CD8+T cells


title: K-562 and HEK293T VASA-seq plate 1

description:
Library name: Sample4
VASA-seq of K-562 and HEK293T

source_name: K-562 and HEK293T

value: K-562 and HEK293T


title: o_sgClu_r4

first: Ninghe

last: Sun

state: Massachusetts

address: 200 Longwood Avenue

institute: Harvard Medical School / Boston Children's Hospital

data_processing:
RNA FASTQ files were processed with the RNAseq pipeline
Assembly: GRCm38_mm10
Supplementary files format and content: FPKM

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
cDNA was generated according to manufacturer’s protocol of SMART-Seq v4 Ultra Low Input RNA Kit
RNA library was generated according to manufacturer’s protocol of Nextera XT DNA Sample Preparation Kit

value: Hematopoietic stem and progenitor cells


title: Combo2-NR-2

description: post-treatment

value: nivolumab and bezafibrate


title: Combo8-NR-2

description: post-treatment

value: post-treatment


title: sWAT_2_Fgf13_Ko

description: Library name: sWAT_Sample 5


title: VM108_Adjacent Kidney

city: Dallas

first: Javier

last: Garcia Bermudez

state: TX

address: 6000 Harry Hines Blvd

department: CRI

institute: UT Southwestern Medical Center

description: Library name: VM43

data_processing:
Ends of sequences were trimmed with remaining adapter or quality scores <25.
Sequencing reads were aligned to the human reference genome (hg19) by STAR 2.7.3.a with default parameters in the 2-pass mod.
Counts for each gene were generated using htseq-count v0.6.1. DEGs were identified by DESeq2 v1.14.1.
Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequence less than 35bp after trimming were removed.
The trimmed Fastq files were aligned to the GRCh38 using HiSAT272 and duplicates were marked with SAMBAMBA. Features (genes, transcripts and exons) were counted using featureCounts73. Differential expression analysis was performed using EdgeR74 and DESeq75. Genes with 0 values for all samples were trimmed from the processed data.
Assembly: hg19
Supplementary files format and content: Excel file includes log2CPM counts for each Sample

source_name: Adjacent Kidney

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific, Cat. No. 15596018) and an Rneasy Mini Kit (Qiagen, Cat. No. 74106). Total RNA was quantified using a Qubit fluorometer and the Invitrogen Qubit RNA High Sensitivity kit (Invitrogen, Cat. No. Q32852). Samples were diluted in ultrapure water prior to sequencing.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. No. E7490L, E7760L) according to manufacturer’s instructions. Libraries were stranded using standard N.E.B indices according to manufacturer’s instructions (New England Biolabs, Cat. No. E7730L, E7335L, E7500L).

value: Adjacent Kidney


title: Young HSC-6

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: Young_6

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

extract_protocol:
total RNA
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

value: hematopoietic stem cells

value: wt


title: o_sgClu_r3


title: Combo6-R-2

description: post-treatment


title: Combo8-NR-1

description: pre-treatment


title: Combo11-R-1

description: pre-treatment


title: IL10KI A2-CAR Treg, donor 3526

description: Library name: 26-A20

value: Treg

value: IL10KI A2-CAR

value: female