title: WT BeWo 48hr FSK biol rep 1

description:
Library name: Sample 3
RNASeq batch 1


title: WT BeWo 2hr Torin1 biol rep 1

status: Public on Dec 18 2024

type: SRA

city: Berkeley

first: Meagan

middle: Nicole

last: Esbin

state: California

address: 475 Li Ka Shing Center

department: Molecular and Cell Biology

country: USA

institute: University of California Berkeley

description:
Library name: Sample 2
RNASeq batch 1

library_source: transcriptomic

data_processing:
Raw data were assessed using FastQC
FASTQ files were pseudoaligned to the hg38 transcriptome using Salmon to quantify transcripts in mapping-based mode (salmon quant -i) using decoy-aware mapping with gencode.v39. transcripts.fa.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook. Raw counts were filtered to remove genes with fewer than 10 reads per sample or fewer than 15 reads summed across all samples. Counts per million reads (CPM) was calculated for the filtered count data using the EdgeR function cpm. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
To create bigwig files for visualization with IGV, mapping of FASTQ files was performed using STAR (with settings --quantMode GeneCounts --outSJfilterReads Unique --outFilterMultimapNmax 1)
Bam files (STAR outputs) were converted to bigwig files using deeptools bamcoverage (with settings --binSize 50 --normalizeTo1x 3049315783 --ignoreDuplicates)
Assembly: hg38
Supplementary files format and content: Comma separated values file contains CPM-normalized count data for each Sample by NCBI Gene ID
Supplementary files format and content: Bigwig file to be used for Genome track visualization (i.e. IGV viewer) of binned reads mapped across the human genome for each Sample
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (FC), p-value (PVAL) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) for each gene across different comparisons between Samples. Comparisons are noted as (Sample X - Sample Y) where positive FC values indicates higher gene expression in Sample X.

molecule: total RNA

organism: Homo sapiens

source_name: BeWo

growth_protocol: BeWo cells (ATCC CCL-98) were cultured at 37°C and 5% CO2 in F-12K medium (Corning or ATCC) supplemented with 10% fetal bovine serum and 10 U/mL penicillin–streptomycin. Cells were passaged by trypsinization every 2–4 days and split at a ratio of 1:3–1:5. Media was changed completely every 24–36 h.

extract_protocol:
RNA was extracted from each well using 500 µL of Trizol followed by two sequential chloroform extractions followed by ethanol precipitation per the Trizol user guide (Thermo Fisher MAN0001271).
500ng total RNA was used as starting material for each sample and then depleted of rRNA using the Illumina rRNA depletion kit (NEB E6310). For Batch 1 samples, 1uL of 1:100 diluted ERCC RNA Spike-In Mix (Thermo #4456740) was first added to the 500ng starting total RNA before rRNA depletion and libraries were prepared for Illumina sequencing using the NEBNext Ultra II directional RNA library preparation kit for Illumina (E7760) per the manufacturer’s protocol. For Batch 2 samples, libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770L) per the manufacturer’s protocol.

treatment_protocol: BeWo cells were plated at 300,000 cells per well into a 6 well plate and allowed to settle 6 h to overnight. Cells were then treated with 0.1% DMSO, 20 μM Forskolin, or 250nM Torin1 for 48 h or left untreated. For 2 hour Torin1 treatment, cells were treated with 0.1% DMSO for 46 h and then switched to 250 nM Torin1 media for 2 h before harvesting. Media for all treatments was changed at 24 h.

tag: cell line

value: BeWo

tag: cell type

value: choriocarcinoma

tag: genotype

value: wild-type

tag: treatment

value: 250nM Torin1 for 2hrs


title: WT, diffuse haplotype, bone marrow, replicate 1

city: Memphis

first: Mitchell

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

data_processing:
Reads were aligned with STAR (v2.7.9a) to the mouse mm10 genome with the following parameters: --readFilesCommand unpigz -c -p 4 --limitBAMsortRAM 67108864000 --outReadsUnmapped None --outSAMtype BAM SortedByCoordinate --outSAM strandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMmapqUnique 60 --outSAMmultNmax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFi lterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10 0000 --alignMatesGapMax 100000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions With inBAM SoftClip --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
Sequencing reads overlapping the mm10 Hbb-bt and Hbb-bs genes, including 1000 bases upsteam and downstream of the genes, and the intergenic region between the genes (chr7:103811548-103828825), were extracted using samtools view command.  Paired end reads were reconstituted by matching sequencing IDs. A reference genome consisting of the Hbb-bt and Hbb-bs genes from mm10 genome (C57BL6/J) and the Hbb-b1 and Hbb-b2 from the BALB/C globin locus region (Genbank record X14061.1) was generated (including 1000 bases upstream and downstream plus intronic sequence).
STAR (2.5.3a) was used to generate an indexed genome from the four globin reference sequence (following non-default parameters used: genomeSAindexNbases=9, sjdbOverhang=99). STAR was then used to align b-globin RNA-SEQ reads to this reference genome. (Non default parameters used : outFilterMismatchNmax 100 , alignIntronMax 500000 , sjdbFileChrStartEnd -, chimSegmentMin 20, chimJunctionOverhangMin 20, outSAMstrandField intronMotif, outBAMcompression -1, outSAMtype BAM Unsorted, outReadsUnmapped Fastx, --outFilterScoreMinOverLread .33 --outFilterMatchNminOverLread .33). For reads mapping to multiple b-globin genes equally well, only one mapping per read pair was retained.
For RNA-SEQ data from the single strain, if the reads mapped equally to Hbb-bs and Hbb-bt, it was classified as ambiguous. If only one of the single globin genes was a top match, but a diffuse gene (Hbb-b1 and/or Hbb-b2) was the top match, then the mapping to the single gene (Hbb-bs or Hbb-bt) was retained. The same decision was applied for diffuse strain data, but genes were switched. HTSEQ-Count was used to identify genes mapping to the four Hbb genes (gene annotation includes entire coordinates from transcriptional start to transcriptin end site).
An annotation file of introns was also created with the first/last 10 bases of the intron not included in the annotation. Running HTSEQ-Count with the introns file was performed to get intron counts. Exon counts for each sample and gene combination was calculated by substracting the intron count from total gene count.
Assembly: mm10
Supplementary files format and content: ec3751bf9ea548ebd1d7018304b2f413  is an xlsx file containing intron and exon counts of the different Hbb and Hba alleles from each samples.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Bone marrow and spleens were harvested from mice of the following genotypes: WT sing, WT diff, HbbTh3/+ sing, HbbTh3/+ diff. For each sample Ter119+ cells were isolated from 3 x 107 live bone marrow or spleen cells respectively with Anti-Ter-119 MicroBeads, mouse (Miltenyi, 130-049-901) on MS Columns (Miltenyi Biotec, 130-042-201). Total RNA was purified from Ter119+ cells with the RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s instructions.
Libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599) according to the manufacturer’s instructions.

tag: tissue

value: Bone marrow

tag: strain

tag: replicate

value: WT diffuse


title: WT, diffuse haplotype, bone marrow, replicate 3


title: WT BeWo Untreated biol rep 1

description:
Library name: Sample 1
RNASeq batch 1

value: Untreated


title: WT, diffuse haplotype, bone marrow, replicate 2


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, bone marrow, replicate 3

value: Hbb[th3/+] diffuse


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, bone marrow, replicate 5


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, bone marrow, replicate 2


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, bone marrow, replicate 1


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, bone marrow, replicate 4


title: Primary T-cell, Patient 89, SF

city: Manchester

first: Jake

last: Butler

address: AV Hill Building, The University of Manchester, Acker Street

country: United Kingdom

institute: University of Manchester

description: Library name: S055C8SF

data_processing:
RNA-seq reads were quality filtered and trimmed and adapters were removed using fastp v0.20.1 (Chen et al. 2018). Counts per transcript were generated using salmon v1.6.0 (Patro et al. 2017), with a decoy aware transcriptome (Gencode hg38 v29) and the validate mappings option enabled. Counts were then aggregated per gene and differential analysis was performed using DESeq2 (Love et al. 2014). Genes with average counts lower than 5 were removed. In all cases, unless otherwise specified, sex was used as a covariate. For other analysis, normalized counts were extracted from DESeq2 and used. No batch effect correction was found to be necessary.
Assembly: hg38
Supplementary files format and content: Salmon counts generated using Salmon v1.6.0

molecule: polyA RNA

source_name: Synovial fluid CD8

extract_protocol:
Between 40ml and 100ml of peripheral blood was collected following informed consent from 55 PsA patients and 19 healthy controls and processed on the same day. Patients and healthy controls were recruited under the National Repository study ethics approval number IRAS 32231, MREC 99/8/084. PBMCs were isolated using Ficoll density gradient centrifugation. EasySep Human CD4+ and CD8+ T cell negative selection kits (StemCell technologies #17952 and #17953) were used to isolate CD4+ and CD8+ T cells respectively. Cells were then aliquoted and prepared for long-term storage separately for each technique used. Synovial fluid extracted from patients with PsA was first treated with hyaluronidase enzyme (Sigma Aldrich #H3884) and then processed in a similar way as the peripheral blood samples.
Approximately 500 thousand to 1 million cells were lyzed and stored in 700uL Qiazol lysis reagent (QIAGEN, ref: 79306). To isolate RNA, 140 uL of chloroform was added. After centrifugation at 12000 x g for 15 min, approximately 350 uL of the upper layer containing the RNA was transferred and mixed with 350 uL of 70% ethanol. RNA isolation was continued from this point using the RNeasy MinElute kit (QIAGEN, ref: 74204) protocol. RNA libraries were then generated by NovoGene UK using a custom protocol based on cDNA synthesis using random hexamer primers and polyA mRNA enrichment. Sequencing was performed on the NovaSeq6000 platform using NovaSeq S4 flow cells at a target depth of 40 million reads per library and generating 150bp paired-end reads.

value: Synovial fluid CD8

value: Patient


title: A23_Single_EryA

data_processing:
Reads were aligned with STAR (v2.5.3a) to the mouse mm10 genome. Default parameters were used except the following: outSAMunmapped=Within, outSAMtype=BAM Unsorted, quantMode=TranscriptomeSAM, outSAMstrandField=intronMotif, outBAMcompression=-1, chimSegmentMin=20, . Sequencing reads overlapping the mm10 Hbb-bt and Hbb-bs genes, including 1000 bases upsteam and downstream of the genes, and the intergenic region between the genes (chr7:103811548-103828825), were extracted using samtools view command.
Paired end reads were reconstituted by matching sequencing IDs. A reference genome consisting of the Hbb-bt and Hbb-bs genes from mm10 genome (C57BL6/J) and the Hbb-b1 and Hbb-b2 from the BALB/C globin locus region (Genbank record X14061.1) was generated (including 1000 bases upstream and downstream plus intronic sequence).
STAR was used to generate an indexed genome from the four globin reference sequence (following non-default parameters used: genomeSAindexNbases=9, sjdbOverhang=99). STAR was then used to align b-globin RNA-SEQ reads to this reference genome. (Non default parameters used : outFilterMismatchNmax 100 , alignIntronMax 500000 , sjdbFileChrStartEnd -, chimSegmentMin 20, chimJunctionOverhangMin 20, outSAMstrandField intronMotif, outBAMcompression -1, outSAMtype BAM Unsorted, outReadsUnmapped Fastx, --outFilterScoreMinOverLread .33 --outFilterMatchNminOverLread .33). For reads mapping to multiple b-globin genes equally well, only one mapping per read pair was retained.
For RNA-SEQ data from the single strain, if the reads mapped equally to Hbb-bs and Hbb-bt, it was classified as ambiguous. If only one of the single globin genes was a top match, but a diffuse gene (Hbb-b1 and/or Hbb-b2) was the top match, then the mapping to the single gene (Hbb-bs or Hbb-bt) was retained. The same decision was applied for diffuse strain data, but genes were switched. HTSEQ-Count was used to identify genes mapping to the four Hbb genes (gene annotation includes entire coordinates from transcriptional start to transcriptin end site).
An annotation file of introns was also created with the first/last 10 bases of the intron not included in the annotation. Running HTSEQ-Count with the introns file was performed to get intron counts. Exon counts for each sample and gene combination was calculated by substracting the intron count from total gene count.
Assembly: mm10
Supplementary files format and content: hbb_hbaCounts.ery_retic.txt is a tab-delimited file containing intron and exon counts of the different Hbb and Hba alleles from each samples.

source_name: Erythroid A

growth_protocol: Primary Ery.A and Ery.B cells were purified from mouse bone marrow and reticulocytes from mouse blood.

extract_protocol:
Ery.A (Ter119hiCD71hiFSChi; basophilic), Ery.B (Ter119hiCD71hiFSClo; late basophilic and polychromatic) and reticulocytes represent increasingly mature erythroblast populations. Liu Y, Pop R, Sadegh C, Brugnara C, Haase VH, Socolovsky M, Suppression of Fas-FasL coexpression by erythropoietin mediates erythroblast expansion during the erythropoietic stress response in vivo. Blood 108, 123–133 (2006). Peripheral blood reticulocytes were purified after staining for RNA (BD Retic-Count).
RNA was purified using Rneasy Plus Mini and Micro kits (Qiagen).
RNA samples were submitted to Novogene (CA, USA) for quality control, library preparation and sequencing.

value: C57BL/6 Hbb th3/+

value: Erythroid A

value: Hbb Single


title: Primary T-cell, Patient 83

description: Library name: PSA5037CD8

source_name: CD8 + T-cell

value: CD8 + T-cell


title: Primary T-cell, Patient 90, SF

description: Library name: S056C8SF


title: A20_Diffuse_EryA

value: Hbb Diffuse


title: Primary T-cell, Patient 80

description: Library name: PSA5036CD4

source_name: CD4 + T-cell

value: CD4 + T-cell


title: Primary T-cell, Patient 85

description: Library name: PSA5040CD4


title: Primary T-cell, Patient 86

description: Library name: PSA5040CD8


title: A18_Diffuse_EryB

source_name: Erythroid B

value: Erythroid B


title: A24_Single_EryB


title: A22_Single_Retic

source_name: Reticulocyte

value: Reticulocyte


title: Primary T-cell, Patient 84

description: Library name: PSA5039CD8


title: Primary T-cell, Patient 88, SF

description: Library name: S055C4SF

source_name: Synovial fluid CD4

value: Synovial fluid CD4


title: Primary T-cell, Patient 77

description: Library name: PSA5017CD8


title: A16_Diffuse_Retic


title: A21_Diffuse_EryB


title: Primary T-cell, Patient 75

description: Library name: PSA5006CD4


title: A19_Diffuse_Retic


title: Primary T-cell, Patient 74

description: Library name: PSA4969CD8


title: Primary T-cell, Patient 78

description: Library name: PSA5019CD4


title: Primary T-cell, Patient 79, SF

description: Library name: PSA5025CD8SF


title: Primary T-cell, Patient 87, SF

description: Library name: PSA5040CD8SF


title: Primary T-cell, Patient 81

description: Library name: PSA5036CD8


title: A17_Diffuse_EryA


title: Primary T-cell, Patient 76

description: Library name: PSA5017CD4


title: A10_Single_Retic


title: Primary T-cell, Patient 70

description: Library name: PSA4963CD8


title: Primary T-cell, Patient 71

description: Library name: PSA4964CD4


title: A9_Single_EryB


title: Primary T-cell, Patient 69

description: Library name: PSA4963CD4


title: A15_Diffuse_EryB


title: A14_Diffuse_EryA


title: A8_Single_EryA


title: Primary T-cell, Patient 82

description: Library name: PSA5037CD4


title: A6_Diffuse_EryB


title: Primary T-cell, Patient 72

description: Library name: PSA4965CD8


title: A5_Diffuse_EryA


title: A12_Single_EryB


title: A13_Diffuse_Retic


title: Primary T-cell, Patient 73

description: Library name: PSA4966CD8


title: A4_Diffuse_Retic


title: A7_Single_Retic


title: Primary T-cell, Patient 68

description: Library name: PSA4962CD8


title: Primary T-cell, Patient 67

description: Library name: PSA4962CD4


title: Primary T-cell, Patient 62

description: Library name: PSA4955CD8


title: A11_Single_EryA


title: Primary T-cell, Patient 66

description: Library name: PSA4959CD8


title: Primary T-cell, Patient 65

description: Library name: PSA4959CD4


title: A1_Single_Retic


title: Primary T-cell, Patient 63

description: Library name: PSA4958CD4


title: A3_Single_EryB


title: Primary T-cell, Patient 64, SF

description: Library name: PSA4958CD8SF


title: Primary T-cell, Patient 61

description: Library name: PSA4954CD8


title: Primary T-cell, Patient 48

description: Library name: P67C4


title: A2_Single_EryA


title: Primary T-cell, Patient 58

description: Library name: PSA4952CD8


title: Primary T-cell, Patient 57

description: Library name: PSA4949CD4


title: Primary T-cell, Patient 46

description: Library name: P60C8


title: Primary T-cell, Patient 60

description: Library name: PSA4954CD4


title: Primary T-cell, Patient 47

description: Library name: P61C8


title: Primary T-cell, Patient 55

description: Library name: PSA4945CD4


title: Primary T-cell, Patient 56

description: Library name: PSA4947CD4


title: Primary T-cell, Patient 44, SF

description: Library name: P58C4SF


title: Primary T-cell, Patient 53, SF

description: Library name: PSA4942CD8SF


title: Primary T-cell, Patient 42, SF

description: Library name: P51C4SF


title: Primary T-cell, Patient 54

description: Library name: PSA4944CD8


title: Primary T-cell, Patient 52

description: Library name: PSA4941CD8


title: Primary T-cell, Patient 43

description: Library name: P51C8


title: Primary T-cell, Patient 41

description: Library name: P51C4


title: B16-F10 tumor overexpressing IL-18 D69A_1

city: Shanghai

first: junchen

last: Shen

address: 320 yueyang road.

country: China

institute: Shanghai institute of immunity and infection

description: IL-18 D69A-1

data_processing:
The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We use fastp to filter.
We use HISAT to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
We mapped clean reads to reference using Bowtie, and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Then, wecalculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R.
We detect DEGs(different expressio genes) with DEGseq and PossionDis as requested.DEGseq is based on the poisson distribution. Parameters: Fold Change >= 2 and Adjusted Pvalue <= 0.05.
With the GO&KEGG annotation result, we classify DEGs according to official classification, and we also perfrom GO&KEGG functional enrichment using phyper, a function of R. Then we calculate false discovery rate (FDR) for each pvalue, in general, the terms which FDR not largerthan 0.05 are defined as significant enriched.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: tumor

extract_protocol:
The tumor tissues were preserved in RNAlater solution (Invitrogen, AM7020) at -80 °C, and RNA was extracted by RNase-Free DNase Set kit (QIAGEN, 79254).
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit following manufacturer's protocols.

value: tumor

value: melanoma cells

value: IL-18 D69A overexpression

value: B16-F10 cells were subcutaneously implanted into the right flank of C57BL/6 mice


title: Primary T-cell, Patient 51

description: Library name: PSA4920CD8


title: B16-F10 tumor overexpressing IL-18 WT_5

description: IL-18 WT-5

value: IL-18 WT overexpression


title: B16-F10 tumor overexpressing IL-18 WT_6

description: IL-18 WT-6


title: Primary T-cell, Patient 40

description: Library name: P5026C8


title: Primary T-cell, Patient 50

description: Library name: PAS4958CD8


title: B16-F10 tumor overexpressing IL-18 D69A_5

description: IL-18 D69A-5


title: Primary T-cell, Patient 49, SF

description: Library name: P69C8


title: Primary T-cell, Patient 45, SF

description: Library name: P59C8SF


title: B16-F10 tumor overexpressing IL-18 D69A_4

description: IL-18 D69A-4


title: B16-F10 tumor overexpressing IL-18 D69A_2

description: IL-18 D69A-2


title: B16-F10 tumor overexpressing IL-18 D69A_3

description: IL-18 D69A-3


title: Primary T-cell, Patient 37

description: Library name: P5023C8


title: Primary T-cell, Patient 38

description: Library name: P5024C8


title: Primary T-cell, Patient 59

description: Library name: PSA4953CD8


title: Primary T-cell, Patient 36

description: Library name: P5022C8


title: Primary T-cell, Patient 35

description: Library name: P5021C8


title: marrow, KO sham, rep3

city: Beijing

first: Haiyan

last: Xue

address: 11th Xizhimen South Street

institute: Peking University People's Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated using NovaSeq control software (v1.6.0), RTA (v3.4.4), and bcl2fastq2 (v2.20).
Raw data (raw reads) of fastq format were firstly processed through fastp software (v0.23.4 -g -q 5 -u 50 -n 15 -l 150). 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm39
Supplementary files format and content: xlsx file of raw counts
Supplementary files format and content: xlsx file of FPKM

source_name: bone marrow

extract_protocol:
Total RNA of the cultured cells was extracted using HiPure Universal RNA Mini Kit(Qiagen, GERMANY) according to the manufacturer's instructions.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). 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. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: bone marrow

value: KO

value: SHAM


title: Primary T-cell, Patient 39

description: Library name: P5026C4

value: Patient


title: B16-F10 tumor overexpressing IL-18 WT_4

description: IL-18 WT-4


title: B16-F10 tumor overexpressing IL-18 WT_3

description: IL-18 WT-3


title: marrow, KO CLP, rep3

value: CLP


title: Primary T-cell, Patient 32

description: Library name: P5019C8


title: B16-F10 tumor overexpressing IL-18 WT_2

description: IL-18 WT-2


title: marrow, WT CLP, rep3

value: WT


title: marrow, WT sham, rep3


title: Primary T-cell, Patient 28

description: Library name: P5014C8

value: CD8 + T-cell


title: marrow, KO CLP, rep2


title: Primary T-cell, Patient 25

description: Library name: P5013C4


title: Primary T-cell, Patient 26

description: Library name: P5013C8


title: marrow, KO CLP, rep1


title: marrow, KO sham, rep2


title: Hippocampus, AAV-CaMKIIα-TAF15 stereotaxic injection, 31 days, TAF15 OE 3

city: Hefei

first: Ding

middle: Mei

last: Jie

state: Anhui

address: Huangshanlu

department: life science

institute: the University of science and technology of China

data_processing:
Illumina Casava software used for basecalling.
Remove adapter polluted reads, remove low-quality reads, and remove reads which contain N higher than 5%.
The reference genomes and the annotation file were downloaded from ENSEMBL database(http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Mus_musculus.GRCm38.90.chr
Supplementary files format and content: tab-delimited text files include raw counts for each sample.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: Hippocampus

growth_protocol: Mice were housed in a specific-pathogen-free barrier room with appropriate temperature, humidity, and a 12-hour light-dark cycle.

extract_protocol:
Hippocampus were removed, flash frozen in liquid nitrogen,and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols with Illumina TruSeq RNA Sample Prep Kit.

treatment_protocol: TAF15-AAV or control-AAV were stereotaxically injected with into the bilateral hippocampal CA1 region of  male C57BL/6J mice at 8 weeks of age. The coordinates used for stereotaxic injection are AP -2.3, ML ±2.0, DV -1.5. After the surgery, mice were kept on a warm pad for a short period of recovery, then returned to the home cage and monitored for 24 h.

value: Hippocampus

value: TAF15 OE

value: AAV stereotaxic injection


title: Primary T-cell, Patient 31

description: Library name: P5018C8


title: marrow, KO sham, rep1


title: Primary T-cell, Patient 33

description: Library name: P5020C8


title: Primary T-cell, Patient 30

description: Library name: P5018C4

value: CD4 + T-cell


title: Hippocampus, AAV-CaMKIIα-TAF15 stereotaxic injection, 31 days, TAF15 OE 2


title: Primary T-cell, Patient 21

description: Library name: P5010C4


title: Primary T-cell, Patient 29

description: Library name: P5015C8


title: Primary T-cell, Patient 22

description: Library name: P5010C8


title: Hippocampus, AAV-CaMKIIα-TAF15 stereotaxic injection,31 days, TAF15 OE 1


title: marrow, WT CLP, rep2


title: Primary T-cell, Patient 19

description: Library name: P5009C4


title: marrow, WT CLP, rep1


title: Hippocampus, AAV-control stereotaxic injection, 31 days, Control 3

value: Control


title: Primary T-cell, Patient 18

description: Library name: P5008C8


title: marrow, WT sham, rep1


title: Primary T-cell, Patient 34

description: Library name: P5021C4


title: Hippocampus, AAV-control stereotaxic injection, 31 days, Control 2


title: Primary T-cell, Patient 24

description: Library name: P5012C8


title: Primary T-cell, Patient 17

description: Library name: P5008C4


title: Primary T-cell, Patient 23

description: Library name: P5012C4


title: Hippocampus, AAV-control stereotaxic injection, 31 days, Control 1


title: LB-M-RE-MI-2

city: Xi'an City

first: Bei

last: Liu

state: Shaanxi province

address: No.569 Xinsi Road

institute: Tangdu Hospital

library_source: transcriptomic single cell

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 27bp GEXSCOPE barcode and the 12bp UMI (bases 61-72). Read 2 contains the cDNA information.
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: Bilateral hippocampus

extract_protocol:
Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

tag: group

value: drug-resistant epileptic memory impairment

value: Bilateral hippocampus

tag: Sex

value: male

tag: age

value: 14 weeks


title: Primary T-cell, Patient 16

description: Library name: P5007C8


title: marrow, WT sham, rep2


title: LB-M-RE-MI-1


title: LB-M-RE-MI-3


title: LB-M-Cont-2


title: LB-M-Cont-3


title: LB-M-Cont-1


title: Primary T-cell, Patient 10

description: Library name: P4956C8


title: UTE15M

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Singleron Matrix GEXSCOPE

data_processing:
To produce gene expression matrices, the raw scRNA-seq data were processed using the CeleScope v1.9.0 pipeline (https://github.com/singleron-RD/CeleScope). Briefly, raw reads were initially processed with Cutadapt v1.17 to trim the poly A tail and adapter sequences, and CeleScope to eliminate low-quality reads. Next, we mapped reads to the reference genome GRCm38 (Ensembl version 92 annotation) using STAR v2.6.1a. The feature Counts v2.0.1 programme was used to obtain the UMI and gene counts for each cell after extracting the cell barcode and UMI. Specifically, UMIs and genes with the same barcodes were clustered together and counted. The expression matrices for subsequent analyses were then generated based on the gene counts in each cell.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: uterus

extract_protocol:
The fresh C57BL/6 murine ovaries, oviducts, and uteri were excised from each age group (5D, 5W, 3M, 6M, 9M, 12M, and 15M, n = 6/age group). Tissues from the same organ were then pooled together. Within the first 30 min of the procedure, the collected fresh tissues were placed on ice and soaked in sCelLiveTM Tissue Preservation Solution (Singleron Biotechnology, China). The specimens were cleaned thrice with Hanks Balanced Salt Solution and then digested by Singleron PythoNTM Automated Tissue Dissociation System (Singleron Biotechnology, China) using 3 mL sCelLiveTM Tissue Dissociation Solution for 15 min at 37 °C. Next, the cells were incubated at 25 °C for an additional 10 min to remove the red blood cells following the addition of GEXSCOPE® red blood cell lysis solution (2 mL, Singleron). The solution was then gently suspended in phosphate buffer saline (PBS, HyClone, China) after being centrifuged at 300 × g at 4 °C for 5 min to remove the supernatant. Finally, the samples were stained with trypan blue (Sigma, USA), and cell vitality was analyzed using an inverted microscope (Nikon, Japan).
The Singleron Matrix® Single Cell Processing System was used to load single-cell suspensions (1 × 105 cells/mL) in PBS (HyClone) into the GEXSCOPE® Single Cell Microchip (Singleron Biotechnology, China). The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library kits (Singleron). Briefly, following the removal of the barcoding beads from the microwell chip, reverse transcription was performed on the mRNA that attached to the beads to produce cDNA, and PCR amplification was then performed. Following fragmentation, the amplified cDNA was ligated using sequencing adapters. GEXSCOPE® Single Cell RNA Library Kits (Singleron) were used for the construction of scRNA-seq libraries, in accordance with the manufacturer’s instructions. On an Illumina NovaSeq 6000 with 150-bp paired-end reads, individual libraries were combined after being diluted to 4 nM.

value: uterus


title: UTE12M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 9

description: Library name: P4956C4


title: UTE9M

description: Singleron Matrix GEXSCOPE


title: UTE6M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 8

description: Library name: P48C8


title: Primary T-cell, Patient 11

description: Library name: P4957C4


title: UTE5W

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 12

description: Library name: P4968C4


title: UTE3M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 6

description: Library name: P46C8


title: OVI15M

description: Singleron Matrix GEXSCOPE

source_name: oviduct

value: oviduct


title: OVI12M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 14

description: Library name: P5006C8


title: Primary T-cell, Patient 3

description: Library name: P43C8


title: Primary T-cell, Patient 4

description: Library name: P44C4


title: Primary T-cell, Patient 15

description: Library name: P5007C4


title: Primary T-cell, Patient 2

description: Library name: P42C8


title: Primary T-cell, Patient 1

description: Library name: P42C4


title: OVI3M

description: Singleron Matrix GEXSCOPE


title: UTE5D

description: Singleron Matrix GEXSCOPE


title: OVI9M

description: Singleron Matrix GEXSCOPE


title: OVI6M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 38

description: Library name: NRHV322CD8

value: Healthy


title: OVI5W

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 36

description: Library name: NRHV321CD8


title: OVI5D

description: Singleron Matrix GEXSCOPE


title: OVA15M

description: Singleron Matrix GEXSCOPE

source_name: ovary

value: ovary


title: Primary T-cell, Patient 7

description: Library name: P47C8

value: Patient


title: Primary T-cell, Healthy 37

description: Library name: NRHV322CD4


title: Primary T-cell, Healthy 34

description: Library name: NRHV319CD8


title: Primary T-cell, Healthy 35

description: Library name: NRHV321CD4


title: Primary T-cell, Patient 20

description: Library name: P5009C8


title: OVA6M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Patient 5

description: Library name: P45C8


title: Primary T-cell, Healthy 33

description: Library name: NRHV319CD4


title: OVA9M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 32

description: Library name: NRHV171CD8


title: OVA3M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 30

description: Library name: NRHV121CD8


title: Primary T-cell, Healthy 31

description: Library name: NRHV171CD4


title: OVA5W

description: Singleron Matrix GEXSCOPE


title: OVA5D

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 27

description: Library name: NRHV086CD4


title: Primary T-cell, Healthy 28

description: Library name: NRHV086CD8


title: Primary T-cell, Healthy 29

description: Library name: NRHV121CD4


title: Primary T-cell, Patient 13

description: Library name: P4968C8


title: kidney, PND14, WT, rep2

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

data_processing:
Reads were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the paired-end samples (PND14) or "-s0" for the single-end samples (PND7,PND28).
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Note that each age should be treated as an independent dataset; since age and batch are conflated, results from direct comparisons across ages should be interpreted with caution.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

extract_protocol:
Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.

value: kidney


title: kidney, PND14, WT, rep3

value: WT


title: OVA12M

description: Singleron Matrix GEXSCOPE


title: Primary T-cell, Healthy 25

description: Library name: NRHV005CD4


title: kidney, PND14, WT, rep5


title: Primary T-cell, Healthy 23

description: Library name: NH326C4


title: Primary T-cell, Healthy 22

description: Library name: NH324C8

value: CD8 + T-cell


title: kidney, PND14, WT, rep4


title: kidney, PND14, Glis3 KO, rep4

value: Glis3 KO


title: Primary T-cell, Healthy 21

description: Library name: NH324C4


title: Primary T-cell, Healthy 26

description: Library name: NRHV005CD8


title: kidney, PND14, Glis3 KO, rep2


title: kidney, PND14, Glis3 KO, rep1


title: kidney, PND14, Glis3 KO, rep5


title: Primary T-cell, Healthy 20

description: Library name: NH238C8


title: kidney, PND14, Glis3 KO, rep3


title: Primary T-cell, Healthy 17

description: Library name: HV332CD4


title: dTAGV-1 treated tumor 3

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to mm10 reference genome using STAR program with default parameters
Read counts, TPM and FPKM were calculated using RSEM program.
Differential expression gene analysis was performed using DESeq2 program in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: Tab-delimited gene-by-sample text file with raw gene counts for each sample.

source_name: lung

extract_protocol: Mice were treated with either vehicle or dTAGV-1. Tumor nodules were harvested and subjected to RNA extraction using Qiagen RNA extraction kit.

value: lung


title: control treated tumor

description: 10x Genomics

data_processing:
The whole gene expression matrix from Cell Ranger was fed to Seurat R package for normalization, dimension reduction, and clustering.
Cell clusters were annotated based on canonical cell markers.
Data visualization was achieved using Seurat functions and customized R and Python scripts.
Assembly: mm10
Supplementary files format and content: feature-by-cell count matrix in H5 format

extract_protocol:
Mice were humanely euthanized, and mouse lungs were perfused using sterile PBS through heart perfusion from the left ventricle. The whole lung was cut and minced into small pieces followed by digestion in collagenase D (Sigma) and DNase I (Sigma) in Hank’s Balanced Salt Solution (HBSS) at 37°C for 30 minutes. After incubation, the digested tissue was subjected to a 70-μm cell strainer (ThermoFisher Scientific) to obtain single-cell suspensions. Live cell swere then sorted using DAPI  staining. Cells were then resuspended into single cells at a concentration of 1 x 106 per ml in 1X PBS with 0.4% BSA for 10x genomics processing.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: Mice were treated with either vehicle or dTAGV-1 for a 5-day treatment.

value: vehicle


title: kidney, PND14, WT, rep1


title: dTAGV-1 treated tumor

description: 10x Genomics


title: Primary T-cell, Healthy 18

description: Library name: HV332CD8


title: Primary T-cell, Healthy 15

description: Library name: HV325CD4

value: CD4 + T-cell


title: Primary T-cell, Healthy 16

description: Library name: HV325CD8


title: Primary T-cell, Healthy 19

description: Library name: NH238C4


title: Primary T-cell, Healthy 14

description: Library name: HV295CD8


title: dTAGV-1 treated tumor 1


title: control treated tumor 2


title: Primary T-cell, Healthy 24

description: Library name: NH326C8


title: Primary T-cell, Healthy 13

description: Library name: HV295CD4


title: control treated tumor 1


title: Primary T-cell, Healthy 12

description: Library name: HV290CD8


title: dTAGV-1 treated tumor 2


title: MEF 4in1_Prox1_OE day28 rep2 [timecourse bulk]

city: Heidelberg

first: Moritz

last: Mall

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
timecourse_deseq2.tsv
timecourse_day28_norm_counts.tsv

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
For bulk MEF reprogramming data, we used the primary MEF line as a covariate.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics (all comparisons vs respective timepoint GFP control)
Supplementary files format and content: tsv file with normalised counts

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5 embryos of C57BL/6N (wild-type). MEFs were transduced with indicated lentivirus in MEF medium containing 8 μg/mL polybrene (Sigma) for 16 to 20 h. Medium was exchanged to MEF medium containing 2 μg/mL doxycycline (Sigma) to induce transgene expression. 1 day following doxycycline induction, the medium was supplemented with 0.5× volume Hepatocyte Culture Medium (HCM, Lonza) containing 5% FBS (Life Technologies) and 2 μg/mL doxycycline. On day 2, all medium was exchanged to a mixture of ⅓ MEF medium and ⅔ HCM + 5% FBS and 2 μg/mL doxycycline. On day 3, all medium was exchanged to HCM + 5% FBS and 2 μg/mL doxycycline. Afterwards, the medium was changed every 2 days for the rest of the reprogramming experiment.

extract_protocol:
Cells were harvested at days 2, 7, 14, or 28 by the addition of TRIzol to the cultures (Invitrogen). RNA harvested in TRIzol (Invitrogen) was isolated using the RNA Miniprep kit (Zymo Research).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: MEFs were seeded onto collagen-coated plates and transduced 1 day later with lentivirus encoding rtTA (FUW-rtTA) and 4in1 (LV.4TF) together with GFP (tetO-GFP) or Prox1 (tetO-FLAG-mmProx1), respectively. 2 μg/ml doxycycline (Sigma) was used to induce transgene expression in growth media for indicated days.

value: Primary mouse embryonic fibroblasts

value: 4in1 reprogramming


title: Primary T-cell, Healthy 9

description: Library name: HV168CD4


title: MEF 4in1_GFP_OE day28 rep2 [timecourse bulk]

value: GFP


title: Primary T-cell, Healthy 11

description: Library name: HV290CD4


title: Primary T-cell, Healthy 8

description: Library name: HV151CD8


title: MEF 4in1_Prox1_OE day14 rep2 [timecourse bulk]

description:
timecourse_deseq2.tsv
timecourse_day14_norm_counts.tsv


title: Primary T-cell, Healthy 7

description: Library name: HV151CD4


title: MEF 4in1_Prox1_OE day14 rep1 [timecourse bulk]


title: MEF 4in1_GFP_OE day14 rep2 [timecourse bulk]


title: MEF 4in1_GFP_OE day14 rep1 [timecourse bulk]


title: Primary T-cell, Healthy 6

description: Library name: HV079CD8


title: CO3 MUT,replicate2,snRNA-seq

first: Kexin

last: Li

address: No. 15, Datun Road, Chaoyang District, Beijing, China

institute: Peking Union Medical College

data_processing:
For each snRNA-seq library, cells were processed using CellRanger with default settings. Further filtering was applied to each library, retaining only cells with a minimum of 500 RNA features (nFeature_RNA) and a maximum of 10% mitochondrial gene expression (percent.mt). There were 117765 nuclei that met these criteria. Data analysis was performed using the Seurat package (version 5.0.3) following these steps: normalization of expression by total counts per cell, scaling of the data, identification of highly variable genes, calculation of principal components, identification of nearest neighbors, clustering using the Leiden algorithm, and dimensionality reduction using the UMAP algorithm. Cluster identities were assigned based on established marker genes, as indicated in the figures. Differential expression analysis was done with FindMarkers.
Assembly: mRatBN7.2
Supplementary files format and content: matrix files

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol: The anterior horn of lumbar spinal cord from 40-day-old COXⅢLSL and COXⅢNeuN-Cre rats were used for the isolation of the nuclei, based on methods reported in previous studies15. Nuclei from frozen anterior horn of lumbar spinal cord tissues were isolated using Shbio Nuclei Isolation Kit (SHBIO; Shanghai, China). For cDNA library preparation, 10000 nuclei were used for the Single-cell RNA (scRNA) library construction. The single-nuclei suspension (700-1200 nuclei per ml as determined by the CellDrop FL Cell Counter) were loaded into microfluidic chip of Chip A Single Cell Kit v2.1 (MobiDrop no. S050100301) to generate droplets with MobiNova-100. Each nucleus was encapsulated into a droplet which contained a gel bead linked with up to millions oligos (cell unique barcode). The mRNAs were captured by cell barcodes with cDNA amplification in droplets. According to the manufacturer’s introduction, scRNA-seq libraries were constructed using the High Throughput Single-Cell 3' Transcriptome Kit v2.1 (MobiDrop no. S050200301) and sequenced on illumina platform by Annoroad Gene Technology Co., Ltd.

value: spinal cord

value: neuron


title: MEF 4in1_Prox1_OE day07 rep2 [timecourse bulk]

description:
timecourse_deseq2.tsv
timecourse_day07_norm_counts.tsv


title: Primary T-cell, Healthy 5

description: Library name: HV079CD4


title: WT,replicate2,snRNA-seq


title: MEF 4in1_Prox1_OE day28 rep1 [timecourse bulk]


title: MEF 4in1_Prox1_OE day07 rep1 [timecourse bulk]


title: WT,replicate1,snRNA-seq


title: Primary T-cell, Healthy 3

description: Library name: HV073CD4


title: Primary T-cell, Healthy 2

description: Library name: HV014XCD8


title: MEF 4in1_GFP_OE day07 rep2 [timecourse bulk]


title: MEF 4in1_GFP_OE day28 rep1 [timecourse bulk]


title: WT,replicate3,snRNA-seq


title: MEF 4in1_GFP_OE day07 rep1 [timecourse bulk]


title: Primary T-cell, Healthy 10

description: Library name: HV168CD8


title: Primary T-cell, Healthy 1

description: Library name: HV014XCD4


title: low light, high salt, rep1

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

description: Library name: R_H_20d_1_x

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Leymus chinensis

source_name: leaf

growth_protocol: All the plant materials  were grown in 1/2MS medium under either low light or salt stress

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 3-week-old sheepgrass plants were collected.

value: leaf

value: leaf cells

value: low light, high salt, rep1


title: low light, ck, rep3

description: Library name: R_0_20d_3_x

value: low light, ck, rep3


title: low light, ck, rep2

description: Library name: R_0_20d_2_x

value: low light, ck, rep2


title: low light, high salt, rep2

description: Library name: R_H_20d_2_x

value: low light, high salt, rep2


title: low light, ck, rep1

description: Library name: R_0_20d_1_x

value: low light, ck, rep1


title: Primary T-cell, Healthy 4

description: Library name: HV073CD8

source_name: CD8 + T-cell

value: CD8 + T-cell

value: Healthy


title: PsA5040CD8_SF, HiC

description: Library name: PsA5040CD8_SF

library_source: genomic

data_processing:
Hi-C reads were quality filtered and trimmed and adapters were removed using fastp v0.20.1 (Chen et al. 2018). Reads were then processed and mapped to the GRCh38 genome using HiC-pro v3.0.0 (Servant et al. 2015), using default settings. Hic juicebox files for visualization and analysis were generated using the hicpro2juicebox.sh script using juicer tools v1.22.01. Cool files were generated from the juicebox files using hic2cool (https://github.com/4dn- dcic/hic2cool). TAD calling was done using onTAD (An et al. 2019) with default settings and ICE normalized 40kb resolution maps.
Assembly: hg38
Supplementary files format and content: .hic files that can be used for visualisation. These files can be converted to cool files.

molecule: genomic DNA

source_name: Synovial fluid

extract_protocol:
Between 40ml and 100ml of peripheral blood was collected following informed consent from 55 PsA patients and 19 healthy controls and processed on the same day. Patients and healthy controls were recruited under the National Repository study ethics approval number IRAS 32231, MREC 99/8/084. PBMCs were isolated using Ficoll density gradient centrifugation. EasySep Human CD4+ and CD8+ T cell negative selection kits (StemCell technologies #17952 and #17953) were used to isolate CD4+ and CD8+ T cells respectively. Cells were then aliquoted and prepared for long-term storage separately for each technique used. Synovial fluid extracted from patients with PsA was first treated with hyaluronidase enzyme (Sigma Aldrich #H3884) and then processed in a similar way as the peripheral blood samples.
Approximately 3-5 million cells were crosslinked in 2% formaldehyde for 10 minutes at room temperature and the reaction was then quenched using a solution glycine + BSA. Samples were then washed in PBS and snap frozen on dry ice and then transferred to -80°C for long- term storage. 2 million cells were then used for library preparation following the two-restriction enzyme Arima Hi-C kit (Arima Genomics) and the KAPA HyperPrep kit (Roche #KK8504) manufacturer’s protocol using Illumina TruSeq dual indexes. Library size was checked by TapeStation 4200 (Agilent) and QC was done by quantstudio (Life technologies) using the NEBNext® Library Quant Kit for Illumina (E7630). Sequencing was performed on the NovaSeq6000 platform using NovaSeq S4 flow cells at a target depth of 350 million reads per library and generating 150bp paired-end reads.

value: Synovial fluid

value: Patient


title: PsA5040CD8, HiC

description: Library name: PsA5040CD8

source_name: Blood

value: Blood


title: CO3 MUT,replicate3,snRNA-seq


title: CO3 MUT,replicate1,snRNA-seq


title: MEF 4in1_Prox1_OE day02 rep1 [timecourse bulk]

description:
timecourse_deseq2.tsv
timecourse_day02_norm_counts.tsv

value: Primary mouse embryonic fibroblasts

value: WT


title: Primary T-cell, Patient 27

description: Library name: P5014C4

source_name: CD4 + T-cell

value: CD4 + T-cell


title: PSA5040CD4, HiC

description: Library name: PSA5040CD4


title: MEF 4in1_GFP_OE day02 rep2 [timecourse bulk]

value: 4in1 reprogramming

value: GFP


title: normal light, high salt, rep2

description: Library name: Q_H_20d_2_x

value: leaf

value: normal light, high salt, rep2


title: normal light, high salt, rep3

description: Library name: Q_H_20d_3_x

value: leaf cells

value: normal light, high salt, rep3


title: normal light, low salt, rep2

description: Library name: Q_L_20d_2_x

value: normal light, low salt, rep2


title: MEF 4in1_GFP_OE day02 rep1 [timecourse bulk]


title: normal light, high salt, rep1

description: Library name: Q_H_20d_1_x

value: normal light, high salt, rep1


title: PsA5037CD8, HiC

description: Library name: PsA5037CD8


title: PSA5039CD8, HiC

description: Library name: PSA5039CD8


title: normal light, ck, rep3

description: Library name: Q_0_20d_3_x

value: normal light, ck, rep3


title: MEF 4in1_Prox1_OE day02 rep2 [timecourse bulk]


title: MEF all remaining barcodes [scRNA-seq]

data_processing:
Single-cell RNA-seq data were analyzed using 10x Genomics Cell Ranger (v4.0.0) and Seurat (v4.0). Cells containing fewer than 1,000 features, containing fewer than 2,000 reads, or with mitochondrial genes comprising over 20% of genes, were discarded.
Cell doublets were removed using Scrublet with a threshold of 0.35.
8-nt HTO sequences are provided in hashtag_oligos.tsv. Reads were obtained from Undetermined_*.fastq.gz with zcat Undetermined_*.fastq.gz | grep -v "@" | grep -v "+" > file1 followed by cat file1 | grep -e CAGCAAAAAAA -e CAGGAAAAAAA -e CAGTAAAAAAA | gzip > input_hashing_bc_counts.txt.gz.
HTO reads were taken from this file, sorted into bins based on their 8-nt HTO sequences, then assigned to a cell based on the 10x barcode in the read.
Cells were demultiplexed based on their hashtag oligos by running Seurat HTODemux() recursively on the cell-to-HTO dictionary generated in the previous step.
Expression values of cell cycle genes were regressed out using vars.to.regress in ScaleData() to reduce heterogeneity caused by cycling cells.
Assembly: mm10
Supplementary files format and content: barcodes.mtx.gz from Cellranger
Supplementary files format and content: features.mtx.gz from Cellranger
Supplementary files format and content: matrix.mtx.gz from Cellranger
Supplementary files format and content: hashtag_oligos.tsv tab-separate file with information on barcode sequences and associated biological condition and replicate

extract_protocol:
Cells were harvested at days 2, 7, or 14. Cultures dissociated into single cells after two PBS washes by Accutase digestion. Cells were lifted using cell scrapers, then suspensions were then passed through 70 μm filters into 9 mL of pre-warmed MEF medium. Cells were pelleted (800 RPM, 5 min) and resuspended in 1 mL HBSS + 0.04% BSA to > 3.5 million cells/mL, then fixed through the addition of 4× volume of ice-cold methanol to a final concentration of 80% methanol. Cells were then stored at -20° C.
Barcoding oligonucleotides for multiplexing were designed based upon the ClickTag scheme and ordered with a 5’ amine group label. A methyltetrazine group was conjugated to the oligos via the 5’-amine group. Membrane proteins on the fixed cells were conjugated to an amine-trans-cyclooctene group. Subsequent incubation of oligos and cells according to the ClickTag protocol allowed chemical labeling of cells. ~10,000 cells were multiplexed and loaded per GEM well in the Chromium Controller (10x Genomics), and the Chromium Single Cell 3' v2 reagent kit was used according to the manufacturer’s instructions for gene expression library generation. We performed modifications at the cDNA and library preparation steps as suggested in the ClickTag protocol to generate barcoded oligonucleotide libraries in parallel. Gene expression and barcode libraries were then diluted to equimolar amounts, pooled at a 9 to 1 ratio, and 26 + 98 bp paired-end sequencing was performed using NovaSeq 6000 platform (Illumina).

tag: timepoint

value: day 02, day 07, and day 14


title: PsA5037CD4, HiC

description: Library name: PsA5037CD4


title: normal light, ck, rep2

description: Library name: Q_0_20d_2_x

value: normal light, ck, rep2


title: normal light, ck, rep1

description: Library name: Q_0_20d_1_x

value: normal light, ck, rep1


title: Hep3B Prox1 OE rep 3

description: Library name: Hep3B Prox1 rep 3

data_processing:
Raw reads were quality-checked with fastqc (v0.11.8), trimmed with trimmomatic (v0.38), and aligned to UCSC hg38 with bowtie2 (v2.3.4.3).
Aligned reads were cleaned and base-recalibrated (to take account of Tn5 insertion biases) with samtools (v1.10) and picard (v2.18.16). Reads were filtered with bedtools (v2.27.1), samtools, and picard.
Peaks were called using macs2 (2.1.2) and coverage was calculated with deeptools (v3.1.3). Final quality checks were performed with multiqc (v1.6).
Differential peak analysis was performed with DiffBind (v3.4.11) as described in the authors’ vignette (same version).
Assembly: hg38
Supplementary files format and content: individual bigwig coverage files

growth_protocol: Hep3B grown in DMEM (Invitrogen) containing 10% foetal bovine serum (Sigma), non-essential amino acids, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen) were transduced with pLIX-Puro-hsPROX1 lentivirus. Puromycin (2 μg/ml) selection was performed for 2 days to generate stable cell lines.

extract_protocol:
Cells on culture plates were washed twice with PBS and detached by Accutase digestion (4-6 min, RT) followed by ATAC processing. Cell suspensions were placed into an equal volume of MEF medium followed by centrifugation (500g, 5 min, 4°C) before resuspension in ice-cold PBS + 1% BSA. Cells were then strained through a 70 μm filter, centrifuged (500g, 5 min, 4°C), and 50,000 cells resuspended in 50 μL of ice-cold cell lysis buffer containing 0.1% NP-40 and 0.01% digitonin in wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA in ddH2O) for 3-5 minutes. 1 mL of ice-cold wash buffer was then added to stop cell lysis, and nuclei were centrifuged (500g, 10 min, 4°C). 4.5 μL of each of the tagmentation oligos, Tn5_ME and Tn5-R1N, were annealed in oligo annealing buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, and 10 mM EDTA final concentration in ddH2O) by heating at 95°C (3 min) followed by a ramp down by 1°C to 25°C. The same procedure was performed for Tn5_ME and Tn5-R2N. Tn5 was assembled with annealed oligos by combining 50 μL Tn5 (1 mg/mL stock) with 25 μL annealed Tn5_ME and Tn5-R1N and 25 μL Tn5_ME and Tn5-R2N. Nuclei were resuspended in 40 μL tagmentation buffer (38.8 mM Tris-acetate, 77.6 mM K-acetate, 11.8 Mg-acetate, 18.8% dimethylformamide, and 0.12% NP-40 in ddH2O), to which 5 μL ice-cold PBS + 1% BSA and 5 μL pre-assembled Tn5 was added. Samples were incubated on a Thermomixer (37°C, 30 min, 500 rpm) before being subjected to MinElute (Qiagen) cleanup to extract tagmented DNA.
Eluted DNA was pre-amplified with P5 and P7 primers using the NEBNext HF 2x PCR Master Mix (New England Biolabs) in a thermocycler set to 72°C (5 min), 98°C (30 sec), and 5 cycles of 98°C (10 sec), 63°C (30 sec), and 72°C (1 min). A qPCR side reaction was performed with the resulting pre-amplified libraries to determine the necessary additional cycles (5 cycles fewer than the number of cycles corresponding to ⅓ of max fluorescence) for complete amplification. After finishing amplification, 50 μL of each library was subjected to 2-sided size selection by addition of 27.5 μL (0.55x) AMPure XP beads, incubation (5 min), transfer of supernatant to new tubes, addition of 42.5 μL (1.4x) AMPure XP beads to the supernatant, incubation (5 min), three washes with 80% ethanol, and elution of DNA.

treatment_protocol: 2 μg/ml doxycycline (Sigma) was used to induce Prox1 expression (PROX1 overexpression) in growth media for 2 days and compared to no doxycycline treated cells (Control).

value: Hepatocellular carcinoma

value: PROX1 overexpression


title: MEF unreprogrammed_or_Myod1_OE barcodes [scRNA-seq]

description:
GEM01_barcodes.tsv.gz
GEM01_matrix.mtx.gz
GEM01_features.tsv.gz

value: Primary mouse embryonic fibroblasts

value: day 02 and day 07


title: normal light, low salt, rep3

description: Library name: Q_L_20d_3_x

value: normal light, low salt, rep3


title: MEF Myod1_OE day02 [scRNA-seq]

value: WT

value: 4in1 reprogramming

value: day 07


title: PsA5026CD8, HiC

description: Library name: PsA5026CD8

value: Blood

value: CD8 + T-cell

value: Patient


title: MEF unreprogrammed day02 [scRNA-seq]

value: day 02


title: Hep3B Control rep 2

description: Library name: Hep3B Control rep 2

value: Control


title: PsA5026CD4, HiC

description: Library name: PsA5026CD4

value: CD4 + T-cell


title: Hep3B Control rep 3

description: Library name: Hep3B Control rep 3


title: Hep3B Prox1 OE rep 1

description: Library name: Hep3B Prox1 rep 1


title: MEF 4in1_OE day14 barcodes [scRNA-seq]

description:
GEM06_barcodes.tsv.gz
GEM06_features.tsv.gz
GEM06_matrix.mtx.gz
GEM07_barcodes.tsv.gz
GEM07_features.tsv.gz
GEM07_matrix.mtx.gz

value: day 14


title: normal light, low salt, rep1

description: Library name: Q_L_20d_1_x

value: leaf

value: leaf cells

value: normal light, low salt, rep1


title: PSA5025CD8SF, HiC

description: Library name: PSA5025CD8SF

value: Synovial fluid


title: MEF 4in1_Prox1_OE day14 [scRNA-seq]

description:
GEM07_barcodes.tsv.gz
GEM07_features.tsv.gz
GEM07_matrix.mtx.gz

value: Primary mouse embryonic fibroblasts


title: PSA5040CD8, ATAC

description: Library name: PSA5040CD8

data_processing:
ATAC-seq reads were quality filtered and trimmed and adapters were removed using fastp v0.20.1 (Chen et al. 2018). Reads were then mapped using bowtie2 v2.4.4 (Langmead and Salzberg 2012) using the very-sensitive pre-set. Duplicates were removed using the MarkDuplicates functionality of picard tools (Institute 2019) and mitochondrial reads were removed, as well as removing low quality alignments (MAPQ<30) and keeping only properly paired reads. Coverages were generated from cleaned alignments using the bamCoverage functionality from DeepTools2 (Ramírez et al. 2016). Peaks were called using macs2 v2.2.7.1 (Zhang et al. 2008). The ATAC-seq processing pipeline is available on GitHub (https://github.com/ChenfuShi/ATAC_ChIP_pipeline). Data for all samples was then analysed in R using DiffBind (Stark and Brown 2011). A consensus peakset was generated using peaks that were present in at least 5 samples. Peak size was set to 500bp. Cross library normalization was performed using the DESeq2 normalization method (DBA_NORM_NATIVE) but using only reads in peaks (DBA_LIBSIZE_PEAKREADS), as different samples had significantly different proportion of reads in peaks, which would bias the default normalization method. Counts were extracted at this point for further analysis, except for differential binding analysis, which was performed within DiffBind, using the DESeq2 method. No batch effect correction was found to be necessary. We found that quantile normalization slightly improved results, such as separation of cell types on the PCA plot and correlation between expression and peak height of promoter peaks, and as such we used quantile normalized counts for all downstream analysis.
Assembly: hg38
Supplementary files format and content: Narrow peak file,in bed format, showing locations of Macs2 called peaks on narrow mode

extract_protocol:
Between 40ml and 100ml of peripheral blood was collected following informed consent from 55 PsA patients and 19 healthy controls and processed on the same day. Patients and healthy controls were recruited under the National Repository study ethics approval number IRAS 32231, MREC 99/8/084. PBMCs were isolated using Ficoll density gradient centrifugation. EasySep Human CD4+ and CD8+ T cell negative selection kits (StemCell technologies #17952 and #17953) were used to isolate CD4+ and CD8+ T cells respectively. Cells were then aliquoted and prepared for long-term storage separately for each technique used. Synovial fluid extracted from patients with PsA was first treated with hyaluronidase enzyme (Sigma Aldrich #H3884) and then processed in a similar way as the peripheral blood samples.
Approximately 500 thousand cells were frozen in RecoveryTM Cell Culture Freezing Medium (Thermofisher #12648010) and stored at -80°C. An aliquot of 50 thousand cells was then used for ATAC-seq library preparation following the Omni-ATAC protocol as released by the Kaersten lab (Corces et al. 2017; Amanda Ackermann 2019). Library size was checked by TapeStation 4200 (Agilent) and QC was done by quantstudio (Life technologies) using the NEBNext® Library Quant Kit for Illumina (E7630). Sequencing was performed on the NextSeq2000 platform at a target depth of 50 million reads per library and generating 50bp paired-end reads.


title: PSA5040CD8SF, ATAC

description: Library name: PSA5040CD8SF


title: PSA5040CD4, ATAC

description: Library name: PSA5040CD4


title: PSA5039_CD8, ATAC

description: Library name: PSA5039_CD8


title: MEF 4in1_GFP_OE day14 [scRNA-seq]

description:
GEM06_barcodes.tsv.gz
GEM06_features.tsv.gz
GEM06_matrix.mtx.gz

value: GFP


title: PSA5037CD8, ATAC

description: Library name: PSA5037CD8


title: PsA5023CD8, HiC

description: Library name: PsA5023CD8


title: PsA5024CD8, HiC

description: Library name: PsA5024CD8


title: PSA5037_CD4, ATAC

description: Library name: PSA5037_CD4


title: gcn4Δ MMS rep 3

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: barcode: CCTTCGTTGC-ATCGGAGTGC

data_processing:
Reads were checked for initial quality using FastQC 0.11.9 and adapters removed via automatic detection by fastp. Reads were then mapped to the transcriptome using Salmon 1.10.1 with libraryType IU, gcBias, seqBias, and validate Mappings flags set. The transcriptome was generated by using the R64-3-1 cDNAs from SGD, with 200 nt upstream and downstream of the CDS added. Only those genes whose ORF was classified as verified or unknown were kept. The transcriptome was indexed using Salmon with the k-mers option set to 31.
Salmon quantification files were imported into DESeq2 1.38.3 using Tximport 1.26.1. The matrix design was set to compare the effect of strain, treatment with MMS, and interaction between strain and treatment with MMS. The wild-type strain and untreated condition were set as the reference levels. Resultant fold changes were adjusted using the ashr package.
Assembly: SGD R64-3-1
Supplementary files format and content: Microsoft Excel file containing differential gene expression analysis for the interaction effect of MMS treatment and genotype

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: S. cerevisiae BY4741 strains were grown in YPD medium to OD ~0.6 before treatment

extract_protocol:
Cells were flash frozen and RNA was collected using a hot phenol extraction method
Total RNA integrity was determined using Agilent Bioanalyzer. Library preparation was performed with 5 to 10 µg of total RNA with a Bioanalyzer RNA Integrity Number (RIN) greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer by heating at 94 degrees for 8 minutes. Fragments were reverse transcribed using SuperScript III RT enzyme (ThermoFisher Scientific) and random hexamers, as per manufacturer's instructions, to yield cDNA. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were not treated (NT) or treated with 0.1% methyl methanesulfonate (MMS) for one hour

value: yeast cell

tag: ploidy

value: haploid

value: BY4741 MATa gcn4{delta}::KAN


title: PsA5036CD8, HiC

description: Library name: PsA5036CD8


title: MEF 4in1_OE day07 barcodes [scRNA-seq]

description:
GEM04_barcodes.tsv.gz
GEM04_features.tsv.gz
GEM04_matrix.mtx.gz
GEM05_barcodes.tsv.gz
GEM05_features.tsv.gz
GEM05_matrix.mtx.gz

value: WT

value: 4in1 reprogramming

value: day 07


title: Hep3B Prox1 OE rep 2

description: Library name: Hep3B Prox1 rep 2

value: Hepatocellular carcinoma

value: PROX1 overexpression


title: MEF 4in1_Prox1_OE day07 [scRNA-seq]

description:
GEM05_barcodes.tsv.gz
GEM05_features.tsv.gz
GEM05_matrix.mtx.gz


title: PsA5022CD8, HiC

description: Library name: PsA5022CD8

value: Blood

value: CD8 + T-cell

value: Patient


title: gcn4Δ MMS rep 2

description: barcode: TCGGACAACG-CTCATTAACG


title: PsA5036CD4, ATAC

description: Library name: PsA5036CD4

value: CD4 + T-cell


title: PsA5021CD4, HiC

description: Library name: PsA5021CD4


title: gcn4Δ MMS rep 1

description: barcode: AGCAGACATT-GAACACGCCT


title: MEF 4in1_OE day02 barcodes [scRNA-seq]

description:
GEM02_barcodes.tsv.gz
GEM02_features.tsv.gz
GEM02_matrix.mtx.gz
GEM03_barcodes.tsv.gz
GEM03_features.tsv.gz
GEM03_matrix.mtx.gz

value: day 02


title: Hep3B Control rep 1

description: Library name: Hep3B Control rep 1

value: Control


title: PsA5026CD8, ATAC

description: Library name: PsA5026CD8


title: PsA5021CD8, HiC

description: Library name: PsA5021CD8


title: MEF 4in1_GFP_OE day07 [scRNA-seq]

description:
GEM04_barcodes.tsv.gz
GEM04_features.tsv.gz
GEM04_matrix.mtx.gz


title: PsA5026CD4, ATAC

description: Library name: PsA5026CD4


title: MEF 4in1_GFP_OE day02 [scRNA-seq]

description:
GEM02_barcodes.tsv.gz
GEM02_features.tsv.gz
GEM02_matrix.mtx.gz


title: MEF 4in1_Prox1_OE day02 [scRNA-seq]

description:
GEM03_barcodes.tsv.gz
GEM03_features.tsv.gz
GEM03_matrix.mtx.gz


title: gcn4Δ NT rep 2

description: barcode: AATCGAACTC-TTAGACCTTC


title: PSA5025CD8SF, ATAC

description: Library name: PSA5025CD8SF

value: Synovial fluid


title: PsA5019CD8, HiC

description: Library name: PsA5019CD8


title: PsA5019CD4, HiC

description: Library name: PsA5019CD4


title: Liver HCC tumour shRen endpoint rep2

description:
hcc_shprox1_deseq2.tsv
hcc_shprox1_norm_counts.tsv

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics (vs shRen control as baseline)
Supplementary files format and content: tsv file with normalised counts

source_name: liver

extract_protocol:
At humane endpoint euthanasia, primary mouse liver tumor samples were dissected and placed into TRIzol (Invitrogen). Samples were crushed and then homogenized using QIAshredder (Qiagen).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: For hydrodynamic tail vein injection (HDTVI), 2 mL of sterile 0.9% NaCl solution, corresponding to 10% of body weight, containing the plasmids of interest was injected into the tail vein of 8-week-old female C57BL/6N mice within 5 to 7 s. Each mouse was injected with 20 µg of pX330-sgRNA-Tp53 (p53 KO) and 2 µg of CMV-Sleeping Beauty transposase plus 10 µg of pT3-EF1a-MYC-IRES-rtTA (Myc OE), together with 20 µg of miR-E shProx1 (Prox1 KD) or miR-E shRhen (control) including a GFP reporter were co-injected.

value: liver

tag: genotype background

value: Myc OE + Tp53 KO

value: Renilla luciferase KD

value: endpoint

value: control


title: gcn4Δ NT rep 1

description: barcode: AGGTATTCGG-GAGTCGCTTC

value: yeast cell

value: haploid

value: BY4741 MATa gcn4{delta}::KAN


title: Liver HCC tumour shRen endpoint rep1


title: PsA5018CD8, HiC

description: Library name: PsA5018CD8


title: PsA5023CD8, ATAC

description: Library name: PsA5023CD8


title: mbf1Δ MMS rep 2

description: barcode: ACTGTAAGCA-AGTCCGCTTG

value: BY4741 MATa mbf1{delta}::NAT


title: mbf1Δ MMS rep 3

description: barcode: AAGGTGTTAG-TAAGCGCGTG


title: PsA5036CD8, ATAC

description: Library name: PsA5036CD8


title: PsA5024CD8, ATAC

description: Library name: PsA5024CD8


title: PsA5018CD4, HiC

description: Library name: PsA5018CD4


title: PsA5020CD8, HiC

description: Library name: PsA5020CD8


title: PsA5022CD8, ATAC

description: Library name: PsA5022CD8


title: PsA5017CD8, HiC

description: Library name: PsA5017CD8


title: Liver HCC tumour shProx1 endpoint rep2

value: Prox1 KD


title: gcn4Δ NT rep 3

description: barcode: CCGAAGATAA-TGGATTAACG


title: mbf1Δ NT rep 3

description: barcode: CCATTGTCAA-ACAATCGCTG


title: PsA5017CD4, HiC

description: Library name: PsA5017CD4

value: Blood


title: Liver HCC tumour shProx1 endpoint rep1


title: PsA5021CD8, ATAC

description: Library name: PsA5021CD8

value: CD8 + T-cell


title: MEF 4in1_EnR_OE day07 rep2

description:
fusions_deseq2.tsv
fusions_norm_counts.tsv

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
For bulk MEF reprogramming data, we used the primary MEF line as a covariate.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics (all comparisons vs DBD control)
Supplementary files format and content: tsv file with normalised counts

extract_protocol:
Cells were harvested at day 7 by the addition of TRIzol to the cultures (Invitrogen). RNA harvested in TRIzol (Invitrogen) was isolated using the RNA Miniprep kit (Zymo Research).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: MEFs were seeded onto collagen-coated plates and transduced 1 day later with lentivirus encoding rtTA (FUW-rtTA) and 4in1 (LV.4TF) together with GFP (tetO-GFP), or Prox1 (tetO-FLAG-mmProx1), or Prox1 DBD (tetO-FLAG-mmProx1-DBD), or EnR-Prox1 DBD (tetO-FLAG-EnR-mmProx1-DBD), or VP64-Prox1 DBD (tetO-FLAG-VP64-mmProx1-DBD), respectively. 2 μg/ml doxycycline (Sigma) was used to induce transgene expression in growth media for 7 days.

value: Primary mouse embryonic fibroblasts

value: WT

value: 4in1 reprogramming

value: EnR

value: EnR fusion


title: PsA5021CD4, ATAC

description: Library name: PsA5021CD4

value: CD4 + T-cell

value: Patient


title: MEF 4in1_EnR_OE day07 rep1


title: PsA5020CD8, ATAC

description: Library name: PsA5020CD8


title: mbf1Δ NT rep 1

description: barcode: CCACTGAGCT-ACCTGTCTTG


title: mbf1Δ NT rep 2

description: barcode: AGAATGTGGT-TTAGCCGATA


title: PsA5019CD8, ATAC

description: Library name: PsA5019CD8


title: MEF 4in1_VP64_OE day07 rep2

value: VP64 fusion


title: PsA5014CD4, HiC

description: Library name: PsA5014CD4


title: MEF 4in1_VP64_OE day07 rep1


title: PsA5019CD4, ATAC

description: Library name: PsA5019CD4


title: PsA5013CD8, HiC

description: Library name: PsA5013CD8


title: gcn2Δ MMS rep 3

description: barcode: TGACCTGCTG-ATCTGACGGA

value: BY4741 MATa gcn2{delta}::KAN


title: PsA5018CD8, ATAC

description: Library name: PsA5018CD8


title: gcn2Δ MMS rep 2

description: barcode: CGCCAGAATC-ACACGAACAA


title: PsA5013CD4, HiC

description: Library name: PsA5013CD4


title: MEF 4in1_ProxDBD_OE day07 rep1

value: DBD

value: Prox1DBD (negative control)


title: PsA5018CD4, ATAC

description: Library name: PsA5018CD4


title: gcn2Δ MMS rep 1

description: barcode: CAGCATAACA-GCCATCCTTG

value: yeast cell

value: haploid


title: gcn2Δ NT rep 3

description: barcode: AACAGGCAAG-TTCATGGAAG


title: MEF 4in1_Prox1_OE day07 rep2

value: Prox1 (positive control)


title: PsA5014CD8, HiC

description: Library name: PsA5014CD8


title: PSA5017_CD4, ATAC

description: Library name: PSA5017_CD4


title: PSA5012_CD4, HiC

description: Library name: PSA5012_CD4


title: MEF 4in1_Prox1_OE day07 rep1


title: PsA5015CD8, HiC

description: Library name: PsA5015CD8


title: PSA5017_CD8, ATAC

description: Library name: PSA5017_CD8


title: gcn2Δ NT rep 2

description: barcode: AATCTCAGGC-TCACCAGGAC


title: MEF 4in1_ProxDBD_OE day07 rep2


title: PSA5010_CD4, HiC

description: Library name: PSA5010_CD4


title: PsA5015CD8, ATAC

description: Library name: PsA5015CD8


title: wt MMS rep 3

description: barcode: CCGTATCACA-TAGCTAACGT

value: BY4741 MATa


title: MEF 4in1_GFP_OE day07 rep1

value: GFP

value: GFP (control)


title: MEF 4in1_GFP_OE day07 rep2

value: Primary mouse embryonic fibroblasts


title: PsA5014CD8, ATAC

description: Library name: PsA5014CD8

value: Blood

value: CD8 + T-cell


title: gcn2Δ NT rep 1

description: barcode: CCTTGCCGTA-TAGTACACAG


title: mbf1Δ MMS rep 1

description: barcode: GTAGTACAGT-TGTCCAGGTG

value: BY4741 MATa mbf1{delta}::NAT


title: PSA5012_CD8, HiC

description: Library name: PSA5012_CD8


title: MEF_Prox1(fl/fl) 4in1_dcreGFP_OE day14 rep2

description:
flox_prox1_deseq2.tsv
flox_prox1_norm_counts.tsv

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
For bulk MEF reprogramming data, we used the primary MEF line as a covariate.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics
Supplementary files format and content: tsv file with normalised counts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5 embryos of C57BL/6J (Prox1 fl/fl). MEFs were transduced with indicated lentivirus in MEF medium containing 8 μg/mL polybrene (Sigma) for 16 to 20 h. After 1 day, the medium was supplemented with 0.5× volume Hepatocyte Culture Medium (HCM, Lonza) containing 5% FBS (Life Technologies). On day 2, all medium was exchanged to a mixture of ⅓ MEF medium and ⅔ HCM + 5% FBS. On day 3, all medium was exchanged to HCM + 5% FBS. Afterwards, the medium was changed every 2 days for the rest of the reprogramming experiment.

extract_protocol:
Cells were harvested at day 14 by the addition of TRIzol to the cultures (Invitrogen). RNA harvested in TRIzol (Invitrogen) was isolated using the RNA Miniprep kit (Zymo Research).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: MEFs were seeded onto collagen-coated plates and transduced 1 day later with lentivirus encoding 4in1 (LV.4TF) together with Cre-recombinase (FUW-GFP-Cre; Prox1 KO) or non-functional delta Cre-recombinase (FUW-GFP-dCre; WT Prox1 (control)), respectively. Cells were reprogrammed for 14 days.

value: 4in1 + dcre-GFP

value: WT Prox1 (control)


title: PsA5009CD4, HiC

description: Library name: PsA5009CD4

value: CD4 + T-cell

value: Patient


title: PsA5014CD4, ATAC

description: Library name: PsA5014CD4


title: wt MMS rep 1

description: barcode: TGATCGAGGC-CTTAGCTGGC


title: MEF_Prox1(fl/fl) 4in1_dcreGFP_OE day14 rep1


title: wt MMS rep 2

description: barcode: TCATCGACTA-TAGCGGTTCG


title: PsA5013CD8, ATAC

description: Library name: PsA5013CD8


title: MEF_Prox1(fl/fl) 4in1_creGFP_OE day14 rep2

value: 4in1 + cre-GFP

value: Prox1 KO


title: PsA5013CD4, ATAC

description: Library name: PsA5013CD4


title: PsA5010CD8, HiC

description: Library name: PsA5010CD8


title: MEF_Prox1(fl/fl) 4in1_creGFP_OE day14 rep1


title: PsA5006CD8, HiC

description: Library name: PsA5006CD8


title: PsA5007CD4, HiC

description: Library name: PsA5007CD4


title: PsA5012_CD8, ATAC

description: Library name: PsA5012_CD8


title: wt NT rep 1

description: barcode: AACTCCAAGA-CTCACTACTC


title: PSA5008_CD4, HiC

description: Library name: PSA5008_CD4


title: PSA5008_CD8, HiC

description: Library name: PSA5008_CD8


title: wt NT rep 3

description: barcode: TCTAGAGTGC-TTCCTCACGT


title: PsA5009CD8, HiC

description: Library name: PsA5009CD8


title: PsA5010CD8, ATAC

description: Library name: PsA5010CD8


title: PsA5012_CD4, ATAC

description: Library name: PsA5012_CD4


title: Liver IgG rep 5

description: Library name: Liver IgG rep 5

data_processing:
CUT&RUN data were analysed using the nf-core/cutandrun pipeline v1.0.0 with Nextflow version 21.05.0. Reads were aligned to mm10 or hg38. Software versions: bedtools (v2.30.0), bowtie2 (2.4.2), deeptools (v3.5.0), DESeq2 (v1.28.0), fastqc (v0.11.9), multiqc (v1.11), picard (v2.23.9), python (v3.8.3), samtools (v1.10), Genrich (v0.6.1)(https://github.com/jsh58/Genrich), TrimGalore (v0.6.6), ucsc (v377).
Consensus peaks were defined by running Genrich -m 30 -e chrM -r -l 5 -q 0.3.
To determine peaks containing motifs, we mapped the PROX1 binding motif (CIS-BP ID: M03445_2.00) onto mm10 or hg38, extended each resulting motif peak to a total width of 50 bp, and ran bedtools intersect -wa on the CUT&RUN consensus peaks and motif peaks, respectively.
Genes defined as direct target genes based upon CUT&RUN were determined by running Homer annotatePeaks.pl on the final peak set and filtering for genes with a peak within ±1kb of their TSS.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: individual bigwig coverage files
Supplementary files format and content: Narrow peak files
Library strategy: CUT&Run

source_name: Liver

growth_protocol:
MEF: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5 embryos of C57BL/6N (wild-type). Wild-type MEFs were transduced with rtTA (FUW-rtTA) and tetO-FLAG-mmProx1 (Prox1 overexpression) lentivirus in MEF medium containing 8μg/ml polybrene (Sigma) for 16 to 20h. Medium was exchanged to MEF medium containing 2μg/ml doxycycline (Sigma) to induce Prox1 overexpression (Prox1 overexpression) for two days followed by nuclei harvesting for CUT&RUN.
Liver: Mouse livers were harvested from 2 to 3-month-old wildtype C57BL/6J mice and directly processed for nuclei isolation using liver swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2) with the help of a douncer. Homogenized tissue was passed through a 70 μm strainer and centrifuged (400g, 5 min, 4°C). Tissue pellets were resuspended in liver lysis buffer (10 mM Tris pH 7.5, 1% NP-40, 2 mM MgCl2, 10% Glycerol, 3 mM CaCl2) and centrifuged again. Pellets, now containing hepatocyte nuclei, were washed twice in PBS. These nuclei were processed for CUT&RUN.
Hep3B: Hep3B grown in DMEM (Invitrogen) containing 10% foetal bovine serum (Sigma), non-essential amino acids, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen) were transduced with pLIX-Puro-hsPROX1 (PROX1 overexpression) lentivirus. Puromycin selection was performed (2 μg/ml) for 2 days to generate stable cell lines. Medium was exchanged to growth medium containing 2 μg/ml doxycycline (Sigma) to induce PROX1 expression (PROX1 overexpression) for two days followed by nuclei harvesting for CUT&RUN.

extract_protocol:
Cells were harvested with Accutase and strained through a 70 um strainer followed by CUT&RUN processing. 250,000 cells were washed twice with wash buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and 1X Roche Complete Protease Inhibitor), then resuspended in wash buffer and added to Concanavalin-A beads (Polysciences) pre-activated in cold binding buffer (20 mM HEPES-KOH pH 7.5, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2). The bead-cell suspension was rotated (RT, 10 min). The supernatant was removed on a magnet and the beads were resuspended in antibody buffer (0.2 mM EDTA, 0.05% w/v digitonin in wash buffer). Primary antibody (as indicated) or control (rabbit IgG) was added at 1:100 v/v, and cells were incubated on a nutator (overnight, 4°C). Beads were washed twice in digitonin-wash buffer (0.05% w/v digitonin in wash buffer), resuspended in 700 ng/mL pAG-MNase (Protein Expression and Purification Core Facility, EMBL, Heidelberg) in digitonin-wash buffer, and rotated (4°C, 1 h). pAG-MNase-loaded beads were then washed twice in digitonin-wash buffer, resuspended in digitonin-wash buffer, and placed on ice. 1 uL of 100 mM CaCl2 was added to induce chromatin digestion, and the mixture was incubated on ice (30 min). 50 uL of 2x stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% w/v digitonin, 50 ug/mL RNase A, 50 ug/mL glycogen, 0.5 ng/mL spike-in E. coli DNA) was added, and the suspension incubated at 37°C for 10 minutes to release chromatin fragments from cells.
The supernatant was subjected to phenol-chloroform extraction, and purified DNA fragments were used for library preparation with NEBNext DNA Library Prep Kit for Illumina (NEB E7645). Libraries were then sequenced (paired-end, 2x40 bp) on the NextSeq 550 platform (Illumina).

value: Liver

value: Hepatocyte

tag: chip antibody

value: Rabbit IgG (Sigma 12-370)


title: PsA5010CD4, ATAC

description: Library name: PsA5010CD4


title: Liver IgG rep 4

description: Library name: Liver IgG rep 4


title: PsA5006CD4, HiC

description: Library name: PsA5006CD4


title: PsA4969CD8SF, HiC

description: Library name: PsA4969CD8SF

value: Synovial fluid


title: wt NT rep 2

description: barcode: CGGAGCGATA-CTTAACAAGG

value: yeast cell

value: haploid

value: BY4741 MATa


title: Liver IgG rep 3

description: Library name: Liver IgG rep 3


title: PsA5009CD8, ATAC

description: Library name: PsA5009CD8


title: PsA4968CD8, HiC

description: Library name: PsA4968CD8


title: PsA5009CD4, ATAC

description: Library name: PsA5009CD4


title: Liver IgG rep 2

description: Library name: Liver IgG rep 2


title: Liver IgG rep 1

description: Library name: Liver IgG rep 1


title: PsA4968CD4, HiC

description: Library name: PsA4968CD4


title: PSA5008CD8, ATAC

description: Library name: PSA5008CD8


title: PSA4967CD4, HiC

description: Library name: PSA4967CD4


title: PSA4963_CD8, HiC

description: Library name: PSA4963_CD8


title: Liver Prox1 rep 4

description: Library name: Liver Prox1 rep 4

value: Rabbit anti-Prox1 (Reliatech 102-PA32)


title: Liver Prox1 rep 3

description: Library name: Liver Prox1 rep 3


title: PSA4962_CD8, HiC

description: Library name: PSA4962_CD8

value: Blood


title: PsA5007CD8, ATAC

description: Library name: PsA5007CD8

value: CD8 + T-cell


title: Liver Prox1 rep 2

description: Library name: Liver Prox1 rep 2


title: PSA4963_CD4, HiC

description: Library name: PSA4963_CD4


title: PsA5006CD8, ATAC

description: Library name: PsA5006CD8


title: PSA5007CD4, ATAC

description: Library name: PSA5007CD4


title: Liver Prox1 rep 1

description: Library name: Liver Prox1 rep 1


title: PSA4961_CD8, HiC

description: Library name: PSA4961_CD8


title: PSA4969CD8, ATAC

description: Library name: PSA4969CD8


title: PSA4962_CD4, HiC

description: Library name: PSA4962_CD4


title: MEF IgG rep 2

description: Library name: MEF IgG rep 2

source_name: Primary mouse embronic fibroblasts

value: Primary mouse embronic fibroblasts

value: Primary mouse embryonic fibroblasts

value: Prox1 overexpression


title: PsA4959CD8SF, HiC

description: Library name: PsA4959CD8SF


title: MEF IgG rep 1

description: Library name: MEF IgG rep 1


title: PSA4960_CD8, HiC

description: Library name: PSA4960_CD8


title: PsA4969CD8_SF, ATAC

description: Library name: PsA4969CD8_SF


title: Liver Prox1 rep 5

description: Library name: Liver Prox1 rep 5


title: PsA4968CD8, ATAC

description: Library name: PsA4968CD8


title: PSA4968CD4, ATAC

description: Library name: PSA4968CD4

value: CD4 + T-cell


title: PSA4959_CD8, HiC

description: Library name: PSA4959_CD8

value: Patient


title: PsA4959CD4, HiC

description: Library name: PsA4959CD4


title: PSA4967CD4, ATAC

description: Library name: PSA4967CD4


title: MEF Flag rep 3

description: Library name: MEF Flag rep 3

value: Rabbit anti-FLAG (Cell Signaling Technology 14793)


title: PsA5008_CD4, ATAC

description: Library name: PsA5008_CD4


title: MEF Flag rep 1

description: Library name: MEF Flag rep 1


title: PSA4966CD8, ATAC

description: Library name: PSA4966CD8


title: MEF IgG rep 3

description: Library name: MEF IgG rep 3


title: PsA4958CD8, HiC

description: Library name: PsA4958CD8


title: Exercise_2

first: Shujing

last: Feng

address: Qingyuan ring road

institute: Shanghai university of sport

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: xls file includes TPM for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were examined using Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RQN values were determined by Agilent5300. The requirements for a single library were 1 μg of total RNA, concentration ≥ 30 ng/μL, RQN > 6.5, and OD260/280 between 1.8 and 2.2.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: skeletal muscle

value: Exercise


title: PSA5006CD4, ATAC

description: Library name: PSA5006CD4


title: PsA4965CD8, ATAC

description: Library name: PsA4965CD8


title: ScY01

city: Tianjin

first: Qinhong

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence， then mapped to reference genome using Bowtie 1.2.0 with default parametres
Abundance measurements by script  geneexp_stat
Differential gene expression by R package DEGseq with method MARS, a p-value cutoff of 0.001 or less and an absolute fold-change threshold of 2.0 or greater
Genome_build: R64
Supplementary_files_format_and_content: Transcriptome profiles of ScY and ScY01.xlsx: Windows Excel file include abundance for each sample and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_ScY01 vs. ScY.xlsx: Windows Excel file include different expression gene list

source_name: Early-log phase cells grown on YP medium containing 200 g/l glucose at 40ºC

extract_protocol:
Cells of ScY and ScY01 were grown on YP medium containing 200 g/l glucose at 40ºC at 200 rpm for 14 h ~ 16 h to the early-log phase, and harvested in Falcon tubes precooled in liquid N2 by centrifuging for 5 minutes at 4000 rpm (3220 × g). The supernatant was discarded, and the pellet was stored at −80°C until further use. Total RNA extraction, library construction and sequencing were conducted by Majorbio Company (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: evolved thermotolerance strain


title: ScY

value: ScY

value: wild type


title: Exercise_1


title: PSA4958CD4SF, HiC

description: Library name: PSA4958CD4SF

value: Synovial fluid


title: PsA4958CD4, HiC

description: Library name: PsA4958CD4


title: PsA4964_CD8, ATAC

description: Library name: PsA4964_CD8


title: PSA4964CD4, ATAC

description: Library name: PSA4964CD4


title: NRK-52E cells, TGF-beta1 + 3D-EVs-3

city: Guangzhou

first: Qiang

last: Guo

state: Guangdong

address: No. 26, Erheng Road, Yuancun, Tianhe District

institute: Sun-Yat Sen university, The sixth affiliated Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(parameter;default)
Clean reads were mapped to  Rattus_norvegicus  genome using by Hisat2（v2.2.0）
The expression level of genes were calculated by StringTie （v2.1.2） and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads.
DEseq2（1.26.0） was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 and adjusted P value <= 0.05 were considered to be significantly different expressed genes.
GO enrichment analysis and KEGG enrichment analysis were performed using clusterProfiler, a function of R. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value < 0.05)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: NRK-52E cells were maintained in DMEM supplemented 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the treated NRK-52E cells using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
The RNA samples were processed for RNA-seq library construction using the Hieff NGS® RNA Lib Prep Primer Mix for Illumina® (Yeasen, 13335ES96).

treatment_protocol: NRK-52E cells were incubated in DMEM with 10% FBS until 80% convergence, and treated with 10ug/ml TGF-beta1 24h to induced renal fibrosis,and then treated with 2D- or 3D-EVs(5*10^8 particles/ml) for another 48h.

value: Tubular epithelial cells

value: WT

value: Renal fibrosis

value: TGF-beta1 + 3D-EVs


title: MEF Flag rep 2

description: Library name: MEF Flag rep 2


title: PsA4963_CD8, ATAC

description: Library name: PsA4963_CD8

value: Blood

value: CD8 + T-cell


title: PsA4957CD4, HiC

description: Library name: PsA4957CD4


title: Control_2

value: Control


title: PSA4954_CD8, HiC

description: Library name: PSA4954_CD8


title: PSA4958CD8SF, HiC

description: Library name: PSA4958CD8SF


title: NRK-52E cells, TGF-beta1 + 3D-EVs-1


title: PsA4963_CD4, ATAC

description: Library name: PsA4963_CD4