title: HLE-LOH34.31 [UT_TH12]

description: replicate 3


title: HLF-WT45 [UT_TH159_1]

status: Public on Dec 27 2023

type: SRA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: replicate 1

library_source: transcriptomic

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

molecule: total RNA

organism: Homo sapiens

source_name: HLF cells (human HCC)

growth_protocol: All cells were cultured in DMEM medium at 37 °C and 5% CO2

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Cells were left untreated

tag: genotype


title: ID15279_adipose_0yr

city: Chicago

first: Wenhe

last: Lin

state: Illinois

address: 920 E 58th St

country: USA

institute: University of Chicago

data_processing:
RNA-seq data were aligned to the baboon reference genome Panubis1.0 with STAR v2.7.7a. FASTQC was used to confirm that the reads were of high quality. Gene-level expression quantification was performed using featureCounts. Quality controls were performed on two levels using a similar pipeline for GTEx. On the sample level, we first identified and removed sample swaps and contaminations where a sample was not matched to its genotype or contained a mixture of two or more samples using verifyBamID. We removed outlier samples based on expression profile using PCA. We checked sex correctness by examining gene expression for genes on the Y chromosome for each sample. On the gene level, gene expression values for all samples from a given tissue were normalized using the following procedure: 1) read counts were normalized between samples using trimmed mean of M-values (TMM); 2) genes were selected based on expression thresholds of ≥0.1 TPM in ≥10% of samples, and > 3 reads (unnormalized) in ≥10% of samples for both diet conditions; 3) expression values for each gene were inverse normal transformed across samples. After the quality controls, we obtained 570 high-quality RNA samples and 20,224 genes for downstream analyses.
Assembly: Panubis1.0
Supplementary files format and content: raw count matrix of all samples (n=588)
Supplementary files format and content: raw count matrix of post-QC samples (n=570)

organism: Papio anubis

source_name: adipose

extract_protocol:
Approximately 10 mg of each frozen tissue sample was homogenized in 1ml QIAzol Lysis Reagent (79306, QIAGEN) using BeadBug 6 Microtube Homogenizer (D1036, Benchmark Scientific) with 1.5mm Zirconium beads (D1032-15, Benchmark Scientific). RNA was immediately extracted from the homogenate using QIAGEN RNeasy Universal Kit (73404, QIAGEN). RNA concentration and quality was measured using Agilent RNA 6000 Nano Kit and RNA 6000 Pico Kit (5067-1511 & 5067-1513, Agilent) on Agilent 2100 Bioanalyzer.
TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina); TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina)
96 libraries from 16 animals in batch 1 were performed using TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina) and were sequenced 50 base pairs, single-end using the Illumina HiSeq4000 according to manufacturer instructions with the goal of achieving at least 15 million reads per sample. Each sequencing lane contained 24 multiplexed samples from different RNA extraction batches. 498 libraries from 83 animals in batch 2 were performed using TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina) and were sequenced 50 base pairs, paired-end using the Illumina NovaSeq6000 according to manufacturer instructions with the goal of achieving at least 30 million reads per sample. Each sequencing lane contained 84 multiplexed samples from different RNA extraction batches. Samples from the same animal were always in the same RNA extraction, library preparation, and sequencing batches. Samples from different animals were randomized in every processing step to avoid potential batch effects.

treatment_protocol: The animals were feeding a high cholesterol, high fat diet for two years, switching from a low cholesterol, low fat diet.

tag: tissue

value: adipose

tag: animal id

tag: treatment

value: LCLF

tag: time


title: HLF-WT41 [UT_TH106_4]

description: replicate 1


title: ID15175_adipose_2yr

value: HCHF


title: INO80_1

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

library_source: genomic

data_processing:
Base- and modified basecalling were performed with megalodon (v2.3.3) and guppy (v5.0.11) using the res_dna_r941_min_modbases-all-context_v001 model and default parameters.
ARS sequences derived from genome build/assembly Saccharomyces_cerevisisae.R64-1-1 targeted for affinity purification, an in vitro assembled nucleosomal array of 12x601 sequences and a spike-in naked plasmid DNA added in the experiments served as spike-in controls to normalize for methylation efficiencies.
Assembly: Saccharomyces_cerevisiae.R64-1-1
Supplementary files format and content: comma separated files that contain binary information about methylation

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Logarithmic yeast cells were grown in YPR medium and arrested with alpha-factor together with addition of 2% galactose to induce site-specific recombination of native replication origin chromatin domains. Cells were harvested and frozed for subsequent affinity purification.

extract_protocol:
Cell pellets were lysed with dry ice in a commercial coffee grinder and chromatin domains affinity-purified as described in the manuscript. The purified chromatin circles were then treated with the M.CviPI/M.SssI (GpC/CpG-5-methyl-Cytosine-specific) and EcoGII (methyl-6-Adenine-specific) DNA methyltransferases. Methylated DNA was then isolated using Phenol-chloroform extraction.  EcoGII (methyl-6-Adenine-specific) DNA methyltransferases,
MinIONTM Seqencing Library Preparation (Oxford Nanopore Sequencing)
Nanopore long-read sequencing for direct detection of methylated bases

tag: cell lines

tag: cell type

value: yeast cells

value: Y0127:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS305_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR ;ies6delta::his

value: Y0129:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS316_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR;ies6delta::his

value: Y0130:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS315_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR ;ies6delta::his

value: Y0128:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS313_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR ;ies6delta::his


title: ID15175_adipose_0yr


title: HLF-LOH41.94 [UT_TH106_15]

description: replicate 3


title: ID15175_liver_0yr

source_name: liver

value: liver


title: INO80_2


title: ID14948_muscle_2yr

source_name: muscle

value: muscle


title: Control_3

value: Y0065:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS305_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0069:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS316_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0091:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS315_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0094:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS313_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0084:MATa; ade2-1; ura3-1; trp1-1; leu2-3,112; his3-11; can1-100 URA3::LEU2 pTEF2 LEXA-TAP pGAL RecR rDN1::L_RS_LEXA_ARS_RS_5S_35S_L bar1::his3


title: HLF-LOH41.94 [UT_TH106_13]

description: replicate 1


title: ID14948_liver_2yr


title: ID14948_muscle_0yr


title: ID14948_liver_0yr


title: classical cells from a 68 year old with donor id BAT013 DAT128

type: genomic

city: Novato

first: Alan

last: Tomusiak

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: none provided

scan_protocol: For both experiments, DNA was quantified using QubitTM HS dsDNA quantification reagents. Bisulfite conversion and DNA methylation assessment were performed by Diagenode. For all experiments involving FACS, post-sort validations were performed to verify cell sort purity by analyzing sorted populations via flow cytometry. The Clock Foundation assisted with facilitating DNA methylation assessment and data transfer for the initial CD8+ experiment.

data_processing:
PreprocessFunNorm from the minfi package was used to pre-process the Illumina data.
FunNorm pre-processed Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy8

source_name: source dna from classical cells from a 68 year old with donor id BAT013

label_protocol: Both CD8+ cells and remaining PBMCs were washed, stained with 1:500 LIVE/DEADTM Fixable Near-IR Dead Cell staining kit and washed again. CD8+ cells were stained with a CD4/CD8 antibody cocktail (Supplementary Table 2), and the remaining PBMCs were stained with a B Cell/NK Cell/Monocyte antibody cocktail (Supplementary Table 3), after blocking with human IgG. All three fractions were then subjected to FACS analysis using a BD FACSAriaTM II instrument. DNA was isolated using a Zymo Quick-DNA/RNATM Microprep Plus kit.

extract_protocol: 2 million PBMCs were frozen immediately after extraction. The remaining cells were then positively selected for a CD4 fraction using the EasySepTM Human CD4 Positive Selection Kit II. The CD4 cells were stained with 1:500 LIVE/DEADTM Fixable Near-IR Dead Cell staining kit, washed, and stained with CD4/CD8 antibody cocktail (Supplementary Table 2), and the remaining cells were positively selected for a CD8 fraction using the EasySepTM Human CD8 Positive Selection Kit II.

tag: age

tag: Sex

value: Female

value: monocyte

value: classical


title: pbmc cells from a 68 year old with donor id BAT013 DAT130

label: Cy5 and Cy10

source_name: source dna from pbmc cells from a 68 year old with donor id BAT013

value: pbmc


title: HLF-LOH87 [UT_TH106_12]

description: replicate 3


title: pbmc cells from a 68 year old with donor id BAT013 DAT127

label: Cy5 and Cy7


title: pbmc cells from a 68 year old with donor id BAT013 DAT129

label: Cy5 and Cy9


title: ID14948_adipose_0yr

value: adipose

value: LCLF


title: ID15175_muscle_0yr


title: ID15175_liver_2yr

value: HCHF


title: ID14944_liver_2yr


title: ID14944_liver_0yr


title: HLE-LOH34.31 [UT_TH10]

description: replicate 1

source_name: HLE cells (human HCC)


title: ID14944_muscle_0yr


title: HCC68-WT3 [UT_TH1]

description: replicate 1

source_name: HCC68 cells (human HCC)


title: naive cells from a 68 year old with donor id BAT013 DAT125

label: Cy5 and Cy5

source_name: source dna from naive cells from a 68 year old with donor id BAT013

value: naive


title: switched_memory cells from a 68 year old with donor id BAT013 DAT126

label: Cy5 and Cy6

source_name: source dna from switched_memory cells from a 68 year old with donor id BAT013


title: ID14924_liver_2yr


title: ID14924_adipose_2yr


title: ISW2_1

value: yeast cells

value: Y0105:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS305_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR ;isw2delta::ura3

value: Y0106:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS316_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR;isw2delta::ura3

value: Y0102:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS315_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR ;  isw2delta::ura3

value: Y0107:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS313_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR;isw2delta::ura3


title: ID14924_muscle_0yr

value: muscle


title: cd8_em_temra cells from a 68 year old with donor id BAT013 DAT122

label: Cy5 and Cy3

source_name: source dna from cd8_em_temra cells from a 68 year old with donor id BAT013


title: ID14924_liver_0yr

value: liver


title: ID15175_muscle_2yr


title: ID14924_adipose_0yr


title: ID14922_muscle_2yr


title: siNUDT18_rep3

growth_protocol: HLF cells were cultured in DMEM medium at 37 °C and 5% CO2

treatment_protocol: Cells were transfected using 1 nM final concentration of siPools targeting NUDT17, NUDT18 or a negative control.


title: cd8_cm cells from a 68 year old with donor id BAT013 DAT121

source_name: source dna from cd8_cm cells from a 68 year old with donor id BAT013


title: ID14922_liver_2yr


title: ID14944_adipose_0yr


title: ID14948_adipose_2yr


title: ID14922_muscle_0yr


title: siCTRL_rep3

value: siCtrl


title: cd8_naive cells from a 68 year old with donor id BAT013 DAT124

label: Cy5 and Cy4

source_name: source dna from cd8_naive cells from a 68 year old with donor id BAT013


title: cd4_cm cells from a 68 year old with donor id BAT013 DAT120

source_name: source dna from cd4_cm cells from a 68 year old with donor id BAT013


title: HLF-LOH41.94 [UT_TH106_14]

description: replicate 2


title: HLF-LOH87 [UT_TH106_11]

description: replicate 2


title: ID14924_muscle_2yr


title: ID14922_adipose_2yr


title: cd56_bright cells from a 68 year old with donor id BAT013 DAT123

source_name: source dna from cd56_bright cells from a 68 year old with donor id BAT013


title: siNUDT17+siNUDT18_rep2

value: siCombi


title: ID14922_liver_0yr


title: ID14922_adipose_0yr


title: siNUDT17+siNUDT18_rep3


title: ID14916_muscle_2yr


title: siNUDT17_rep3


title: cd4_naive cells from a 68 year old with donor id BAT013 DAT119

source_name: source dna from cd4_naive cells from a 68 year old with donor id BAT013

value: Female


title: siNUDT18_rep2

source_name: HLF cells (human HCC)


title: ID14916_liver_2yr


title: pbmc cells from a 66 year old with donor id BAT012 DAT117

source_name: source dna from pbmc cells from a 66 year old with donor id BAT012

value: Male


title: ID14916_muscle_0yr


title: ID14916_adipose_2yr

source_name: adipose


title: siNUDT17_rep2


title: siCTRL_rep2


title: ID14916_liver_0yr

source_name: liver


title: ID14867_muscle_2yr

source_name: muscle


title: siNUDT17+siNUDT18_rep1


title: cd56_bright cells from a 66 year old with donor id BAT012 DAT115

source_name: source dna from cd56_bright cells from a 66 year old with donor id BAT012


title: siNUDT18_rep1


title: ID14867_liver_2yr


title: ID14867_adipose_2yr


title: siNUDT17_rep1


title: ID14867_liver_0yr


title: cd8_cm cells from a 66 year old with donor id BAT012 DAT113

source_name: source dna from cd8_cm cells from a 66 year old with donor id BAT012


title: ID14867_adipose_0yr


title: cd8_naive cells from a 66 year old with donor id BAT012 DAT112

source_name: source dna from cd8_naive cells from a 66 year old with donor id BAT012


title: ID14852_liver_2yr


title: ID14852_muscle_2yr


title: naive cells from a 66 year old with donor id BAT012 DAT116

source_name: source dna from naive cells from a 66 year old with donor id BAT012


title: pbmc cells from a 66 year old with donor id BAT012 DAT114


title: siCTRL_rep1


title: Bone-marrow-derived cells, 2h incubation with spherical nanoparticles (SNPs), 3

city: Knoxville

first: Paul

last: Dalhaimer

state: Tennessee

address: 1512 Middle Drive, Room 420

department: Chemical and Biomolecular Engineering

institute: University of Tennessee

data_processing:
Reads were trimmed and filtered with fastp (v0.23.2) using parameters `--length_required 31 --detect_adapter_for_pe`.
Trimmed and filtered reads were aligned to the Ensembl Mus musculus genome build GRCm39 version 109 using STAR (v2.7.10a).
Subread featureCounts (v2.0.1) was used to generate a counts matrix of fragments within genes with parameters `-s 0 -p`.
Assembly: Ensembl GRCm39 version 109
Supplementary files format and content: Tab-delimited text files with header line, gene metadata, and raw count of fragments within gene exons.

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone-marrow-derived macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Life Technologies) followed by on-column purification and Dnase I digestion using the RNA Clean & Concentrator-5 (Zymo Research) kit according to the manufacturer's recommendations.
Libraries were contructed using the SMART-Seq® mRNA LP with UMIs (Takara Bio) kit according to the manufacturer's protocol.

treatment_protocol: Bone marrow from BALB/c mice was incubated with macrophage-colony stimulating factor (M-CSF) for 5-7 days. The resulting macrophages were polarized to M1-like with LPS and IFNgamma for 24 hours.

value: Bone marrow

tag: strain

value: BALB/c derived

value: macrophage

value: LPS + IFNgamma

tag: agent

value: SNP


title: ID14847_liver_2yr

value: HCHF


title: cd8_em_temra cells from a 66 year old with donor id BAT012 DAT109

source_name: source dna from cd8_em_temra cells from a 66 year old with donor id BAT012


title: Bone-marrow-derived cells, 2h incubation with spherical nanoparticles (SNPs), 2


title: Bone-marrow-derived cells, 2h incubation with spherical nanoparticles (SNPs), 1


title: ID14847_muscle_0yr

value: LCLF


title: ID14852_muscle_0yr


title: cd4_naive cells from a 66 year old with donor id BAT012 DAT110

source_name: source dna from cd4_naive cells from a 66 year old with donor id BAT012


title: Bone-marrow-derived cells, 2h incubation with human high density lipoprotein (hHDL), 3

value: hHDL


title: ID14852_liver_0yr


title: ID14847_adipose_2yr

value: adipose


title: ID14847_liver_0yr


title: ID14847_adipose_0yr


title: ID14847_muscle_2yr


title: ID14867_muscle_0yr


title: switched_memory cells from a 57 year old with donor id BAT011 DAT108

source_name: source dna from switched_memory cells from a 57 year old with donor id BAT011


title: classical cells from a 57 year old with donor id BAT011 DAT106

source_name: source dna from classical cells from a 57 year old with donor id BAT011

value: monocyte

value: classical


title: Bone-marrow-derived cells, 2h incubation with human high density lipoprotein (hHDL), 1


title: Bone-marrow-derived cells, 2h incubation with human high density lipoprotein (hHDL), 2


title: ID14833_liver_2yr


title: naive cells from a 57 year old with donor id BAT011 DAT107

source_name: source dna from naive cells from a 57 year old with donor id BAT011

value: naive


title: ID14852_adipose_0yr


title: cd4_cm cells from a 66 year old with donor id BAT012 DAT111

source_name: source dna from cd4_cm cells from a 66 year old with donor id BAT012


title: ID14852_adipose_2yr


title: Bone-marrow-derived cells, 2h incubation with volume equivalent of PBS to either hHDL or SNPs, 3

value: PBS


title: ID14833_adipose_2yr


title: pbmc cells from a 57 year old with donor id BAT011 DAT105

source_name: source dna from pbmc cells from a 57 year old with donor id BAT011

value: pbmc


title: Bone-marrow-derived cells, 2h incubation with volume equivalent of PBS to either hHDL or SNPs, 2


title: ID14833_muscle_0yr

value: muscle


title: cd8_em_temra cells from a 57 year old with donor id BAT011 DAT104

source_name: source dna from cd8_em_temra cells from a 57 year old with donor id BAT011

value: Female


title: ID14833_liver_0yr

value: liver


title: ID14833_adipose_0yr


title: Bone-marrow-derived cells, 2h incubation with volume equivalent of PBS to either hHDL or SNPs, 1

value: Bone marrow


title: cd8_cm cells from a 57 year old with donor id BAT011 DAT103

source_name: source dna from cd8_cm cells from a 57 year old with donor id BAT011


title: ID14473_muscle_2yr


title: ID14473_liver_2yr


title: cd8_naive cells from a 57 year old with donor id BAT011 DAT102

source_name: source dna from cd8_naive cells from a 57 year old with donor id BAT011


title: ID14473_muscle_0yr


title: ID14473_adipose_2yr

source_name: adipose


title: 5xFAD+L_LEC, rep 3

city: Haikou

first: Feifan

last: Zhou

address: No 58, Renmin Avenue, Haikou, Hainan province

country: China

institute: School of Biomedical Engineering, Hainan University

description:
5xFAD+L3_LEC_fpkm
all.genes.expression.annot.WT.xls

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, low quality sequences and reads containing poly-N with Trimmomatic software. All the downstream analyses were based on the clean data with high quality.
The clean reads were aligned to the reference genome using the software Hisat2, and the genome file was mm10.StringTie software was used to search the new transcripts, and the genome annotation version was mm10.
Gene expression profiling was based on the number of reads. FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels.
DESeq2 was selected to identifying differentially expressed genes (DEGs). Genes with an adjusted Pvalue < 0.05 and abs (log2(fold change)) >1 were assigned as DEGs.
Assembly: mm10

source_name: meningeal lymphatic endothelial cells

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen,15596018)

value: meningeal lymphatic endothelial cells

value: light


title: pbmc cells from a 66 year old with donor id BAT012 DAT118

source_name: source dna from pbmc cells from a 66 year old with donor id BAT012

value: Male


title: ID14473_adipose_0yr


title: 5xFAD+L_LEC, rep 1

description:
5xFAD+L1_LEC_fpkm
all.genes.expression.annot.WT.xls


title: 5xFAD+L_LEC, rep 2

description:
5xFAD+L2_LEC_fpkm
all.genes.expression.annot.WT.xls


title: cd56_bright cells from a 57 year old with donor id BAT011 DAT101

source_name: source dna from cd56_bright cells from a 57 year old with donor id BAT011


title: ID14833_muscle_2yr

source_name: muscle


title: pbmc cells from a 57 year old with donor id BAT011 DAT100


title: ID14369_muscle_2yr


title: ID14369_adipose_2yr


title: ID14369_liver_2yr

source_name: liver


title: ID14916_adipose_0yr


title: pbmc cells from a 57 year old with donor id BAT011 DAT99


title: ID14369_muscle_0yr


title: 5xFAD_LEC, rep 2

description:
5xFAD2_LEC_fpkm
all.genes.expression.annot.WT.xls


title: ID14369_liver_0yr


title: ID14473_liver_0yr


title: 5xFAD_LEC, rep 4

description:
5xFAD4_LEC_fpkm
all.genes.expression.annot.WT.xls


title: 5xFAD_LEC, rep 1

description:
5xFAD1_LEC_fpkm
all.genes.expression.annot.WT.xls


title: ID14355_muscle_2yr


title: HLF-LOH87 [UT_TH106_10]

description: replicate 1

source_name: HLF cells (human HCC)


title: cd4_cm cells from a 57 year old with donor id BAT011 DAT98

source_name: source dna from cd4_cm cells from a 57 year old with donor id BAT011


title: cd4_naive cells from a 57 year old with donor id BAT011 DAT97

source_name: source dna from cd4_naive cells from a 57 year old with donor id BAT011


title: ID14355_liver_2yr


title: WT_LEC, rep 4

description:
WT4_LEC_fpkm
all.genes.expression.annot.WT.xls

value: WT


title: ID14355_liver_0yr


title: pbmc cells from a 35 year old with donor id BAT010 DAT95

source_name: source dna from pbmc cells from a 35 year old with donor id BAT010


title: pbmc cells from a 35 year old with donor id BAT010 DAT96


title: WT_LEC, rep 3

description:
WT3_LEC_fpkm
all.genes.expression.annot.WT.xls


title: ID14355_adipose_2yr

value: HCHF


title: ID14355_adipose_0yr

value: LCLF


title: ID14355_muscle_0yr


title: WT_LEC, rep 2

description:
WT2_LEC_fpkm
all.genes.expression.annot.WT.xls


title: cd8_cm cells from a 35 year old with donor id BAT010 DAT93

source_name: source dna from cd8_cm cells from a 35 year old with donor id BAT010


title: cd8_em_temra cells from a 35 year old with donor id BAT010 DAT94

source_name: source dna from cd8_em_temra cells from a 35 year old with donor id BAT010


title: ID14350_liver_2yr


title: ID14350_liver_0yr


title: ID14350_muscle_2yr


title: ID14350_adipose_2yr


title: WT_LEC, rep 1

description:
WT1_LEC_fpkm
all.genes.expression.annot.WT.xls


title: ID14369_adipose_0yr


title: ID14350_adipose_0yr


title: ID14290_muscle_2yr


title: 5xFAD+L_M, rep 2

description:
5xFAD+L02_fpkm
all.genes.expression.annot.LT.xls

source_name: meninge

value: meninge


title: ID14290_liver_2yr


title: 5xFAD+L_M, rep 4

description:
5xFAD+L04_fpkm
all.genes.expression.annot.LT.xls


title: classical cells from a 35 year old with donor id BAT010 DAT92

source_name: source dna from classical cells from a 35 year old with donor id BAT010


title: 5xFAD+L_M, rep 1

description:
5xFAD+L01_fpkm
all.genes.expression.annot.LT.xls


title: ID14290_adipose_2yr

value: adipose


title: cd4_naive cells from a 35 year old with donor id BAT010 DAT90

source_name: source dna from cd4_naive cells from a 35 year old with donor id BAT010


title: ID14290_muscle_0yr


title: ID14290_liver_0yr


title: cd56_bright cells from a 35 year old with donor id BAT010 DAT91

source_name: source dna from cd56_bright cells from a 35 year old with donor id BAT010


title: 5xFAD_M, rep 4

description:
5xFAD04_fpkm
all.genes.expression.annot.LT.xls


title: ID14290_adipose_0yr


title: cd8_naive cells from a 35 year old with donor id BAT010 DAT88

source_name: source dna from cd8_naive cells from a 35 year old with donor id BAT010


title: ID14154_muscle_2yr


title: 5xFAD_M, rep 2

description:
5xFAD02_fpkm
all.genes.expression.annot.LT.xls


title: ID14154_liver_2yr


title: 5xFAD_M, rep 1

description:
5xFAD01_fpkm
all.genes.expression.annot.LT.xls


title: switched_memory cells from a 35 year old with donor id BAT010 DAT89

source_name: source dna from switched_memory cells from a 35 year old with donor id BAT010


title: cd4_cm cells from a 35 year old with donor id BAT010 DAT87

source_name: source dna from cd4_cm cells from a 35 year old with donor id BAT010


title: ID14154_adipose_2yr

source_name: adipose


title: WT_M, rep 4

description:
WT04_fpkm
all.genes.expression.annot.LT.xls


title: ID14154_liver_0yr


title: pbmc cells from a 35 year old with donor id BAT010 DAT86


title: ID14077_muscle_2yr


title: ID14154_muscle_0yr


title: ID14154_adipose_0yr


title: naive cells from a 35 year old with donor id BAT010 DAT85

source_name: source dna from naive cells from a 35 year old with donor id BAT010


title: ID14077_liver_2yr


title: WT_M, rep 3

description:
WT03_fpkm
all.genes.expression.annot.LT.xls


title: ID14077_adipose_2yr


title: ID14077_muscle_0yr

source_name: muscle


title: ID14077_liver_0yr

source_name: liver


title: pbmc cells from a 47 year old with donor id BAT007 DAT84

source_name: source dna from pbmc cells from a 47 year old with donor id BAT007


title: WT_M, rep 2

description:
WT02_fpkm
all.genes.expression.annot.LT.xls


title: cd8_cm cells from a 47 year old with donor id BAT007 DAT83

source_name: source dna from cd8_cm cells from a 47 year old with donor id BAT007


title: WT_M, rep 1

description:
WT01_fpkm
all.genes.expression.annot.LT.xls


title: ID14062_muscle_2yr


title: 5xFAD+L_HP, rep 4

description:
5xFAD+L4_HP_fpkm
all.genes.expression.annot.LT.xls

source_name: hippocampus

value: hippocampus


title: ID14077_adipose_0yr


title: cd8_naive cells from a 47 year old with donor id BAT007 DAT82

source_name: source dna from cd8_naive cells from a 47 year old with donor id BAT007


title: ID14062_liver_2yr


title: ID14062_adipose_2yr


title: cd4_em_temra cells from a 47 year old with donor id BAT007 DAT81

source_name: source dna from cd4_em_temra cells from a 47 year old with donor id BAT007


title: 5xFAD+L_HP, rep 3

description:
5xFAD+L3_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID14062_muscle_0yr


title: ID14062_liver_0yr


title: cd4_cm cells from a 47 year old with donor id BAT007 DAT80

source_name: source dna from cd4_cm cells from a 47 year old with donor id BAT007


title: switched_memory cells from a 47 year old with donor id BAT007 DAT79

source_name: source dna from switched_memory cells from a 47 year old with donor id BAT007


title: 5xFAD+L_HP, rep 1

description:
5xFAD+L1_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID14058_liver_2yr


title: ID14058_muscle_2yr


title: ID14062_adipose_0yr


title: 5xFAD_HP, rep 4

description:
5xFAD4_HP_fpkm
all.genes.expression.annot.LT.xls


title: 5xFAD+L_HP, rep 2

description:
5xFAD+L2_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID14058_muscle_0yr


title: ID14058_adipose_2yr


title: 5xFAD_HP, rep 3

description:
5xFAD3_HP_fpkm
all.genes.expression.annot.LT.xls


title: naive cells from a 47 year old with donor id BAT007 DAT78

source_name: source dna from naive cells from a 47 year old with donor id BAT007


title: ID14058_adipose_0yr


title: classical cells from a 47 year old with donor id BAT007 DAT77

source_name: source dna from classical cells from a 47 year old with donor id BAT007

value: monocyte

value: classical


title: ID14016_muscle_2yr


title: ID14058_liver_0yr


title: 5xFAD_HP, rep 2

description:
5xFAD2_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID14016_liver_2yr


title: cd56_bright cells from a 47 year old with donor id BAT007 DAT76

source_name: source dna from cd56_bright cells from a 47 year old with donor id BAT007


title: ID14016_muscle_0yr


title: 5xFAD_HP, rep 1

description:
5xFAD1_HP_fpkm
all.genes.expression.annot.LT.xls


title: cd8_em_temra cells from a 47 year old with donor id BAT007 DAT75

source_name: source dna from cd8_em_temra cells from a 47 year old with donor id BAT007


title: ID14016_liver_0yr


title: switched_memory cells from a 55 year old with donor id BAT006 DAT74

source_name: source dna from switched_memory cells from a 55 year old with donor id BAT006


title: WT_HP, rep 4

description:
WT4_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID14016_adipose_0yr


title: WT_HP, rep 3

description:
WT3_HP_fpkm
all.genes.expression.annot.LT.xls


title: naive cells from a 55 year old with donor id BAT006 DAT73

source_name: source dna from naive cells from a 55 year old with donor id BAT006

value: naive


title: ID13644_liver_2yr


title: ID13644_adipose_2yr

source_name: adipose


title: classical cells from a 55 year old with donor id BAT006 DAT72

source_name: source dna from classical cells from a 55 year old with donor id BAT006


title: WT_HP, rep 1

description:
WT1_HP_fpkm
all.genes.expression.annot.LT.xls


title: ID13644_liver_0yr


title: ID13644_muscle_0yr

source_name: muscle


title: ID12719_muscle_2yr


title: ID12719_adipose_2yr


title: MLL-AF9 cells in NSG  mice, biol rep 3

city: Tokyo

first: Susumu

last: Goyama

address: 4-6-1 Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

data_processing: The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

source_name: Bone marrow

growth_protocol: We transduced MLL-AF9 (coexpress GFP) into mouse bone marrow progenitor cells, and transplanted the cells into sublethally irradiated recipient mice. All recipient mice developed AML around 2 months after transplantation. We collected GFP+ leukemia cells from spleens of the moribund mice, and enriched for leukemia stem cell activity by serial transplantation through secondary, tertiary, and quaternary recipient mice after sublethal irradiation. The MLL-AF9-expressing AML cells were then maintained in non-irradiated recipient mice through serial (more than 10 times) transplantations. These aggressive MLL-AF9 cells were then transplanted into WT, Rag2-/- or NSG mice to determine the role of specific immune cells in the development of AML

extract_protocol: Total RNA was extracted from 3.0 x 106 GFP+ leukemia cells using RNeasy Mini Kit (Qiagen). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

tag: cell line

value: MLL-AF9 cells

value: Mouse bone marrow cells expressing MLL-AF9

value: NSG


title: MLL-AF9 cells in NSG  mice, biol rep 4


title: pbmc cells from a 55 year old with donor id BAT006 DAT69

source_name: source dna from pbmc cells from a 55 year old with donor id BAT006

value: Female

value: pbmc


title: ID14016_adipose_2yr


title: ID12719_liver_0yr

source_name: liver

value: liver


title: ID12719_muscle_0yr

value: muscle


title: MLL-AF9 cells in NSG  mice, biol rep 2

value: Bone marrow


title: pbmc cells from a 55 year old with donor id BAT006 DAT70


title: ID13644_muscle_2yr


title: ID12681_liver_2yr


title: cd8_naive cells from a 55 year old with donor id BAT006 DAT67

source_name: source dna from cd8_naive cells from a 55 year old with donor id BAT006


title: ID12681_adipose_2yr


title: ID12681_muscle_2yr


title: ID12719_adipose_0yr


title: ID12681_muscle_0yr


title: cd56_bright cells from a 55 year old with donor id BAT006 DAT66

source_name: source dna from cd56_bright cells from a 55 year old with donor id BAT006


title: ID12681_liver_0yr


title: ID13644_adipose_0yr


title: MLL-AF9 cells in Rag2-/-  mice, biol rep 3


title: ID12681_adipose_0yr


title: ID12481_muscle_2yr


title: pbmc cells from a 55 year old with donor id BAT006 DAT71


title: cd8_em_temra cells from a 55 year old with donor id BAT006 DAT65

source_name: source dna from cd8_em_temra cells from a 55 year old with donor id BAT006


title: ID12719_liver_2yr


title: MLL-AF9 cells in Rag2-/-  mice, biol rep 2


title: ID12481_liver_2yr


title: cd8_cm cells from a 55 year old with donor id BAT006 DAT68

source_name: source dna from cd8_cm cells from a 55 year old with donor id BAT006


title: MLL-AF9 cells in Rag2-/-  mice, biol rep 1


title: ID12481_adipose_2yr


title: MLL-AF9 cells in NSG  mice, biol rep 1


title: ID12481_muscle_0yr


title: ID12481_liver_0yr


title: cd4_naive cells from a 55 year old with donor id BAT006 DAT63

source_name: source dna from cd4_naive cells from a 55 year old with donor id BAT006


title: pbmc cells from a 56 year old with donor id BAT005 DAT62

source_name: source dna from pbmc cells from a 56 year old with donor id BAT005

value: Male


title: ID12423_liver_2yr

value: HCHF


title: ID12481_adipose_0yr

value: LCLF


title: MLL-AF9 cells in C57BL/6 mice, biol rep 4

value: WT


title: MLL-AF9 cells in C57BL/6 mice, biol rep 3


title: MLL-AF9 cells in Rag2-/-  mice, biol rep 4


title: MLL-AF9 cells in C57BL/6 mice, biol rep 2


title: MLL-AF9 cells in C57BL/6 mice, biol rep 1


title: ID12423_adipose_0yr

value: adipose


title: cd8_em_temra cells from a 56 year old with donor id BAT005 DAT60

source_name: source dna from cd8_em_temra cells from a 56 year old with donor id BAT005


title: ID12282_muscle_2yr


title: ID12282_liver_2yr


title: WT_HP, rep 2

description:
WT2_HP_fpkm
all.genes.expression.annot.LT.xls

source_name: hippocampus

value: hippocampus


title: cd4_cm cells from a 55 year old with donor id BAT006 DAT64

source_name: source dna from cd4_cm cells from a 55 year old with donor id BAT006


title: MLL-AF9 cells obtained after serial transplantations, biol rep 4

data_processing:
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.
Raw gene counts were derived from the read alignments by Rsubread.1 (v2.12.3)28 and further transferred into count per million (CPM) by edgeR2 (v3.40.2).

growth_protocol: We transduced MLL-AF9 (coexpress GFP) into mouse bone marrow progenitor cells, and transplanted the cells into sublethally irradiated recipient mice. All recipient mice developed AML around 2 months after transplantation. We collected some GFP+ cells as newly genarated AML cells to extract RNAs. We enriched for leukemia stem cell activity of the remaining GFP+ cells by 5 times serial transplantations to generate aggressive AML cells.

extract_protocol: Total RNA was extracted from 3.0 x 106 GFP+ leukemia cells using RNeasy Mini Kit (Qiagen).


title: classical cells from a 56 year old with donor id BAT005 DAT58

source_name: source dna from classical cells from a 56 year old with donor id BAT005

value: monocyte


title: ID12282_adipose_2yr


title: MLL-AF9 cells obtained after serial transplantations, biol rep 3


title: cd56_bright cells from a 56 year old with donor id BAT005 DAT57

source_name: source dna from cd56_bright cells from a 56 year old with donor id BAT005


title: ID12282_muscle_0yr


title: MLL-AF9 cells obtained after serial transplantations, biol rep 2


title: ID12282_adipose_0yr

source_name: adipose


title: ID12282_liver_0yr


title: ID12423_adipose_2yr


title: MLL-AF9 cells obtained after serial transplantations, biol rep 1


title: ID12218_muscle_2yr


title: switched_memory cells from a 56 year old with donor id BAT005 DAT55

source_name: source dna from switched_memory cells from a 56 year old with donor id BAT005


title: ID12218_liver_2yr


title: pbmc cells from a 56 year old with donor id BAT005 DAT61


title: ID12423_muscle_0yr

source_name: muscle


title: ID12423_liver_0yr


title: ID12218_adipose_2yr


title: cd8_cm cells from a 56 year old with donor id BAT005 DAT59

source_name: source dna from cd8_cm cells from a 56 year old with donor id BAT005


title: ID12218_muscle_0yr


title: Newly generated MLL-AF9 cells, biol rep 4

source_name: Bone marrow


title: naive cells from a 56 year old with donor id BAT005 DAT54

source_name: source dna from naive cells from a 56 year old with donor id BAT005


title: ID12218_adipose_0yr


title: ID12218_liver_0yr

source_name: liver


title: Newly generated MLL-AF9 cells, biol rep 3


title: Newly generated MLL-AF9 cells, biol rep 2


title: MCF7 cells control

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17, Chuo-Ku

department: Pathology

institute: Sapporo Medical University

description: MCF7 Eribulin 0nM

data_processing:
The bulk-RNA-Seq results were analyzed using the CLC Genomics Workbench Version 12.0.2 (Filgen Inc.).
Assembly: hg19
Supplementary files format and content: Excel file includes counts and RPKM values for each Sample

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using Rneasy mini plus kit (Qiagen). 3.0 ug of total RNA was used for the construction of sequencing libraries.
The libraries for sequencing were constructed using TruSeq Stranded mRNA (Illumina) according to the protocol.

treatment_protocol: MCF7 cells were treated by Eribulin (10nM) for 2 days.

value: breast cancer

value: Wild type

value: non-treated


title: cd8_naive cells from a 56 year old with donor id BAT005 DAT53

source_name: source dna from cd8_naive cells from a 56 year old with donor id BAT005


title: MCF7 cells treated by Eribulin

description: MCF7 Eribulin 10nM

value: Eribulin


title: cd4_em_temra cells from a 56 year old with donor id BAT005 DAT52

source_name: source dna from cd4_em_temra cells from a 56 year old with donor id BAT005


title: pbmc cells from a 56 year old with donor id BAT005 DAT56


title: LN_FRC_D14_3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Lymph Node

extract_protocol: For freshly-isolated samples, 500-1000 cells were double-sorted into 5ul TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich). Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

tag: cell subtype

value: Lymph Node

value: Fibroblastic reticular cells


title: Newly generated MLL-AF9 cells, biol rep 1

value: MLL-AF9 cells

value: Mouse bone marrow cells expressing MLL-AF9


title: LN_FRC_D14_2


title: LN_FRC_D14_4


title: cd4_naive cells from a 56 year old with donor id BAT005 DAT50

source_name: source dna from cd4_naive cells from a 56 year old with donor id BAT005


title: AML12 cells, KI 8

city: Zaragoza

first: Jesus

last: Osada

state: Spain

address: C/ Miguel Servet 177

department: Biochemistry and Molecular Biology

country: Spain

institute: Universidad de Zaragoza

data_processing:
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. These clean data were further mapped to pre-defined reference genome generating mapped data. Assessment on insert size and sequencing randomness were processed on mapped data as library quality control. Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization.
Assembly: eference genome was pre-defined for the analysis. The download address is: https://www.ncbi.nlm.nih.gov/genome/?term=Mus+musculus. HISAT2[2] is a highly efficient system for mapping RNA-seq reads, which is a more advanced version of TopHat2/Bowtie2.HISAT2 uses a Burrows-Wheeler Transform and Ferragina-Manzini（FM）index based search. HISAT2 uses one global graph FM index (GFM) to represent general population, as well as small indexes (local indexes) combined with several alignment strategies in order to achieve more efficient alignment. StringTie[3] was applied to assemble the mapped reads. The algorithm is established based on optimality theory. It utilizes a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantify transcripts representing multiple spliced variants for each gene locus.
Supplementary files format and content: Fragments Per Kilobase of transcript per Million (FPKM)  values for each Sample

molecule: polyA RNA

extract_protocol:
RNA was extracted from AML12 cells using  Quick-RNA MiniPrep kit (Cat.No:R1055, ZYMO Research Irvine, CA, USA). Purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0, Agilent 2100, etc. Only RNA with good quality could move on to following procedures.
Qualified RNA were processed for library construction. The procedures are described as follow: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.
In order to ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration. Library with concentration larger than 2 nM is acceptable.

value: alpha mouse liver 12

value: TXNDC5 Knockin


title: AML12 cells, KI 7


title: CR5

city: Weifang

first: Wenxia

last: Su

address: No 7166, Baotong West Street

institute: Weifang Medical University

data_processing:
Total RNA was extracted from the MNCs of AML patients using the mirVanaTM microRNA isolation kit. The samples with rRNA Ratio [28s/18s] ≥ 1.5 and RNA Integrity Number (RIN) ≥ 8 were adopted.
Small RNA libraries were constructed for 10 samples (5 initially diagnosed AML and 5 CR AML) using the “The NEBNext Multiplex Small RNA Library Prep Set for Illumina” according to the manufacturer’s recommendations. The libraries were subsequently sequenced on HiSeq2500.
FASTQ files with raw data obtained from RNA-Seq experiments were checked with FastQC software and cleaned with cutadapt-1.7.1 and fastx-toolkit-0.0.14 softwares. This was followed by adapter trimming and sequence alignment with GRCh37 human genome assembly database using bowtie-1.1.1. Known miRNA reads aligned to pre-miRNA sequences in miRBase v22. rRNA, tRNA, snRNA, other ncRNA aligned to the corresponding sequences in Rfam (release 11.0). Repeat regions aligned to the corresponding sequences in RepBase (version 20.04).
The unaligned potential novel miRs were clustered with miRDeep2 and theirunique IDs were generated. Read normalization was performed with TPM (Transcripts Reads Number Per Million), and differentially expressed microRNAS (DEMs) were identified in 5 paired bone marrow samples by R package edgeR/limma.
The microRNAs with adjusted p values < 0.05, and fold change (FC) ≥ 2 representing positive log2FC (> 1.0) and negative log2FC (< −1.0) were considered to be significantly different. Interesections of DEMs in 5 paired bone marrow samples were achieved by R package.
Assembly: hg38
Supplementary files format and content: B_Group_VS_C_Group known miRNA.xlsx.gz
Supplementary files format and content: known_precursor.summaryTable.xls.gz
Supplementary files format and content: B_Group_VS_C_Group novel miRNA.xlsx.gz
Supplementary files format and content: novel_precursor.summaryTable.xls.gz

source_name: bone marrow

extract_protocol: RNA libraries for RNA-seq was prepared using NEBNext Multiplex Small RNA library prep set folllowing manufacture's  protocols

tag: disease

value: acute myeloid leukemia (AML)

tag: timepoint

value: complete remission

value: bone marrow

value: primary cell

value: Mononuclear cells


title: CR3


title: LN_FRC_D5_4

value: WT


title: CR2


title: AML12 cells, KI 5


title: pbmc cells from a 30 year old with donor id BAT004 DAT49

source_name: source dna from pbmc cells from a 30 year old with donor id BAT004

value: Female

value: pbmc


title: AML12 cells, KI 6


title: LN_FRC_D5_3


title: AML12 cells, WT 8


title: cd4_cm cells from a 56 year old with donor id BAT005 DAT51

source_name: source dna from cd4_cm cells from a 56 year old with donor id BAT005

value: Male


title: LN_FRC_D5_2


title: cd4_naive cells from a 30 year old with donor id BAT004 DAT46

source_name: source dna from cd4_naive cells from a 30 year old with donor id BAT004


title: pbmc cells from a 30 year old with donor id BAT004 DAT48


title: CR1


title: LN_FRC_D14_5


title: AML12 cells, WT 7


title: LN_FRC_D5_1


title: LN_FRC_D14_1


title: pbmc cells from a 30 year old with donor id BAT004 DAT45


title: CR4


title: LN_Ly6CLoMM_D14_2

value: Monocyte-Macrophage


title: AML4

value: initial diagnosis


title: switched_memory cells from a 30 year old with donor id BAT004 DAT44

source_name: source dna from switched_memory cells from a 30 year old with donor id BAT004


title: LN_Ly6CLoMM_D14_1

value: Lymph Node


title: AML12 cells, KO 8

value: TXNDC5 Knockdown


title: naive cells from a 30 year old with donor id BAT004 DAT43

source_name: source dna from naive cells from a 30 year old with donor id BAT004

value: naive


title: LN_Ly6CHiMM_D14_3


title: cd4_cm cells from a 30 year old with donor id BAT004 DAT47

source_name: source dna from cd4_cm cells from a 30 year old with donor id BAT004


title: AML3


title: LN_Ly6CHiMM_D14_2


title: AML12 cells, KO 6


title: AML2


title: AML1


title: classical cells from a 30 year old with donor id BAT004 DAT42

source_name: source dna from classical cells from a 30 year old with donor id BAT004

value: monocyte

value: classical


title: cd56_bright cells from a 30 year old with donor id BAT004 DAT41

source_name: source dna from cd56_bright cells from a 30 year old with donor id BAT004


title: AML12 cells, KO 7

value: alpha mouse liver 12


title: AML5

value: acute myeloid leukemia (AML)


title: AML12 cells, KO 5


title: cd8_cm cells from a 30 year old with donor id BAT004 DAT40

source_name: source dna from cd8_cm cells from a 30 year old with donor id BAT004


title: LN_Ly6CHiMM_D14_1


title: cd8_naive cells from a 30 year old with donor id BAT004 DAT39

source_name: source dna from cd8_naive cells from a 30 year old with donor id BAT004


title: BM neutrophils, WT, H3K27Ac, control, rep3

city: La Jolla

first: Ben

last: Croker

address: 9500 Gilman Drive

department: Department of Pediatrics

institute: University of California San Diego

data_processing:
Sequencing reads were mapped to mm9 reference genome using BWA v0.7.17 aligner. Hotspot peak caller was used to identify peaks of read density.
Assembly: mm9
Supplementary files format and content: coverage track in bigwig format was prepared using bamCoverage function of the deepTools
Library strategy: CUT&Tag

source_name: bone marrow neutrophil

extract_protocol:
2 × 10^5cells were washed in 200 μL of wash buffer [20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, and 1× protease inhibitors] by gentle pipetting, and then resuspended in 1.5 mL wash buffer. Ten microliters of concanavalin A–coated magnetic beads (Bangs Laboratories, ca.) were activated and then added to 2 × 105cells with incubation on an end-over-end rotator at room temperature for 10 min. The supernatant was removed, and bead-bound cells were resuspended in 50 μL of antibody buffer [20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, one Roche Complete Protease Inhibitor EDTA-Free tablet, 0.05% digitonin, 0.1% BSA, and 2 mM EDTA]. Rabbit polyclonal Anti-Histone H3 (citrulline R2 + R8 + R17) antibody (Abcam, ab5103) was added to bead-bound cells (1:50 dilution) and incubated on a nutator overnight at 4°C. As a control, histone H3 (acetyl K27)  (Abcam ab4729) was added to bead-bound cells (1:50 dilution) and incubated on a nutator overnight at 4°C. After removing the supernatant in the next morning, the cells were incubated with Donkey Anti-Rabbit Immunoglobulin G (IgG) antibody (1:100 dilution, Jackson Immunoresearch) in 100ul antibody buffer on a nutator at room temperature for 1 hour. The control cells were incubated with Rabbit Anti-Mouseimmunoglobulin G (IgG) antibody (1:100 dilution, Jackson Immunoresearch). Bead-bound cells were washed twice with 1mL dig-wash buffer [20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, and 0.05% digitonin] to remove the unbound antibodies. 2.5 μL of CUTANA™ pAG-Tn5 (EpiCypher) was added into 50 μl of dig-300 buffer [20 mM HEPES (pH 7.5), 300 mM NaCl, 0.5 mM spermidine, one Roche Complete Protease Inhibitor EDTA-Free tablet, and 0.01% digitonin], and was mixed with the bead-bound cells and then rotated at room temperature for 1 hour. Bead-bound cells were washed twice in 1mL of dig-300 buffer to remove unbound pA-Tn5 protein. Next, cells were resuspended in 300 μl of tagmentation buffer [20 mM HEPES (pH 7.5), 300 mM NaCl, 0.5 mM spermidine, 1 Roche Complete Protease Inhibitor EDTA-Free tablet, 0.01% digitonin, and 10 mM MgCl2] and incubated at 37°C for 1 hour. To stop tagmentation and solubilize DNA fragments, 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K (Thermo Fisher Scientific) were added to each sample, and were further incubated at 55°C for 60 min. To extract the DNA, cells were mixed with 300 µL PCI (Thermo Fisher), centrifuged at 16,000 x g for 3min, and then mixed with 300 µL Chloroform (Sigma). The aqueous layer was added into 300 µL 100% ethanol, centrifuged at 4 °C 16000 x g for 10 min, and then rinsed with 1 ml 100% ethanol. The DNA was dissolved in 30 µL 1 mM Tris-HCl (pH 8), 0.1 mM EDTA.
To generate the sequencing libraries, the mixture was mixed with a universal i5 primer and a uniquely barcoded i7 primer and then amplified with the NEBNext HiFi 2x PCR Master mix (NEB, M0541). The libraries were cleaned-up with SPRI paramagnetic beads (Beckman Coulter) and washed with 80% ethanol, and then dissolved in 25 µL 10 mM Tris-HCl (pH 8). TapeStation D1000 capillary electrophoresis was performed to Determine the size distribution and concentration of libraries.
Paired-end Illumina sequencing were performed on the barcoded libraries following the manufacturer’s instructions.

value: bone marrow neutrophil

value: ice

tag: antibody


title: AML12 cells, WT 5-6


title: LN_Ly6CLoMM_D5_2


title: BM neutrophils, WT, H3K27Ac, control, rep2


title: pbmc cells from a 30 year old with donor id BAT002 DAT38

source_name: source dna from pbmc cells from a 30 year old with donor id BAT002


title: PAEC_47, passage_3

city: Providence

first: Navneet

last: Singh

state: Rhode Island

address: 593 Eddy Street, POB Suite 334

department: Medicine

institute: Brown University

description:
EC063P3
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

data_processing:
Quality control performed using FastQC (Babraham Bioinformatics, Cambridge, UK)
Supplementary files format and content: tab-limited text files include raw counts for each sample

source_name: pulmonary artery endothelial cell

growth_protocol: Pulmonary artery catheter tips with balloon were placed directly into one well of a 24 well plate with Attachment Factor Solution (Cell Applications, Inc; San Diego, CA) and washed with fresh media (EndoGRO-vascular endothelial growth factor [VEGF] complete media kit; Millipore Sigma, Billerica, MA) every two days.Cells were then seeded into T-25 and T-75 flasks until passaged cells reached confluence over the next four to five days.

extract_protocol:
RNA was extracted from frozen cell pellets by Genewiz (Azenta) per their protocol.
Libraries were constructed by Genewiz (Azenta) per their protocol.

value: pulmonary artery endothelial cell

tag: ph group/control

value: Group 1 PAH

tag: ph subtype

value: HPAH

tag: passaged specimen

value: Passage 3


title: PAEC_47, passage_4

description:
EC063P4
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

tag: tissue

value: Passage 4


title: LN_Ly6CLoMM_D5_1

tag: genotype

value: WT


title: PAEC_45

description:
EC040A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 2 PH

value: CpcPH


title: pbmc cells from a 30 year old with donor id BAT002 DAT37

value: Female

value: pbmc


title: LN_Ly6CHiMM_D5_3

value: Lymph Node

value: Monocyte-Macrophage


title: BM neutrophils, WT, H3K27Ac, control, rep1

tag: treatment


title: BM neutrophils, WT, H3Cit, control, rep3


title: LN_Ly6CHiMM_D5_2


title: pbmc cells from a 30 year old with donor id BAT002 DAT36


title: LN_Ly6CHiMM_D5_1


title: switched_memory cells from a 30 year old with donor id BAT002 DAT35

source_name: source dna from switched_memory cells from a 30 year old with donor id BAT002


title: BM neutrophils, WT, H3Cit, control, rep2


title: BM neutrophils, WT, H3Cit, control, rep1


title: PAEC_43

description:
EC033A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 3 PH


title: LN_Ly6CLoMM_D5_3

source_name: Lymph Node


title: PAEC_42

description:
EC032A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: M504

city: Brighton

first: Katherine

middle: Ann

last: Staines

address: Lewes Road

country: United Kingdom

institute: University of Brighton

data_processing:
Sequenced reads were trimmed for adaptor sequences and for quality (minimum 20) using trim-galore v0.6.5.
Trimmed reads were quantified using kallisto quant
kallisto quantifications were converted to gene level by tximport, then normalised and analysed for differential expression using DESeq2
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file. Matrix table with raw gene counts for every gene and every sample, generated by tximport

source_name: metatarsal cartilage tissue, 50mPa

extract_protocol:
The RNA was extracted from hip and metatarsal cartilage tissues using the following protocol: after collection tissue samples were pooled (n=6 metatarsals and n=2 hip caps for each sample), transferred to eppendorf tubes and frozen at -80ºC. Tissue (<100mg) were defrosted on ice and 1ml Trizol was added to each sample; tissues were homogenised  making sure to keep them cool by putting on ice every 15secs. Samples were Incubated at room temperature for a minimum of 10 minutes to allow for cell lysis and centrifuged at 12,000 g for 15 minutes at 4 °C to pellet the excess tissue, whilst retaining RNA in solution. The supernatant was transferred to a clean tube and 200 μL of chloroform added. After vigorous shaking for 20 seconds the samples were incubated at room temperature for 3 minutes and then centrifuged at 12,000 g for 15 minutes at 4 °C to enable phase separation. The upper, aqueous phase was transferred to a new eppendorf avoiding the Interface. 1 volume of 70% ethanol was added and the samples were mixed thoroughly by vortexing. 700 μl of the sample was transferred to an RNeasy Mini spin column (Qiagen). From this point onwards the manufacturer's recommendation were followed. The elution was done in 30μl of RNase free water and repeated twice with the first eluate. The concentration and purity of the RNA samples were assessed by measurments on the Nanodrop One C spectrophotometer (Labtech) and the quality of the RNA was assessed on a TapeSation 4200 (Agilent Technologies).
The libray construction kit was the Universal Plus Total RNA-seq with Nuquant (Tecan Genomics) which produces stranded RNAseq libraries with Illumina compatible adaptors and unique dual indexes.Input total RNA was between 20 and 200 ng and the amplification cycles were optimized by QPCR based on the manufacturer's recommendations. The cycles of amplifications varied based on the optimization by QPCR on 1/10 of the available volume before amplificatioj and were determined so that the chosen number of cycles were in the middle exponential PCR amplification curve.The procedure followed was as specified by the manufacturer's recommendation except for a technical error made during library preparation which affected the strandness of the following samples HC3, H501, H502, H503, H504, M504. Those samples were analysed using the unstranded library analysis pipeline while the reminder of the samples were analysed using the stranded library analysis pipeline :HC1, HC2, H51, H52, H53, H54, MC1, MC2, MC3, MC4, M501, M502, M503. Samples H502 and HC4 were ultimately identified as outliers and were eliminated from the final data analysis.
RNA seq.The RNA samples had a RINe value which varied from low to medium (1.5-7).DV200 quality metric (the percentage of RNA fragments above 200 nt) which is part the TapeStation 4200 software was used to assess the quality of partially degraded RNA and the analysis showed a range between 53.51-87.4%. Given the variable range of RNA sample quality the library construction strategy exploited the depletion of ribosomal RNA rather than the purification of mRNAs from total RNA.The probe mix for mouse and the Universal Plus any deplete module used was part of the library construction kit that was used to prepare the RNAseq libraries: Universal Plus Total RNA kit with NuQuant (Tecan Genomics)

treatment_protocol: Femoral heads were isolated from 4-week-old male C57/Bl6 mice. Embyronic metatarsals were isolated from E15 embryos of C57/Bl6 mice. After 24 hours of culture, hips caps and metatarsals were placed into the hydrostatic pressure vessel and subjected to 0mPa (control), 5mPa (physiological) or 50mPa (injurious) hydrostatic pressure for 1 hour. Following mechanical stimulation, tissues were placed back into the incubator and cultured for a further 24 hours in the respective media

value: metatarsal cartilage

value: unknown

tag: library type

value: unstranded


title: naive cells from a 30 year old with donor id BAT002 DAT34

source_name: source dna from naive cells from a 30 year old with donor id BAT002

value: naive


title: PAEC_41, passage_4

description:
EC031P4
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: pulmonary artery endothelial cell


title: BM neutrophils, WT, H3K27Ac, S63845, rep3

tag: cell type

value: bone marrow neutrophil


title: M503

value: stranded


title: cd56_bright cells from a 30 year old with donor id BAT002 DAT32

source_name: source dna from cd56_bright cells from a 30 year old with donor id BAT002

tag: age


title: PAEC_41, passage_3

description:
EC031A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Passage 3


title: M502

tag: Sex


title: BM neutrophils, WT, H3K27Ac, S63845, rep1


title: cd8_em_temra cells from a 30 year old with donor id BAT002 DAT31

source_name: source dna from cd8_em_temra cells from a 30 year old with donor id BAT002


title: PAEC_46

description:
EC056A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: M501

tag: strain


title: PAEC_44

description:
EC034A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: BM neutrophils, WT, H3Cit, S63845, rep3


title: cd8_cm cells from a 30 year old with donor id BAT002 DAT30

source_name: source dna from cd8_cm cells from a 30 year old with donor id BAT002


title: PAEC_39

description:
EC028A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 1 PAH

value: CTD


title: PAEC_40

description:
EC029A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 2 PH


title: BM neutrophils, WT, H3Cit, S63845, rep2


title: M54

source_name: metatarsal cartilage tissue, 5mPa


title: PAEC_38

description:
EC026A
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: CpcPH


title: cd8_naive cells from a 30 year old with donor id BAT002 DAT29

source_name: source dna from cd8_naive cells from a 30 year old with donor id BAT002

value: Female


title: cd4_cm cells from a 30 year old with donor id BAT002 DAT28

source_name: source dna from cd4_cm cells from a 30 year old with donor id BAT002


title: BM neutrophils, WT, H3Cit, S63845, rep1


title: Mouse P30 Disc Replicate 3

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data was processed using the Cellranger pipeline (Version 3.0.2, 10x Genomics) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome with the include introns parameter and creation of feature-barcode matrices.
Poor quality cells (< 200 genes or >5% mitochondrial genes) and doublets (> 6000 genes) were excluded.
Gene expression was natural long transformed and normalized using the Seurat v4 toolkit and R Statistical Software (v4.1.2; R Core Team 2021).
Assembly: mm10
Supplementary files format and content: barcodes.tsv: cellular barcodes present in dataset, gzipped
Supplementary files format and content: features.tsv: IDs of quantified genes, gzipped
Supplementary files format and content: matrix.mtx: a matrix of count values, gzipped

source_name: Intervertebral disc

extract_protocol:
Spinal columns were excised from mice postmortem. Under a dissecting microscope, dorsal boney elements and the spinal cord were removed leaving the isolated ventral spinal column comprising the vertebrae and discs. Whole discs in the lumbar, thoracic and caudal regions were isolated by cutting through the vertebral boney endplates with a scalpel, and bisected to expose the NPs. Isolated discs were placed in a phosphate buffered saline containing 25 mM HEPES and 0.1% FBS, finely diced, then digested in collagenase for 30 mins. After digestion, cells were strained through a 50 µm filter. TdTomato+ cells were then enriched using fluorescence activated cell sorting.
Libraries were generated using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3 per manufacturer’s instructions.

value: Intervertebral disc


title: PAEC_36

description:
EC023A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: M52


title: classical cells from a 30 year old with donor id BAT002 DAT33

source_name: source dna from classical cells from a 30 year old with donor id BAT002

value: monocyte

value: classical


title: cd4_naive cells from a 30 year old with donor id BAT002 DAT27

source_name: source dna from cd4_naive cells from a 30 year old with donor id BAT002


title: M53


title: M51


title: PAEC_35

description:
EC021A
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: CHD


title: BM neutrophils, WT, H3K27Ac, S63845, rep2


title: MC4

source_name: metatarsal cartilage tissue, 0mPa

value: metatarsal cartilage


title: Mouse P30 Disc Replicate 2

description: 10x Genomics


title: PAEC_34

description:
EC020A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 4 PH


title: Mouse P30 Disc Replicate 1

description: 10x Genomics


title: cd8_temra cells from a 29 year old with donor id R45504 DAT25

source_name: source dna from cd8_temra cells from a 29 year old with donor id R45504

value: Male


title: cd8_temra cells from a 77 year old with donor id R45805 DAT26

source_name: source dna from cd8_temra cells from a 77 year old with donor id R45805


title: MC3

value: unknown


title: PAEC_33

description:
EC018A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

source_name: pulmonary artery endothelial cell

value: pulmonary artery endothelial cell

value: Group 3 PH


title: MC2

value: stranded


title: PKD1 KO kidney 3, F4/80-high cystic, biol rep 2

city: Leiden

first: Sevtap

middle: Aysu

last: Yasinoglu

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Standard quality metrics for the raw data set was determined using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.25) QC tools
Sequence reads were trimmed to remove possible adapter sequences using fastp v0.20.1.
For each sample, trimmed reads were mapped to the mouse genome mm10 2020-A using STAR2 v2.5.4. Gene count tables were generated using HTSeq v0.11.0 with gene annotation Ensembl GRCm38, version M23, Release 98.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values file, containing raw counts for each sample

source_name: Kidney

growth_protocol: iKspCre-Pkd1del mice have a homozygously bred kidney–specific, tamoxifen–inducible Cre and two LoxP sites that flank exons 2–11 of the Pkd1 gene. The mice received tamoxifen (12.5 mg/kg) by oral gavage on days PN18 and PN19 to induce adult-onset PKD. Cyst development was monitored using MRI to sacrifice mice at the mild cystic phase of the disease.

extract_protocol:
The total RNA was extracted with TRI reagent following standard protocols.
RNA libraries for RNA-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit from Illumina®  (E6420) according to the manufacturer’s instructions

treatment_protocol: Kidneys used for this experiment were embedded in TissueTek and snap-frozen using pre-cooled isopentane, and stored in a -80°C freezer.

value: Kidney

value: Pkd1 KO


title: PKD1 KO kidney 3, F4/80-high cystic, biol rep 1


title: PAEC_37

description:
EC025A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: cd8_temra cells from a 70 year old with donor id R45804 DAT22

source_name: source dna from cd8_temra cells from a 70 year old with donor id R45804


title: cd8_temra cells from a 60 year old with donor id R45740 DAT23

source_name: source dna from cd8_temra cells from a 60 year old with donor id R45740


title: PKD1 KO kidney 2, F4/80-high cystic, biol rep 2


title: PAEC_32

description:
EC017A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: H504

source_name: hip cartilage tissue, 50mPa

value: hip cartilage

value: male

value: unstranded


title: cd8_temra cells from a 73 year old with donor id R45741 DAT24

source_name: source dna from cd8_temra cells from a 73 year old with donor id R45741


title: MC1


title: cd8_temra cells from a 30 year old with donor id R45690 DAT21

source_name: source dna from cd8_temra cells from a 30 year old with donor id R45690


title: cd8_em cells from a 77 year old with donor id R45805 DAT20

source_name: source dna from cd8_em cells from a 77 year old with donor id R45805


title: H503


title: PAEC_30

description:
EC013A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 2 PH


title: PAEC_31

description:
EC014A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: PKD1 KO kidney 1, F4/80-high cystic, biol rep 2


title: PAEC_29

description:
EC011A
PAEC RNAseq Counts_GEO1.09.11.23.xlsx


title: PKD1 KO kidney 2, F4/80-high cystic, biol rep 1


title: PAEC_28

description:
EC010A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: CpcPH


title: H501


title: cd8_em cells from a 29 year old with donor id R45504 DAT19

source_name: source dna from cd8_em cells from a 29 year old with donor id R45504


title: H502


title: PAEC_27

description:
EC009PA
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: PKD1 KO kidney 1, F4/80-high cystic, biol rep 1


title: cd8_em cells from a 73 year old with donor id R45741 DAT18

source_name: source dna from cd8_em cells from a 73 year old with donor id R45741


title: PKD1 KO kidney 3, F4/80-low cystic, biol rep 2


title: PKD1 KO kidney 3, F4/80-low cystic, biol rep  1


title: cd8_em cells from a 60 year old with donor id R45740 DAT17

source_name: source dna from cd8_em cells from a 60 year old with donor id R45740


title: H54

source_name: hip cartilage tissue, 5mPa


title: PAEC_26

description:
EC004A
PAEC RNAseq Counts_GEO1.09.11.23.xlsx


title: PKD1 KO kidney 2, F4/80-low cystic, biol rep 2


title: cd8_em cells from a 70 year old with donor id R45804 DAT16

source_name: source dna from cd8_em cells from a 70 year old with donor id R45804

value: Female


title: PAEC_25

description:
1111N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 1 PAH

value: CTD


title: H53


title: PKD1 KO kidney 2, F4/80-low cystic, biol rep 1


title: PAEC_24

description:
1109N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 5 PH


title: H52


title: cd8_em cells from a 34 year old with donor id R45553 DAT15

source_name: source dna from cd8_em cells from a 34 year old with donor id R45553


title: H51


title: cd8_em cells from a 30 year old with donor id R45690 DAT14

source_name: source dna from cd8_em cells from a 30 year old with donor id R45690


title: PAEC_23

description:
1108N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx


title: PKD1 KO kidney 1, F4/80-low cystic, biol rep 1


title: PAEC_22

description:
1105N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: HPAH


title: HC3

source_name: hip cartilage tissue, 0mPa


title: PKD1 KO kidney 3, non-cystic, biol rep 2

value: Male


title: cd8_cm cells from a 77 year old with donor id R45805 DAT13

source_name: source dna from cd8_cm cells from a 77 year old with donor id R45805


title: cd8_cm cells from a 73 year old with donor id R45741 DAT11

source_name: source dna from cd8_cm cells from a 73 year old with donor id R45741


title: cd8_cm cells from a 29 year old with donor id R45504 DAT12

source_name: source dna from cd8_cm cells from a 29 year old with donor id R45504


title: PKD1 KO kidney 3, non-cystic, biol rep 1

source_name: Kidney


title: PAEC_21

description:
1102N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

source_name: pulmonary artery endothelial cell


title: PAEC_20, control

description:
1101N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: Control


title: HC1


title: PAEC_19

description:
1100N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: pulmonary artery endothelial cell


title: cd8_cm cells from a 60 year old with donor id R45740 DAT10

source_name: source dna from cd8_cm cells from a 60 year old with donor id R45740


title: PAEC_18, bio_rep_2

description:
EC035A
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

tag: biological replicate

value: Biological Replicate 2


title: PKD1 KO kidney 2, non-cystic, biol rep 1


title: cd8_cm cells from a 70 year old with donor id R45804 DAT9

source_name: source dna from cd8_cm cells from a 70 year old with donor id R45804


title: PKD1 KO kidney 1, non-cystic, biol rep 2


title: PKD1 KO kidney 1, F4/80-low cystic, biol rep 2


title: cd8_cm cells from a 30 year old with donor id R45690 DAT7

source_name: source dna from cd8_cm cells from a 30 year old with donor id R45690


title: PAEC_17

description:
1096N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: IPAH


title: cd8_cm cells from a 34 year old with donor id R45553 DAT8

source_name: source dna from cd8_cm cells from a 34 year old with donor id R45553


title: PAEC_18, bio_rep_1

description:
1098N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: Biological Replicate 1


title: PKD1 KO kidney 1, non-cystic, biol rep 1

value: Kidney

value: Pkd1 KO


title: cd8_naive cells from a 29 year old with donor id R45504 DAT6

source_name: source dna from cd8_naive cells from a 29 year old with donor id R45504


title: TNFα+VEGF+Ramucirumab-1

type: RNA

city: Seongnam-si, Gyeonggi-do

first: Jihyun

last: Lee

address: 30, Changeop-ro 40beon-gil, Sujeong-gu

country: South Korea

institute: Tiumbio

description: Intensity (CEL) Data files are generated by Affymetrix® GeneChip Command Console® Software(AGCC). The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT).

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: HUVEC cell, TNFα+VEGF+Ramucirumab

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: HUVECs were cultured in EBM-2 culture media (containing human epidermal growth factor, vascular endothelial growth Factor, R3-Insulin-like growth factor-1, Ascorbic acid, Hydrocortisone, human fibroblast growth factor-Beta, Heparin, and Gentamicin/Amphotericin-B and FBS) (Lonza). Cells were incubated at 37℃, 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from HUVECs using Direct-zol RNA MiniPrep (Zymoresearch, Irvine, CA, USA) according to the manufacturer’s recommendations.
cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

tag: cell line

value: HUVEC

tag: agent

value: TNFα+VEGF+Ramucirumab

value: Umbilical cord


title: TNFα+VEGF+Ramucirumab-3


title: cd8_naive cells from a 73 year old with donor id R45741 DAT5

source_name: source dna from cd8_naive cells from a 73 year old with donor id R45741


title: PAEC_16, control

description:
1093N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx


title: PAEC_15, control

description:
1091N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx


title: TNFα+VEGF+Ramucirumab-2


title: HC2

value: hip cartilage

value: male

value: stranded


title: PAEC_14

description:
1087N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 3 PH


title: TNFα+VEGF+Vactosertib-2

source_name: HUVEC cell, TNFα+VEGF+Vactosertib

value: TNFα+VEGF+Vactosertib


title: cd8_naive cells from a 60 year old with donor id R45740 DAT4

source_name: source dna from cd8_naive cells from a 60 year old with donor id R45740


title: cd8_naive cells from a 70 year old with donor id R45804 DAT3

source_name: source dna from cd8_naive cells from a 70 year old with donor id R45804

value: Female


title: TNFα+VEGF+Vactosertib-3


title: TNFα+VEGF+Vactosertib-1


title: cd8_naive cells from a 34 year old with donor id R45553 DAT2

source_name: source dna from cd8_naive cells from a 34 year old with donor id R45553

value: Male


title: PAEC_13

description:
1086N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: Group 1 PAH


title: PAEC_12

description:
1084N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: pulmonary artery endothelial cell

value: Group 2 PH

value: CpcPH


title: PAEC_11

description:
1078N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx


title: cd8_naive cells from a 30 year old with donor id R45690 DAT1

source_name: source dna from cd8_naive cells from a 30 year old with donor id R45690


title: TNFα+VEGF+TU2218-3

source_name: HUVEC cell, TNFα+VEGF+TU2218


title: TNFα+VEGF+TU2218-2


title: PAEC_10

description:
1067N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: IPAH


title: PAEC_9

description:
1066N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 5 PH


title: experiment 1 replicate 3, scRNAseq

city: Tempe

first: Leandra

last: Brettner

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Mechanisms of Evolution

institute: Arizona State University

description: SPLiTseq

data_processing:
Due to an unforeseen and irreversible data loss, 3 of the 14 files were truncated, resulting in minor loss of approximately 5% of the data. The trimmed files are indicated with _trim.
The original, untruncated fastq files were processed into barcode-by-gene count matrices using STARsolo version 2.7.9a. These files were unaffected by the data loss.
Assembly: R46 s288c and/or sc5314 V4
Supplementary files format and content: tab separated value and matrix files

organism:
Saccharomyces cerevisiae
Candida albicans

source_name: mixed sample (s228c, ATCC 3147)

extract_protocol:
At the time of sampling, 3 mL of yeast cultures were immediately spun down in a room temperature centrifuge at 3000G for 5 minutes. The media supernatant was removed, and the cell pellet was resuspended in 2 mL of cold 4% formaldehyde in molecular grade PBS. The cells were then fixed cold in a 4C refrigerator for approximately 18 hours. After fixation, the samples were spun down in a 4C centrifuge at 3000G for 5 minutes. The formaldehyde supernatant was removed, and the pellet was resuspended in 1 mL cold molecular grade 100 mM Tris HCl pH 7 plus 0.1 U/uL SUPERase-In RNase inhibitor (Invitrogen) to quench the formaldehyde. Cells were then centrifuged, resuspended in 250 uL of a zymolyase enzymatic solution of 0.1M Na2EDTA, 1M sorbitol, and 0.005 U/uL zymolyase (Zymo Research) (pH ~7.5), and incubated at 37C for 15 minutes. At the end of the incubation, 1 mL of cold PBS plus 0.1 U/uL SUPERase-In RNase inhibitor and 0.1 U/uL Enzymatics RNase inhibitor (Enzymatics) was immediately added, and the cells were centrifuged at 4C, 3000G for 5 minutes. The cells were then resuspended in 250 uL of cold 0.4% Triton X-100 in PBS plus RNase inhibitors and incubated on ice for 3 minutes. Again, 1 mL of cold PBS plus RNase inhibitors was added at the end of the 3 minutes and the cells were centrifuged. They were then resuspended in 500 uL of cold PBS plus RNase inhibitors, vortexed on high for ~30 seconds, and lightly filtered through a 40 µm pluriStrainer (pluriSelect). The cells were then counted using a Beckman Coulter Cell Counter and diluted to 1 million cells/mL into fresh cold PBS plus RNase inhibitors.
The cells were then processed according to the standard SPLiTseq protocol. Briefly, in situ reverse transcription and ligation steps were performed and then the cells were lysed and cDNA collected and amplified for sequencing.

value: mixed sample (s228c, ATCC 3147)

value: yeast cells

tag: ploidy

value: diploid

value: naive

value: log growth


title: experiment 2 replicate 1, scRNAseq

description: SPLiTseq

source_name: mixed sample (s228c, ATCC 3147, BY4741)

value: mixed sample (s228c, ATCC 3147, BY4741)

value: diploid, haploid

value: mixed sample (naive, MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P PGK1 -mCherry-KanMX6 ybr209w{delta}::B103-HphMX6, and MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P GAL1 -YFP-KanMX6 ybr209w{delta}::BC3-HphMX6)


title: experiment 2 replicate 2, scRNAseq

description: SPLiTseq

value: mixed sample (naive, MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P PGK1 -mCherry-KanMX6 ybr209w{delta}::B103-HphMX6, and MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P GAL1 -YFP-KanMX6 ybr209w{delta}::BC3-HphMX7)


title: HC4

source_name: hip cartilage tissue, 0mPa

value: hip cartilage

value: male

value: stranded


title: PAEC_8

description:
1063N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

source_name: pulmonary artery endothelial cell

value: pulmonary artery endothelial cell

value: Group 3 PH


title: TNFα+VEGF-3

source_name: HUVEC cell, TNFα+VEGF

value: HUVEC

value: TNFα+VEGF

value: Umbilical cord


title: TNFα+VEGF+TU2218-1


title: TNFα+VEGF-2


title: PAEC_7, bio_rep_5, passage_4

description:
EC003C4P
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: Group 1 PAH

value: PoPH

value: Passage 4


title: TNFα+VEGF-1


title: PAEC_7, bio_rep_4

description:
EC003A
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Biological Replicate 4


title: TNFα-2

source_name: HUVEC cell, TNFα

value: TNFα


title: PKD1 KO kidney 2, non-cystic, biol rep 2

source_name: Kidney

value: Male

value: Kidney

value: Pkd1 KO


title: Drug-perturbed, replicate 2, Gene Expression Library

city: Helsinki

first: Shuyu

last: Zheng

state: Uusimaa

address: Biomedicum 1U, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v7.1.0 ( https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Cell quality control was performed using Seurat v4.0.4 ( https://satijalab.org/seurat/)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files for cell annotation and matrix files for UMI counts

source_name: KURAMOCHI

extract_protocol:
All samples were detatched and resuspended in PBS + 0.04% BSA buffer.
Libraries were performed according to the manufacter’s instructions [Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), 10x Genomics].

treatment_protocol: Kuramochi cells were seeded in 6-well plates at around 50% confluence overnight. Small molecules (Ixazomib citrate 0.36μM, Delanzomib 0.12μM, Bortezomib 0.04μM, Carfilzomib 0.008μM, Pyrrolidinedithiocarbamate ammonium 0.2μM, Sitagliptin 3.3μM, GW843682X 0.36μM, Clofarabine 10μM, Nocodazole 0.04μM, Pevonedistat hydrochloride 0.33μM, or Pevonedistat hydrochloride 1μM) or DMSO as control were added for 24h in duplicates. Then cells were simultaneously washed and detached from plates.

value: KURAMOCHI

value: High grade serous ovarian cancer cell

value: Treated by DMSO, Ixazomib_citrate, Delanzomib, Bortezomib, Carfilzomib, Pyrrolidinedithiocarbamate_ammonium , Sitagliptin, GW843682X, Clofarabine, Nocodazole, Pevonedistat_hydrochloride_L, or Pevonedistat_hydrochloride_H


title: Case CTL_16

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

label: Cy3 and Cy5

source_name: IDHmut Astro_ctl

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: disease state

value: IDHmut Astro_ctl

tag: material

value: FFPE

value: M

value: brain


title: experiment 1 replicate 1, scRNAseq

description: SPLiTseq

value: mixed sample (s228c, ATCC 3147)

value: yeast cells

value: diploid

value: naive

value: log growth


title: TNFα-3

value: HUVEC

value: Umbilical cord


title: Case ID_13

source_name: IDHmut Astro_MS

value: IDHmut Astro_MS

value: F


title: PAEC_7, bio_rep_5, passage_3

description:
EC003C3P
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: pulmonary artery endothelial cell

tag: ph group/control

value: Group 1 PAH

value: PoPH

value: Passage 3

value: Biological Replicate 5


title: Case CTL_18

value: IDHmut Astro_ctl

value: FFPE


title: TNFα-1

value: TNFα


title: Case CTL_17

value: brain


title: Drug-perturbed, replicate 2, Cell Multiplexing Library

description: 10x Genomics

value: KURAMOCHI

value: High grade serous ovarian cancer cell

value: Treated by DMSO, Ixazomib_citrate, Delanzomib, Bortezomib, Carfilzomib, Pyrrolidinedithiocarbamate_ammonium , Sitagliptin, GW843682X, Clofarabine, Nocodazole, Pevonedistat_hydrochloride_L, or Pevonedistat_hydrochloride_H


title: vehicle-3

source_name: HUVEC cell, vehicle

value: vehicle


title: PAEC_7, bio_rep_2

description:
1056N4
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

tag: ph subtype

value: Biological Replicate 2


title: PAEC_7, bio_rep_1

description:
1056N3
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Biological Replicate 1


title: Drug-perturbed, replicate 1, Gene Expression Library

description: 10x Genomics


title: Drug-perturbed, replicate 1, Cell Multiplexing Library

description: 10x Genomics


title: B 120, rep2

city: New Delhi

first: Agam

middle: Prasad

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22.
Supplementary_files_format_and_content: Excel files include RPKM values for each mRNA of respective samples.

organism: Candida albicans

source_name: whole organism total RNA

growth_protocol: Candida albicans NCCPF 400034 was grown at 37 °C overnight in YPD medium. The cells were then washed with PBS and counted using the hemocytometer.

extract_protocol:
RNA was extracted using the Ribopure Yeast Kit (Ambion).  The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum +butanol grown samples and sequencing was performed using Genome Analyzer IIx for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.

treatment_protocol: The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) supplemented with 1 % butanol and incubated in 5 % CO2 at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida cells were treated as control and RNA was sequenced using next generation techniques.

value: 120 minutes in serum + butanol


title: vehicle-2

value: HUVEC

value: Umbilical cord


title: vehicle-1


title: B 120, rep1


title: PAEC_5

description:
1048N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: pulmonary artery endothelial cell

value: Group 2 PH

value: CpcPH


title: G08-C

city: Montreal

first: Lorenzo

last: Ferri

state: Quebec

address: 1650 Cedar Avenue

department: Surgery & Oncology

country: Canada

institute: McGill University

description:
CRUK_storming_cancer_gastric_all_cells_2022_v2.h5ad
CRUK_storming_cancer_gastric_epithelial_2022_v2.h5ad
CRUK_storming_cancer_gastric_fibroblasts_2022_v2.h5ad

data_processing:
fastqs generated with bcl2fastq (2.20.0.422) for illumina or by fgbio (1.3.0) for MGI G400
After polyA-trimming via cutadapt (v3.2), reads were pseudoaligned to the GRCh38 reference transcriptome (ENSEMBL release 96) with kallisto (v0.46.2) using the default kmer size of 31. The pseudoaligned reads were processed into a cell-bygene count matrix using bustools (0.40.0). Cell barcodes were filtered using the whitelist (v3) provided by 10xGenomics. All further processing was done in scanpy (v1.9.1).
Cell barcodes with less than 1000 counts or less than 500 genes expressed were removed. Cell barcodes with more than 20% mitochondrial gene expression were removed. Doublet cells were identified using scrublet, removing any cell barcode with a scrublet score > 0.2. Only coding genes were retained in the final count matrix. Expression profiles were normalized by total counts, the 4000 most highly variable genes identified, renormalized, log-transformed and z-scored. The data was projected onto the first 50 principal components.
Detailed bioinformatics methods found in the supplementary materials: https://www.sciencedirect.com/science/article/pii/S001650852300731X#appsec1
Assembly: GRCh38/ENSEMBL release 96
Supplementary files format and content: hdf5 file with anndata objects

source_name: Gastric adenocarcinoma

extract_protocol:
single cell capture using 10x genomics 3' mRNA library contruction from cells (v3)
After the dissociation protocol, using the single cell 3’ v3 protocol (10x Genomics), the cells were captured with the maximum target of 6000 cells.  During the capture the transcripts are first converted to cDNA and amplified.  The cell barcode and unique molecular identifier are added during the first strand synthesis of the double stranded cDNA.  The full length cDNA is then further processed to fragment the library to size for short read sequencing and amplified further to add the sequencing adapters and capture library index.

treatment_protocol: Tissue specimens were dissected and dissociated into single cell suspentions

value: Gastric adenocarcinoma

tag: tumor stage

value: Female


title: PAEC_4

description:
1046N1
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

tag: tissue

value: Group 1 PAH

value: CHD


title: B 45, rep2

value: 45 minutes in serum + butanol


title: B 45, rep1


title: G08-A

value: NS


title: Case ID_18

value: IDHmut Astro_MS

value: FFPE

value: M

value: brain


title: PAEC_3

description:
1024N2
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: IPAH


title: G08-B

value: T


title: PAEC_2

description:
1012N2
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: Group 5 PH


title: G07-C

source_name: Diffuse-type adenocarcinoma

value: Diffuse-type adenocarcinoma


title: Case ID_06

value: F


title: G07-D


title: PAEC_1

description:
1005N2
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

value: pulmonary artery endothelial cell

value: HIV


title: G07-B


title: B 20, rep1

value: 20 minutes in serum + butanol


title: Male subcortical_Mouse 4

city: San Francisco

first: Marci

middle: F

last: Rosenberg

address: 1651 4th Street

department: Psychiatry

institute: UCSF

data_processing:
Samples were analyzed as previously described (Vainchtein et al. 2018; R. T. Han et al. 2023). Briefly, after assessing read quality with FastQC (v0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), samples were aligned to the Mus musculus genome (Ensembl GRC m39) using STAR aligner (v2.6.0) (Dobin et al. 2013). Aligned reads were then counted with HTSeq (v0.9.0) (Anders, Pyl, and Huber 2015), and loaded into R, where count normalization and differential expression analysis (between cortical vs. subcortical astrocytes) was performed using DESeq2 (v1.35.0) (Love, Huber, and Anders 2014).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized counts for each sample
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Astrocytes

extract_protocol:
After thawing the lysed astrocytes in RLT Plus buffer, mRNA was isolated from each sample using the RNeasy Plus Micro Kit (74034, Qiagen)
cDNA libraries were then prepared using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

value: Astrocytes

value: Male

tag: genotype

value: WT


title: 45_minutes_Serum_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each mRNA of respective samples.

extract_protocol:
RNA was extracted using the Ribopure Yeast Kit (Ambion).  The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum grown samples and sequencing was performed using Genome Analyzer IIX for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.

treatment_protocol: The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) with 5 % CO2 and incubated at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida was treated as control and the extracted RNA was sequenced using the next generation sequencing techniques.

tag: protocol

value: serum

tag: time point

value: 120 minutes


title: G07-A

value: Female

value: N (normal stomach)


title: 45_minutes_Serum_1


title: Case ID_03

value: IDHmut Astro_MS

value: FFPE


title: Case CTL_15

value: IDHmut Astro_ctl

value: M

value: brain


title: 2xH1047R HeLa clone_1

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

institute: School of Life Sciences, University of Dundee

data_processing:
Nextflow (version 20.07.1) nf-core RNAseq pipeline (version 1.1), with Spliced Transcripts Aligment to a Reference (STAR) for read alignment to the human genome (Homo_sapiens.GRCh38.96.gtf) and featureCounts for counting of mapped reads (multimapped reads were discarded)
All subsequent analysis steps using the raw gene counts were performed in R. Filtering of low gene expression counts was performed with the TCGAbiolinks package with quantile value 0.75 (chosen empirically based on the observed count distribution).
Read count normalization was performed with the gene length-corrected trimmed mean of M-values (GeTMM) method.
The mean-variance relationship was modelled with voom(), followed by linear modelling and computation of moderated t-statistics using the lmFit() and eBayes() functions in the limma package.
The associated p-values for assessment of differential gene expression were adjusted for multiple comparisons with the Benjamini-Hochberg method at false-discovery rate (FDR) = 0.05. Adjustments were performed with option = “separate”, comparing PIK3CAH1047R mutant clones against wild-type clones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing all raw gene counts for each sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in complete medium consisting of DMEM (with 4 mM L-Glutamine and 1 mM sodium pyruvate; Thermo Fisher Scientific #41966-029) supplemented with another 2 mM of L-Glutamine (Sigma #G7513) and 10 % fetal bovine serum (FBS; Pan-Biotech #P30-8500).

extract_protocol:
Direct-zol RNA Miniprep Kit from ZymoResearch (#R2051)
NEB Next® Ultra™ RNA Library Prep Kit (NEB #E7770)

treatment_protocol: Cells were fed fresh growth medium 3 hours prior to colelction for RNA extraction.

value: HeLa

tag: cell type

value: cervical cancer

value: PIK3CA H1047R on two alleles, exon21 frameshift on the third

tag: clone


title: 20_minutes_Serum_2

value: 45 minutes


title: Female subcortical_Mouse 3

tag: Sex

tag: age


title: experiment 1 replicate 2, scRNAseq

description: SPLiTseq

value: mixed sample (s228c, ATCC 3147)

value: yeast cells

value: diploid

value: naive

tag: treatment

value: log growth


title: PAEC_7, bio_rep_3

description:
1056N5
PAEC RNAseq Counts_GEO2.09.11.23.xlsx

value: pulmonary artery endothelial cell

value: Group 1 PAH

value: PoPH

tag: biological replicate

value: Biological Replicate 3


title: B 20, rep2

tag: strain

value: 20 minutes in serum + butanol


title: 1xH1047R HeLa clone_2

tag: cell line

value: PIK3CA H1047R on one allele, exon21 frameshift on the remaining two


title: 20_minutes_Serum_1

value: serum


title: Case CTL_11

tag: disease state

value: IDHmut Astro_ctl

value: FFPE

value: F

value: brain


title: Male subcortical_Mouse 1

value: Astrocytes

value: Male

value: WT


title: Female subcortical_Mouse 2

value: Female


title: 1xH1047R HeLa clone_1

value: HeLa

value: cervical cancer


title: 120_minutes_Serum_2

value: 20 minutes


title: Case CTL_13

tag: material

value: M


title: 120_minutes_Serum_1


title: 2xWT, 1xFS HeLa clone

value: PIK3CA WT on two alleles, exon21 frameshift on the third


title: Case CTL_12


title: 3xWT HeLa clone_2

value: PIK3CA WT


title: Case CTL_10